ACADEMIC SENATE: SAN DIEGO DIVISION, 0002 UCSD, LA JOLLA, CA 92093-0002 (858) 534-3640 FAX (858) 534-4528

October 27, 2020

PROFESSOR STEPHEN HEDRICK, Professor Division of Biological Sciences

PROFESSOR MITCHELL KRONENBERG, Professor Division of Biological Sciences

PROFESSOR KIT POGLIANO, Dean Division of Biological Sciences

PROFESSOR ASA GUSTAFSSON, Chair Biomedical Sciences Graduate Program

SUBJECT: Proposal to establish PhD Specialization in Immunology

At its October 12, 2020 meeting, the Graduate Council approved the proposal to establish a PhD specialization in Immunology, to be offered to students in the Division of Biological Sciences and the Biomedical Sciences Graduate Program. The Council supports the creation of the following degree titles:

 PhD in Biology with a Specialization in Immunology  PhD in Biomedical Sciences with a Specialization in Immunology

Final approval from the Representative Assembly is required to establish the new degree titles. Prior to forwarding the proposal for placement on an upcoming Representative Assembly agenda, please provide an addendum to the proposal that clarifies the requirements for doctoral committee membership for the specialization to Senate Associate Director Lori Hullings ([email protected]). Rather than provide links to the committee membership for each program, please clearly state the committee membership for a student in the Immunology specialization. It would be helpful to include if a co-chair is required if the Immunology faculty advisor is not from the student’s home department and who is eligible to serve as the tenured outside member.

If approved, the new degree titles will be available to students in Fall Quarter 2021.

Sincerely,

Lynn Russell, Chair Graduate Council

cc: M. Allen J. Antony S. Constable S. Garfin T. Javidi C. Lyons R. Rodriguez Hullings, Lori

From: Hullings, Lori Sent: Monday, November 2, 2020 9:20 AM To: Hedrick, Stephen Cc: Talia Delamare; Mitchell Kronenberg; Antony, James; Allen, Mary; Russell, Lynn; Pogliano, Kit; Gustafsson, Asa; Constable, Steven; Javidi, Tara; Rodriguez, Ray Subject: PhD Specialization in Immunology: Addendum to doctoral committee requirements

Dear Professor Hedrick,

The Graduate Council approved the addendum (copied below) clarifying the doctoral committee requirements for the PhD Specialization in Immunology with one modification (underlined in the text below). I will add this to the proposal.

Thank you for quickly responding to the Graduate Council’s request.

Best, Lori

The composition of the Doctoral Committee for students in the PhD specialization in Immunology will be enforced in accordance with University and home department regulations. The committee must have a minimum of five members and adhere to the requirements established by Biological Sciences or Biomedical Sciences. The chair of the committee will be a member of the respective graduate programs, either Biological Sciences or Biomedical Sciences. We expect the chair of the committee should also be a member of the Program in Immunology faculty; however, the directors will consider a petition for an outside mentor subject to the same criteria used for Program membership: Appointment at UC San Diego; an interest in some field of study related to immunology; and stable funding consistent with support of a pre-doctoral fellow’s research. The dissertation committee will be chosen by the dissertation advisor and the student, consistent with the requirements set forth by the two graduate programs and the Dean of Graduate Division. We recommend that two faculty members affiliated with the Program in Immunology be included in the committee, though this is not an absolute requirement.

From: Hedrick, Stephen Sent: Friday, October 30, 2020 12:07 PM To: Hullings, Lori Cc: Talia Delamare ; Mitchell Kronenberg Subject: Addendum to doctoral committee requirements

Dear Lori:

Please find an attached addendum or clarification of our requirements for a doctoral committee in the Specialization in Immunology. If you have any further questions, please do not hesitate to contact me at one of the coordinates listed below.

Best regards,

Steve

1 UC San Diego Administrative Cover Sheet: New Academic Degree Programs/Remote Courses

DOCUMENT TYPE AND BRIEF DESCRIPTION: Proposal for a Specialization in Immunology within the Biological and Biomedical Sciences PhD programs.

HEAD OF INITIATING OFFICE:

Stephen Hedrick, PhD Distinguished Professor Molecular Biology and [email protected] Cell & Mol. Medicine

Signature:

RETURN DOCUMENT TO:

Talia Delamare 858-752-6548 [email protected] Mail Code

ROUTING TITLE DATE IN ORDER SIGNATURE DATE OUT

Executive Vice Chancellor - Academic Affairs 10 7/23/20

Vice Chancellor - Health Sciences

Vice Chancellor - Marine Sciences

Office of Resource Administration: Steve Ross Steven Ross 9 Steven Ross (Jun 16, 2020 17:17 PDT)

Office of Resource Administration: Name, Title

Dean of Undergraduate Education

Dean of the Graduate Division - Mary Allen in case 8 of Dean Antony

Dean: Kit Pogliano - Biological Sciences 7 STEVEN R GARFIN,MD 6 Dean: Steve Garfin - Biomedical Sciences STEVEN R GARFIN,MD (Jul 14, 2020 10:06 PDT)

5 Teaching + Learning Commons: Name, Title

Department Chair: Name, Department 4

Department Chair: Name, Department 3

1 Other: Name, Title

1 Other: Name, Title

Please refer to Procedures for Administrative Review of New Academic Programs and Remote Courses for appropriate routing details

Ph.D. Degree in Biological or Biomedical Sciences with a Specialization in Immunology Program Information Doctor of Philosophy degree in Biological Sciences (BS) or Biomedical Sciences (BMS) with a specialization in Immunology Proposed Start Date 09/01/2020 Brief description of the program This proposed graduate study program will award a Ph.D. with a specialization in Immunology as part of graduate training in the UC San Diego BMS and BS graduate programs. Students will be accepted to one of these two programs, and they will satisfy all of the requirements of their chosen program. In addition, the specialization will promote an immersive educational experience in immunology that includes participation in immunology coursework, original research, seminars given by renowned speakers, biweekly research presentations by peers, a weekly journal club, and a yearly area-wide immunology conference. The specialization will be overseen by the Program in Immunology; a newly-established Center that represents a lasting partnership between UC San Diego and the La Jolla Institute for Immunology (LJI). It is composed of more than 70 world-class faculty members, with 23 from LJI, and the remainder from UC San Diego across campus departments and Health Sciences.

The Ph.D. specialization in Immunology will blend existing and new courses designed to familiarize students with the program faculty and expose them to facilities and techniques that are widely used in the field. New courses include “Bioinformatics for Immunologists” that has been developed and “Immunological Basis of Disease” that is being planned and will be developed to complement courses currently given. The coursework is intended to provide a sound theoretical foundation to the broad aspects of immunology along with opportunities for sub-specialization. All necessary resources are in place to support this specialization. We propose to allow existing students to enroll in the specialization beginning Fall 2020 and to admit the first new class of students Fall 2021.

Modality of the program On-Site Name of the institution’s two most closely related programs to the proposed program Immunology is presently an area of emphasis or track within the BMS program. Immunology thesis research is available to students in laboratories in the BS program; but without any designation that this is an area of interest. Anecdotal reports and interviews with present students indicate, however, that student applicants with an interest in immunology often do not target UC San Diego for graduate school.

Number of new courses being required for this program “Bioinformatics for Immunologists” - This course has been approved by the Health Sciences Graduate Programs Education Committee (GPEC). Number of new faculty members required for this program: 0 Significant additional equipment or facilities needed for this program: None Significant additional financial resources needed: None Significant additional library/learning resources needed: None

A proposal for an interdisciplinary Ph.D. Specialization in Immunology

Supported by the

As part of the graduate programs in the Biomedical Sciences (BMS) and the Division of Biological Sciences (BS) at UC San Diego

Date of preparation: August 10, 2020

Contact Information Sheet

Program Directors:

Stephen M. Hedrick Mitchell Kronenberg Distinguished Professor President and Chief Scientific Officer Molecular Biology La Jolla Institute for Immunology Cellular and Molecular Medicine Adjunct Professor, Div. Biological Sciences University of California San Diego University of California San Diego [email protected] [email protected] 5121 Natural Sciences Building 9420 Athena Circle 9500 Gilman Drive La Jolla, CA 92037 La Jolla, CA 92093-0377 858-752-6540-office 858-534-6269-office 858-353-6702-mobile 858-353-1807-mobile

Proposal for a Graduate Specialization in Immunology-UC San Diego

Other Contacts:

Lanisa Medina Talia Delamare cMAV Program Manager Project Manager, Executive Offices University of California, San Diego La Jolla Institute for Immunology 9500 Gilman Dr. MC 0063 [email protected] San Diego, CA, 92093-0063 9420 Athena Circle [email protected] La Jolla, CA 92037 858-822-2561- office 858-752-6548- office

Program Admin: To be named

Page 2 Proposal for a Graduate Specialization in Immunology-UC San Diego

Table of Contents Executive Summary 4 I. Introduction and Organization 5 I.1. Aims and objectives of the Specialization in Immunology 5 I.2. Historical development of the field and historical development of departmental strength 6 in the field I.3. Timetable for development of the Specialization 7 I.4. Relation of the proposed Specialization to existing programs on campus and the Campus 8 Academic Plan I.5. Administration 9 I.6. Admissions Committee 9 I.7. Academic Committee 9 I.8. Dissertation Committee 9 I.9. Plan for evaluation 10 II. Specialization 10 II.1. Undergraduate preparation and requirements for admission 10 II.2. Program of study 10 II.2.a. Faculty mentors 10 II.2.b. Plan: mentorship and student tracking 11 II.2.c. Specialization requirements in addition to those of the degree-granting unit 11 II.3. Field examinations 13 II.4. Examinations and yearly meetings 13 II.4.a. Dissertation committee 13 II.4.b. Milestone Exams 13 II.4.c. Yearly exams 13 II.4.d. Dissertation 13 II.4.e. Oral defense 14 II.5. Special requirements over and above Graduate Division minimum requirements 14 II.6. Relationship of Master’s and Doctor’s Program 14 II.7. Special preparation for careers in academic science, teaching, and industry 14 II.7.a. Pedagogy 14 II.7.b. Industry Careers 15 III. Projected Need 15 III.1. Student demand 15 III.2. Opportunities for placement of graduates 16 III.3. Importance to the discipline 16 III.4. Ways in which the Specialization will meet the needs of society 16 III.5. Relationship of the Specialization to research and/or professional interests of the faculty 17 III.6. Specialization differentiation 17 IV. Faculty 17 V. Courses 17 V.1. Core coursework 17 V.2. Alternative Bioinformatics Courses: 19 V.3. Related coursework available to students to substitute for required courses by petition 19 VI. Resource Requirements 20 VII. Graduate Student Support 20 VIII. Governance 20 Page 3 Proposal for a Graduate Specialization in Immunology-UC San Diego

Appendix I Faculty Biographies 21

Executive Summary This proposed graduate study program will award a Ph.D. specialization in Immunology as part of graduate training in the Biomedical Sciences (BMS) and Division of Biological Sciences (BS) graduate programs. Students will be accepted to one of these two programs, and they will satisfy all of the requirements of their chosen program. Minor exceptions will be described in this application. In addition, the specialization will promote an immersive educational experience in immunology that includes participation in immunology coursework, original research, seminars given by renowned speakers, biweekly research presentations by peers, a weekly journal club, and a yearly area-wide immunology conference. The specialization will be overseen by the Program in Immunology; a newly-established Center that represents a lasting partnership between UC San Diego and the La Jolla Institute for Immunology (LJI). It is composed of more than 70 world-class faculty members, with 23 from LJI, and the remainder from UC San Diego across campus departments and Health Sciences (https://immunology.ucsd.edu).

At UC San Diego, the participating units include a large number of faculty from the Health Sciences including the Departments of Medicine (and divisions therein), Dermatology, Pediatrics, Cellular and Molecular Medicine, and Pharmacology. Most of the campus faculty come from the Division of Biological Sciences, although there are members from the Division of Physical Sciences and the School of Engineering as well. The resulting degree will be (name of Ph.D. program) with a "Specialization in Immunology.” The inception of this specialization comes at a time of excitement and interest in the immune system as the key to fighting cancer, chronic inflammatory diseases and emerging infectious diseases and pandemics. The Specialization will at once facilitate training the next generation of immunologists, and catalyze programmatic cohesion and create even greater cooperation between Program in Immunology members. Success in immunology requires students to understand diverse scientific methods and approaches that are often specialized for studies of adaptive and innate immunity. These include human genome analysis, e.g., to identify regions, genes, and pathways under strong selective pressure; bioinformatics to decipher large data sets related to gene expression as well as non-coding information of the genome; analysis of organismal and cellular metabolism and its influence on immune homeostasis; the broad interface between the immune system and the microbiome; host-pathogen co-evolution; and the many facets of immune regulation that can be manipulated to ameliorate inflammatory diseases or enhance specific responses for the purpose of clearing chronic viral infections or neoplastic disease. We envision a training program with a strong basis in molecular and cellular immunology, but with opportunities for students to gain proficiency in highly- specialized modes of inquiry, such as structural biology or informatics. The primary targets for the Immunology Specialization will be those students with an undergraduate degree in biology, chemistry or engineering, and with experience in a discipline related to the immune system, the interplay between hosts and their pathogens, or tumor immunology. If students wish to enter the specialization without having formal training in immunology, we will propose several means of remedial coursework. The Ph.D. degree in Immunology will blend existing and new courses. New courses in Bioinformatics for Immunologists and Immunological Basis of Disease will be developed to complement courses currently given. The coursework is intended to provide a sound theoretical foundation to the broad aspects of immunology along opportunities for sub-specialization.

Page 4 Proposal for a Graduate Specialization in Immunology-UC San Diego

All necessary resources are in place to support this specialization. We propose to allow existing students to opt for the specialization and enroll in the lecture courses beginning Fall 2020 and to admit the first new class of students Fall 2021.

Section I. Introduction and Organization 1. Aims and objectives of the program We wish to create a training program in immunology that will attract and educate the best students in the country and the world at large. This includes organizing an intellectually- and programmatically-diverse faculty to consider graduate pedagogy as an end in itself as well as a means of achieving research preeminence. We will “brand” Graduate Studies in Immunology through intrinsic excellence but make this excellence apparent through a substantial web presence including social media participation. We already have an annual symposium that will help to attract the attention of prospective students. Our larger goal for The Program in Immunology is to secure an allegiance and participation of faculty and students that transcends institutional and departmental affiliations, similar to what has been achieved at UC San Diego in the neurosciences. We believe that this can best be achieved by the creation of a Specialization in Immunology within existing graduate programs of study. The overarching objective of the Graduate Studies in Immunology is to develop a diverse pool of well-trained scientists that will pioneer the next breakthroughs in fundamental research and human health. We propose that this requires the following. Students will achieve a broad understanding of biomedical disciplines and obtain the skills to independently acquire the knowledge needed to advance immunological research. They will achieve the ability to think critically and independently and to identify important research questions—we will do this through coursework, review of topical literature, review of on-going research carried out by colleagues, and exposure to breaking research presented by leaders in the field. In presenting their own research proposals, students will be encouraged think about pushing forward the boundaries of their areas of study. We propose that with this combination of exposure and participation, students will acquire a strong foundation in scientific reasoning, rigorous research design, experimental methods, quantitative approaches, and data analysis and interpretation. Students will understand the process of initiating, conducting, interpreting, and presenting rigorous and reproducible biomedical research and will do so with increasing self-direction. As a natural consequence of working in a laboratory environment and presenting results in several forums, students will acquire the ability to work effectively with colleagues from a variety of cultural and scientific backgrounds and to promote inclusive and supportive scientific research environments. With experience in teaching and data presentations, students will acquire the skills to teach and communicate scientific research methodologies and findings to a wide variety of audiences. Because diversity at all levels is integral to research and training excellence, the Specialization in Immunology will enhance diversity in the biomedical enterprise by paying particular attention to groups traditionally underrepresented in the biomedical sciences. In order to facilitate those efforts, a faculty member will be appointed as the Minority Outreach Liaison for the Program and will be tasked with ensuring our ongoing dedication in this area. He or she will work closely with Dr. Gentry Patrick who oversees graduate equity, diversity and inclusiveness for the Biological Sciences. The liaison will also work closely with San Diego State University (ranked Top 7 in the nation for racial and ethnic diversity) and California State University San Marcos (designated as a Hispanic-serving Institution) in order to bring awareness for this local opportunity. Campus opportunities are available to take part in initiatives focused on ethnic and gender diversity and inclusion at UC San Diego, and all Ph.D. students with a Specialization in Immunology will be encouraged to participate.

Page 5 Proposal for a Graduate Specialization in Immunology-UC San Diego

Formal coursework will include instruction that follows the requirements of the BMS or Biological Sciences programs, but in addition, includes specialized courses in bioinformatics, immunology, and a planned course in the immunological basis of disease. Upon choosing a dissertation advisor, students will obtain most of their education in the thought and action required to carry out original research. We acknowledge that much of an advanced graduate education comes in the form of daily or weekly interactions with other laboratory members, including the student’s faculty mentor. Equally important is the self-driven acquisition of knowledge from the literature and the trials of experimental science. As an adjunct to this process, and cited above, students will attend frequent outside seminars delivered by world-renowned scientists sponsored by the Program in Immunology, they will attend a weekly journal club, a bi-weekly Research-in-program colloquium, and an annual La Jolla Immunology Conference—all of which are well established, well-funded, and have been in existence for years. Students will meet yearly with their dissertation committee. Although we have support from local biotechnology companies to support many of our activities, the specialization itself does not require additional funding. However, there is little doubt that the creation of this specialization will enhance applications for training grants made to the National Institutes of Health. 2. Historical development of the field and historical development of departmental strength in the field In 1901, Emil von Behring was awarded the first Nobel Prize in Medicine "for his work on serum therapy, especially its application against diphtheria, by which he has opened a new road in the domain of medical science and thereby placed in the hands of the physician a victorious weapon against illness and deaths." In addition to developing serum therapy, von Behring and Kitasato first understood that the vaccines developed by Jenner, Pasteur and Koch worked because “iso-bodies” injected into a host produced “anti-bodies.”1 Thus we began to understand perhaps the greatest medical intervention of all time, the use of vaccines to create immunity in individuals and, through herd-immunity, the elimination of many infectious diseases from the population at large. The field of immunology is again poised to make monumental advances in the treatment of human disease. While there is still much to be learned about infectious diseases, as illustrated by the current pandemic, basic studies characterizing the control of lymphocyte activation have been translated into therapeutics that are transforming medical practice, specifically in autoimmune and inflammatory diseases and cancer. Advances in cancer immune therapy were awarded the Nobel Prize in physiology and medicine in 2018, emphasizing the prominence of immunology discoveries. In addition, bio-therapeutics, and particularly anti-cytokine antibodies, have provided great relief to a large number of patients suffering from auto-inflammatory conditions. Understanding of the vast and intricate mechanisms of immunity is converging with new genetic tools and big data, and the result will be an ability to specifically reprogram lymphocytes and other cells of the hematopoietic system. Such is the great promise of a new generation of treatments tailored to individual human dysfunction. Within the UC San Diego community, we have the basic components to be leaders in this scientific and clinical revolution. In fact, the Torrey Pines mesa has a long history of strength in immunology, led initially by the Scripps Research Institute (not to be confused with SIO). While immunology at Scripps Research has contracted, we have developed a top-rated basic and clinical immunology faculty at UC San Diego. We are ranked 23rd in the world in the US News and World Report listing of Best Global Universities for Immunology, where UC San Diego is listed at 16th in the Best Global Universities Overall2. We believe that the breadth and impact of our immunology group could be far greater. A reason for our confidence is that the group of faculty

1 From 1901 von Behring Nobel address 2 US News and World Report, Best Global Universities for Immunology Page 6 Proposal for a Graduate Specialization in Immunology-UC San Diego working on immunology-related problems is dispersed among different schools and divisions and lacks the visibility and programmatic cohesion that will be a goal of a unified graduate training providing a Specialization in Immunology. Most recently, UC San Diego has created a close affiliation with the La Jolla Institute for Immunology (LJI), also one of the top-rated immunology organizations in the world3. Our partnership provides an exciting opportunity to create an over-arching effort to promote graduate studies in Immunology on the UCSD campus that capitalizes on the vast faculty talent in the two institutions, creating an organization that is more than the sum of its parts. In addition to this academic strength in immunology, the UCSD School of Medicine has recently opened the Altman Clinical and Translational Research Institute (ACTRI) that will host clinical trials with emphasis on autoimmune and inflammatory diseases and an Advanced Cell Therapy Laboratory that will be capable of GMP production of engineered cells for cell and immune therapies. UC San Diego additionally has a top-rated program in bioengineering, affording a unique potential to rapidly translate genetic and cellular therapeutics into medical practice. To complete the landscape, local pharmaceutical and biotechnology companies are investing heavily in immunology research, particularly for the treatment of cancer. We are poised at a critical moment in the history of medicine, and UC San Diego is positioned to lead this revolution. We view a unified, inter-departmental Specialization in Immunology as a key element in making UC San Diego a leader for immunology research within the University of California system, and moreover, one that is comparable to any immunology effort in the world. 3. Timetable for development of the Specialization This initiative started as an ambitious plan to create an interinstitutional Program in Immunology that would promote research and education. This would include a research seminar series of distinguished lecturers, a seed grant program, support of the annual La Jolla Immunology Conference, a UCSD Immunology web presence, and a free-standing Graduate Program. All these entities are in place with the exception of a graduate program. After extensive discussions with the relevant parties on campus, we have decided to instead support a Specialization in Immunology as a part of the BMS and BS graduate programs. We have all the components in place including graduate Immunology electives, an annual meeting of the La Jolla Immunologists, an active (and oversubscribed) research-in-progress bi-weekly (once every two weeks) meeting, a weekly journal club, and monthly research seminar series—all of which are generously supported by the EVCs office, the UCSD Health Sciences, the La Jolla Institute, and local biotech companies. Our students will be required to actively participate in each of these for the duration of their graduate careers. Furthermore, we have created a web presence that is already putting UC San Diego at a higher rank in web searches related to “graduate training immunology” (immunology.ucsd.edu). Interested students are directed to the two umbrella graduate programs: Biomedical Sciences (BMS) and Biological Sciences (BS), and with this specialization, there will be specific instructions for application to the programs and the requirements for a specialization. We also plan to add two courses to the graduate course offerings: 1) Bioinformatics for Immunologists; 2) Immunological basis of disease. The first course has a course director and faculty participants identified. This course has been approved by the Health Sciences Graduate Programs Education Committee (GPEC). The second course is still in the planning stage, and although we are excited about offering this course largely taught by active clinicians, it is not required to start the specialization. Our time-table is to admit current BMS and Biology graduate students in 2020 with the first class of new students to matriculate in the Fall of 2021.

3 Thomson Reuters rating immunology programs based on citations/paper ranks LJI 5th and UC San Diego 16th in the world Page 7 Proposal for a Graduate Specialization in Immunology-UC San Diego

4. Relation of the Specialization to existing programs on campus and the Campus Academic Plan Immunology is presently a subdiscipline within both the Biomedical Sciences (BMS) and Biological Sciences (BS) programs; however, anecdotal reports and interviews with present students indicate that student applicants with an interest in immunology do not target UC San Diego for graduate school. We have not had visibility as an organized and unified place for graduate training in immunology. On PhDs.org UC San Diego does not rank in Immunology and Infectious Disease Graduate Schools. Neither do we make the list of graduate programs in California from the American Association of Immunologists. Our goal is to enhance the present pool of BMS and BS applicants interested in immunology as a discipline. In addition to attracting students with a predetermined interest in immunology, an important aspect of the Specialization in Immunology is to provide an intellectual and cultural home for students to become completely immersed in the scientific issues surrounding host immunity as it relates to infectious diseases, autoimmunity, and cancer. All aspects of cell biology, molecular biology, and physiology can be important for discovery in immunology, but we wish to promote the acquisition of this knowledge and the use of innovative techniques with a directed focus. Our seminars, colloquium, and courses will reflect the broad reach that mechanisms of immunity have on literally every aspect of life, from the details of protein translation as it limits viral replication to the physiology of systemic inflammation and the resulting diseases of abundance and age. However, the dominant theme in classwork, literature discussions, research, and presentations will be selective advantage afforded by the diverse mechanisms of immunity. The mission of the new Specialization in Immunology is congruent with several major goals of the UC San Diego Academic Plan. Goal 1-Educational Experience. We wish to educate students to solve problems and innovate in a diverse and interconnected world. To support this goal, we will add new courses and research experiences in emerging fields, such as bioinformatics data analysis and genetic re-programming of cells important for immune function. This program may also increase the Ph.D. student population—a major goal of the UC San Diego academic plan. As noted above, it will modestly increase the international student population as well. Goal 2-Cultivate a diverse and inclusive community. Program in Immunology faculty members participate on BMS and BS admission committees, and they will solicit applications from underrepresented minority students and appoint a Minority Inclusion Liaison to further facilitate those efforts. We hope to accomplish this through participation in outreach programs at local undergraduate institutions, the American Association of Immunologists annual meeting, the Annual Biomedical Research Conference for Minority Students (ABRCMS), and the Society for Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS). We have ensured and will continue to ensure that there is representation by gender and ethnicity in seminar speakers. Goal 3-Advance the frontiers of knowledge, shape new fields, and disseminate discoveries that transform lives. Immunology impacts most aspects of human life and all aspects of human health. All of the diseases of an aging population are, in essence, diseases of chronic inflammation—the hallmark of a dysregulated immune system. These include cardiovascular disease, diabetes, many forms of cancer, autoimmunity (3% of the American population), and many forms of neurodegenerative diseases. Vaccines have removed many of the “crowd epidemic” diseases from the developed world, and with increasing application they are greatly reducing the incidence of killer diseases such as measles and cholera world-wide. A frontier ahead includes treatments to prevent or treat a class of persistent infectious agents, such as the vaccine to protect against human papilloma virus, the cause of most cervical and head and neck cancer. The HPV vaccine appears to be able to prevent these deadly diseases if widely implemented, and similar vaccines could potentially diminish the effects of other persistent and latent human viruses including hepatitis B and cytomegalovirus. In addition, we are finally learning lessons that may allow us to modulate the immune system to prevent

Page 8 Proposal for a Graduate Specialization in Immunology-UC San Diego immunopathologies or alternatively, enhance an ongoing immune response as a therapeutic treatment for some forms of cancer. Although immunology as a discipline has developed many tools that can be applied to improve human health, a major goal of graduate studies in immunology is to advance human knowledge. We have come to appreciate that immunity as broadly understood cannot be dissociated from the co-evolution of free-living hosts and their commensal and pathogenic microbes and viruses. We have only scratched the surface of this intricate, complex, and constantly-evolving relationship. The next generation of students will incorporate microbiology as a new dimension in the study of immunity. We assert that immunology is central to the campus academic goal of “Enriching Human Life and Society.” 5. Administration The Specialization in Immunology will be administered by the Program in Immunology directors, currently Professors Hedrick and Kronenberg. Day-to-day management of this Graduate specialization will fall to the Program Administrator. The Program currently has funds for a part-time administrator for three years, and we will work to fund this position in future years through other mechanisms that could include Institutional allowance associated with an NIH T32 training grant ($4200/student), campus allocations, or local biotechnology company donations. The Program in Immunology has constituted a Leadership Council, which serves as a steering committee that meets semi-annually. The inauguration of this graduate specialization has been an emphasis of this group. The members of the Leadership Council are: A. Altman (LJI), J.T. Chang (UCSD-Medicine-GI Div.), E. Cohen (UCSD, Moores Cancer Center), M. Corr (UCSD, Medicine-Div. Rheum., Allergy, Immunol.), P.B. Ernst (UCSD-Pathology), A.W. Goldrath (UCSD-Division of Biology), T.M. Handel (UCSD-Pharmaceutical Sciences), S. M. Lippman (UCSD–Director of Moores Cancer), V. Nizet (UCSD--Pediatrics), S. Schoenberger (LJI), and M. Zanetti (UCSD, Moores Cancer Center ), along with Drs. Hedrick and Kronenberg. 6. Admissions Committee Each year the Leadership Council will choose an Immunology Program faculty member to represent the program on the admissions committees constituted by the BS Graduate Program and the BMS graduate program. Since admission into the specialization requires simultaneous admission into the BMS or BS, it is understood that the assigned faculty members will act only as regular committee members. Criteria for admission to the specialization will include those of the degree-granting units, with an additional component that considers the applicant’s interest in immunology. This component would look for direct laboratory experience and letters recommendation that support the applicant’s interest in some field related to immunology. 7. Academic Committee The Leadership Council will choose a representative from each participating department/program to serve on the Academic Committee. This committee will evaluate and coordinate the courses, oversee the streamlining of existing courses and the development of new courses, and make decisions on student performance and petition when special situations arise. 8. Dissertation Committee The Graduate Division has specific and strict guidelines on the composition of a Dissertation Committee. The Dissertation Committee is chosen by the Dissertation advisor and the student, must be approved by the Program Chair and the Dean of Graduate Division, and is appointed by the Graduate Division. The Dissertation Committee must have a minimum of 5 members and at least three must be from within the faculty of the graduate program in question. The BMS and BS programs have additional requirements that must be followed as described in BMS Guidelines (https://biomedsci.ucsd.edu/about/BMS-Guidelines_2019- 20.pdf) and Biological Sciences Grad Handbook (https://biology.ucsd.edu/_files/education/grad/biology-grad- Page 9 Proposal for a Graduate Specialization in Immunology-UC San Diego handbook.pdf). In addition, the Specialization will require that the faculty mentor and two other committee members come from the Program in Immunology. 9. Plan for evaluation In keeping with established campus procedures, we plan an internal review by the Leadership Council approximately three years after admitting the first class of students. This review will evaluate the students’ participation and performance, as well as faculty participation and departmental support. Amendments to the specialization will be made based on this evaluation. Additionally, this specialization will be included in campus-wide reviews of graduate programs. Section II. Program 1. Undergraduate preparation and requirements for admission Students admitted to the BMS or BS programs may enroll in the Specialization in Immunology after the first year, with rotations complete, and an expressed interest in doing thesis research in an immunology laboratory. Enrollment will also be available to students entering the BMS or BS programs. Admitted students will have satisfied the requirements for admission specified for the BMS or BS programs depending on the target of their application. As such, we expect students commencing graduate studies in immunology will have completed an undergraduate degree in any field related to biology, chemistry or engineering that also includes basic molecular and cell biology courses. For matriculation in the Specialization, students should have taken the equivalent of at least one undergraduate course in immunology. Those otherwise qualified students who have not taken an undergraduate course in immunology can fulfill this requirement by taking the week-long American Association of Immunologists Introductory Course in Immunology, presently held during the summer at the UCLA campus. Students can also fulfill this requirement by taking an upper- division summer course in immunology at any accredited college or university. The program administrator will work with admitted students to make sure they fulfill this requirement. This specialization will be built on the strength of the existing programs. To accomplish this, the proposed structure of the Ph.D. specialization is that each program will award a Ph.D. degree with a new “Specialization in Immunology.” Each student will be expected to fulfill the requirements of respective programs, but in addition, take advantage of the resources, courses, seminars, colloquia, and meetings sponsored by the Program in Immunology. In addition, all Ph.D. students in Immunology must receive passing grades in the required Immunology classes before they are permitted to take the candidacy exam. 2. Program of study a. Faculty mentors The eligible mentors for students enrolled in the Specialization in Immunology will consist of UC San Diego and LJI faculty members 1) with a full-time or adjunct appointment at UC San Diego AND 2) membership in the BS or BMS programs. There are members in the Program in Immunology who are not currently members of the BS or BMS programs, and they will not be able to take students. The Specialization in Immunology requires that faculty mentors be members of the awarding graduate programs. The areas of investigation in immunology will follow that of the faculty, and thus will span the breadth of immunology and host-pathogen interactions. We assume that the topics of interest will change with advances in knowledge and with the evolving interests of the faculty; but the focus will inevitably be centered on the fundamental processes that determine the organismal, cellular, and molecular mechanisms that have evolved to counter infectious, neoplastic, or autoimmune diseases. In addition to the traditional studies of resistance to infectious agents and neoplastic disease, the program will include studies covering the immunopathology that affects the cardiovascular system, the nervous system, and systemic metabolism. We hope to synergize with graduate studies in microbiology currently found in BMS and BS, especially involving host-microbial interactions, both

Page 10 Proposal for a Graduate Specialization in Immunology-UC San Diego disease-related and commensal, and seek to participate in coursework directed at the emerging field of study related to the microbiome. b. Plan: mentorship and student tracking In addition to the campus mandated annual spring evaluation for each PhD student, entering students enrolled in the Specialization in Immunology will be assigned an incoming faculty advisor from the eligible list who will help guide rotation choices for the student and will provide other needed information and advice. The student will choose laboratory rotations and ultimately a faculty mentor primarily based on the faculty membership in the respective graduate programs, BMS and BS. The rules for rotations and faculty mentors for each of the programs are somewhat arcane, but we will work with the administrators of each of the programs. The candidate and mentor will mutually decide upon a dissertation topic. The doctoral dissertation will then be approved by a 5-member Dissertation Committee, a committee that meets the general requirements of the Graduate Division and the degree conferring program.

In the instance that the student matriculates through the Biological Sciences, there will be an option for direct admission. The option may be exercised when a faculty member and a prospective student mutually agree that the student will join the faculty member’s laboratory as a condition of admission. In this case, the faculty member must assume stipend and tuition costs immediately upon the student’s matriculation. The direct admission must be approved by the admissions committee with the understanding that the applicant has substantial laboratory experience and that he or she will complete a dissertation in the lab of choice. c. Specialization requirements in addition to those of the degree-granting unit Students are expected to fulfill the requirements of their home graduate programs. The basic course requirements for BMS and BS are reproduced below; however, the student and her mentor will work with the respective graduate administers to make certain that the student's course program meets requirements. Basic requirements for Biomedical Sciences Required courses-All in Year 1 BIOM 200A/B Molecules to Organisms: Concepts and Approaches BIOM 200C Intro to Computational Biology for Biomedical Research BIOM 201 Seminars in Biomedical Research BIOM 202 Laboratory Rotation (one 12-week or two 6-week) BIOM 219 Ethics in Scientific Research BIOM 285 Statistical Inference Choice of 3 BGGN 225 Graduate Immunology* BIOM 226 Hormone Action BIOM 252 Genetics and Genomics BIOM 253 Immunology and Immuneregulation* BIOM 255A/B Molecular Basis of Drug Action and Disease Therapy BIOM 256 Molecular Basis of Cancer *Courses required for Immunology Specialty

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Choice of 2* BIOM 272/277 Seminars in Genetics, Genomics and Mol. Cell Biology BIOM 275 Seminars in Pharmacology BIOM 276 Seminars in Physiology We will add a course designation for the ongoing Immunology seminar series (BIOM 27x) to be taken in lieu of one of these offerings.

Basic requirement for Biological Sciences Graduate Program Course Description Quarter BGGN 200 Graduate School Fundamentals Fall BGGN 205 Communicating Science to the Public Spring BGGN 206A Concepts of Reasoning and Experimentation (CORE) I Fall BGGN 206B Concepts of Reasoning and Experimentation (CORE) II Winter BGGN 208 Graduate Boot Camp Fall? BGGN 213 Foundations of Bioinformatics Fall & Winter BGGN 216 Graduate Biostatistics Spring

Each program has provisions for electives, and these electives will be fulfilled by taking Bioinformatics for Immunologists4, and 2 out of the 3 following courses: BGGN 225-Graduate Immunology and BIOM253- Immunology and Immuneregulation; BGGN 232-Innate Immunity. When the Immunological basis of disease4 course is approved, this can be substituted as a fourth option. These courses can be taken either in the first or second years. An important aspect of this training program will be bioinformatics and quantitative analysis. As such, the students will be required to take a trio of courses. For BS students, this will include required courses BGGN 213 and BGGN 216 Graduate Biostatistics plus Bioinformatics for Immunologists (a newly-designed course). For BMS students, BIOM 285 Statistical Inference and Bioinformatics for Immunologists (a newly-designed course). The third course can be one of the required courses for BS students, with instructor permission, or another course related to analysis and bioinformatics that is suitable given the background of the student. The Program directors and Program administrator will work with the students and the Graduate advisors in BMS and BS to come up with a set of courses that satisfy the degree program and the Specialization. All students will be expected to sign up for, and attend the weekly Journal club in Immunology BGJC 204 and the research in progress course, BGSE 205. They will be encouraged/required by their mentors to attend the monthly Immunology seminar series, and the annual La Jolla Immunology conference. Students will be required to serve as an instructional assistant as required by their parent graduate program. The exact course will be determined by the needs of the department with input from the student. 3. Field examinations Not Applicable

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4. Examinations and yearly meetings a. Dissertation committee The dissertation committee composition was discussed in Section I-8. A list of the Dissertation Committee Members must be submitted for approval by the end of the Spring quarter of the second year. The Dissertation Committee serves an advisory role in the conduct of the Dissertation research, the full committee, assembled according to the Graduate Division rules, serves as the student's Advancement to Candidacy Examination Committee. b. Milestone Exams

The BMS program requires a Research Proposition during the summer of the 1st year and fall of the 2nd year. The Research Proposition is a grant-writing and oral presentation exercise in lieu of a comprehensive Qualifying Exam. The purpose is for the dissertation advisor and student to work together at an early stage to develop the student's research project, choose potential members of his/her Committee, teach student grant writing and oral presentation skills, test the student's grasp of core material relating to the student's research project, and provide the basis for a fellowship application. The Advancement to Candidacy review, should demonstrate that the student has made substantial progress on a thesis research and can chart a coherent course to the completion of the research. This should include significant and substantive findings that will likely lead to a first-author paper. Students must Advance to Candidacy no later than the end of their 3rd year. The details of these exams are described in BMS Guidelines, and will not be repeated here. For the BS program, all students are required to take a First-Year Comprehensive Examination. The exam tests general knowledge and skills in biological sciences with emphasis on material covered in the core curriculum. It is a qualifying exam, which means that performance on the exam, along with performance on rotations and in the core courses, will be used to determine continuation in the program. The second-year Proposition Examination will focus on the student’s dissertation proposal and include both a written report and an oral defense. The principal aims of this exam are for the student to demonstrate proficiency in the background literature relevant to the field in which he/she plans to carry out research and for her/him present a defensible dissertation proposal. Advancement to Candidacy, as above, should demonstrate that the student has made substantial progress on a thesis research and can chart a coherent course to the completion of the research. This should include significant and substantive findings that will likely lead to a first-author paper. Students should take the Advancement to Candidacy exam by the end of year three but no later than end of the 4th year. c. Yearly exams Before the start of each academic year, only in years in which there is no milestone exam (see above) typically in the summer, students will schedule a meeting with their entire Dissertation Committee, including their dissertation advisor. The student will present his or her dissertation project including background of the problem to be addressed, conceptual and technical approaches, feasibility, and experimental progress. If the student appears to be struggling, the Dissertation Committee may ask to meet more frequently or ask for written updates. Program in Immunology directors will receive a copy of the committee report, and act if there appear to be difficulties in the student's progress. d. Dissertation The doctoral dissertation is the essential component of the Ph.D. program. The guidelines for students in the Specialization will be those mandated by the Graduate Division and the respective graduate programs. Generally, students are encouraged to begin dissertation research activity as early as possible, but no later than the second year of their graduate studies. A topic will be selected by the student under the advice and guidance of the dissertation advisor. The topic will be presented to the committee and approved by Dissertation Committee as a consequence of successful completion of the Advancement to Candidacy Page 13 Proposal for a Graduate Specialization in Immunology-UC San Diego exam. All students will write a dissertation that introduces the state of the field and the outstanding questions therein, the logic of their investigations, results, and interpretation. If the advisor agrees, students may substitute published papers for part of the results section, although we will emphasize to the students and their mentors that papers not primarily written by the student should not be a substitute for a dissertation. By way of constructing an introduction, we will encourage students to write a review for publication on their topic of expertise, in addition to a research publication. Acceptance of the dissertation by the five-member dissertation committee follows Graduate Division guidelines. A draft of the dissertation shall be given to each dissertation committee member at least four weeks before the final examination described below. e. Oral defense The entire Dissertation Committee will conduct a final oral examination, which will deal primarily with questions arising out of the relationship of the dissertation to the field of Immunology. The final examination will be conducted in two parts. The first part consists of an approximately 50-minute public presentation by the candidate followed by a period of questions pertaining to the presentation. The second part of the examination will immediately follow the first part; this is a closed session between the student and the committee and will consist of a period of questioning by the committee members. Title and abstract of the oral presentation will be distributed to all faculty and students of departments that participate in the Program in Immunology Program, who are invited to attend the public presentation portion of the examination. 5. Special requirements over and above Graduate Division minimum requirements Students will be required to meet annually with their Dissertation Committee, or more often if deemed necessary. Students completing the immunology specialization will have the same doctoral time limits as other BMS and Biology students. While a first-author publication is not an absolute requirement, it is expected that the student has a complete body of work that is consistent with one or more publications as first author. 6. Relationship of Master’s and Doctoral programs Not applicable 7. Special preparation for careers in academic science, teaching, and industry a. Pedagogy Introducing students to the teaching of science at the university level is an essential part of becoming a practicing scientist. It is required for a successful academic career; but, perhaps as important, it promotes a scientist’s organization and clarity of thought in any endeavor. To truly understand a topic is to be able to present it clearly to a less-informed audience. In addition, the process of presenting a scientific topic can include the identification of unanswered questions, which is often a springboard to new directions of research. The Specialization in Immunology expects that all students, regardless of career path, will develop a high regard for excellence in teaching as well as research. To prepare graduates for a career in science, all students will be required to serve as an instructional assistant (IA) for at least one quarter. The requirements differ for the BS and BMS programs, BS has a more extensive teaching requirement that includes the Guide for Instructional Assistants created by the Division of Biological Sciences and BGGN 500, Introduction to College Biology Education, concurrent with the quarter in which they serve as an IA. As an IA, students will have the opportunity to work closely with existing faculty to develop teaching and course administration skills. As an IA, the students will not necessarily be assigned to an immunology course; as needs arise, the students may participate in cell biology, biochemistry, molecular biology, bioinformatics, or other related courses. Additionally, students will be required to participate in the Immunology Journal Club, BGJC 204 run by John Chang or the equivalent. Here students Page 14 Proposal for a Graduate Specialization in Immunology-UC San Diego will develop their oral presentation skills by discussing current research papers to an audience of faculty, postdocs, and graduate students. Presentation skills will be further enhanced by presentations in an ongoing Research in Immunology, BGSC 205, that meets every other week. b. Industry careers Given UC San Diego's location and proximity to local biotech and pharmaceutical firms, our location uniquely positions us to prepare graduates for careers in Biotechnology. A goal of the Specialization in Immunology will be to seek partnerships with area biotech firms, and provide students with the opportunity to visit and possibly intern in area laboratories or develop industry collaborations. We have interest thus far from the Genomics Institute of the Novartis Foundation (GNF), Pfizer, BioLegend and Celgene Corporation. BioLegend has agreed to financially support a different outstanding early stage student for one year over a five-year period. There is no expectation or requirement that this student will have an interest in a career in biotechnology. Regarding internships, the details will have to be negotiated to address liability and intellectual property issues and ensure consistency with University of California policies. III. Projected need (This section is required for a new free-standing program, but it is possibly not required for a specialization) 1. Student demand We anticipate continuous demand for graduate education in immunology. The trajectory of the number of studies in immunology is upward, partially due to the interest in tumor immunotherapy—the Science magazine breakthrough of the year for 2013, the subject of the 2018 Nobel Prize, and the foremost topic in cancer biology. More recently, the COIVD 19 pandemic has made the general public more aware than ever not only of the powerful benefit of vaccines, but of herd immunity, and neutralizing antibodies, contagion and other concepts. Immunology is funded through several NIH institutes (NIAID, NCI, NHLBI, NIDDK, NIA, etc.); and students "follow the money.” The announcement of a "moon-shot" for cancer research is heavily focused on immunotherapy, and this can only increase the interest in and funding for immunological studies as well as the anticipated funding for infectious disease research. Everyone knows someone with an overt autoimmune disease, whether it is rheumatoid arthritis, systemic lupus erythematosus, psoriasis, or Type I diabetes. Most people who live past retirement age will be affected by one of the chronic inflammatory diseases, such as cardiovascular disease, Alzheimer's disease, or Type II diabetes. Separately, many people are concerned about the extensive vaccination schedule to which we subject our children. Thus, immunology is a field of study that touches almost everyone, necessitating little effort to make a connection with students looking for a scientific career. According to a report published by Fortune Business Insights, titled “IMMUNOLOGY MARKET: GLOBAL MARKET ANALYSIS, INSIGHTS AND FORECAST, 2019-2026,” the market was valued at US$ 77,365.4 Mn in 2018. Fortune Business Insights has predicted that the market will reach US$143,833.2 Mn by 2026. This speaks to a prediction of continued growth in the economics of immune-related diseases. Immunology is also characterized by biological novelty. Presumably a result of unending evolutionary selection by the universe of pathogens, the immune system is characterized by the most extreme and unusual of biological processes in vertebrates. Somatic gene recombination, somatic gene conversion, somatic hypermutation, the vast polymorphism of the major histocompatibility complex, or the stem-cell like qualities of highly differentiated lymphocytes–all of these characteristics are not found outside of the adaptive immune system. While the mechanisms underlying these mysteries have been largely described, we have not plumbed the depths of immune mechanisms and how they interface with disease progress or healthy physiology. Most recently, the interplay between the body's microbiome and the immune system has been glimpsed in data showing the power of commensal bacteria to affect an arm of the immune system that mediates many

Page 15 Proposal for a Graduate Specialization in Immunology-UC San Diego of the autoimmune diseases. Another area of active research is the interface between the immune system and persistent infectious agents, mainly viruses. Most vaccines have been developed against acutely infectious agents—those that are cleared by a surviving patient. Vaccines to prevent persistent viruses, bacteria, or protozoans, have proven much more difficult to produce; yet, hundreds of millions of people are plagued by hepatitis B, hepatitis C, HIV, malaria, and tuberculosis. Formulating vaccines to diminish these diseases presents a monumental challenge for the next generations of biomedical researchers. 2. Opportunities for placement of graduates Traditionally, we aim to train Ph.D. graduates to embark on an academic career. Such has long been the goal of NIH training grants, and indeed this remains a point of focus—to graduate brilliant young scientists to lead the world in understanding the complexities of immunity in all its forms. We will design the training program to encourage students with an interest in basic science for its own sake; however, the landscape of scientific training is changing. A 2014 National Academies report on "The Postdoctoral Experience Revisited" estimated only 23% of postdoctoral fellows land a tenure track academic job (p. 57), and some estimates are lower. A recent Advisory Committee to the NIH director was charged to develop a model for a sustainable and diverse U.S. biomedical research workforce, reporting "The model should include an assessment of present and future needs in the academic research arena, but also current and future needs in industry, science policy, education, communication, and other pathways” (emphasis added). As such, NIH has acknowledged that a large number of graduate students use their training to work outside of traditional universities and academic research institutions. This view is particularly relevant for students in California. The California Life Sciences Industry Report (2018) listed: 3,249 life sciences companies in California had 1,274 new therapies in the development pipeline. Life sciences companies directly employed 298,709 people in California – the most in the nation – with annual wages averaging $113,000. California has a 53.2% share of the nation’s life sciences VC investment. Finally, NIH distributed $3.8 billion in research grants to California institutions to drive basic research, outpacing all other states. Certainly, studies targeted to immunological therapeutics were responsible for much of this investment. 3. Importance to the discipline. Immunology is currently a growing field of study: as stated above, most of the diseases of an aging population in the developed world result from chronic inflammation associated with a western diet, exercise (or lack thereof), sleep deprivation, and the absence of early life exposure to parasitic organisms with which our immune systems co-evolved. This is in addition to autoimmunity found in the population at a rate of ~3%. Additionally, we must consider the awareness and hope that immunotherapy may be the key to overcoming cancers that currently cannot be treated. Moreover, the topic of vaccinations is still very polarizing; and yet we have critical need for new vaccines to counteract emerging diseases, chronic infectious agents, and annual influenza. In the 2017-18 season, influenza was responsible for ~80,000 deaths in the US, and a recent study by economist Corey White showed that each rise in influenza vaccination rate of 1% results in 807 fewer deaths, mostly in seniors. SARS-CoV-2 will easily surpass that number of US deaths. For these reasons, there is a continuing need for trained immunologists. 4. Ways in which the Specialization will meet the needs of society A thread that weaves through this application is that immunology affects virtually every aspect of human health. We embrace the challenge of providing answers to some of the most vexing medical questions of our time—means of harnessing the immune system to eliminate cancer, inflammation associated with neurodegenerative diseases, and others human illnesses. Society will almost certainly benefit from well- trained, motivated, newly-educated researchers working on problems associated with the immune system.

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5. Relationship of the Specialization to research and/or professional interests of the faculty In Appendix I we list 51 faculty who joined the Program in Immunology. More than half of these individuals are members are UCSD faculty or adjuncts who are members of the BS and/or BS programs. The recruitment of graduate students with a stated interest in immunology will almost certainly enhance the research of our already illustrious faculty and will stimulate others in the group to join graduate programs and undertake graduate education and training. 6. Specialization differentiation The UC San Diego specialization will be distinguished by its relationship with the La Jolla Institute, providing students with access to the faculty and resources of a closely-affiliated institute specializing in the study of immunity. Our Program will be complemented by the strengths of the faculty in the Division of Biological Sciences specializing in immunology, as well as Program in Immunology faculty across the campus and the School of Medicine. Leveraging the strengths of a unique partnership with the La Jolla Institute, coupled with a strong basic science foundation and translational research, will result in a compelling Immunology Program. IV. Faculty We have an academically-diverse faculty interested in immunity, with UC San Diego home departments including Bioengineering; Cellular and Molecular Medicine; Dermatology; Gastroenterology (within the Department of Medicine); Molecular Biology; Hematology-Oncology (within the Department of Medicine); Pathology; Pediatrics; Pharmacology; School of Pharmacy; Division of Rheumatology, Allergy & Immunology (within the Department of Medicine); and Surgery (Appendix I). V. Courses for the Specialization in Immunology

BGGN 225: Graduate Immunology (4) The course is devoted to immunology and is organized as a combined lecture-tutorial course stressing classical as well as current literature. Each week will constitute an independent section. Topics will include cellular interactions involved in the immune response and the molecular biology unique to lymphocytes and their receptors. Instructor(s): Li-fan Lu and Elina Zuniga

BIOM 253: Immunology and Immuneregulation (3) This course will examine the innate and adaptive immune responses of humans to microbial infection. In parallel, we will explore the virulence mechanisms through which certain medically-important viruses, bacteria, fungi, and parasites subvert host defense to produce infectious disease. Emphasis will be placed on basic genetic and cellular approaches to understanding microbial pathogenesis and host susceptibility, including progress toward novel antibiotic and immune stimulatory therapies. Instructor(s): Maurizio Zanetti

New: Bioinformatics for Immunologists (4) This new course is designed to be a more advanced and technical, hands-on course in bioinformatics that is especially skewed toward problems in immunology. The course will present problems in immunology and how to use newly-acquired and publicly-accessible datasets to address those problems. Examples and problem sets will access and analyze data from sources such as the NCBI Gene Expression Omnibus, ImmGen, and the Immune Epitope database. Additional topics will include analysis of antibody and T cell antigen receptor repertoires, prediction of peptide epitopes for T cell recognition, and the functionality of

Page 17 Proposal for a Graduate Specialization in Immunology-UC San Diego nature killer cell receptors. Basic programming knowledge is required. Instructor(s): Ferhat Ay, Hannah Carter, and Olivier Harismendy

BGGN 232: Innate Immunity (4) The course will discuss the current understanding of innate immunity, including in organisms such as plants and invertebrates. Through readings and weekly presentations, students will learn the basic concepts of innate immunity including how immunity can be disrupted by pathogen effectors. Recent findings in these rapidly advancing fields will be covered. The course will include weekly seminar-style presentations in which each student will present once during the quarter. Instructor(s): Steven Briggs and Emily Troemel

BGJC 204. Journal Club in Molecular and Cellular Immunology (1)

Weekly presentations and discussions pertaining to research results reported in recently published literature. Prerequisite: none for graduate students. Undergraduates must be seniors or enrolled in BISP 199. (S/U grades only.) (F,W,S)

BGSE 205. Graduate Research Seminar (1)

Discussions of recent research in various aspects of biological research conducted by third- and fourth- year doctoral students in the Division of Biological Sciences. (S/U grades only.) (F,W,S)

BGGN 299. Thesis Research in Biology (1–12) Directed research on dissertation topic. S/U grades only. Instructor(s): Mentors TBD

2. Alternative or possible third Bioinformatics Courses for BMS students: PHAR 201: Bioinformatics 1 - Biological Data Representation and Analysis (4) Bioinformatics is driven by the need to understand complex biological systems for which data are accumulating at exponential or near exponential rates. Such an understanding relies on the effective representation of these data and the ability to analyze these data. This is a broad topic and we focus on macromolecular structure data, which is suitably complex, to introduce the principles of formal data representation, reductionism, comparison, classification, visualization, and biological inference. As such the course also serves as an introduction to Structural Bioinformatics Instructor(s): Philip E. Bourne BGGN 214. Introduction to Q-Biology (4) The course goal is to discuss and work through examples where quantitative biology approaches were necessary to yield novel biological insights. Problems will be presented with a historic perspective to instill a philosophy for when, how, and why q-bio approaches are most effective. The course may also appeal to physics and engineering graduate students. Instructor(s): Gurol Suel BGGN 237/CMM 262: Quantitative Methods in Genetics and Genomics (4) This course is designed to teach experimental and analytical approaches in modern genetics and genomics. Students will focus on several topic areas, developing techniques from experimental design through data analysis. Instructor(s): Gene Yeo MED 263: Bioinformatics Applications to Human Disease (4) Students learn background knowledge and practical skills for investigating the biological basis for human disease. Using bioinformatics applications, they (1) query biological and genetic sequence databases relevant to human health, (2) manipulate sequence data for alignment, recombination, selection, and

Page 18 Proposal for a Graduate Specialization in Immunology-UC San Diego phylogenetic analysis, (3) normalize microarray data and identify differentially expressed genes and biomarkers between patient groups, (4) annotate protein data and visualize protein structure, and (5) search the human genome and annotate genes relevant to human diseases. Instructor(s): Lucia Ohno-Machado and Olivier Harismendy

3. Related coursework available to students to substitute for required courses by petition SPPS 215: Human Disease (3) This introduction to human disease includes etiology and mechanisms of common disease states and integrates pathology with previous core curriculum. Students will focus on an understanding of disease processes and the dynamics of changes related to drug therapy. Instructor(s): Lawrence Hansen BGGN 238A: Integrative Microbiology I (4) To introduce students with structural and functional properties of microorganisms and with the role of microbes in the world. Course will emphasize the integrative aspects of microbiology. First course in series. Instructor(s): Joe Pogliano BGGN 238B: Integrative Microbiology II (4) This course introduces students to structural and functional properties of microorganisms and to the role of microbes in the world. Course will emphasize the integrative aspects of microbiology. Second course in series. Instructor(s): Doug Bartlett BGGN 292: Professional Pathways in Biological Sciences (1) Students meet experienced science professionals from a wide variety of backgrounds, including academia, science industry, and allied roles. Through discussions with these professionals, students will refine and improve their professional skills, including communication and presentation expertise, and develop a personal career action plan. Instructor(s): Ella Tour BIOM 209. Lipid Cell Signaling Genomics, Proteomics, and Metabolomics (2) Overview of new systems biology “omics” approaches to lipid metabolism and cell signaling including interrogating gene and lipid databases, techniques for lipidomics, and implications for profiling and biomarker discovery in blood and tissues relevant to inflammatory and other human diseases. Recommended: one quarter of undergraduate biochemistry. BIOM 224. Topics in Cancer Research (2) Each quarter will focus on an important area of cancer research such as immunology (fall), growth regulation (winter), and cancer genetics (spring). One-hour lecture coordinated with a one-hour seminar with the opportunity to meet with the invited speaker. BIOM 232. In vivo Cellular and Molecular Imaging (1) Strategies such as positron emission tomography, magnetic resonance imaging, and ultrasound for nondestructively imaging molecular and cell biological events inside living animals and eventually human patients. Emphasis on detecting angiogenesis, apoptosis, and expression of tumor-specific genes.

VI. Resource requirements We do not anticipate additional costs in faculty, library acquisition, or computing. Core courses in the program will be staffed by shifting existing efforts from current immunology tracks in the BS and BMS programs and by involving more adjunct faculty in regular class room teaching. No new equipment costs will be associated with these courses.

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VII. Graduate Student Support Support for graduate students after the first year comes from a variety of sources including research grants to faculty mentors, NIH training grants, individual fellowships such as those from NSF, private funds such as those from BioLegend, allocations for teaching assistants and others. The campus has initiated a five-year funding guarantee. It is a goal of the Graduate Specialization in Immunology to obtain an NIH-funded Training Grant in Immunology. VIII. Governance Governance and management of the graduate program will be the responsibility of the Program in Immunology Directors, the Program in Immunology Leadership Council, and Program Administrator. The Program in Immunology Directors will have final responsibility for the overall effectiveness, coordination, and management of the specialization. They will assure that there is communication and coordination among the BS and BMS programs, participating faculty and students, the Leadership Council and the Program Administrator. The Program in Immunology Directors will oversee overall operation and administration of Graduate Studies in Immunology Specialization, day-to-day operations with advice from the Leadership Council and Program Administrator. Importantly, while the Directors will have final responsibility for these areas, whenever possible, the Leadership Council will be included in the process of making major decisions.

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Appendix I Faculty Biographies

PROGRAM DIRECTORS

STEPHEN HEDRICK, Chancellor's Associates Chair VII and Distinguished Professor of Molecular Biology, UC San Diego (Ph.D., UC Irvine)

Stephen Hedrick, Ph.D., and his lab are interested in the sum of lymphocyte dynamics, including, but not limited to, lymphocyte survival and quiescence, lymphocyte expansion and survival, and alternate forms of lymphocyte programmed death. The regulation of lymphocytes is important for almost all of the diseases affecting an aging population: immune hypersensitivity, including asthma; autoimmunity, such as rheumatoid arthritis and psoriasis; cardiovascular disease; cancer; and metabolic diseases such as Type II diabetes.

Selected Publications

1. Hedrick, S. M. (2018). The Imperative to Vaccinate. The Journal of Pediatrics. https://doi.org/10.1016/j.jpeds.2018.06.041 2. Tsau, J. S., Huang, X., Lai, C.-Y., & Hedrick, S. M. (2018). The Effects of Dendritic Cell Hypersensitivity on Persistent Viral Infection. Journal of Immunology (Baltimore, Md. : 1950), 200(4), 1335–1346. https://doi.org/10.4049/jimmunol.1601870 3. Delpoux, A., Michelini, R. H., Verma, S., Lai, C.-Y., Omilusik, K. D., Utzschneider, D. T., … Hedrick, S. M. (2018). Continuous activity of Foxo1 is required to prevent anergy and maintain the memory state of CD8+ T cells. The Journal of Experimental Medicine, 215(2), 575–594. https://doi.org/10.1084/jem.20170697

MITCHELL KRONENBERG, President and CSO, La Jolla Institute; Adjunct Professor, UC San Diego (Ph.D., California Institute of Technology)

Mitchell Kronenberg, Ph.D., and his team study T cells – white blood cells responsible for recognizing and responding to foreign invaders, such as microbes. The laboratory focuses on natural killer T cells, a subset of T lymphocytes that recognize glycolipids, or combinations of sugar and fat. Their research also investigates how the immune system is regulated at barriers such as intestinal mucosae.

Selected Publications

1. Zhao, M., Svensson, M. N. D., Venken, K., Chawla, A., Liang, S., Engel, I., … Kronenberg, M. (2018). Altered thymic differentiation and modulation of arthritis by invariant NKT cells expressing mutant ZAP70. Nature Communications, 9(1), 2627. https://doi.org/10.1038/s41467-018-05095-7 2. Crosby, C. M., & Kronenberg, M. (2018). Tissue-specific functions of invariant natural killer T cells. Nature Reviews. Immunology. 18: 559-574, 2018. 3. Seo, G.-Y., Shui, J.-W., Takahashi, D., Song, C., Wang, Q., Kim, K., Mikulski, Z., Chandra, S., Giles, D.A., Zahner, S., Kim, P.-H., Cheroutre, H., Colonna, M., and Kronenberg, M. (2018) LIGHT-HVEM Signaling in Innate Lymphoid Cell Subsets Protects Against Enteric Bacterial Infection. Cell Host & Microbe. 24: 248-260.

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LEADERSHIP COUNCIL MEMBERS

AMNON ALTMAN, Director of Scientific Affairs and Professor of Cellular Biology, La Jolla Institute; Adjunct Professor of Medicine, UC San Diego (Ph.D, Weizmann Institute)

Amnon Altman, Ph.D., and his team study T lymphocytes – white blood cells formed in the thymus that are essential in the body’s fight against infection and disease. In particular, they study the biochemical changes that occur in T lymphocytes when an antigen activates a binding site on the surface of the T cell, called the T Cell Antigen Receptor (TCR). Dr. Altman and his laboratory have already identified several proteins critical to the proper activation of T cells, including an enzyme called protein kinase C theta (PKCθ), essential for T cell activation and survival, and, more recently, a T cell subset whose primary role is to prevent excessive immune responses carrying the risk of autoimmunity and inflammation.

Selected Publications

1. Pedros, C., Canonigo-Balancio, A. J., Kong, K.-F., & Altman, A. (2017). Requirement of Treg- intrinsic CTLA4/PKCη signaling pathway for suppressing tumor immunity. JCI Insight, 2(23). https://doi.org/10.1172/jci.insight.95692 2. Hashimoto, M., Nagao, J.-I., Ikezaki, S., Tasaki, S., Arita-Morioka, K.-I., Narita, Y., … Tanaka, Y. (2017). Identification of a Novel Alternatively Spliced Form of Inflammatory Regulator SWAP-70- Like Adapter of T Cells. International Journal of Inflammation, 2017, 1324735. https://doi.org/10.1155/2017/1324735 3. Joshi, R. N., Binai, N. A., Marabita, F., Sui, Z., Altman, A., Heck, A. J. R., … Schmidt, A. (2017). Phosphoproteomics Reveals Regulatory T Cell-Mediated DEF6 Dephosphorylation That Affects Cytokine Expression in Human Conventional T Cells. Frontiers in Immunology, 8, 1163. https://doi.org/10.3389/fimmu.2017.01163

JOHN CHANG, Associate Professor of Medicine in Residence, UC San Diego; Adjunct Associate Professor of Developmental Immunology, La Jolla Institute (M.D., University of Pennsylvania)

John Chang, M.D., and his lab study the cellular and molecular mechanisms underlying T lymphocyte fate specification. The Chang lab’s goal is to understand the molecular mechanisms enabling activated T lymphocytes to give rise to differentially-fated progeny. They have found that T lymphocytes exploit an evolutionarily conserved process—asymmetric cell division—during the course of an immune response in order to generate the diverse cell fates required for robust immunity and have also recently demonstrated a functional role for asymmetric division, mediated by the polarity protein atypical PKC, in specification of memory lymphocyte fates.

Selected Publications

1. Dulai, P. S., Boland, B. S., Singh, S., Chaudrey, K., Koliani-Pace, J. L., Kochhar, G., … Cao, C. (2018). Development and Validation of a Scoring System to Predict Outcomes of Vedolizumab Treatment in Patients With Crohn’s Disease. Gastroenterology. https://doi.org/10.1053/j.gastro.2018.05.039 2. Klann, J. E., Kim, S. H., Remedios, K. A., He, Z., Metz, P. J., Lopez, J., … Chang, J. T. (2018). Integrin Activation Controls Regulatory T Cell-Mediated Peripheral Tolerance. Journal of Immunology (Baltimore, Md. : 1950), 200(12), 4012–4023. https://doi.org/10.4049/jimmunol.1800112 Page 22 Proposal for a Graduate Specialization in Immunology-UC San Diego

3. Garcia, D. A., Baek, C., Estrada, M. V., Tysl, T., Bennett, E. J., Yang, J., & Chang, J. T. (2018). USP11 Enhances TGFβ-Induced Epithelial-Mesenchymal Plasticity and Human Breast Cancer Metastasis. Molecular Cancer Research: MCR, 16(7), 1172–1184. https://doi.org/10.1158/1541- 7786.MCR-17-0723

PETER ERNST, Director of the Center of Veterinary Sciences and Comparative Medicine and Professor of Pathology, UC San Diego; Co-Director of the UC Veterinary Medical Center, San Diego (D.V.M., University of Guelph and Ph.D., McMaster University)

Peter Ernst, D.V.M., Ph.D., and his lab are interested in the area of comparative (human to mouse) mucosal immunology with specific projects in immune-epithelial cell interactions involved in the microbial pathogenesis of acute and chronic diseases of the gastrointestinal tract. Their current emphasis in on the role of adenosine as an anti-inflammatory mediator and how it protects from disruption in the microbiota that trigger disease.

Selected Publications

1. Tyler, C. J., Pérez-Jeldres, T., Ehinger, E., Capaldo, B., Karuppuchamy, T., Boyer, J. D., … Rivera- Nieves, J. (2018). Implementation of Mass Cytometry as a Tool for Mechanism of Action Studies in Inflammatory Bowel Disease. Inflammatory Bowel Diseases. https://doi.org/10.1093/ibd/izy214 2. Ernst, P. B., & Carvunis, A.-R. (2018). Of mice, men and immunity: a case for evolutionary systems biology. Nature Immunology, 19(5), 421–425. https://doi.org/10.1038/s41590-018-0084-4 3. Kurashima, Y., Yamamoto, D., Nelson, S., Uematsu, S., Ernst, P. B., Nakayama, T., & Kiyono, H. (2017). Mucosal Mesenchymal Cells: Secondary Barrier and Peripheral Educator for the Gut Immune System. Frontiers in Immunology, 8, 1787. https://doi.org/10.3389/fimmu.2017.01787

ANANDA GOLDRATH, Tata Chancellor's Endowed Professorship V in Molecular Biology Professor and Chair Section in Molecular Biology, UC San Diego (Ph.D., University of Washington)

Ananda Goldrath, Ph.D., and her lab seek to understand how T cell memory is generated and maintained by identifying the transcriptional and signaling events that regulate the survival and differentiation of T cells as they navigate the immune response and become long-lived memory T cells. Relatively little is known about how the microenvironmental milieu impacts the transcriptional network controlling T cell effector function and memory differentiation; the Goldrath lab is examining the impact of microenvironment on gene expression in the context of infection. Ultimately, the Goldrath lab is investigating new ways to induce the immune system to provide protection from infection and eradicate malignancies.

Selected Publications

1. Wang, D., Diao, H., Getzler, A. J., Rogal, W., Frederick, M. A., Milner, J., … Pipkin, M. E. (2018). The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation. Immunity, 48(4), 659–674.e6. https://doi.org/10.1016/j.immuni.2018.03.028 2. Milner, J. J., & Goldrath, A. W. (2018). Transcriptional programming of tissue-resident memory CD8+ T cells. Current Opinion in Immunology, 51, 162–169. https://doi.org/10.1016/j.coi.2018.03.017 3. Smith-Raska, M. R., Arenzana, T. L., D’Cruz, L. M., Khodadadi-Jamayran, A., Tsirigos, A., Goldrath, A. W., & Reizis, B. (2018). The Transcription Factor Zfx Regulates Peripheral T Cell Self-Renewal and Proliferation. Frontiers in Immunology, 9, 1482. https://doi.org/10.3389/fimmu.2018.01482

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TRACY M. HANDEL, Professor of Pharmacology, UC San Diego (Ph.D., California Institute of Technology)

Dr. Handel's laboratory takes a multidisciplinary approach including cell and molecular biology, biochemistry, biophysics and structural biology to study the structure and function of chemokines and chemokine receptors. A major area of study includes determining the structure of chemokine receptors in complex with their natural protein ligand. The work by the Handel lab will form the basis for a new drug discovery initiative targeting the chemokine receptor, CCR2; the laboratory also studies the structural and dynamic basic for receptor activation, again to facilitate drug discovery.

Selected Publications

1. Proudfoot, A. E., Handel, T. M., & Graham, G. (2018). Editorial: Chemokines - beyond chemotaxis. Cytokine, 109, 1. https://doi.org/10.1016/j.cyto.2018.04.036 2. Ortiz Zacarías, N. V, Lenselink, E. B., IJzerman, A. P., Handel, T. M., & Heitman, L. H. (2018). Intracellular Receptor Modulation: Novel Approach to Target GPCRs. Trends in Pharmacological Sciences, 39(6), 547–559. https://doi.org/10.1016/j.tips.2018.03.002 3. Proudfoot, A. E. I., Johnson, Z., Bonvin, P., & Handel, T. M. (2017). Glycosaminoglycan Interactions with Chemokines Add Complexity to a Complex System. Pharmaceuticals (Basel, Switzerland), 10(3), 70. https://doi.org/10.3390/ph10030070

SCOTT LIPPMAN, Director, Moores Cancer Center, Associate Vice Chancellor of Cancer Research and Care, and Professor of Medicine, UC San Diego (M.D., Johns Hopkins)

Scott Lippman, M.D., is internationally-recognized for his research in precancer biology and cancer interception, to eradicate neoplasia before invasion. His NCI-funded Erlotinib Prevention of Oral Cancer (EPOC) trial involving targeting precancer genetic driver and immune defects began an era of molecular selection in this field. He leads the 2018 Stand Up To Cancer (SU2C) Pancreatic Cancer Interception Dream Team in transformative research, including developing cancer vaccines, launching the new field of immune interception and setting new standards for precision medicine. He chaired the NCI Pre-Cancer Atlas (PCA) Think Tank, NCI Cancer Moonshot PCA demonstration project, and led the Lancet Oncol Commission prevention effort to catalyze global collaborations to accelerate patient benefit.

Selected Publications

1. Pierzynski, J. A., Ye, Y., Lippman, S. M., Rodriguez, M. A., Wu, X., & Hildebrandt, M. A. T. (2018). Socio-demographic, Clinical, and Genetic Determinants of Quality of Life in Lung Cancer Patients. Scientific Reports, 8(1), 10640. https://doi.org/10.1038/s41598-018-25712-1 2. Martin, D., Degese, M. S., Vitale-Cross, L., Iglesias-Bartolome, R., Valera, J. L. C., Wang, Z., … Gutkind, J. S. (2018). Assembly and activation of the Hippo signalome by FAT1 tumor suppressor. Nature Communications, 9(1), 2372. https://doi.org/10.1038/s41467-018-04590-1 3. Zhang, T., Wang, Q., Fredimoses, M., Gao, G., Wang, K., Chen, H., … Dong, Z. (2018). The Ashitaba (Angelica keiskei) chalcones 4-hydroxyderricin and xanthoangelol suppress melanomagenesis by targeting BRAF and PI3-K. Cancer Prevention Research, canprevres.0092.2018. https://doi.org/10.1158/1940-6207.CAPR-18-0092

VICTOR NIZET, Professor of Pediatrics and Pharmacy, UC San Diego (M.D., Stanford University)

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Dr. Nizet’s laboratory interests lie in understanding the fundamental mechanisms of bacterial pathogenesis and the innate immune system, with a special focus on invasive and antibiotic-resistant pathogens. Using a variety of molecular genetic approaches, the laboratory discovers and characterizes bacterial virulence factors involved in cytotoxicity, adherence, invasion, inflammation, molecular mimicry, and resistance to immunologic clearance. They have shown that the basic information gained through this platform can lead to novel treatment strategies for infectious diseases, involving targeted neutralization of bacterial virulence phenotypes and pharmacologic augmentation of host innate immune function.

Selected Publications

1. Sakoulas, G., Geriak, M., & Nizet, V. (2018). Is a Reported Penicillin Allergy Sufficient Grounds to Forgo the Multidimensional Antimicrobial Benefits of β-Lactam Antibiotics? Clinical Infectious Diseases. https://doi.org/10.1093/cid/ciy557 2. Alisson-Silva, F., Liu, J. Z., Diaz, S. L., Deng, L., Gareau, M. G., Marchelletta, R., … Varki, A. (2018). Human evolutionary loss of epithelial Neu5Gc expression and species-specific susceptibility to cholera. PLoS Pathogens, 14(6), e1007133. https://doi.org/10.1371/journal.ppat.1007133 3. Askarian, F., Wagner, T., Johannessen, M., & Nizet, V. (2018). Staphylococcus aureus modulation of innate immune responses through Toll-like (TLR), (NOD)-like (NLR) and C-type lectin (CLR) receptors. FEMS Microbiology Reviews. https://doi.org/10.1093/femsre/fuy025

STEPHEN SCHOENBERGER, Professor of Developmental Immunology, La Jolla Institute; Adjunct Professor, UC San Diego (Ph.D., UC Los Angeles)

Stephen Schoenberger and his team focus on achieving a mechanistic understanding of the generation and regulation of T cell responses in the context of in vivo infection and tumor development. One area of concern will help to inform superior vaccination strategies for cancer and infectious disease; a second line of research is directed towards the development of preclinical animal models of cancer immunotherapy, both in the context of adoptive immunotherapy as well as neoantigen-specific cancer vaccines. Lastly, the laboratory is part of a clinical Head and Neck Cancer immunotherapy Program at UC San Diego’s Moores Cancer Center that is focused on treating patients through neoantigen-specific immunotherapy.

Selected Publications

1. Ascierto, P. A., Puzanov, I., Agarwala, S. S., Bifulco, C., Botti, G., Caracò, C., … Thurin, M. (2018). Perspectives in melanoma: Meeting report from the Melanoma Bridge (30 November-2 December, 2017, Naples, Italy). Journal of Translational Medicine, 16(1), 207. https://doi.org/10.1186/s12967- 018-1568-6 2. Schoenberger, S. P. (2017). Is It Possible to Develop Cancer Vaccines to Neoantigens, What Are the Major Challenges, and How Can These Be Overcome? Targeting the Right Antigens in the Right Patients. Cold Spring Harbor Perspectives in Biology, a028837. https://doi.org/10.1101/cshperspect.a028837 3. Hope, J. L., Pulendran, B., Schoenberger, S. P., & Katsikis, P. D. (2016). 1st International Conference on Human & Translational Immunology. Nature Immunology, 18(1), 1–4. https://doi.org/10.1038/ni.3635

MAURIZIO ZANETTI, Professor Emeritus, Moores Cancer Center, UC San Diego (M.D., University of Padua)

The laboratory of Maurizio Zanetti, M.D., investigates the immune system and ways to manipulate the immune response in distinct but interrelated areas of investigations. The lab employs immunochemical and Page 25 Proposal for a Graduate Specialization in Immunology-UC San Diego cellular immunology tools, together with molecular biology and gene analysis techniques, to investigate the nature of selected aspects of the immune response and, contextually, develop principle-based new ways to regulate the immune response against cancer and viral pathogens. The Zanetti lab developed the first physiological, genetically-programmable, cell-based method to immunize against cancer cells and pathogens; discovered the immunogenicity of telomerase reverse transcriptase in humans defining the chemical characteristics of what can be regarded as the first universal tumor antigen; and unexpectedly determined that endoplasmic reticulum stress is transmissible from tumor cells to myeloid cells.

Selected Publications

1. Kouznetsova, V. L., Hu, H., Teigen, K., Zanetti, M., & Tsigelny, I. F. (2018). Cripto stabilizes GRP78 on the cell membrane. Protein Science, 27(3), 653–661. https://doi.org/10.1002/pro.3358 2. Vitiello, A., & Zanetti, M. (2017). Neoantigen prediction and the need for validation. Nature Biotechnology, 35(9), 815–817. https://doi.org/10.1038/nbt.3932 3. Rodvold, J. J., Kesari, S., & Zanetti, M. (2017). A community affair in the tumor microenvironment. Oncotarget, 8(63), 106173–106174. https://doi.org/10.18632/oncotarget.22586

PROGRAM MEMBERS

FERHAT AY, Assistant Professor of Computational Biology, La Jolla Institute; Assistant Adjunct Professor, UC San Diego (Ph.D., University of Florida)

Dr. Ay and his lab focus on understanding gene regulation in complex organisms and diseases by developing novel methods that leverage high-throughput genomics and epigenomics data. Ay develops computational methods that are based in statistics, machine learning, optimization and graph theory. He is particularly interested in the analysis and modeling of the 3D genome architecture from high-throughput chromatin conformation capture data to understand how changes in this 3D architecture affect cellular outcome such as development, differentiation, gene expression, and disease phenotypes.

Selected Publications

1. Bunnik, E. M., Cook, K. B., Varoquaux, N., Batugedara, G., Prudhomme, J., Cort, A., … Le Roch, K. G. (2018). Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages. Nature Communications, 9(1), 1910. https://doi.org/10.1038/s41467-018- 04295-5 2. Chakraborty, A., & Ay, F. (2017). Identification of copy number variations and translocations in cancer cells from Hi-C data. Bioinformatics (Oxford, England), 34(2), 338–345. https://doi.org/10.1093/bioinformatics/btx664 3. Chakraborty, A., & Ay, F. (2018). The role of 3D genome organization in disease: From compartments to single nucleotides. Seminars in Cell & Developmental Biology. https://doi.org/10.1016/j.semcdb.2018.07.005

NUNZIO BOTTINI, Professor of Medicine, UC San Diego; Adjunct Professor of Cellular Biology, La Jolla Institute (M.D. and Ph.D., University of Rome Tor Vergata)

Page 26 Proposal for a Graduate Specialization in Immunology-UC San Diego

The Bottini laboratory studies the mechanism of action of signaling molecules encoded by human autoimmune disease-predisposing genes and also analyses signal transduction pathways in pathological specimens from patients. The first focus of the laboratory is on phosphatase genes that increase risk of autoimmune disease; Dr. Bottini was the first to report that a mutation in the PTPN22 gene, encoding a phosphatase, increases the risk of autoimmunity in humans. A second focus is studying biochemical signaling (focusing in particular on the role of phosphatases) in tissue resident cells in arthritis, scleroderma, and other diseases.

Selected Publications 1. Sacchetti, C., Bai, Y, Stanford SM, Di Benedetto P, Cipriani P, Santelli E, Piera-Velazquez S, Chernitskiy V, Kiosses WB, Ceponis A, Kaestner KH, Boin F, Jimenez SA, Giacomelli R, Zhang ZY, Bottini N. (2017). PTP4A1 promotes TGFβ signaling and fibrosis in systemic sclerosis. Nat Commun, Oct 20;8(1):1060. doi: 10.1038/s41467-017-01168-1. 2. Stanford SM, Bottini N. (2017). Targeting Tyrosine Phosphatases: Time to End the Stigma Trends Pharmacol Sci. 2017 Jun;38(6):524-540. doi: 10.1016/j.tips.2017.03.004. Epub 2017 Apr 12. Review. 3. Zhao, M., Svensson, M. N. D., Venken, K., Chawla, A., Liang, S., Engel, I., … Kronenberg, M. (2018). Altered thymic differentiation and modulation of arthritis by invariant NKT cells expressing mutant ZAP70. Nature Communications, 9(1), 2627. https://doi.org/10.1038/s41467-018-05095-7

JACK BUI, Director, Stem Cell Processing, Pathology Hematologic Malignancies Program, Moores Cancer Center and Associate Professor in Residence, UC San Diego (Ph.D. and M.D., UC San Diego)

Dr. Bui's laboratory is interested in how the innate immune system recognizes developing tumor cells. Toward this end, they have generated a bank of tumor cell lines which they believe are enriched in recognition structures that activate innate immune components, including natural killer (NK) cells and macrophages. Bui and his colleagues hope to understand the molecular basis of this recognition. Using microarray studies, they plan to identify tumor-expressed surface molecules and cytokines that may influence NK and macrophage function.

Selected Publications

1. Strnadel, J., Carromeu, C., Bardy, C., Navarro, M., Platoshyn, O., Glud, A. N., … Marsala, M. (2018). Survival of syngeneic and allogeneic iPSC-derived neural precursors after spinal grafting in minipigs. Science Translational Medicine, 10(440), eaam6651. https://doi.org/10.1126/scitranslmed.aam6651 2. Klann, J. E., Kim, S. H., Remedios, K. A., He, Z., Metz, P. J., Lopez, J., … Chang, J. T. (2018). Integrin Activation Controls Regulatory T Cell-Mediated Peripheral Tolerance. Journal of Immunology (Baltimore, Md. : 1950), 200(12), 4012–4023. https://doi.org/10.4049/jimmunol.1800112 3. Meier, A., Gross, E. T. E., Schilling, J. M., Seelige, R., Jung, Y., Santosa, E., … Bui, J. D. (2018). Isoflurane Impacts Murine Melanoma Growth in a Sex-Specific, Immune-Dependent Manner: A Brief Report. Anesthesia and Analgesia, 126(6), 1910–1913. https://doi.org/10.1213/ANE.0000000000002902

HANNAH CARTER, Assistant Professor of Medicine, UC San Diego (Ph.D., Johns Hopkins University School of Medicine)

Page 27 Proposal for a Graduate Specialization in Immunology-UC San Diego

Dr. Hannah Carter’s research focuses on computationally modeling how DNA mutations in tumor genomes impact intracellular biological processes and cellular behaviors, and how these cellular level changes cause cancer. The Carter lab uses computational tools to study the relationship between genotype and cancer- associated phenotypes at multiple scales. In 2013, Dr. Carter received a prestigious NIH Early Independence Award for her project, Network Approaches to Identify Cancer Drivers from High-Dimensional Tumor Data.

Selected Publications

1. Marty, R., de Prisco, N., Carter, H., & Font-Burgada, J. (2018). MHC-I genotype drives early immune selection of oncogenic mutations. Molecular & Cellular Oncology, 5(2), e1409863. https://doi.org/10.1080/23723556.2017.1409863 2. Ozturk, K., Dow, M., Carlin, D. E., Bejar, R., & Carter, H. (2018). The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine. Journal of Molecular Biology, 430(18), 2875–2899. https://doi.org/10.1016/j.jmb.2018.06.016 3. Zhang, W., Bojorquez-Gomez, A., Velez, D. O., Xu, G., Sanchez, K. S., Shen, J. P., … Ideker, T. (2018). A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nature Genetics, 50(4), 613–620. https://doi.org/10.1038/s41588-018-0091-2

HILDE CHEROUTRE, Professor of Developmental Immunology, La Jolla Institute; Adjunct Professor of Medicine, UC San Diego (Ph.D., Ghent University)

Hilde Cheroutre, Ph.D., and her team are studying the development, function, and regulation of white blood cells, a type of T lymphocytes. The laboratory is investigating how the immune system provides protection at “interfaces,” or places where the outside world comes in contact with the inside of the body, such as skin, lungs, mouth, and the largest surface of all, the intestine. The laboratory is investigating how the immune system succeeds in differentiating between the two and what causes the system to fail, allowing the antigens to invade the body.

Selected Publications

1. Saadalla, A. M., Osman, A., Gurish, M. F., Dennis, K. L., Blatner, N. R., Pezeshki, A., … Khazaie, K. (2018). Mast cells promote small bowel cancer in a tumor stage-specific and cytokine-dependent manner. Proceedings of the National Academy of Sciences of the United States of America, 115(7), 1588–1592. https://doi.org/10.1073/pnas.1716804115 2. Verstichel, G., Vermijlen, D., Martens, L., Goetgeluk, G., Brouwer, M., Thiault, N., … Vandekerckhove, B. (2017). The checkpoint for agonist selection precedes conventional selection in human thymus. Science Immunology, 2(8), eaah4232. https://doi.org/10.1126/sciimmunol.aah4232 3. Larange, A., & Cheroutre, H. (2016). Retinoic Acid and Retinoic Acid Receptors as Pleiotropic Modulators of the Immune System. Annual Review of Immunology, 34(1), 369–394. https://doi.org/10.1146/annurev-immunol-041015-055427

HIUTUNG “HIU” CHU, Assistant Professor of Pathology, UC San Diego; Adjunct Assistant Professor, La Jolla Institute (Ph.D., UC Davis)

The Chu lab’s primary research goal is understanding mechanisms that direct immune tolerance in the gut. Chu and her team are particularly interested in identifying the common language by which symbiotic bacteria induce commensal-driven immune responses. The lab is pioneering research into how the immune system tolerates a foreign and complex microbial community, and whether this tolerogenic balance is disrupted Page 28 Proposal for a Graduate Specialization in Immunology-UC San Diego during intestinal pathologies; these discoveries will subsequently inform them of basic processes that can be targeted for the development of novel, personalized therapeutic approaches to inflammatory diseases.

Selected Publications

1. Chu, H. (2017). Host gene-microbiome interactions: molecular mechanisms in inflammatory bowel disease. Genome Medicine, 9(1), 69. https://doi.org/10.1186/s13073-017-0459-4 2. Chairatana, P., Chu, H., Castillo, P. A., Shen, B., Bevins, C. L., & Nolan, E. M. (2016). Proteolysis Triggers Self-Assembly and Unmasks Innate Immune Function of a Human α-Defensin Peptide. Chemical Science, 7(3), 1738–1752. https://doi.org/10.1039/C5SC04194E 3. Chu, H., Khosravi, A., Kusumawardhani, I. P., Kwon, A. H. K., Vasconcelos, A. C., Cunha, L. D., … Mazmanian, S. K. (2016). Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Science (New York, N.Y.), 352(6289), 1116–1120. https://doi.org/10.1126/science.aad9948

MICHAEL CROFT, Professor of Immune Regulation, La Jolla Institute; Associate Adjunct Professor of Medicine, UC San Diego (Ph.D., Sussex University)

Croft and his team focus on a number of molecules that are members of the tumor necrosis factor (TNF) and tumor necrosis factor receptor (TNFR) family, a group of proteins believed to play important roles in the ability of the immune system to guard the body against harmful microorganisms. The TNFR molecules studied by Dr. Croft and his laboratory are expressed on T lymphocytes and other cells of the immune system and emerging evidence is suggesting they are crucial for the effective function of these cells in many types of immune response. Dr. Croft is the primary inventor on a number of patents directed at autoimmune/inflammatory disease therapy targeting the TNF family, and he has consulted for many major pharmaceutical firms.

Selected Publications

1. Bitra, A., Doukov, T., Croft, M., & Zajonc, D. M. (2018). Crystal structures of the human 4-1BB receptor bound to its ligand 4-1BBL reveal covalent receptor dimerization as a potential signaling amplifier. The Journal of Biological Chemistry, 293(26), 9958–9969. https://doi.org/10.1074/jbc.RA118.003176 2. Publicover, J., Gaggar, A., Jespersen, J. M., Halac, U., Johnson, A. J., Goodsell, A., … Baron, J. L. (2018). An OX40/OX40L interaction directs successful immunity to hepatitis B virus. Science Translational Medicine, 10(433), eaah5766. https://doi.org/10.1126/scitranslmed.aah5766 3. da Silva Antunes, R., Mehta, A. K., Madge, L., Tocker, J., & Croft, M. (2018). TNFSF14 (LIGHT) Exhibits Inflammatory Activities in Lung Fibroblasts Complementary to IL-13 and TGF-β. Frontiers in Immunology, 9, 576. https://doi.org/10.3389/fimmu.2018.00576

SHANE CROTTY, Professor of Vaccine Discovery, La Jolla Institute; Adjunct Professor UC San Diego (Ph.D., UC San Francisco)

Dr. Crotty’s research focus is on the underlying immunology of vaccines, particularly the development of potent antibody responses and memory, with a predominant focus on the important role of CD4 T cells in these processes. The Crotty lab has helped established that follicular helper T cells (Tfh) are a distinct type of differentiated CD4 T cell uniquely specialized in B cell help, and that Tfh differentiation is controlled by the transcription factor Bcl6. Crotty has made major advances in the area of T cell help to B cells and through this work has become an internationally-recognized leader in the field of Tfh cell biology. Page 29 Proposal for a Graduate Specialization in Immunology-UC San Diego

Selected Publications

1. Havenar-Daughton, C., Sarkar, A., Kulp, D. W., Toy, L., Hu, X., Deresa, I., … Crotty, S. (2018). The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen. Science Translational Medicine, 10(448), eaat0381. https://doi.org/10.1126/scitranslmed.aat0381 2. Cho, S., Lee, H.-M., Yu, I.-S., Choi, Y. S., Huang, H.-Y., Hashemifar, S. S., … Lu, L.-F. (2018). Differential cell-intrinsic regulations of germinal center B and T cells by miR-146a and miR-146b. Nature Communications, 9(1), 2757. https://doi.org/10.1038/s41467-018-05196-3 3. da Silva Antunes, R., Babor, M., Carpenter, C., Khalil, N., Cortese, M., Mentzer, A. J., … Sette, A. (2018). Th1/Th17 polarization persists following whole-cell pertussis vaccination despite repeated acellular boosters. The Journal of Clinical Investigation. https://doi.org/10.1172/JCI121309

MATTHEW DAUGHERTY, Assistant Professor of Molecular Biology, UC San Diego (Ph.D., UC San Francisco)

The Daugherty lab applies evolutionary principles, with virology and mechanistic biochemistry, to understand how the immune system has evolved to defend against pathogens and how pathogens counter-evolve to defeat host immunity. One of the approaches the lab takes is to use comparative genomics to identify characteristic signatures of pathogen-driven innovation. Their ultimate goal is to understand the rapidly- evolving molecular means by which hosts and pathogens battle each other, while also providing insight into how genetic variation resulting from these conflicts contributes to differences in human susceptibility to infectious diseases.

Selected Publications

1. Moens, U., Calvignac-Spencer, S., Lauber, C., Ramqvist, T., Feltkamp, M. C. W., Daugherty, M. D., … Ictv Report Consortium. (2017). ICTV Virus Taxonomy Profile: Polyomaviridae. The Journal of General Virology, 98(6), 1159–1160. https://doi.org/10.1099/jgv.0.000839 2. Chavarría-Smith, J., Mitchell, P. S., Ho, A. M., Daugherty, M. D., & Vance, R. E. (2016). Functional and Evolutionary Analyses Identify Proteolysis as a General Mechanism for NLRP1 Inflammasome Activation. PLoS Pathogens, 12(12), e1006052. https://doi.org/10.1371/journal.ppat.1006052 3. Calvignac-Spencer, S., Feltkamp, M. C. W., Daugherty, M. D., Moens, U., Ramqvist, T., Johne, R., … Ehlers, B. (2016). A taxonomy update for the family Polyomaviridae. Archives of Virology, 161(6), 1739–1750. https://doi.org/10.1007/s00705-016-2794-y

MICHAEL DAVID, Professor of Biological Sciences, UC San Diego (Ph.D., University of Vienna)

The David lab aims to elucidate the mechanisms by which interferons (IFNs) exhibit diverse biological effects. The lab investigates the following areas: characterization of signal transduction mechanisms that permit IFNs to activate transcription of defined cellular genes; definition of cellular and molecular events governing immunomodulatory properties of interferons; elucidation of pathways by which the immune system recognizes infection and initiates an innate immune response. The laboratory is also interested in innate immune processes governing induction of interferon production following pathogen recognition.

Selected Publications

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1. Stabell, A. C., Hawkins, J., Li, M., Gao, X., David, M., Press, W. H., & Sawyer, S. L. (2016). Non- human Primate Schlafen11 Inhibits Production of Both Host and Viral Proteins. PLOS Pathogens, 12(12), e1006066. https://doi.org/10.1371/journal.ppat.1006066 2. Almaden, J. V., Liu, Y. C., Yang, E., Otero, D. C., Birnbaum, H., Davis-Turak, J., … Hoffmann, A. (2016). B-cell survival and development controlled by the coordination of NF- B family members RelB and cRel. Blood, 127(10), 1276–1286. https://doi.org/10.1182/blood-2014-10-606988 3. Otero, D. C., Fares-Frederickson, N. J., Xiao, M., Baker, D. P., & David, M. (2015). IFN-β Selectively Inhibits IL-2 Production through CREM-Mediated Chromatin Remodeling. The Journal of Immunology, 194(11), 5120–5128. https://doi.org/10.4049/jimmunol.1403181

ANTONIO DE MAIO, Professor of Surgery and Neuroscience, UC San Diego (Ph.D., Weizmann Institute of Science)

The De Maio laboratory has found that response to injury is modulated by several confounding factors, including genetic background, sex, age, diet, and environment. As the major factor associated with morbidity and mortality injury is an overwhelming inflammatory response, the group is using mouse genetics to identify genes that regulate the inflammatory process as potential therapeutic targets. The lab is also actively engaged in training of basic scientists, future academic surgeons, and students at the undergraduate, graduate, and medical school levels.

Selected Publications

1. Bickler, S. W., Wang, A., Amin, S., Halbach, J., Lizardo, R., Cauvi, D. M., & De Maio, A. (2018). Urbanization in Sub-Saharan Africa: Declining Rates of Chronic and Recurrent Infection and Their Possible Role in the Origins of Non-communicable Diseases. World Journal of Surgery, 42(6), 1617– 1628. https://doi.org/10.1007/s00268-017-4389-5 2. Liu, Z., Cauvi, D. M., Bernardino, E. M. A., Lara, B., Lizardo, R. E., Hawisher, D., … De Maio, A. (2018). Isolation and characterization of human urine extracellular vesicles. Cell Stress & Chaperones. https://doi.org/10.1007/s12192-018-0902-5 3. Arispe, N., & De Maio, A. (2018). Memory Loss and the Onset of Alzheimer’s Disease Could Be Under the Control of Extracellular Heat Shock Proteins. Journal of Alzheimer’s Disease: JAD, 63(3), 927–934. https://doi.org/10.3233/JAD-180161

WENXIAN FU, Assistant Professor of Pediatrics, UC San Diego (Ph.D., Peking University)

Dr. Fu’s research focuses on the immune regulatory mechanisms that lead to type 1 diabetes, with the goal of discovering new preventive and therapeutic strategies. His lab is also exploring new imaging methods for predicting the risk of developing type 1 diabetes before patients are diagnosed with the disease. Specifically, the Fu lab is interested in examining the regulatory mechanisms in the pathogenesis of autoimmune type 1 diabetes and other complex diseases in which tissue inflammation is a key component of the disease pathogenesis.

Selected Publications

1. Chen, K., Jih, A., Osborn, O., Kavaler, S. T., Fu, W., Sasik, R., … Kim, J. J. (2018). Distinct gene signatures predict insulin resistance in young mice with high fat diet-induced obesity. Physiological Genomics, 50(3), 144–157. https://doi.org/10.1152/physiolgenomics.00045.2017

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2. Lee, J., Liao, R., Wang, G., Yang, B.-H., Luo, X., Varki, N. M., … Feng, G.-S. (2017). Preventive Inhibition of Liver Tumorigenesis by Systemic Activation of Innate Immune Functions. Cell Reports, 21(7), 1870–1882. https://doi.org/10.1016/j.celrep.2017.10.064 3. Yuan, X., Yang, B.-H., Dong, Y., Yamamura, A., & Fu, W. (2017). CRIg, a tissue-resident macrophage specific immune checkpoint molecule, promotes immunological tolerance in NOD mice, via a dual role in effector and regulatory T cells. ELife, 6. https://doi.org/10.7554/eLife.29540

MARK GINSBERG, Distinguished Professor of Medicine, UC San Diego (M.D., State University of New York, Downstate Medical Center)

Early studies from the Ginsberg laboratory established that the matrix protein fibronectin binds to specific cell surface receptors, members of a widely-distributed protein family, now termed integrins, that are essential for normal development and functioning of both vertebrates and invertebrates. A specific interaction of integrin cytoplasmic domains with talin, a cytoskeletal protein, proved to be the key to inside out signaling. The present focus of the Ginsberg lab is to analyze the structural basis of inside out signaling–how the signal traverses the plasma membrane–and how cells regulate the talin-integrin interaction.

Selected Publications

1. Zeineddine, H. A., Girard, R., Saadat, L., Shen, L., Lightle, R., Moore, T., … Awad, I. A. (2018). Phenotypic characterization of murine models of cerebral cavernous malformations. Laboratory Investigation; a Journal of Technical Methods and Pathology. https://doi.org/10.1038/s41374-018- 0030-y 2. Klann, J. E., Kim, S. H., Remedios, K. A., He, Z., Metz, P. J., Lopez, J., … Chang, J. T. (2018). Integrin Activation Controls Regulatory T Cell-Mediated Peripheral Tolerance. Journal of Immunology (Baltimore, Md.: 1950), 200(12), 4012–4023. https://doi.org/10.4049/jimmunol.1800112 3. Sun, H., Lagarrigue, F., Gingras, A. R., Fan, Z., Ley, K., & Ginsberg, M. H. (2018). Transmission of integrin β7 transmembrane domain topology enables gut lymphoid tissue development. The Journal of Cell Biology, 217(4), 1453–1465. https://doi.org/10.1083/jcb.201707055

CHRISTOPHER K. GLASS, Professor of Cellular and Molecular Medicine and Professor of Medicine, UC San Diego (M.D. and Ph.D., UC San Diego)

Dr. Glass’s primary interests are to understand the mechanisms by which sequence-specific transcription factors, co-activators, and co-repressors regulate the development and function of macrophages. A major direction of his laboratory has been to define the genome-wide locations and functions of these proteins through the use of assays that are based on massively parallel DNA sequencing. The combination of these technologies with molecular, genetic, lipidomic, and cell-based approaches is providing new insights into mechanisms that regulate macrophage gene expression and function that are relevant to inflammatory diseases including diabetes, atherosclerosis, and neurodegenerative diseases.

Selected Publications

1. Schlachetzki, J. C. M., Prots, I., Tao, J., Chun, H. B., Saijo, K., Gosselin, D., … Winkler, J. (2018). A monocyte gene expression signature in the early clinical course of Parkinson’s disease. Scientific Reports, 8(1), 10757. https://doi.org/10.1038/s41598-018-28986-7 2. Link, V. M., Romanoski, C. E., Metzler, D., & Glass, C. K. (2018). MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements. Nucleic Acids Research. https://doi.org/10.1093/nar/gky491

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3. Que, X., Hung, M.-Y., Yeang, C., Gonen, A., Prohaska, T. A., Sun, X., … Witztum, J. L. (2018). Oxidized phospholipids are proinflammatory and proatherogenic in hypercholesterolaemic mice. Nature, 558(7709), 301–306. https://doi.org/10.1038/s41586-018-0198-8

WENDY HUANG, Assistant Professor of Cellular and Molecular Medicine, UC San Diego (Ph.D., UC San Diego)

The Huang lab examines molecular mechanisms underlying immune-cell development and effector functions and to assess their contributions to immune pathologies in mouse models of colitis and multiple sclerosis. The first focus area of focus is contributions of RNA-helicases and their associated non-coding RNAs to host immune homeostasis and autoimmune pathologies. The second area of inquiry is non- canonical functions for nucleoporins in immunity; the final area of study is tissue-specific post-transcriptional and post-translational mechanisms that orchestrate local immune responses in animal autoimmune disease models of colitis and multiple sclerosis.

Selected Publications

1. Huang, W., Thomas, B., Flynn, R. A., Gavzy, S. J., Wu, L., Kim, S. V., … Littman, D. R. (2015). DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature, 528(7583), 517– 522. https://doi.org/10.1038/nature16193 2. Huang, W., & Littman, D. R. (2015). Regulation of RORγt in Inflammatory Lymphoid Cell Differentiation. Cold Spring Harbor Symposia on Quantitative Biology, 80, 257–263. https://doi.org/10.1101/sqb.2015.80.027615 3. Sano, T., Huang, W., Hall, J. A., Yang, Y., Chen, A., Gavzy, S. J., … Littman, D. R. (2015). An IL- 23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses. Cell, 163(2), 381–393. https://doi.org/10.1016/j.cell.2015.08.061

ALISA HUFFAKER, Assistant Professor of Cell and Developmental Biology, UC San Diego (Ph.D., Washington State University)

Huffaker’s research interests center on plant peptide signals, Peps, which regulate broad spectrum plant defense responses against pathogens and herbivores, and their application to manipulate plant resistance to biotic attack. Current lab efforts are focused on study of Pep-PEPR ligand-receptor interactions and determination of structural requirements for signaling activity, characterization of downstream Pep signaling components identified through genetic screens and profiling of rapid changes in transcriptome and phosphoproteome of maize and Arabidopsis, and development of Pep-based strategies for enhancement of plant immunity against pathogens and pests.

Selected Publications

1. Mafu, S., Ding, Y., Murphy, K. M., Yaacoobi, O., Addison, J. B., Wang, Q., … Zerbe, P. (2018). Discovery, Biosynthesis and Stress-Related Accumulation of Dolabradiene-Derived Defenses in Maize. Plant Physiology, 176(4), 2677–2690. https://doi.org/10.1104/pp.17.01351 2. Nakata, R., Yoshinaga, N., Teraishi, M., Okumoto, Y., Huffaker, A., Schmelz, E. A., & Mori, N. (2018). A fragmentation study of isoflavones by IT-TOF-MS using biosynthesized isotopes. Bioscience, Biotechnology, and Biochemistry, 82(8), 1309–1315. https://doi.org/10.1080/09168451.2018.1465810

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3. Ziemann, S., van der Linde, K., Lahrmann, U., Acar, B., Kaschani, F., Colby, T., … Doehlemann, G. (2018). An apoplastic peptide activates salicylic acid signalling in maize. Nature Plants, 4(3), 172– 180. https://doi.org/10.1038/s41477-018-0116-y

ENFU HUI, Assistant Professor of Cell and Developmental Biology, UC San Diego (Ph.D., University of Wisconsin-Madison)

The Hui lab aims to dissect the mechanisms of immune checkpoints, using cell-free membrane reconstitution, time-resolved live cell microscopy, and cutting-edge cell biology approaches; the lab recently uncovered two novel aspects of PD-L1/PD-1 signaling. In addition, they are investigating whether and how additional immune brakes operate in conjunction with PD-1 to “turn off” T cell activity, seeking to identify the triggering molecules that turn these brakes on, and signal transducers these brakes recruit to suppress the immune response. Their findings could lead to the development of novel biomarkers and drug targets of cancer immunotherapy.

Selected Publications

1. Zhao, Y., Harrison, D. L., Song, Y., Ji, J., Huang, J., & Hui, E. (2018). Antigen-Presenting Cell- Intrinsic PD-1 Neutralizes PD-L1 in cis to Attenuate PD-1 Signaling in T Cells. Cell Reports, 24(2), 379–390.e6. https://doi.org/10.1016/j.celrep.2018.06.054 2. Hui, E., Cheung, J., Zhu, J., Su, X., Taylor, M. J., Wallweber, H. A., … Vale, R. D. (2017). T cell costimulatory receptor CD28 is a primary target for PD-1–mediated inhibition. Science, 355(6332), 1428–1433. https://doi.org/10.1126/science.aaf1292 3. Carbone, C. B., Kern, N., Fernandes, R. A., Hui, E., Su, X., Garcia, K. C., & Vale, R. D. (2017). In vitro reconstitution of T cell receptor-mediated segregation of the CD45 phosphatase. Proceedings of the National Academy of Sciences of the United States of America, 114(44), E9338–E9345. https://doi.org/10.1073/pnas.1710358114

MOHIT JAIN, Assistant Professor of Medicine and Pharmacology, UC San Diego (M.D., Boston University and Ph.D., Boston University)

The Jain lab at UCSD utilizes large-scale biosampling, mass spectrometry-based metabolomics, and computational informatics to map the non-genetic underpinnings of human physiology and disease, including within the immune system. These efforts involve coordinated efforts of analytical chemists, bioengineers, synthetic chemists, statistical epidemiologists, cellular immunologists, and physicians. Current efforts are aimed at probing small molecule metabolite modulators of immune cellular function, in auto-immune based diseases and cancer immunotherapy.

Selected Publications

1. Basu Ball, W., Baker, C. D., Neff, J. K., Apfel, G. L., Lagerborg, K. A., Žun, G., … Gohil, V. M. (2018). Ethanolamine ameliorates mitochondrial dysfunction in cardiolipin-deficient yeast cells. Journal of Biological Chemistry, 293(28), 10870–10883. https://doi.org/10.1074/jbc.RA118.004014 2. Grankvist, N., Watrous, J. D., Lagerborg, K. A., Lyutvinskiy, Y., Jain, M., & Nilsson, R. (2018). Profiling the Metabolism of Human Cells by Deep 13C Labeling. Cell Chemical Biology. https://doi.org/10.1016/j.chembiol.2018.09.004 3. Lagerborg, K. A., Watrous, J. D., Cheng, S., & Jain, M. (2019). High-Throughput Measure of Bioactive Lipids Using Non-targeted Mass Spectrometry. In Methods in molecular biology (Clifton, N.J.) (Vol. 1862, pp. 17–35). https://doi.org/10.1007/978-1-4939-8769-6_2

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MICHAEL KARIN, Distinguished Professor of Pharmacology and Pathology, UC San Diego (Ph.D., UC Los Angeles)

Dr. Karin’s current activity primarily focuses on understanding the relationship between inflammation, cancer, and metabolic disease as well as the signaling mechanisms used by receptors involved in inflammation and innate immunity. In addition to discovering some of the most important stress- and inflammation-responsive signal transduction pathways and establishing molecular links between obesity, inflammation, and cancer, Dr. Karin’s work has revealed new targets for cancer prevention and therapy, as well as for the treatment of non-alcoholic steatohepatitis (NASH) and other metabolic diseases. Dr. Karin was elected as a member of the US National Academy of Sciences in 2005, the National Academy of Medicine in 2011, a fellow of the American Association for Cancer Research Academy in 2017.

Selected Publications

1. Zhong, Z., Liang, S., Sanchez-Lopez, E., He, F., Shalapour, S., Lin, X.-J., … Karin, M. (2018). New mitochondrial DNA synthesis enables NLRP3 inflammasome activation. Nature, 560(7717), 198– 203. https://doi.org/10.1038/s41586-018-0372-z 2. Shalapour, S., Lin, X.-J., Bastian, I. N., Brain, J., Burt, A. D., Aksenov, A. A., … Karin, M. (2018). Author Correction: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. Nature. https://doi.org/10.1038/s41586-018-0304-y 3. Dhar, D., Antonucci, L., Nakagawa, H., Kim, J. Y., Glitzner, E., Caruso, S., … Karin, M. (2018). Liver Cancer Initiation Requires p53 Inhibition by CD44-Enhanced Growth Factor Signaling. Cancer Cell, 33(6), 1061–1077.e6. https://doi.org/10.1016/j.ccell.2018.05.003

DAN KAUFMAN, Professor of Medicine and Director of Cell Therapy, UC San Diego (M.D., Mayo Medical School and Ph.D., Mayo Graduate School)

The Kaufman laboratory uses human pluripotent stem cells to understand the development of blood cells (both hematopoietic stem cells and functional lymphocytes: T cells and NK cells) and related mesodermal cell populations (including bone, endothelial, and smooth muscle/vascular cells). The aim is to use human pluripotent stem cells as a resource to produce blood and immune cells for new clinical applications for treatment of relapsed/refractory cancers – both hematologic malignancies and solid tumors.

Selected Publications

1. Li, Y., Hermanson, D. L., Moriarity, B. S., & Kaufman, D. S. (2018). Human iPSC-Derived Natural Killer Cells Engineered with Chimeric Antigen Receptors Enhance Anti-tumor Activity. Cell Stem Cell, 23(2), 181–192.e5. https://doi.org/10.1016/j.stem.2018.06.002 2. Angelos, M. G., & Kaufman, D. S. (2018). Advances in the role of the aryl hydrocarbon receptor to regulate early hematopoietic development. Current Opinion in Hematology, 25(4), 273–278. https://doi.org/10.1097/MOH.0000000000000432 3. Zhu, H., Lai, Y.-S., Li, Y., Blum, R. H., & Kaufman, D. S. (2018). Concise Review: Human Pluripotent Stem Cells to Produce Cell-Based Cancer Immunotherapy. Stem Cells (Dayton, Ohio), 36(2), 134– 145. https://doi.org/10.1002/stem.2754

TOSHIAKI KAWAKAMI, Professor of Cellular Biology, La Jolla Institute; Adjunct Professor of Dermatology, UC San Diego (M.D. and Ph.D., University of Tokyo)

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Toshiaki Kawakami and his team study signal transduction in the immune and hematopoietic systems. The laboratory has been studying mainly mast cells, an important cell type found in mucosal as well as connective tissues that is responsible for the allergic reactions that trigger itching, wheezing, and sneezing, symptoms of allergic reactions that occur after mast cells are activated. Dr. Kawakami and his colleagues focus on dissecting the complex network of signaling molecules, particularly those involved in the early phase of mast cell activation.

Selected Publications

1. Pincha, N., Hajam, E. Y., Badarinath, K., Batta, S. P. R., Masudi, T., Dey, R., … Jamora, C. (2018). PAI1 mediates fibroblast–mast cell interactions in skin fibrosis. Journal of Clinical Investigation, 128(5), 1807–1819. https://doi.org/10.1172/JCI99088 2. Herro, R., Shui, J.-W., Zahner, S., Sidler, D., Kawakami, Y., Kawakami, T., … Croft, M. (2018). LIGHT–HVEM signaling in keratinocytes controls development of dermatitis. The Journal of Experimental Medicine, 215(2), 415–422. https://doi.org/10.1084/jem.20170536 3. Doré, K. A., Kashiwakura, J., McDonnell, J. M., Gould, H. J., Kawakami, T., Sutton, B. J., & Davies, A. M. (2018). Crystal structures of murine and human Histamine-Releasing Factor (HRF/TCTP) and a model for HRF dimerisation in mast cell activation. Molecular Immunology, 93, 216–222. https://doi.org/10.1016/j.molimm.2017.11.022

THOMAS KIPPS, Professor of Medicine, Evelyn and Edwin Tasch Chair in Cancer Research, and Deputy Director of Research Operations at Moores Cancer Center, UC San Diego (Ph.D. and M.D., Harvard University)

A major focus of Dr. Kipps’ research is the immunobiology and genetics of human B-cell malignancies, with emphasis on chronic lymphocytic leukemia (CLL). His work has provided insight into the ontogeny of B cells that are subject to leukemia transformation and defined the highly-restricted nature of the immunoglobulins expressed in this disease. He has also defined genetic factors contributing to the development and progression of the disease, identified biochemical pathways that enhance the growth or survival of leukemia B cells, identified means with which to elicit host anti-leukemia immune responses through vaccines generated via gene transfer, and identified promising new drugs and biologic agents in the treatment of the disease.

Selected Publications

1. Barr, P. M., Robak, T., Owen, C., Tedeschi, A., Bairey, O., Bartlett, N. L., … Ghia, P. (2018). Sustained efficacy and detailed clinical follow-up of first-line ibrutinib treatment in older patients with chronic lymphocytic leukemia: extended phase 3 results from RESONATE-2. Haematologica, haematol.2018.192328. https://doi.org/10.3324/haematol.2018.192328 2. Choi, M. Y., Widhopf, G. F., Ghia, E. M., Kidwell, R. L., Hasan, M. K., Yu, J., … Kipps, T. J. (2018). Phase I Trial: Cirmtuzumab Inhibits ROR1 Signaling and Stemness Signatures in Patients with Chronic Lymphocytic Leukemia. Cell Stem Cell, 22(6), 951–959.e3. https://doi.org/10.1016/j.stem.2018.05.018 3. Yu, J., Chen, Y., Chen, L., Zhang, L., Rassenti, L. Z., Widhopf, G. F., & Kipps, T. J. (2018). Cirmtuzumab inhibits ibrutinib-resistant, Wnt5a-induced Rac1 activation and proliferation in mantle cell lymphoma. Oncotarget, 9(37), 24731–24736. https://doi.org/10.18632/oncotarget.25340

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LI-FAN LU, Associate Professor of Molecular Biology, UC San Diego (Ph.D., Dartmouth College)

During the last decade a unique mechanism of negative regulation of immune responses and inflammation by a dedicated population of so-called regulatory T (Treg) cells has become the focus of intensive investigation. Expression of the transcription factor Foxp3, a hallmark of Treg cells, is necessary for the establishment and maintenance of a distinct transcriptional program that determines metabolic, signaling, and effector features (e.g., suppressive function), distinguishing these cells from other T cell lineages. The long-term goals of the Lu lab’s research are to identify the molecular determinants of differentiation and function of Treg cells and to ultimately gain insight into the complex biology of these cells.

Selected Publications

1. Becher, B., Waisman, A., & Lu, L.-F. (2018). Conditional Gene-Targeting in Mice: Problems and Solutions. Immunity, 48(5), 835–836. https://doi.org/10.1016/j.immuni.2018.05.002 2. Klann, J. E., Kim, S. H., Remedios, K. A., He, Z., Metz, P. J., Lopez, J., … Chang, J. T. (2018). Integrin Activation Controls Regulatory T Cell-Mediated Peripheral Tolerance. Journal of Immunology (Baltimore, Md. : 1950), 200(12), 4012–4023. https://doi.org/10.4049/jimmunol.1800112 3. Cho, S., Lee, H.-M., Yu, I.-S., Choi, Y. S., Huang, H.-Y., Hashemifar, S. S., … Lu, L.-F. (2018). Differential cell-intrinsic regulations of germinal center B and T cells by miR-146a and miR-146b. Nature Communications, 9(1), 2757. https://doi.org/10.1038/s41467-018-05196-3

GERALD MORRIS, Director, Immunogenetics and Transplantation Laboratory and Assistant Professor of Pathology, UC San Diego (M.D. and Ph.D., Wayne State University)

The Morris laboratory studies T lymphocyte function and development in hematopoietic stem cell transplantation (HSCT). The lab is interested in understanding the molecular events that define the recognition of alloantigens by T cells, and how that results in T cell activation and generation of effector mechanisms ultimately responsible for GVHD. They utilize transgenic animal models, human T cell culture systems, gene expression analyses, and flow cytometry to examine T cells from patients with GVHD in an attempt to define the mechanisms driving disease.

Selected Publications

1. Balakrishnan, A., Gloude, N., Sasik, R., Ball, E. D., & Morris, G. P. (2017). Proinflammatory Dual Receptor T Cells in Chronic Graft-versus-Host Disease. Biology of Blood and Marrow Transplantation: Journal of the American Society for Blood and Marrow Transplantation, 23(11), 1852–1860. https://doi.org/10.1016/j.bbmt.2017.07.016 2. Jani, V., Ingulli, E., Mekeel, K., & Morris, G. P. (2017). Root cause analysis of limitations of virtual crossmatch for kidney allocation to highly-sensitized patients. Human Immunology, 78(2), 72–79. https://doi.org/10.1016/j.humimm.2016.11.003 3. Morris, G. P., & Hedrick, S. M. (2017). A rheostat tuning thymic selection. Nature Immunology, 18(7), 713–714. https://doi.org/10.1038/ni.3778

CORNELIS MURRE, Distinguished Professor of Molecular Biology, UC San Diego (Ph.D., Harvard Medical School)

The Murre lab studies gene regulation in adult stem cells and developing lymphocytes and has a long- standing interest in deciphering the role and regulation of helix-loop-helix proteins in lymphocyte development. Currently, their main interests are in the role of these factors in the control of hematopoietic stem cell homeostasis, B- and T-lineage specification and commitment, aging, inflammatory disease and Page 37 Proposal for a Graduate Specialization in Immunology-UC San Diego their roles in the periphery in the response to invading pathogens. The lab has recently demonstrated that genes encoding for key developmental regulators reposition during developmental progression and now aims to address the question as to why and how genomic regions encoding for developmental regulator reposition during developmental progression.

Selected Publications

1. Murre, C. (2018). ‘Big bang’ of B-cell development revealed. Genes & Development, 32(2), 93–95. https://doi.org/10.1101/gad.311357.118 2. Roy, S., Moore, A. J., Love, C., Reddy, A., Rajagopalan, D., Dave, S. S., … Zhuang, Y. (2018). Id Proteins Suppress E2A-Driven Invariant Natural Killer T Cell Development prior to TCR Selection. Frontiers in Immunology, 9, 42. https://doi.org/10.3389/fimmu.2018.00042 3. Bortnick, A., & Murre, C. (2018). mTECs Aire on the side of caution. Nature Immunology, 19(2), 100–101. https://doi.org/10.1038/s41590-017-0033-7

BJOERN PETERS, Professor of Vaccine Discovery, La Jolla Institute; Associate Adjunct Professor of Medicine, UC San Diego (Ph.D., Humboldt University)

Dr. Peters has worked on the development and validation of computational tools to analyze and predict which parts of a pathogen, allergen, or cancer cell are targeted by immune responses and the identification of differences between immune cells in individuals with opposite disease outcomes. Powerful experimental tools have been developed to detect differences in how cells utilize the diverse parts of the genome; the Peters lab is using these tools to characterize how immune cells from diseased individuals differ from healthy individuals. Finally, the Peters lab is deeply involved in the development of community standards for knowledge representation to promote interoperability and re-use of data.

Selected Publications

1. Dhanda, S. K., Vaughan, K., Schulten, V., Grifoni, A., Weiskopf, D., Sidney, J., … Sette, A. (2018). Development of a novel clustering tool for linear peptide sequences. Immunology. https://doi.org/10.1111/imm.12984 2. Dhanda, S. K., Karosiene, E., Edwards, L., Grifoni, A., Paul, S., Andreatta, M., … Sette, A. (2018). Predicting HLA CD4 Immunogenicity in Human Populations. Frontiers in Immunology, 9, 1369. https://doi.org/10.3389/fimmu.2018.01369 3. da Silva Antunes, R., Babor, M., Carpenter, C., Khalil, N., Cortese, M., Mentzer, A. J., … Sette, A. (2018). Th1/Th17 polarization persists following whole-cell pertussis vaccination despite repeated acellular boosters. Journal of Clinical Investigation. https://doi.org/10.1172/JCI121309

MANUELA RAFFATELLU, Professor of Pediatrics, UC San Diego (M.D., University of Sassari)

The goal of the Raffatellu laboratory is to understand how mucosal responses are orchestrated in response to mucosal pathogens like Salmonella typhimurium. The mucosal immune response has the important function of containing an infection and preventing dissemination of pathogens to systemic sites; however, there is increasing evidence that mucosal pathogens achieve greater colonization during inflammation. The lab is interested in investigating this dichotomy of the host response, and understanding which responses constitute the mucosal barrier during S. typhimurium infection and which favor S. typhimurium colonization of the inflamed gut.

Selected Publications

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1. Lapek, J. D., Mills, R. H., Wozniak, J. M., Campeau, A., Fang, R. H., Wei, X., … Gonzalez, D. J. (2018). Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas. Cell Systems, 6(5), 579–592.e4. https://doi.org/10.1016/j.cels.2018.04.010 2. Raffatellu, M. (2018). Learning from bacterial competition in the host to develop antimicrobials. Nature Medicine, 24(8), 1097–1103. https://doi.org/10.1038/s41591-018-0145-0 3. Gerner, R. R., & Raffatellu, M. (2018). A Worm’s Gut Feelings: Neuronal Muscarinic and Epithelial Canonical Wnt Pathways Promote Antimicrobial Defense. Immunity, 48(5), 839–841. https://doi.org/10.1016/j.immuni.2018.04.035

ANJANA RAO, Professor of Signaling and Gene Expression, La Jolla Institute; Adjunct Professor of Pharmacology, UC San Diego (Ph.D., Harvard University)

Anjana Rao and her team focus on understanding how signaling pathways control gene expression, using T cells and other cells of the immune system as models. They are particularly interested in a pathway of gene expression that is regulated by calcium influx into many different types of cells. A current critical focus involves the TET family of 5-methylcytosine oxidases, which control cell lineage specification in many different systems: profound TET loss-of-function is associated with aggressive cancers, both in human and in mouse model systems, and the lab is examining the mechanisms involved. Anjana Rao is a member of the National Academy of Sciences,

Selected Publications

1. Shepherd, M. S., Li, J., Wilson, N. K., Oedekoven, C. A., Li, J., Belmonte, M., … Kent, D. G. (2018). Single cell approaches identify the molecular network driving malignant hematopoietic stem cell self- renewal. Blood, blood-2017-12-821066. https://doi.org/10.1182/blood-2017-12-821066 2. Tuttle, K. D., Krovi, S. H., Zhang, J., Bedel, R., Harmacek, L., Peterson, L. K., … Gapin, L. (2018). TCR signal strength controls thymic differentiation of iNKT cell subsets. Nature Communications, 9(1), 2650. https://doi.org/10.1038/s41467-018-05026-6 3. Yu, O. M., Benitez, J. A., Plouffe, S. W., Ryback, D., Klein, A., Smith, J., … Brown, J. H. (2018). YAP and MRTF-A, transcriptional co-activators of RhoA-mediated gene expression, are critical for glioblastoma tumorigenicity. Oncogene. https://doi.org/10.1038/s41388-018-0301-5

EYAL RAZ, Professor of Medicine, UC San Diego (M.D., Hebrew University at the Hadassah Medical School)

The research in the Raz lab is focusing on the fundamentals of innate immunity. The lab studies the Toll-like receptor (TLR) and the non-TLR activation pathways by which the host recognizes and responds to any microbial agent. Raz and his team explore the consequences of this activation on antigen presentation by dendritic cells and its impact on priming of naïve CD4 and CD8 T cells as well as the generation of memory T cell responses.

Selected Publications

1. Taniguchi, K., Moroishi, T., de Jong, P. R., Krawczyk, M., Grebbin, B. M., Luo, H., … Karin, M. (2017). YAP–IL-6ST autoregulatory loop activated on APC loss controls colonic tumorigenesis. Proceedings of the National Academy of Sciences, 114(7), 1643–1648. https://doi.org/10.1073/pnas.1620290114 2. Bertin, S., Aoki-Nonaka, Y., Lee, J., de Jong, P. R., Kim, P., Han, T., … Raz, E. (2017). The TRPA1 ion channel is expressed in CD4+ T cells and restrains T-cell-mediated colitis through inhibition of TRPV1. Gut, 66(9), 1584–1596. https://doi.org/10.1136/gutjnl-2015-310710

Page 39 Proposal for a Graduate Specialization in Immunology-UC San Diego

3. Viriyakosol, S., Walls, L., Okamoto, S., Raz, E., Williams, D. L., & Fierer, J. (2018). Myeloid Differentiation Factor 88 and Interleukin-1R1 Signaling Contribute to Resistance to Coccidioides immitis. Infection and Immunity, 86(6). https://doi.org/10.1128/IAI.00028-18

ROBERT RISSMAN, Associate Professor of Neurosciences, UC San Diego (Ph.D., Drexel University College of Medicine)

The goal of Robert Rissman’s basic science research is novel biomarker discovery and experimental neuropathology in Alzheimer’s Disease (AD), Parkinson’s Disease (PD), and preclinical animal models. A major focus of the Rissman lab in AD and PD biomarkers is on the utility and mechanistic underpinnings of neuronal exosomes. Their group has published manuscripts demonstrating the ability of pathologic proteins from neuronal exosomes to predict progression of disease and induce pathology in animal models.

Selected Publications

1. Kim, C., Spencer, B., Rockenstein, E., Yamakado, H., Mante, M., Adame, A., … Masliah, E. (2018). Immunotherapy targeting toll-like receptor 2 alleviates neurodegeneration in models of synucleinopathy by modulating α-synuclein transmission and neuroinflammation. Molecular Neurodegeneration, 13(1), 43. https://doi.org/10.1186/s13024-018-0276-2 2. Spencer, B., Brüschweiler, S., Sealey-Cardona, M., Rockenstein, E., Adame, A., Florio, J., … Masliah, E. (2018). Selective targeting of 3 repeat Tau with brain penetrating single chain antibodies for the treatment of neurodegenerative disorders. Acta Neuropathologica, 136(1), 69–87. https://doi.org/10.1007/s00401-018-1869-0 3. Pottier, C., Zhou, X., Perkerson, R. B., Baker, M., Jenkins, G. D., Serie, D. J., … Rademakers, R. (2018). Potential genetic modifiers of disease risk and age at onset in patients with frontotemporal lobar degeneration and GRN mutations: a genome-wide association study. The Lancet Neurology, 17(6), 548–558. https://doi.org/10.1016/S1474-4422(18)30126-1

JESUS RIVERA-NIEVES, Professor of Medicine, UC San Diego (M.D., University of Puerto Rico, San Juan)

Dr. Rivera-Nieves is a Professor of Medicine in the Division of Gastroenterology and team member at the Inflammatory Bowel Disease Center and the Veterans Administration San Diego Healthcare System. Dr. Nieves-Rivera's research laboratory focuses on treatment strategies for IBD—which includes Crohn’s disease and ulcerative colitis, both characterized by chronic inflammation of the lining of the digestive tract— using unique mouse models that develop Crohn's-like terminal ileitis.

Selected Publications

1. Tyler, C. J., Pérez-Jeldres, T., Ehinger, E., Capaldo, B., Karuppuchamy, T., Boyer, J. D., … Rivera- Nieves, J. (2018). Implementation of Mass Cytometry as a Tool for Mechanism of Action Studies in Inflammatory Bowel Disease. Inflammatory Bowel Diseases. https://doi.org/10.1093/ibd/izy214 2. Dulai, P. S., Boland, B. S., Singh, S., Chaudrey, K., Koliani-Pace, J. L., Kochhar, G., … Cao, C. (2018). Development and Validation of a Scoring System to Predict Outcomes of Vedolizumab Treatment in Patients With Crohn’s Disease. Gastroenterology. https://doi.org/10.1053/j.gastro.2018.05.039 3. McNamee, E. N., & Rivera-Nieves, J. (2017). Defective Lymphatics in Crohn’s Disease: Tertiary Lymphoid Follicles Plug the Gap. Gastroenterology, 152(4), 908–910. https://doi.org/10.1053/j.gastro.2017.01.022

Page 40 Proposal for a Graduate Specialization in Immunology-UC San Diego

WILLIAM SANDBORN, Director, Inflammatory Bowel Disease Center; Chief, Division of Gastroenterology; and Professor of Medicine, UC San Diego (M.D., Loma Linda University)

William Sandborn, M.D., is a board-certified gastroenterologist who is one of the world's top experts in the management of ulcerative colitis and Crohn’s disease. He directs the Inflammatory Bowel Disease Center at UC San Diego Health. In addition, he is chief of the Division of Gastroenterology, vice chair of clinical operations for the Department of Medicine, and a member of the Clinical Practice Oversight Board for UC San Diego Health. A professor in the Department of Medicine at UC San Diego School of Medicine, Dr. Sandborn conducts clinical trials in IBD and leads a team of physicians, research fellows, nurses, and study coordinators.

Selected Publications

1. Jairath, V., Peyrin-Biroulet, L., Zou, G., Mosli, M., Vande Casteele, N., Pai, R. K., … Pai, R. K. (2018). Responsiveness of histological disease activity indices in ulcerative colitis: a post hoc analysis using data from the TOUCHSTONE randomised controlled trial. Gut, gutjnl-2018-316702. https://doi.org/10.1136/gutjnl-2018-316702 2. Feagan, B. G., Panés, J., Ferrante, M., Kaser, A., D’Haens, G. R., Sandborn, W. J., … Böcher, W. O. (2018). Risankizumab in patients with moderate to severe Crohn’s disease: an open-label extension study. The Lancet. Gastroenterology & Hepatology. https://doi.org/10.1016/S2468-1253(18)30233- 4 3. Lichtenstein, G. R., Feagan, B. G., Mahadevan, U., Salzberg, B. A., Langholff, W., Morgan, G. J., … Cohen, R. D. (2018). Pregnancy Outcomes Reported During the 13-Year TREAT Registry: A Descriptive Report. The American Journal of Gastroenterology. https://doi.org/10.1038/s41395-018- 0202-9

ALESSANDRO SETTE, Professor of Vaccine Discovery, La Jolla Institute; Adjunct Professor of Medicine, UC San Diego (Dr. BiolSci, University of Rome)

The laboratory of Dr. Alessandro Sette is defining in chemical terms the specific structures (epitopes) that the immune system recognizes, and uses this knowledge to measure and understand immune responses. The Sette lab’s approach uses epitopes as specific probes to define the immune signatures associated with productive/protective immunity versus deficient immunity/immunopathology. Sette’s disease focus includes HIV, HBV and HCV, emerging diseases and diseases of potential biodefense concern to, most recently, diseases and pathogens relevant to worldwide global health, including dengue viruses, malaria, tuberculosis, and trypanosome infections.

Selected Publications

1. Dhanda, S. K., Vaughan, K., Schulten, V., Grifoni, A., Weiskopf, D., Sidney, J., … Sette, A. (2018). Development of a novel clustering tool for linear peptide sequences. Immunology. https://doi.org/10.1111/imm.12984 2. Dhanda, S. K., Karosiene, E., Edwards, L., Grifoni, A., Paul, S., Andreatta, M., … Sette, A. (2018). Predicting HLA CD4 Immunogenicity in Human Populations. Frontiers in Immunology, 9, 1369. https://doi.org/10.3389/fimmu.2018.01369 3. da Silva Antunes, R., Babor, M., Carpenter, C., Khalil, N., Cortese, M., Mentzer, A. J., … Sette, A. (2018). Th1/Th17 polarization persists following whole-cell pertussis vaccination despite repeated acellular boosters. Journal of Clinical Investigation. https://doi.org/10.1172/JCI121309

Page 41 Proposal for a Graduate Specialization in Immunology-UC San Diego

NISARG SHAH, Assistant Professor of Nanoengineering, UC San Diego (Ph.D., Massachusetts Institute of Technology)

Nisarg Shah’s work focuses on the design and synthesis of polymeric biomaterials that regulate the fate of cells resident in tissues by providing cell-instructive cues to control spatiotemporal cellular behavior. The Shah laboratory focuses on the development of these polymeric systems to mimic aspects of the native extracellular matrix, in their control in space and time, of signaling molecules and cues. Through this design of chemical and biophysical tools to control molecular, cellular, and tissue interactions, they aim to shed new light on the functioning of the immune system which can be used to develop therapies for a broad range of diseases, including cancer, antibiotic-resistant bacterial infection, and autoimmune disease. Technology developed from Shah’s research has been licensed to companies for clinical development.

Selected Publications

1. Darnell, M., Young, S., Gu, L., Shah, N., Lippens, E., Weaver, J., … Mooney, D. (2017). Substrate Stress-Relaxation Regulates Scaffold Remodeling and Bone Formation In Vivo. Advanced Healthcare Materials, 6(1), 1601185. https://doi.org/10.1002/adhm.201601185 2. Shah, N. J., Hyder, M. N., Quadir, M. A., Dorval Courchesne, N.-M., Seeherman, H. J., Nevins, M., … Hammond, P. T. (2014). Adaptive growth factor delivery from a polyelectrolyte coating promotes synergistic bone tissue repair and reconstruction. Proceedings of the National Academy of Sciences of the United States of America, 111(35), 12847–12852. https://doi.org/10.1073/pnas.1408035111 3. Shah, N. J., Geiger, B. C., Quadir, M. A., Hyder, M. N., Krishnan, Y., Grodzinsky, A. J., & Hammond, P. T. (2016). Synthetic nanoscale electrostatic particles as growth factor carriers for cartilage repair. Bioengineering & Translational Medicine, 1(3), 347–356. https://doi.org/10.1002/btm2.10043

EMILY TROEMEL, Professor of Cell and Developmental Biology, UC San Diego (Ph.D., UC San Francisco)

The Troemel lab research focuses on two different pathogens. The first pathogen is a natural intracellular pathogen isolated from a wild-caught C. elegans strain, which they have found defines a genus and species of microsporidia–poorly understood eukaryotic pathogens and emerging pathogens of humans that can cause problems for immunocompromised patients. The second pathogen is an extracellular bacterial pathogen called Pseudomonas aeruginosa, which is a clinically-relevant pathogen that causes opportunistic infections in humans.

Selected Publications

1. Reddy, K. C., Dror, T., Sowa, J. N., Panek, J., Chen, K., Lim, E. S., … Troemel, E. R. (2017). An Intracellular Pathogen Response Pathway Promotes Proteostasis in C. elegans. Current Biology : CB, 27(22), 3544–3553.e5. https://doi.org/10.1016/j.cub.2017.10.009 2. Reinke, A. W., Balla, K. M., Bennett, E. J., & Troemel, E. R. (2017). Identification of microsporidia host-exposed proteins reveals a repertoire of rapidly evolving proteins. Nature Communications, 8, 14023. https://doi.org/10.1038/ncomms14023 3. Reinke, A. W., Mak, R., Troemel, E. R., & Bennett, E. J. (2017). In vivo mapping of tissue- and subcellular-specific proteomes in Caenorhabditis elegans. Science Advances, 3(5), e1602426. https://doi.org/10.1126/sciadv.1602426

AJIT VARKI, Distinguished Professor of Medicine and Cellular & Molecular Medicine; Co-Director, Glycobiology Research and Training Center; Co-Director, UCSD/Salk Center for Academic Research and Training in Anthropogeny (CARTA) (M.D., Christian Medical College, Vellore)

Page 42 Proposal for a Graduate Specialization in Immunology-UC San Diego

The interests of the Varki lab are focused on a family of sugars called the sialic acids, and their roles in biology, evolution, and disease. Currently, active projects are relevant to the roles of sialic acids in microbial infection; the regulation of the immune response; the progression of cancer; and unique aspects of human evolution. The lab is particularly intrigued about finding multiple differences in sialic acid biology between humans and our closest evolutionary cousins, the great apes.

Selected Publications

1. Alisson-Silva, F., Liu, J. Z., Diaz, S. L., Deng, L., Gareau, M. G., Marchelletta, R., … Varki, A. (2018). Human evolutionary loss of epithelial Neu5Gc expression and species-specific susceptibility to cholera. PLoS Pathogens, 14(6), e1007133. https://doi.org/10.1371/journal.ppat.1007133 2. Samraj, A. N., Bertrand, K. A., Luben, R., Khedri, Z., Yu, H., Nguyen, D., … Varki, A. (2018). Polyclonal human antibodies against glycans bearing red meat-derived non-human sialic acid N- glycolylneuraminic acid are stable, reproducible, complex and vary between individuals: Total antibody levels are associated with colorectal cancer risk. PloS One, 13(6), e0197464. https://doi.org/10.1371/journal.pone.0197464 3. Ram, S., Gulati, S., Lewis, L. A., Chakraborti, S., Zheng, B., DeOliveira, R. B., … Rice, P. A. (2018). A Novel Sialylation Site on Neisseria gonorrhoeae Lipooligosaccharide Links Heptose II Lactose Expression with Pathogenicity. Infection and Immunity, 86(8), IAI.00285-18. https://doi.org/10.1128/IAI.00285-18

PANDURANGAN VIJAYANAND, Associate Professor of Vaccine Discovery, La Jolla Institute; Associate Adjunct Professor of Medicine, UC San Diego (M.D., MGR Medical University and Ph.D., University of Southampton)

Dr. Vijayanand and his laboratory have developed a number of techniques to study the molecular profiles of circulating and airway immune cells from patients with asthma and other diseases, using fewer cells than was possible previously. In a pioneering study, he applied these tools to a genome-wide study of disease- related changes in the epigenome—the layer atop the genome that controls gene activity and is altered by the environment—of immune cells isolated from patients with asthma. Dr. Vijayanand also oversees a large- scale effort to map epigenomic modifications in more than a dozen different types of human immune cells from normal individuals to understand how epigenetic variations cause susceptibility to disease.

Selected Publications

1. da Silva Antunes, R., Babor, M., Carpenter, C., Khalil, N., Cortese, M., Mentzer, A. J., … Sette, A. (2018). Th1/Th17 polarization persists following whole-cell pertussis vaccination despite repeated acellular boosters. The Journal of Clinical Investigation. https://doi.org/10.1172/JCI121309 2. Youhanna Jankeel, D., Cayford, J., Schmiedel, B. J., Vijayanand, P., & Seumois, G. (2018). An Integrated and Semiautomated Microscaled Approach to Profile Cis-Regulatory Elements by Histone Modification ChIP-Seq for Large-Scale Epigenetic Studies. In Methods in molecular biology (Clifton, N.J.) (Vol. 1799, pp. 303–326). https://doi.org/10.1007/978-1-4939-7896-0_22 3. Rosales, S. L., Liang, S., Engel, I., Schmiedel, B. J., Kronenberg, M., Vijayanand, P., & Seumois, G. (2018). A Sensitive and Integrated Approach to Profile Messenger RNA from Samples with Low Cell Numbers. Methods in Molecular Biology (Clifton, N.J.), 1799, 275–301. https://doi.org/10.1007/978- 1-4939-7896-0_21

MATTHIAS VON HERRATH, Director of the Center for Type 1 Diabetes Research and Professor of Developmental Immunology, La Jolla Institute; Adjunct Professor of Medicine, UC San Diego (M.D., Freiburg Medical School)

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Dr. Matthias von Herrath is committed to clinical translation of immune-based interventions in autoimmune and metabolic diseases, the latter in particular being an exciting emerging field. His expertise and main strength is working at the interface of experimental research to interpret and refine early phase I/II clinical trials in order to optimize strategies for phase III trials and drug approval. In order to be better able to pursue his goal of clinical translation, Dr. von Herrath accepted the position of Vice President and Head of NovoNordisk’s diabetes R&D Center in autumn of 2011. At NovoNordisk, he built the diabetes translational unit, which is based on less conventional and innovative design, while maintaining his academic laboratory in San Diego.

Selected Publications

1. Sbierski-Kind, J., Kath, J., Brachs, S., Streitz, M., von Herrath, M. G., Kühl, A. A., … Volk, H.-D. (2018). Distinct Housing Conditions Reveal a Major Impact of Adaptive Immunity on the Course of Obesity-Induced Type 2 Diabetes. Frontiers in Immunology, 9, 1069. https://doi.org/10.3389/fimmu.2018.01069 2. Anquetil, F., Mondanelli, G., Gonzalez, N., Rodriguez Calvo, T., Zapardiel Gonzalo, J., Krogvold, L., … von Herrath, M. G. (2018). Loss of IDO1 Expression From Human Pancreatic β-Cells Precedes Their Destruction During the Development of Type 1 Diabetes. Diabetes, db171281. https://doi.org/10.2337/db17-1281 3. Christoffersson, G., Chodaczek, G., Ratliff, S. S., Coppieters, K., & von Herrath, M. G. (2018). Suppression of diabetes by accumulation of non-islet-specific CD8+ effector T cells in pancreatic islets. Science Immunology, 3(21), eaam6533. https://doi.org/10.1126/sciimmunol.aam6533

YE ZHENG, Associate Professor, Salk Institute for Biological Studies; Adjunct Associate Professor of Molecular Biology, UC San Diego (Ph.D., Columbia University)

Dr. Zheng was the first to map the Foxp3 cistrome in regulatory T cells (Tregs), which served as a blueprint for subsequent studies on molecular mechanisms of Treg function and was also the first to identify three intronic conserved non-coding sequences (named CNS1 to 3) at the Foxp3 genomic locus, and recognized that they were likely to be key players in regulation of Foxp3 gene expression. At the Salk Institute, Dr. Zheng has expanded his research into three related areas; first, the Zheng lab is dissecting the molecular mechanisms of regulatory T cell stability and function. Second, they are investigating the role of nuclear hormone receptors (NHRs) in T cell differentiation and function; third, they are probing the role of T cells in aging and metabolic diseases.

Selected Publications

1. Klann, J. E., Kim, S. H., Remedios, K. A., He, Z., Metz, P. J., Lopez, J., … Chang, J. T. (2018). Integrin Activation Controls Regulatory T Cell–Mediated Peripheral Tolerance. The Journal of Immunology, 200(12), 4012–4023. https://doi.org/10.4049/jimmunol.1800112 2. He, N., Fan, W., Henriquez, B., Yu, R. T., Atkins, A. R., Liddle, C., … Evans, R. M. (2017). Metabolic control of regulatory T cell (Treg) survival and function by Lkb1. Proceedings of the National Academy of Sciences, 114(47), 12542–12547. https://doi.org/10.1073/pnas.1715363114 3. Klann, J. E., Remedios, K. A., Kim, S. H., Metz, P. J., Lopez, J., Mack, L. A., … Chang, J. T. (2017). Talin Plays a Critical Role in the Maintenance of the Regulatory T Cell Pool. The Journal of Immunology, 198(12), 4639–4651. https://doi.org/10.4049/jimmunol.1601165

ELINA ZUNIGA, Professor of Molecular Biology, UC San Diego (Ph.D., National University of Cordoba)

Page 44 Proposal for a Graduate Specialization in Immunology-UC San Diego

The immune system is responsible for the tremendous task of fighting a wide range of pathogens to which we are constantly exposed. The Zuniga laboratory studies cellular and molecular aspects of immune responses during acute and chronic viral infections to determine general principles of antiviral immunity, immune-evasion, persistence, and pathogenesis. The ultimate goal is to generate fundamental knowledge on immune-regulation that could help modulate immune responses to prevent or treat infectious diseases and may have implications for other immune-related illnesses.

Selected Publications

1. Loureiro, M. E., Zorzetto-Fernandes, A. L., Radoshitzky, S., Chi, X., Dallari, S., Marooki, N., … Zúñiga, E. (2018). DDX3 suppresses type I interferons and favors viral replication during Arenavirus infection. PLoS Pathogens, 14(7), e1007125. https://doi.org/10.1371/journal.ppat.1007125 2. Harker, J. A., Wong, K. A., Dallari, S., Bao, P., Dolgoter, A., Jo, Y., … Zuniga, E. I. (2018). Interleukin-27R Signaling Mediates Early Viral Containment and Impacts Innate and Adaptive Immunity after Chronic Lymphocytic Choriomeningitis Virus Infection. Journal of Virology, 92(12). https://doi.org/10.1128/JVI.02196-17 3. Macal, M., Jo, Y., Dallari, S., Chang, A. Y., Dai, J., Swaminathan, S., … Zúñiga, E. I. (2018). Self- Renewal and Toll-like Receptor Signaling Sustain Exhausted Plasmacytoid Dendritic Cells during Chronic Viral Infection. Immunity, 48(4), 730–744.e5. https://doi.org/10.1016/j.immuni.2018.03.020

Page 45

Steven Hedrick, MD Professor Molecular Biology 9500 Gilman Drive #0377 La Jolla, CA 92093-0377

Mitchell Kronenberg, PhD President and Chief Scientific Officer La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037

May 15, 2020

Dear Drs. Hedrick and Kronenberg:

I am pleased to support your proposal to establish a Specialization in Immunology within the Biomedical Sciences (BMS) Graduate Program. The proposal demonstrates the benefits of a Specialization in Immunology for focused training and research, as well as the potential benefits for recruiting outstanding graduate students in this rapidly progressing field.

I understand that the BMS Executive Committee agrees that the Specialization in Immunology will benefit the BMS Graduate Program and have little or no impact on the program resources. I further understand that a ladder rank faculty member from the BMS program will serve as Co-Chair of the doctoral committee at all times. In addition, any student pursuing the Specialization in Immunology will be integrated into the broader BMS program and therefore will also complete all courses required by the BMS curriculum.

I believe this program will strengthen the important relationship with our affiliate organization, La Jolla Institute for Immunology and am enthusiastic about the promise of bringing more additional students to the BMS program under the auspices of a Specialization in Immunology.

Sincerely,

Steven R. Garfin, MD Interim Dean, School of Medicine

UC San Diego School of Medicine 9500 Gilman Drive #0602, Suite 1305A  La Jolla, CA 92093-0602  T: (858) 534-1783  F: (858) 534-6573  https://medicine.ucsd.edu

ÅSA B. GUSTAFSSON, Ph.D. PROFESSOR 9500 GILMAN DRIVE, MC 0751 SKAGGS SCHOOL OF PHARMACY AND PHARMACEUTICAL SCIENCES Department of Pharmacology Chair, Biomedical Sciences Graduate Program LA JOLLA, CALIFORNIA 92093-0751 Phone: (858) 822-5569 Fax: (858) 822-7558

March 24, 2020

Dear Drs. Hedrick and Kronenberg,

The Biomedical Sciences (BMS) Graduate Program Executive Committee at UCSD is pleased to support the proposal to establish a Specialization in Immunology. Your proposal clearly demonstrates the benefits of a Specialization in Immunology for focused training and research, as well as increased effectiveness for recruiting outstanding graduate students in this rapidly progressing field. The BMS Executive Committee agrees that the Specialization in Immunology will benefit the BMS Graduate Program and have little or no impact on our program resources.

We are pleased that any BMS graduate student pursuing the Specialization in Immunology will be integrated into the broader program and therefore will also complete the required courses as listed in BMS curriculum. Per UCSD policy, Professors in the Adjunct series may only serve as Chairs of doctoral committees provided a UCSD ladder rank faculty member serves as co-Chair. Furthermore, the ladder rank faculty member must be a member of the BMS program. We do not see this as a problem because there are many ladder rank UCSD faculty who are also in the BMS program.

All entering BMS students are required to participate in BMS orientation. Therefore, we are pleased that the planned Immunology Boot Camp will not conflict with BMS Orientation activities.

Overall, the Executive committee has no reservations and is enthusiastic about the promise of bringing more highly qualified students to the BMS program under the auspices of a Specialization in Immunology.

Sincerely,

Åsa Gustafsson for the BMS Executive Committee Professor of Pharmacy and Pharmacology Chair, Biomedical Sciences Graduate Program in Health Sciences

March 24, 2020

Dear Drs. Hedrick and Kronenberg,

The Graduate Committee of the Division of Biological Sciences at UCSD is pleased to support your proposal for an interdisciplinary PhD Specialization in Immunology. Your proposal articulates very effectively the wider benefits of a Specialization in Immunology for focused PhD training, for research, and for increased visibility for PhD recruitment in this area. The proposed Specialization will strongly benefit the Biological Sciences Graduate Program.

The Graduate Committee noted the following points in its discussion of your proposal.

1. To ensure the success of the Specialization the Committee emphasized the need for strong faculty participation in the Biological Sciences PhD Admissions and Recruitment processes and was pleased to note that three Immunology faculty are currently members of the Graduate Admissions Committee. Faculty involved in PhD training would also be expected to participate in other program activities such as graduate teaching and thesis committee service. 2. The Committee was supportive of students joining the Specialization upon admission (i.e., in the first year) or upon selection of thesis lab (i.e., ‘second year’). The committee emphasized that students should be able to choose at any time to switch from a Specialization to the general Biology PhD degree (BI77). 3. With regard to Immunology faculty eligibility for our four mandatory rotations, the Committee proposes that rotation outside Biological Sciences could be permitted by student petition, subject to approval by the Graduate Committee Chair. 4. As a reminder, and per Graduate Division policy, Adjunct faculty members wishing to serve as thesis advisors for Biological Sciences PhD students will need to identify a Biology Ladder-Rank Faculty member to serve as Doctoral Committee Chair.

Sincerely,

Andrew Chisholm Professor and Associate Dean, Division of Biological Sciences Chair, Biological Sciences Graduate Committee

KIT POGLIANO Dean of Biological Sciences 9500 Gilman Dr. Professor of Molecular Biology La Jolla, CA 92093-0376 Richard C. Atkinson Endowed Chair Phone: (858) 822-5738 Division of Biological Sciences E-mail: [email protected]

May 26, 2020

TO: Stephen Hedrick Professor of Molecular Biology Division of Biological Sciences

Mitchell Kronenberg President and Chief Scientific Officer La Jolla Institute for Immunology

RE: Proposal for PhD Specialization in Immunology

Dear Drs. Hedrick and Kronenberg,

I am pleased to support your proposal for an interdisciplinary PhD Specialization in Immunology. Your proposal articulates very effectively the wider benefits of a Specialization in Immunology for focused PhD training, for research, and for increased visibility for PhD recruitment in this area and for increased visibility of the Biological Sciences Graduate Program more generally. In sum, the proposed Specialization will strongly benefit the Program.

I have noted the following points in the discussion of your proposal.

1. To ensure the success of the Specialization, the Committee emphasized the need for strong faculty participation in the Biological Sciences PhD Admissions and Recruitment processes and was pleased to note that three Immunology faculty are currently members of the Graduate Admissions Committee. Faculty involved in PhD training would also be expected to participate in other program activities such as graduate teaching and thesis committee service. 2. The Committee was supportive of students joining the Specialization upon admission (i.e., in the first year) or upon selection of thesis lab (i.e., ‘second year’). The committee emphasized that students should be able to choose at any time to switch from a Specialization to the general Biology PhD degree (BI77). 3. With regard to Immunology faculty eligibility for our four mandatory rotations, the Committee proposes that rotation outside Biological Sciences could be permitted by student petition, subject to approval by the Graduate Committee Chair. 4. As a reminder, and per Graduate Division policy, Adjunct faculty members wishing to serve as thesis advisors for Biological Sciences PhD students will need to identify a Biology Ladder-Rank Faculty member to serve as Doctoral Committee Chair.

Sincerely,

Kit Pogliano, PhD

5/26/2020 For the Biological Sciences Catalog:

Specialization in Immunology A graduate specialization in Immunology is offered as part of graduate training in the Biomedical Sciences (BMS) and Division of Biological Sciences (BS) graduate programs. Students accepted to the Biological Sciences (BS) graduate program will satisfy all of the degree requirements of that program. In addition, the specialization will promote an immersive educational experience in immunology that includes participation in immunology coursework, seminars given by renowned speakers, biweekly research presentations by peers, a weekly journal club, and a yearly area-wide immunology conference.

Admission to the Specialization and Course Requirements Students admitted to the BS program may enroll in the Specialization in Immunology after entering the program or after the first year with rotations complete. Admitted students will have satisfied the requirements for admission specified for the BS program. Also, we expect students in graduate studies with a specialization in immunology to have completed an undergraduate course in the field or the equivalent before enrolling in the Specialization. Application Requirements Prospective students should apply to and are admitted into the Division of Biological Sciences doctoral program and can choose the Specialization in Immunology by notifying the Immunology Specialization Program Administrator upon admission or at any time up to completing their rotations and choosing a lab for thesis research.

The following items should be combined into a single PDF document and submitted to the Program Administrator ([email protected]):

- Student’s CV or unofficial transcript with proof of undergraduate coursework in Immunology** - Up to one-page statement of student’s interest in interdisciplinary immunology research including career goals - Nomination letter from adviser acknowledging student’s academic ability and immunology interest. **For matriculation in the Specialization, students just starting in the BS graduate program should have taken the equivalent of at least one undergraduate course in immunology. Those otherwise qualified students who have not taken an undergraduate course in immunology can fulfill this requirement by taking the week-long American Association of Immunologists Introductory Course in Immunology, presently held during the summer at the UCLA campus. Students can also fulfill this requirement by taking an upper-division summer course in immunology at any accredited college or university. Students enrolling in the Specialization during or after their rotations can satisfy the requirement by completing graduate course work in Immunology. The program administrator will work with admitted students to make sure they fulfill this requirement.

Specialization Requirements - Complete all course work and other requirements for the biological science doctorate - Completion of 2 of the following 3 courses: Graduate Immunology (BGGN 225) and BIOM253 (Immune and Immuneregulation); BGGN 232 (Innate Immunity) - Completion of a Bioinformatics for Immunologists course - Thesis research must be completed in an approved immunology laboratory Time Limits Students admitted to the specialization in Immunology must meet the time limit requirements as all other doctoral students in the Division of Biological Sciences. It is expected that students will retain the same time to degree as students not pursuing this specialization.

For the Biomedical Sciences Catalog:

Specialization in Immunology A graduate specialization in Immunology is offered as part of graduate training in the Biomedical Sciences (BMS) and Division of Biological Sciences (BS) graduate programs. Students accepted to the Biomedical Sciences (BMS) graduate program will satisfy all of the degree requirements of that program. In addition, the specialization will promote an immersive educational experience in immunology that includes participation in immunology coursework, seminars given by renowned speakers, biweekly research presentations by peers, a weekly journal club, and a yearly area-wide immunology conference.

Admission to the Specialization and Course Requirements Students admitted to the BMS program may enroll in the Specialization in Immunology after entering the program or after the first year with rotations complete. Admitted students will have satisfied the requirements for admission specified for the BMS program. Also, we expect students in graduate studies with a specialization in immunology to have completed an undergraduate course in the field or the equivalent before enrolling in the Specialization. Application Requirements Prospective students should apply to and are admitted into the Division of Biomedical Sciences doctoral program and can choose the Specialization in Immunology by notifying the Immunology Specialization Program Administrator upon admission or at any time up to completing their rotations and choosing a lab for thesis research.

The following items should be combined into a single PDF document and submitted to the Program Administrator ([email protected]):

- Student’s CV or unofficial transcript with proof of undergraduate coursework in Immunology** - Up to one-page statement of student’s interest in interdisciplinary immunology research including career goals - Nomination letter from adviser acknowledging student’s academic ability and immunology interest. **For matriculation in the Specialization, students just starting in the BMS graduate program should have taken the equivalent of at least one undergraduate course in immunology. Those otherwise qualified students who have not taken an undergraduate course in immunology can fulfill this requirement by taking the week-long American Association of Immunologists Introductory Course in Immunology, presently held during the summer at the UCLA campus. Students can also fulfill this requirement by taking an upper-division summer course in immunology at any accredited college or university. Students enrolling in the Specialization during or after their rotations can satisfy the requirement by completing graduate course work in Immunology. The program administrator will work with admitted students to make sure they fulfill this requirement.

Specialization Requirements - Complete all course work and other requirements for the biomedical science doctorate - Completion of 2 of the following 3 courses: Graduate Immunology (BGGN 225) and BIOM253 (Immune and Immuneregulation); BGGN 232 (Innate Immunity) - Completion of a Bioinformatics for Immunologists course - Thesis research must be completed in an approved immunology laboratory Time Limits Students admitted to the specialization in Immunology must meet the time limit requirements as all other doctoral students in the Division of Biomedical Sciences. It is expected that students will retain the same time to degree as students not pursuing this specialization.