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Gardner Tufts COHA Fellowship 2020

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Gardner Tufts COHA Fellowship 2020 CTSA Translational Research Fellowship Opportunity in Comparative Cancer Genomics at Tufts Cummings School of Veterinary Medicine Description of Fellowship Training Environment The purpose of this 2-year research fellowship opportunity is to provide residency-trained veterinary specialists with advanced instruction and mentoring in comparative cancer genomics. The Fellow will be involved in research aimed at dissecting the genomic landscape of specific canine tumors (osteosarcoma, hemangiosarcoma, lymphoma) and using those data to interrogate relevant molecular pathways for potential therapeutic intervention. The goal of the fellowship is to provide the trainee with a comprehensive set of tools that will support a future career as a clinician-scientist in the setting of academic medicine. Fellows will work within the laboratories of Drs. Cheryl London and Heather Gardner, gaining bench-based skill sets including cell- culture, a variety of assays to assess tumor cell phenotype (flow cytometry, assessment of proliferation/apoptosis, invasion assays, etc), DNA/RNA purification, PCR/RT-qPCR, cloning, gene editing (CRISPR), western blotting and chromatin immunoprecipitation (ChIP), among others. Additionally, the Fellow will learn basic tools associated with analysis of genomic data including R/R Studio and command-line based open-source software (DESeq2, EdgeR, SnpEff, etc.). The Fellow will obtain a visiting scientist position at the Broad Institute, permitting access to correlative genomics data and computational expertise within the Vertebrate Genomics Group (directed by Dr. Karlsson). The Research Fellow will devote at least 80% of their effort to benchtop research and analysis of data. The remaining 20% of time may be spent embedded within the Clinical Trials Office at the Cummings School to participate in ongoing translational oncology studies and/or engaging in clinical duties related to their research (i.e., sample collection, etc.). In this clinical setting, the Fellow will be responsible for assisting with all aspects of clinical trials conducted in oncology patients presenting to the Foster Hospital for Small Animals under the supervision of Dr. London. The Fellow will also have opportunities to rotate through the pediatric oncology service at the University of Massachusetts Medical School (with Dr. Shohet). Lastly, Jackson Laboratory is now a partner with Tufts University and we have initiated a large collaborative effort to develop and credential canine PDX models, with the goal of establishing a canine immune system in the mouse, much like humaniZed mouse systems. This is being undertaken at the JAX Farmington campus, a short drive from the Grafton Cummings School. The fellow will be involved, as appropriate, in working with the JAX faculty to evaluate the PDX tumors at the histologic and genomic levels. Goals of the Fellowship 1. Gain expertise in a variety of laboratory techniques including cell culture, gene editing methods, cloning, western blotting, flow cytometry among others. 2. Become familiar with methods for genomic interrogation (RNAseq, whole exome sequencing, whole genome sequencing and CHiP sequencing) and associated analytic tools. 3. Develop fundamental knowledge regarding animal models of cancer, specifically mouse xenograft and PDX systems. 4. Demonstrate an understanding of how molecular techniques can be used to support comparative and translational research. 5. Improve communication and presentation skills in both small and large venues 6. SynthesiZe relevant literature and apply it to research questions including hypothesis generation and formulation of a research plan 7. Gain expertise in grant and paper writing 8. Develop tools to become comfortable working in a team science setting. Fellowship Mentoring Team Heather Gardner, DVM, PhD, ACVIM(O), Primary Mentor: Assistant Research Professor, Cummings School of Veterinary Medicine at Tufts University. Dr. Gardner in a veterinary medical oncologist with broad training in clinical trials and comparative genomics. She has a number of active collaborations with the Broad Institute, the Translational Genomics Research Institute and the Children’s Hospital of Philadelphia. Her research efforts center on leveraging the canine tumor genome to inform comparative and translational research. Dr. Gardner will provide primary oversight to the Fellow. She has co-mentored research projects for several veterinary residents, undergraduate and graduate students. Cheryl London, DVM, PhD, ACVIM(O), Co-Mentor: Anne Engen and Dusty Professor in Comparative Oncology, Director of the Clinical Trials Office, Cummings School of Veterinary Medicine at Tufts University; Research Professor at the Graduate School of Biomedical Sciences and School of Medicine at Tufts University. Dr. London is an expert in the field of translational sciences and comparative medicine, using spontaneous models of cancer in dogs. She led the establishment of successful Veterinary Clinical Trials programs at both OSU and Tufts and she maintains an active research laboratory in the Immunology Department at Tufts School of Medicine. She is heavily involved in the Tufts Clinical and Translational Science Institute (CTSI), serving as Director of the Research Collaboration Team and the One Health Optional Module. Dr. London has been the primary mentor/research advisor for 8 MS students, 5 PhD students, 14 Medical Oncology Residents/Fellows, and 3 Postdoctoral Fellows. Several have gone on to advanced careers in industry and academics. Importantly, all of her prior PhD students were DVMs enrolled in a dual program; in each case their thesis work was undertaken during the course of their residency programs (two anatomic pathology, two clinical pathology, two medical oncology) and she is therefore familiar with the need to balance laboratory-based research with clinical responsibilities in the setting of veterinary medicine. Elinor Karlsson, PhD: Associate Professor in Bioinformatics and Integrative Biology at the University of Massachusetts Medical School; Director of the Vertebrate Genomics Group at the Broad Institute of MIT and Harvard. Dr. Karlsson has expertise in vertebrate genomics, with her research program spanning the genetics that drive canine behaviors to genomic alterations in canine cancers. She has extensive experience with various techniques to analyZe genomics data, bioinformatics and integration of data from multiple genomics platforms within and across species. Dr. Karlsson has several active collaborations with Drs. Gardner and London, with studies spanning both genomics-based analytic techniques and clinical trials in pet dogs with cancer. These coordinated efforts supported successful R27 and R01 applications for which Dr. Karlsson is the PI and Drs. London and Gardner are co-PI/co-investigator. Jason Shohet, MD, PhD: Division Chief for Pediatric Hematology/Oncology at University of Massachusetts Medical School; Associate Professor of Pediatrics at University of Massachusetts Medical School. Dr. Shohet’s research focuses on the development of less toxic therapies for childhood cancers and cancer stem cell biology. As such, he provides a clinical context to assist with translation of experimental results and application to human patients. Wonyeong Kang, DVM, PhD: Associate Research Scientist, The Jackson Laboratory. Dr. Kang is leading an effort to generate a canine PDX core resource for future translational work. She plans to caninize these models to provide a better tool for immune-oncology studies. Dr. Kang will assist the Fellow with making connections to the community at JAX in Farmington CT engaged in canine comparative oncology work, ranging from the PDX models to generation of canine iPSCs and genomics of canine brain tumors. Norma Terrin, PhD: Scientific Director of the Biostatistics, Epidemiology and Research Design (BERD) Center within the Tufts Clinical and Translational Science Institute (CTSI) and Professor at Tufts University School of Medicine. Dr. Terrin will contribute her experience with respect to experimental design and statistical analysis, particularly with respect to animal model work. Programmatic training opportunities available to the fellow: The mentoring team has designed a set of comprehensive training opportunities that take advantage of the complementary sets of expertise available to the Fellow and leverages ongoing partnerships between Tufts University/Tufts CTSI/Tufts Medical Center, the Broad Institute and The Jackson Laboratory. The following workshops and seminar series are available through Tufts CTSI, providing instruction in multiple facets of comparative and translational research: grant writing, comparative effectiveness research seminars, good clinical practice (GCP), developing and managing your research career, research design and data analysis. The CTSI has several resources to support training in team science that are geared to junior faculty as well. Through the visiting scientist appointment at the Broad Institute, the Fellow will be able to attend workshops and seminar series, including advanced informatics classes, yearly CRISPR focused short courses and monthly cancer program meetings, which brings together scientists from across the diverse landscape of Boston academic and industry stakeholders. Additional workshops are available through both the Broad Institute and Tufts CTSI for fellows interested in gaining skills in bioinformatics techniques related to their research. Lastly, the Fellow will have opportunities to spend
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