Table of Contents

Letter from Organizers ………………………… 2-3

Symposium Schedule …………………………….. 4

Annual JMBGSA Keynote Address ……………………………….. 5-6

Research Abstracts – Oral ………………………………. 7-10 Symposium Abstracts – Poster …………………………… 11-23

Participants ……………………………………… 24

Sponsors …………………………………………. 27

Friday March 24, 2017

10:00AM - 4:30PM

Atrium – Life Sciences Building Busch Campus,

1 Letter from Organizers participate as judges and give students feedback on their work. Since this event would not be possible without the participation of Welcome to the 11th Annual Graduate Student Symposium our fellow graduate students, we applaud their efforts and thank hosted by the Joint Molecular Biosciences Graduate Student them for their poster presentations and talks. We would like to Association (JMBGSA) of Rutgers University. We are delighted to offer a very special thank you to all our generous sponsors as well have you join us today to support the outstanding work that for supporting graduate student research at Rutgers. Thank you for graduate students in the Molecular Biosciences Graduate Programs joining us for this symposium and we hope you enjoy your time have been producing throughout their different stages of graduate spent here today! learning. As a student organization, the goal of JMBGSA is to Sincerely, facilitate the professional development of graduate students and JMBGSA Executive Board 2016-2017 promote opportunities for social interaction with their peers. By presenting their work to a critical audience, graduate students are able to hone important presentation skills and receive input on their work from faculty and peers from various departments. With these goals in mind, we organize the annual symposium and look to the university community to make it a success. Through this symposium, we hope to not only showcase the graduate student research, but also to provide a platform for professional interaction between students, faculty and administration. We are proud to be able to provide the avenue for students from different fields of bioscience research to showcase their scientific endeavors. Through both the oral and poster presentations, we seek to highlight some of the interesting basic and translational research that is being conducted at Rutgers. We want to take this opportunity to acknowledge our gratitude to our faculty advisor, Dr. Janet Alder, for her incredible guidance and support during the planning process of this and other events throughout the year. We also want to thank the graduate student offices of both the Graduate School – New Brunswick (GSNB) and the Graduate School of Biomedical Sciences (GSBS) for their help and support. We gratefully acknowledge the faculty members who have taken time out from their busy schedules to

2 3 Symposium Schedule Keynote Address

Dr. Steven K. Libutti Registration and 9:30 - 10:00AM Introduction Director of Rutgers Institute of New Jersey Vice Chancellor for Cancer Programs for Rutgers Biomedical and Health Sciences at Rutgers University 10:00 - 11:00AM Oral Presentations I "Of Mice and Men(in) and What I 11:00 - 12:00PM Poster Presentations I have Learned from Both”

12:00 - 1:00PM Keynote Address A graduate of Harvard College, Dr. Steven Libutti received his MD from the College of 1:00 - 2:00PM LUNCH Physicians and Surgeons. Following his residency in surgery, he completed a fellowship in Surgical Oncology and 2:00 - 3:00PM Poster Presentations II Endocrine Surgery in the Surgery Branch of the National Cancer Institute and was ultimately a tenured Senior 3:00 - 4:00PM Oral Presentations II Investigator and Chief of the Tumor Section in the Surgery Branch, NCI. Dr. Libutti served as Director for the Montefiore Einstein Center for Cancer Care in City and 4:00 - 4:30PM Award Ceremony was a Professor and Vice Chairman of the Department of Surgery and a Professor in the Department of Genetics at Albert Einstein College of Medicine and Montefiore Health System. In January 2017, he became the Director of Rutgers Cancer Institute of New Jersey.

4 5 In addition to being an accomplished clinical surgeon, Dr. Oral Presentations Libutti is a world-renowned scientist. The goal of Dr. Libutti's research program is to develop novel cancer therapies through a #1. Preclinical Analysis of the Notch Gamma Secretase Inhibitor BMS- better understanding of the complex interactions within the tumor 906024 in Combination with Chemotherapy in the Treatment of Lung Adenocarcinoma microenvironment. He is particularly interested in understanding of Authors: Morgan KM., Lee F., Michaud E., Fischer BS., Pine SR. tumor neovascular formation and the interaction between tumor Notch signaling is aberrantly activated in approximately one third of non-small cells, endothelial cells and the components of the tumor cell lung cancer (NSCLC) cases, primarily through loss of the endogenous microenvironment including fibroblasts and cancer stem cells. Dr. inhibitor, Numb, or via gain-of-function mutations in the Notch1 receptor, and is Libutti's approach to the study of these interactions has been associated with poor overall survival. We characterized the interaction between BMS-906024, a clinically relevant gamma secretase inhibitor (GSI) that inhibits through the utilization of a variety of in vitro and in vivo model Notch activation, and front-line chemotherapy in preclinical models of NSCLC. systems. Drug synergy MTS assays consisting of treatment with BMS-906024, cisplatin or paclitaxel, or the combination of GSI and chemotherapy were performed on a panel of human NSCLC cell lines, most of which were derived from Dr. Libutti has authored more than 270 peer reviewed adenocarcinomas. Analysis of the drug effects with CalcuSyn yielded journal articles and holds seven U.S. patents. He also serves as significantly greater synergy for the GSI BMS-906024 combined with paclitaxel Editor-in-Chief of Cancer Gene Therapy. He is the recipient of than with cisplatin (average CI = 0.54 vs 0.85, respectively; P = 0.001). Additionally, MTS assays performed on an extended panel of 31 NSCLC cell both the National Cancer Institute and National Institutes of Health lines demonstrated that the synergy between BMS-906024 and paclitaxel was Director’s Awards and has been recognized as a top doctor and top significantly greater in Kras/Braf-wildtype than –mutant cells (average CI = 0.43 vs 0.90, respectively; P=0.0026), while there was no correlation with EGFR cancer doctor by Castle Connelly as well as one of the best doctors or TP53 status. Treatment of cell line- and patient-derived lung adenocarcinoma in New York by New York Magazine. xenografts in mice confirmed enhanced antitumor activity for the combination of BMS-906024 and paclitaxel via decreased cell proliferation and increased apoptosis. These results are a step toward identification of the optimal combination of the GSI BMS-906024 with standard chemotherapies, as well as potential biomarkers that may predict patient response to Notch-targeted therapy. Funding: National Cancer Institute (KMM, SRP); Bristol-Myers Squibb (SRP)

#2. Mass Spectrometric Analysis of TRPM7 Phosphorylation Reveals Regulatory Mechanisms of the Channel-Kinases Authors: Cai N., Bai Z., Nanda V., Runnels L.W.

Transient Receptor Potential Melastatin 7 (TRPM7) was the first ion channel identified to contain a functional kinase domain. As a cation-permeating channel, TRPM7 is essential for controlling whole-body magnesium homeostasis and is involved in various cellular processes such as cell proliferation, adhesion, and migration. While much progress has been made in elucidating the function of the channel, little is known about the function and regulation of the kinase domain. To fill this gap in knowledge, we performed a comprehensive mass spectrometric analysis of TRPM7 phosphorylation and

6 7 uncovered multiple in vivo autophosphorylation sites on TRPM7. To test represent novel therapeutic opportunities to improve prognosis for these whether autophosphorylation affects the function of TRPM7’s kinase, we patients. conducted a series of amino acid substitution analyses and identified two potential regulatory autophosphorylation sites: S1565, located on the exchange #4. Cellular Zinc Homeostatic Mechanisms Function as an On/Off Switch domain outside of the kinase’s catalytic core, and S1777, located at the catalytic for Zinc Metallochaperone Mediated Reactivation of Mutant p53 center of the kinase domain. When phosphomimetic substitutions of either Authors: Samuel Kogan, Xin Yu, Darren Carpizo glutamate or aspartate were introduced at these two sites, the kinase activities of the proteins were severely compromised as assessed by in vitro kinase assays. TP53 is the most commonly mutated gene in cancer; however, no effective anti- This analysis in addition to structural modeling suggests a novel mechanism of cancer drug targeting mutant p53 exists. Restoring wild type structure and TRPM7 autophosphorylation in controlling TRPM7 kinase activity. This study function to mutant p53 has been one of the holy grails of cancer drug research. will serve as the first step towards understanding the regulatory mechanisms of We recently discovered a class of small molecules (zinc metallochaperones, the channel-kinase and further allow us to investigate how this unique ion ZMC), which restores wild type structure and function specifically to zinc- channel takes part in various important cellular processes. deficient p53 mutants by delivering zinc to cells as an ionophore. The p53 This work was supported by the generous support of the National Institutes of protein requires zinc for proper folding and loss of zinc binding is a common Health NIGMS (GM080753) to LWR, and American Heart Association mechanism for inactivating p53. In vitro pharmacodynamics studies (p21 Predoctoral Fellowship (15PRE24890008) to NC. levels) of ZMC1 indicated that over a 24 hour time period, the drug function comes on at 2 hours, peaks at 6 hours, and is off by 8-10 hours. We #3. Integrative proteogenomic analyses to identify essential genes in poorly hypothesized that the regulation of this on/off function is governed by cellular prognostic high-grade serous ovarian cancer zinc homeostatic mechanisms that function to restore zinc to its physiologic Authors: Khella, C. A., Karagoz, K. B., Gatza, M. L. levels. We first investigated the dynamics of zinc levels in cancer cells treated with ZMC1 using a fluorescent zinc reporter and found that zinc levels peaked High-grade serous ovarian cancer is the most lethal gynecological cancer and at 4-6 hours, which preceded the peak in p21 protein levels, followed by accounts for ~22,440 new cases and 14,080 deaths each year. The poor returning to baseline by 8-10 hours. We examined the expression of the entire prognosis for these patients can be partially attributed to diagnosis at later stages suite of 36 zinc regulatory genes by RNAseq and found that ZMC1 induced the and tumor progression due to developed resistance to primary platinum-taxane- greatest increase in MT1A, MT2A and ZnT1. Using the CRISPR-cas9 system, based therapy. To investigate the underlying mechanisms regulating resistance we deleted MT1A and MT2A and examined the cellular zinc dynamics and and poor prognosis for these patients, we performed integrated genomic sensitivity to ZMC1. Not only were the baseline levels higher, but the maximum analyses incorporating gene expression, proteomic, and phosphoproteomic data. peak and duration of zinc induction were higher than controls. When we Analysis of gene expression data from human tumors (n=297) determined that examined the pharmacodynamics of ZMC1 by p21 western blot we observed HER2, KRAS, STAT3, HCK, and epiregulin signaling are significantly higher and longer duration of p21 levels. Cell growth inhibition experiments upregulated in poor prognostic patients (<2 year survival) compared to long- revealed that the cells were markedly more sensitive to ZMC1. Together these term survivors (>5 years). Analysis of quantitative mass-spectrometry-based data support the hypothesis that cellular zinc homeostatic mechanisms function phosphoproteome data from human tumors demonstrated that phosphorylated as an on/off switch to regulate the mechanism of ZMCs. EGFR, HER2, and HCK are significantly overexpressed in these tumors and Acknowledgements: NCI (1R01CA200800-01), Breast Cancer Research enrichment analyses determined that insulin, mTOR, MAPK, and focal adhesion Foundation signaling are activated. To identify potential therapeutic opportunities that correspond to activated signaling in poorly prognostic patients, we analyzed data #5. Negative regulatory network between the aurora kinases protects from a genome-wide RNAi screen to identify essential genes in taxane-resistant female gamete euploidy ovarian cancer cell lines. These analyses demonstrate that AKT1, IGF1R, Authors: Alexandra Nguyen, Amanda Gentilello, Karen Schindler PIK3CA, CDK6 and FGF12 are essential for cell viability in taxane-resistant ovarian cancer cell lines. Collectively, our proteogenomic analyses of human The aurora kinases (AURKs) are critical regulators of cell division. Mammalian ovarian cancer demonstrate that poorly prognostic tumors are characterized by germ cells express 3 AURK homologs (A, B, C), unlike mitotic cells which increased ERBB-associated signaling leading to increased PI3K, mTOR, and require 2 (A, B). AURKB and AURKC are more similar in sequence and JAK-STAT activity. Importantly, our analyses suggest that targeting druggable AURKC has assumed the mitotic functions of AURKB during female meiosis I essential genes in these pathways (i.e. AKT1, PIK3CA, CDK6, and IGF1R) may leaving the requirement for AURKB unknown. To determine the requirement

8 9 for AURKB in female meiosis we generated an oocyte-specific knockout mouse strain. In contrast to oocytes lacking Aurkc, where oocytes are healthy because Poster Presentations of AURKB compensation, oocytes lacking Aurkb were aneuploid. But, surprisingly these Aurkb-/- oocytes had increased AURKC activity. We then #1. The C-terminal region of the yeast mitochondrial transcription factor generated mice with one copy of Aurkc in the Aurkb-/- oocyte background to ask Mtf1 has distinct roles in transcription initiation if reducing AURKC levels could rescue the failure phenotype; utilizing oocytes Authors: Basu U., Deshpande A.P., Sultana S., Patel S.S. without AURKB and AURKC as controls. Reduction of Aurkc in half did not rescue, but to our surprise oocytes lacking both kinases were indistinguishable Mitochondria are double-membrane bound organelles in eukaryotic cells. Their from WT. Here we show that AURKA, the homolog restricted to spindle poles, cardinal role in energy production makes mitochondria a key player in compensates for the loss of AURKB and AURKC; localizing to chromosomes metabolic, degenerative, and age-related diseases. Thus, processes involved in and phosphorylating AURKB/C substrates. Interestingly, this compensation is the maintenance and expression of the mitochondrial DNA are crucial to dependent on the absence of AURKC as expression of the kinase restricts understand. Our lab studies the mechanism of transcription initiation, the first AURKA to spindle poles. These studies show, for the first time, the ability for step in mitochondrial gene regulation, in mitochondria using yeast as a model AURKA to functionally complement AURKB/C in vivo. Importantly, these data system. Expression of the yeast mitochondrial DNA is driven by two-component shed new light on a negative regulatory network among the kinases, which may transcription machinery containing the core RNA polymerase Rpo41, which is be critical for generating euploid gametes. homologous to T3/T7 phage RNA polymerases, and a transcription factor Mtf1, This work was supported by grants from the NIH (F31HD089591: A.L.N.; which is required for promoter melting and specific transcription initiation. To R01GM112801-02: K.S.). understand the role of the C-terminal region(C-tail) of Mtf1 which is not resolved in crystal structure, we purified recombinant Mtf1 mutant proteins with #6. Record Growth Rate and Exceptional Photoprotection Powered by an increasing deletions of the C-tail. Our studies show that the Mtf1 mutants can Adaptable Light Conversion Mechanism in the Microalga Chlorella ohadii efficiently bind to the promoter DNA, can melt the -4 to +2 promoter region Authors: Ananyev, G., Gates, C., Treves, H., Dismukes, G.C. similar to wild-type Mtf1 to form the open complex. We report that the C-tail of Mtf1 aids in template alignment and consequently promotes the binding of the The desert microalga Chlorella ohadii was reported to grow at extreme light initiating NTPs. The C-tail also prevents initiation with nanoRNAs and plays a intensities with minimal photoinhibition, tolerate frequent de/re-hydrations and crucial role in transitioning from transcription initiation to elongation. Combined to lack photoprotection by antenna-based non-photochemical quenching. Here with other biochemical studies, we propose that the C-tail of Mtf1 is involved in we investigate the molecular mechanisms using PSII charge separation quantum regulating key steps in transcription initiation. yield (variable fluorescence, Fv/Fm) and both linear (PSII-LEF) and cyclic This study is supported by National Institute of General Medical Sciences (PSII-CEF) electron flow within PSII (by flash-induced O2). Cells grown at low (NIGMS) [R35GM118086 to S.S.P.] and American Heart Association (AHA) (20), high (200), and extreme (2000) light intensities (µE/m2/s) grow [16PRE30400001 to U.B.] increasingly faster by shifting from PSII-LEF to PSII-CEF to maintain photochemical energy conversion and increase photoprotection, respectively. #2. Aresenic Trioxide as targeted therapy for harboring TRIM33- Low light grown cells have small antennae (332 Chl/PSII), use mainly PSII-LEF RET -fusion proteins (95%), and produce high O2 quantum yield (0.06 mol O2/mol PSII), converting Authors: Husam Al-hraishawi, Atul Kulkarni and Shridar Ganesan 40% of PSII charge separations. High light grown cells have smaller antenna and lower PSII-LEF (63%). Extreme light grown cells have only 42 Chl/PSII Aberrant rearrangements in chromosome structure occur in many hematological (no LHCII antenna), minimal PSII-LEF (10%), and grow faster than any known and solid tumors. During the past decade, the number of newly identified phototroph (doubling time 1.3 h). Adding a synthetic quinone that displaces QB chromosomal rearrangements has rapidly increased because of the widespread decreases PSII-LEF and increases PSII-CEF, pinpointing the chokepoint for use of high-throughput sequencing. For chromosomal rearrangements to occur, electron/proton branching between these two pathways. Adding excess quinone two double-strand breaks of DNA in distinct regions of the genome are linked to supplement the PQ pool fully uncouples PSII-CEF from its natural regulation by canonical non-homologous end joining (NHEJ) of the breakpoints. and produces maximum PSII-LEF. Upon dark adaptation PSII-LEF reverts to Ultimately, some fused genes exhibit constitutive activation due to a powerful PSII-CEF as a transient protection mechanism to conserve water and minimize new promoter or enhancer resulting from the rearrangement, or by removing the cost of antenna biosynthesis. sequences important for transcriptional or functional control. Tyrosine kinases fusions represent a large portion of fusion genes which are constitutively active.

10 11 Unsurprisingly, due to rearrangements from genomic instability, cancers driven #4. Role of Autophagy in Kras-Driven Non-Small Cell Lung Cancer by these kinases develop resistance after treatment with kinase inhibitors over (NSCLC) with LKB1 Loss extended periods of time. Thus, we need to target the fused partners of Authors: Vrushank Bhatt, Stephen C. Van Nostrand, Wali Kamran, Jessie constitutively active fusion proteins to lower the probability of the cancer Yanxiang Guo acquiring resistance. Arsenic trioxide (ATO) has been shown promote PML/RARA degradation by the proteasome after binding to the PML moiety. Autophagy degrades and recycles macromolecules for cells to survive PML is a TRIM family member, which have highly conserved N-terminal starvation. In genetically engineered mouse models (GEMMs) for human regions and have been implicated in many fusion gene-related cancers. We NSCLC, autophagy supports Kras-driven lung tumor growth with or without hypothesize that ATO can target these fusion genes and ameliorate the cancer Trp53. Tumor suppressor liver kinase B1 (LKB1) activates 5’-adenosine driven in part by these TRIM members. monophosphate protein kinase (AMPK) to maintain energy homeostasis. LKB1 mutation is detected in 20-30% of NSCLC. Hypothesis: Loss of LKB1 promotes #3. Compromised BRCA1-PALB2 interaction is associated with breast cell growth but also limits adaptation to metabolic stress, and this property can cancer risk be further compromised by loss of autophagy. we found that Atg7 deficiency Authors: Tzeh Keong Foo, Marc Tischkowitz, Srilatha Simhadri, Talia Boshari, significantly extended the lifespan of mice bearing Atg7 deficient tumors with Kathleen A. Burke, Samuel H. Berman, Nadia Zayed, Yuan Chun Ding, Susan both LKB1 and p53 deletion, but had no effect on mice bearing Atg7 null L. Neuhausen, Britta Weigelt, Jorge S. Reis-Filho, William D. Foulkes and Bing tumors with LKB1 loss alone. Surprisingly, in mice bearing Atg7 deficient Xia tumors with LKB1 loss alone, immunohistochemistry for ATG7 shows that 20% of tumors still expressed ATG7, indicating that loss of LKB1 selectively The major breast cancer suppressor proteins BRCA1 and BRCA2 are physically suppresses autophagy deficient tumor growth, leading to WT tumor cell and functionally linked by PALB2 (partner and localizer of BRCA2), a third differentiation and death. Furthermore, 25% of tumor derived cell lines (TDCLs) tumor suppressor, in the homologous recombination (HR)-mediated DNA repair generated from “Atg7 null tumors” were still expressing ATG7. Atg7 null pathway critical for tumor suppression. Heterozygous mutation carriers in TDCLs were more sensitive to glucose, glutamine and serum starvation, than PALB2 have been reported to have increased risk of breast, ovarian and Atg7 WT TDCLs. Tumor metabolomics show that levels of certain amino acids pancreatic cancer. While truncating mutations are generally pathogenic, involved in methionine metabolism pathway and urea cycle, were lower in Atg7 interpretation of missense variants in BRCA genes remains challenging. null tumors with LKB1 loss compared to Atg7 WT tumors. Therefore, a clear Although patient-derived missense variants that disrupt PALB2 binding have understanding of mechanisms underlying autophagy and metabolic pathways been identified in BRCA1 and BRCA2, none was reported for PALB2. Here, we that fuel tumor cell survival under metabolic stress would be useful to develop describe the identification of a novel PALB2 variant, c.104T>C [p.L35P], that novel therapies. segregated in a family with strong history of breast cancer. Functional analyses Funding: K22 CA190521, P30 CA72720. showed that L35P abrogates the PALB2-BRCA1 interaction, resulting in impaired HR and sensitivity to platinum salts and PARP inhibitors. Whole- #5. The N-terminus of SBP2 is a Requirement for Selenoprotein P Synthesis exome sequencing of breast tumor from a c.104T>C carrier revealed a somatic, Authors: Pinkerton MH, Shetty S, Vetick M, Copeland PR truncating mutation in the second allele of PALB2, with the tumor displays hallmark genomic features of tumors with BRCA mutations and HR defects. A UGA stop codon is recoded to accommodate the incorporation of the 21st Using a combination of traditional clinical genetics, tumor whole-exome amino acid selenocysteine (Sec), which is essential for human health. For UGA sequencing and in-depth functional analyses, we have provided direct evidence to be recoded a specialized set of cis and trans factors are required and consist to cement the pathogenicity of L35P. Parallel analyses of other germline variants of: an mRNA with an in frame UGA codon, a selenocysteine insertion sequence in the PALB2 N-terminal BRCA1-binding domain also identified multiple (SECIS) in the 3’ untranslated region, a SECIS binding protein 2 (SBP2), a variants that affect HR function to varying degrees, suggesting their possible specific translation elongation factor (eEFSec), and a selenocysteine tRNA. The contribution to cancer development. Our findings establish p.L35P as the first N-terminus of SBP2 is believed to have no direct role in Sec incorporation pathogenic missense mutation in PALB2 identified to date and directly because the C-terminus of SBP2 is sufficient for the incorporation of Sec into demonstrate the requirement of the PALB2-BRCA1 interaction for breast cancer selenoproteins that have one Sec codon. Having recently developed an in vitro suppression. translation system in wheat germ requiring the addition of all Sec-incorporation factors, we found that translation of SELENOP, which contains 10 Sec codons, is defective in that only early termination products are made. This contrasts with

12 13 mammalian systems where full length protein is predominantly found. This synaptic activity. The phosphatidylinositol-4,5-bisphosphate 3-kinase/Akt/ observation, combined with the fact that neither SELENOP nor the N-terminus mammalian target of rapamycin (PI3K/Akt/mTOR) pathway has been of SBP2 are found in invertebrates, points to a specialized function for the N- implicated in the modulation and regulation of synaptic strength, activity, terminus of SBP2 related to SELENOP synthesis. To validate the relationship maturation, and axonal regeneration. The present study focuses on the between the N-terminus of SBP2 and SELENOP, C-terminal and full length physiology and survival of neurons following manipulation of Akt and several SBP2 were compared for in vitro translation of SELENOP. We found that the downstream targets, such as GSK3β, FOXO1, and mTORC1, prior to NMDA production of full length SELENOP is heavily dependent on the presence of the injury. Our analysis reveals that exposure to sublethal levels of NMDA does not SBP2 N-terminus. alter phosphorylation of Akt, S6, and GSK3β at two and twenty four hours following injury. Electrophysiological recordings show that NMDA-induced #6. The strontium inorganic mutant of the water oxidizing center injury causes a significant decrease in spontaneous excitatory postsynaptic (CaMn4O5) of PSII improves WOC efficiency but slows electron flux currents at both two and twenty four hours, and this phenotype can be prevented through the terminal acceptors by inhibiting mTORC1 or GSK3β, but not Akt. Additionally, inhibition of Authors: Gates, C., Ananyev, G., Dismukes, G.C. mTORC1 or GSK3β promotes neuronal survival following NMDA-induced injury. Thus, NMDA-induced excitotoxicity involves a mechanism that requires Herein we extend prior studies of biosynthetic strontium replacement of calcium the permissive activity of mTORC1 and GSK3β, demonstrating the importance in PSII-WOC core particles to characterize whole cells. Previous studies of of these kinases in the neuronal response to injury. Thermosynechococcus elongatus found a lower rate of light-saturated O2 from isolated PSII-WOC(Sr) cores and 5-8× slower rate of oxygen release. We find #8. Integrative Genomic Analysis Identify Molecular Subtypes of Lung similar properties in whole cells, and show it is due to a 20% larger Arrhenius Carcinoids activation barrier for O2 evolution. Cellular adaptation to the sluggish PSII- Authors: Laddha, S. V., Da Silva, E, Robyzk, K., Untch, B.R., Tang, L.H., WOC(Sr) cycle occurs in which flux through the QAQB acceptor gate becomes Chan, C.S limiting for turnover rate in vivo. Benzoquinone derivatives that bind to QB site remove this kinetic chokepoint yielding 31% greater O2 quantum yield (QY) of Lung carcinoids are a rare and slow growing type of primary lung neoplasms. PSII-WOC(Sr) vs. PSII-WOC(Ca). QY and efficiency of the WOC(Sr) catalytic The understanding of tumorigenesis and molecular subtyping of these carcinoids cycle are greatly improved at low light flux, due to fewer misses and backward is incomplete. Here, we investigated the genomic and molecular alterations in transitions and 3-fold longer lifetime of the unstable S3 state, attributed to lung carcinoids and uncover subtypes of lung carcinoids with distinct biological, greater thermodynamic stabilization of the WOC(Sr) relative to the photoactive clinical features and identify a set of novel gene signatures and biomarkers. We tyrosine YZ. More linear and less cyclic electron flow through PSII occurs per performed targeted sequencing of a 354-cancer gene panel (n=29), mRNA PSII-WOC(Sr). The organismal response to the more active PSII centers in Sr- sequencing (n=30) and DNA methylation assay (n=18) on lung carcinoids grown cells at 45°C is to lower the number of active PSII-WOC per Chl, (including 13 atypical and 17 typical samples). We identified mutated genes producing comparable oxygen and energy per cell. We conclude that redox and enriched in histone covalent modifier/chromatin remodeler (with MEN1 and protonic energy fluxes created by PSII are primary determinants for optimal ARID1A being recurrently mutated), DNA repair and protein kinases pathways. growth rate of T. elongatus. We further conclude that the (Sr-favored) Unsupervised clustering and principle component analysis on gene expression intermediate-spin S=5/2 form of the S2 state is the active form in the catalytic and DNA methylation data showed 3 robust subtypes: Subtype 1(S1), Subtype cycle relative to the low-spin S=1/2 form. 2(S2) and Subtype 3(S3). MEN1 gene mutations were found exclusively in S2 subtype. S3 subtype is enriched for typical carcinoids, predominately found at #7. Role of Akt-independent mTORC1 and GSK3β signaling in sublethal endobronchial lung (pval < 0.001) and has better recurrence free survival (pval < NMDA-induced injury and the recovery of neuronal electrophysiology and 0.003). Immunohistochemistry of two biomarkers is sufficient to stratify the survival three (ASCL1 positive only for S1, S100 positive only for S2) subtypes. Przemyslaw Swiatkowski, P., Nikolaeva, I., Kumar, G., Zucco, A., Akum, B.F., Patel, M.V., D'Arcangelo, G., and Firestein, B.L.

Glutamate-induced excitotoxicity, mediated by overstimulation of N-methyl-D- aspartate (NMDA) receptors, is a mechanism that causes secondary damage to neurons. The early phase of injury causes loss of dendritic spines and changes to

14 15 #9. PipelineDog: a simple and flexible pipeline construction and compared to that observed in mice challenged with melanoma alone. In tissues maintenance tool from concomitantly challenged mice, a 90% reduction (relative to uninfected, Authors: A. Zhou, Y. Zhang, Y. Sun, J. Xing melanoma-bearing mice) in myeloid-derived suppressor cells (MDSCs) was observed via flow cytometry. These findings contrast with the results of Data manipulations and analysis are essential components of bioinformatics previously run experiments in our laboratory in which concomitantly challenged research. Such studies require multiple data manipulation and analysis steps, mice exhibited faster tumor progression than uninfected counterparts, when necessitating the integration of these steps into pipelines. An analysis pipeline influenza was administered at an earlier stage in tumor development. Further defines an analysis workflow by specifying the order and configuration of research will be conducted to elucidate the dual role of non-oncogenic, acute various analysis tools, and their input/output data. Although pipelines can be infection in promoting the development of early-stage, subclinical tumors, and coded in a scripting language like BASH or python, such scripts usually suffer in thwarting progression of established tumors. The focus of future experiments from limited readability and poor reusability. For enhanced reusability, a design will be to decipher the immunological and non-immunological mechanisms that allows clear decoupling and easy reassembly of individual steps is needed, governing tumor progression in the presence versus absence of infection. but it is challenging to implement this design in these general-purpose scripting languages. #11. Activating Endogenous Neural Stem Cells for Traumatic Brain Injury To address these challenges, there have been several attempts, e.g., the Common Treatment Workflow Language (CWL) and Workflow description language (WDL). Authors: Anderson, J., Cai, L. However, they still suffer from either heightened development cost, or limited application scope. In this study, we developed a new assisted pipeline building Traumatic brain injury (TBI) affects people of all ages and can lead to tool, PipelineDog, to deliver both simplicity and flexibility. This tool is a temporary or permanent loss of motor and cognitive function. Current comprehensive web-based pipeline building IDE. A simple to read and write therapeutics minimize secondary injury but do not promote functional recovery. YAML syntax defines analysis commands and their flow. An innovative Neurogenesis in the adult brain can be induced by TBI, indicating the potential LEASH expression system allows dynamic alteration of command input/output. of activating the endogenous neural stem cells (NSCs) in repair and With analysis steps and pipelines’ IO parameters easily controlled by LEASH regeneration. However, the mechanism of injury-induced neurogenesis remains and nicely isolated in PipelineDog scripts, pipeline reusability and to be determined. In this work, we have investigated NSC activation after injury maintainability are greatly enhanced. PipelineDog’s web GUI, together with using a closed head injury (CHI) model with Notch1CR2-GFP transgenic mice. assisted features such as parsing, format validation, a template library, and In this transgenic animal, CR2 enhancer directs the expression of green online repositories, enables pipeline construction and maintenance with a fluorescent protein (GFP) exclusively in NSCs. We show that brain injury minimal amount of coding, while maintaining outstanding reusability and increased endogenous NSC activation and the expression of brain injury makers flexibility. in injured tissues. We plan to further investigate the genes driving NSC activation after TBI on a single cell level to identify specific genes driving NSC #10. Non-Oncogenic Acute Viral Infection Slows Growth of Established activation. Increased understanding of genes driving NSC activation after TBI Tumors in Concomitantly Challenged Hosts will aid in the development of new targets and therapeutics for treatment of TBI. Authors: Newman, J.H., Li, S., Chesson, B., Schenkel, J.M., Silk, A. , Zloza, A. #12. The Role of Genetic Polymorphisms in a Mouse Model of Traumatic The ability of the immune system to identify cancer cells as abnormal and to Brain Injury and Personalized Treatment Approaches execute the destruction of such cells is dependent upon a multitude of biological Authors: Giarratana, A.O., Fish, L., Schloss, R., Thakker-Varia, S., Yarmush, factors. It has been reported that cancer patients have an increased incidence of M., Alder, J. infection relative to that observed in the general population, bringing forth the question of how concomitant immune challenges affect the capability of the Traumatic Brain Injury (TBI) is a serious and potentially life threatening clinical immune system to mount a specific, anti-tumor response, and ultimately, the rate problem. Clinicians have long noticed that certain patients recover better after of cancer progression and overall long-term survival. To address this, C57BL/6 TBI, and identifying what makes some patients more susceptible is a vital step mice were concurrently challenged with B16 F10 melanoma and PR8/H1N1/A in understanding the underlying mechanisms through which TBI causes its influenza. Influenza was administered intranasally, subsequent to the deleterious effects. The goal of this study was to determine the effect of specific development of palpable tumors. We observed that mice concomitantly single nucleotide polymorphisms (SNPs) which may lend insight into whether challenged with melanoma and influenza exhibited reduced tumor growth when individuals with these genetic alleles might be at higher risk than the general

16 17 population for poor recovery following TBI and to explore approaches to #14. TGF-B1 Evokes Human Airway Smooth Muscle Shortening and treating them. We have investigated behavioral and cellular outcomes in Hyperresponsiveness: A New Job Description? genetically engineered mice with the ApoE4 and BDNF Val66Val Authors: C.A. Ojiaku, G. Cao, W. Zhu, S.S. An, R.A. Panettieri polymorphisms following repeated, mild TBI. We have found that ApoE4 and Val66Met mice trend towards having a larger injury volume as assessed by MRI The factors contributing to airway hyperresponsiveness (AHR), a defining and increased levels of neurodegeneration, apoptosis, and gliosis compared to characteristic of asthma, have yet to be completely elucidated. Transforming ApoE3 and Val66Val mice. We have also begun to identify a personalized growth factor beta 1 (TGF-B1), a cytokine elevated in the airway of asthmatic approach to treating genetically susceptible individuals by targeting the pathway patients, is known for its role in airway remodeling and inflammation in asthma altered in those genotypes. Human mesenchymal stromal cells have been shown pathogenesis. However, the role of TGF-B1 in modulating airway to secrete neurotrophins such as BDNF. We have utilized different approaches hyperresponsiveness in human airway smooth muscle (HASM) remains unclear. such as encapsulation and pre-treatment with different factors in order to We hypothesize that TGF-B1 directly induces HASM shortening and AHR increase their therapeutic efficacy. We have found that encapsulation and through activation of Smad2/3 signaling. pretreatment of the MSCs with forskolin may help skew their secretome towards We show that TGF-B1 (100 ng/ml) induces acute (15 min) and chronic (24 h) a more positive one. This study lays the groundwork for further investigation bronchoconstriction in human precision-cut lung slices (hPCLS). Both baseline into the genetics that play a role in recovery after TBI and potential therapeutics. and methacholine-induced HASM cell stiffness was significantly increased at 4 h and 24 h following 100 ng/ml TGF-B1 treatment. Additionally, TGF-B1 (10 #13. Predicting the Zeta Potential of Molecular Structures: An Application ng/ml) treatment acutely and chronically increased basal and agonist-induced for Structure-Based Drug Design myosin light chain (MLC) phosphorylation in HASM cells, but had little effect Authors: Grisham, D. R., Nanda, V. on HASM cell calcium mobilization. Additionally, knockdown of Smad2/3 decreased acute MLC phosphorylation by TGF-B1 (10 ng/ml) in HASM cells. In addition to designing a new molecular structure, drug design involves Together, our findings show that TGF-B1 contributes to asthma pathogenesis consideration of the delivery method in which the drug is administered. An through direct induction of HASM shortening and modulation of HASM AHR. appropriate delivery method is typically a biocompatible solution allowing the The mechanism by which TGF-B1 induces HASM shortening and AHR may active drug to remain at a specific concentration. Designing such a solution is involve the acute activation Smad2/3 signaling. Together, these data suggest a commonly done using the drug’s zeta potential, which is its effective charge novel role for TGF-B1 and Smad2/3 in asthma pathogenesis. energy in solution. This work proposes and tests a protocol for predicting the zeta potential of a molecular structure given specified solution conditions; thus, #15. Expression of short stature homeobox 2 Transcription Factor During providing a shortcut to the drug design problem saving time and resources spent Otic Development at the lab bench. The primary model of the proposed protocol is based on a Authors: Laureano,A.S., Flaherty,K., Sabaawy,H.E., Kwan,K.Y. Gouy-Chapman electric double layer (EDL) around the structure of consideration and can be extended to a Gouy-Chapman-Stern EDL if modeling Syndromic hearing loss is highly heterogeneous genetic disorder. The discovery specific ion effects is desired. The protocol is tested on a number of proteins in and study of genetic factors that contribute to syndromic hearing loss allows for different ionic environments using their measured electrophoretic mobilities. As the advancement of early screening methods, diagnosis and treatment. Studying shown by this work, excellent agreement between experimental and modeled molecular factors that govern the development of the inner ear will lead to a values can be obtained by appropriate consideration of the electrophoretic better understanding of the etiology behind syndromic hearing loss. Using effects impacting the EDL during electrophoresis. This work holds significance molecular biology and bioinformatics tools, the short stature homeobox 2 gene in providing a computational method for speeding up the drug design process, (SHOX2) was identified as a candidate transcription factor involved in the early allowing potential new drug solutions to be made faster. process of auditory neuron development. To better understand and recapitulate the role of SHOX2 in human inner ear development zebrafish was chosen as a model organism. Zebrafish, like humans possess both orthologues from the SHOX gene family, SHOX and SHOX2. Whereas mice only have the SHOX2 in their genome. Zebrafish shox2 has not been previously identified in the inner ear. Utilizing in situ hybridization, shox2 transcripts were first detected in the otic placode at 16 hours post fertilization (hpf) during zebrafish development. shox2 is dynamically expressed throughout zebrafish development and continues

18 19 to be present in otic cell types at 18, 24, 48, and 72 hpf. At these time points, goal we hope to resolve the mechanism of RNAi-mediated gene regulation and shox2 can also be observed in the cranial ganglia and hindbrain regions. To its role in epigenetic memory. further assess the importance of shox2 in the developing inner ear, antisense morpholinos were used to reduce expression of shox2 starting from the one cell #17. Identifying factors involved in coordination of heterochromatin stage. At 72 hpf, embryos were observed and tested for abnormal behavior. The inheritance and DNA replication observed behaviors in shox2 morphants include circling, lack of avoidance Authors: Reilly, E., Zaratiegui, M. behavior and spasms. These behaviors suggested inner ear and neurological deficits. Single fish were acquired after behavioral testing and subjected to Epigenetic modifications can transform chromatin into two distinct states: an qPCR to assess shox2 levels. Embryos with low shox2 levels correlated to ‘open’ form knownas euchromatin, or ‘closed’ and highly compact abnormal behaviors. Similarly, embryos with low levels of shox2 after heterochromatin. Maintaining or switching between these chromatin states in a morpholino injection showed a trend in the decrease of the hair cell (atoh1a) and temporally and spatially defined manner is essential for coordinating gene neuronal (neurog1) transcripts. These results provide evidence for the regulation and ensuring genome organization and stability. Position effect involvement of shox2 in early otic neurosensory development of hair cells and variegation (PEV), first observed in Drosophila melanogaster, is an epigenetic otic neurons. We propose that shox2 is essential for determining hair cell and phenomenon characterized by variable expression of a reporter gene due to neuronal fate. Generation of a mutant shox2 using genome editing and stochastic heterochromatic spreading with stable inheritance of these expression employing various reporter lines in zebrafish line will help elucidate the patterns once they are established. We performed a genetic screen for PEV functional role of shox2 in inner ear development. mutants in Schizosaccharomyces pombe by transposable element mediated mutagenesis. Surprisingly, integration density profiling of the mutagenized #16. Role of heterochromatin in RNAi-mediated transcriptional regulation genes enriched in the screen after several rounds of selection for loss of in C. elegans pericentromeric heterochromatin silencing produced a number of essential genes Authors: Natallia Kalinava, Julie Ni, Esteban Chen, Kimberly Peterman, Sam involved in DNA replication. One of the biggest open questions in epigenetics is Gu how heterochromatic marks are faithfully inherited by subsequent generations after disruption by the replication fork in the process of DNA replication and We wish to understand the molecular and genetic basis of transcriptional cell division. To address this, we are developing a method to couple isolation of regulation mediated by nuclear small interfering RNA (siRNA). In many actively replicating regions with proteomic analysis of specific genomic loci to organisms, nuclear siRNA can guide transcriptional silencing and/or determine whether the components of the replication fork and associated heterochromatin formation at the homologous genomic regions. Such proteins differ between heterochromatic and euchromatic genomic regions. heterochromatin response can be maintained over several generations in C. Using this method, we aim to gain insight into the mechanism by which elegans. However, the function of the heterochromatin response remains elusive. heterochromatin inheritance is coordinated with DNA replication to ensure that We use biochemical, genetic and whole-genome approaches to investigate the heterochromatin is maintained throughout the cell cycle and transmitted to requirements of H3K9me3 heterochromatin for initiation and maintenance of subsequent generations with a high degree of fidelity. transcriptional silencing in germline nuclear RNAi pathway in C. elegans. First, we identified three histone methyltransferase (HMT) – MET-2, SET-25 #18. The uncharacterized Rho GAP Y34B4A.8 is required for epithelial and SET-32 that, in combination, are required for the full H3K9me3 response in morphogenesis in C. elegans the germline nuclear RNAi pathway. Surprisingly, complete depletion of Authors: Raduwan, H. and Soto, MC. H3K9me3 in met-2 set-25;set-32 mutants does not result with transcriptional de- silencing. We concluded, that H3K9me3 is dispensable for the maintenance of During embryonic development, epithelial cells must develop and maintain RNAi-mediated transcriptional silencing. We are performing genome wide apicobasal polarity and healthy cell-cell junctions as they move past other transcription characterization to investigate the effect of H3K9me3 on tissues in the process of morphogenesis. Defects in this process can lead to birth transcriptional silencing in the absence of RNAi repression. In addition, using defects, or premature death. Studies have shown that epithelial morphogenesis is CRISPR-cas9 editing we are repairing HRDE-1 Argonaute to test if regulated by the Rho GTPases, molecular switches that become activated by transcriptional silencing can be fully re-established in the H3K9me3 HMTs binding to GTP, and deactivated by hydrolyzing GTP to become GDP. The mutant background. cycle of GTP- and GDP- binding was regulated by GTP exchange factor protein Our current work will help to define the role of H3K9me3 HMTs in initiation (GEF) and GTPase-activating protein (GAP), respectively. This family of and maintenance of RNAi-mediated transcriptional silencing. As a long-term proteins regulates cell morphology and activity by regulating the actin

20 21 cytoskeleton. However, the precise regulation of these GTPases in the possibility of using G9a inhibitors to target cancers with certain DNA repair developing embryo is not well understood. Our lab uses the model organism defects. Caenorhabditis elegans to study the regulation of epithelial cell morphogenesis by the Rho GTPases on two important epithelial tissues, the epidermal and #20. Interstitial Release of Cisplatin from Triggerable Liposomes Enhances intestinal cells. Embryos defective in epithelial morphogenesis have failed cell Efficacy against Triple Negative Breast Cancer Solid Tumor Analogues migrations of the epidermis, which results in extrusion of the internal organs to Authors: Stras, S. , Holleran, T. , Howe, A., Sofou, S. the outside of the embryo. In addition, the intestinal cells are disorganized, potentially due to defect in junction regulation. By focusing on the Rho GAP Breast cancer is the 2nd leading cause of cancer related deaths in women. Triple regulators of those Rho GTPases, genetic screens to identify suppressors of the negative breast cancer (TNBC) is a subgroup of breast cancer associated with hypomorphic Rho GTPase mutants revealed an uncharacterized protein, poor prognosis and a higher chance of cancer reoccurrence outside the breast. Y34B4A.8 to play a role in epithelial morphogenesis. Knockout of this gene was To enable treatment of TNBC solid tumors, we study a tunable (pH-sensitive) able to partially rescue embryonic lethality of Cdc-42 RNAi depletion, delivery carrier of cisplatin (CDDP) - a clinically accepted major line of therapy suggesting that it is regulating Cdc-42 via its GAP domain. Using CRISPR/Cas9 for TNBC. These tunable liposomes are to be injected into the blood stream and technique, we generated a tagged version of Y34B4A.8 to visualize its enter the tumor exploiting the enhanced permeability and retention (EPR) effect. localization using confocal microscopy. We found that Y34B4A.8 assumes Within the tumor there is an inherent drop in pH (~6.0-6.7), which causes the specific apical localization on the intestine early in the embryo, as the intestines liposomes to become leaky and release their contents within the tumor become polarized. This polarized localization lasts until adulthood. In addition, interstitium. This is desirable because it leads to decreased off-target toxicities in Y34B4A.8 is enriched at the leading edge of migrating epidermal cells, similar the body, which are extensive and debilitating when treating a patient with free to F-actin. Despite this polarized localization, Y34B4A.8 null mutants have only cisplatin. We demonstrate the efficacy of the pH responsive liposomes with in a low percentage of embryos with morphogenesis defects, suggesting that there vitro experiments, both 2-D monolayers and 3-D tumor analogues (spheroids), are other proteins that are redundant with Y34B4A.8. This study identified using two TNBC cell lines. pH responsive liposomes, when compared to Y34B4A.8 as a driver of epithelial cell morphogenesis during C. elegans conventional liposomes, are more efficacious at pH 6.0, and are also the only development, through the action of the Cdc-42 Rho GTPase. liposomal construct we investigated to effectively control spheroid growth over time. #19. G9a methyltransferase plays a role in ATM-dependent DNA Damage Response Authors: Rodriguez-Colon, L., Ginjala, V., Kulkarni, A., Ansari, S., Ganesan, G.

Induction of DNA damage leads to a choreographed set of local chromatin changes that ensures an efficient recruitment of DNA repair factors. One principal regulator of the DNA Damage Response (DDR) signaling pathway is ATM kinase, which phosphorylates key factors at early stages of the response. G9a protein methyltransferase has been identified as a novel substrate for ATM. We have found that G9a localizes to sites of DNA damage in an ATM- dependent fashion and that inhibition of its activity affects recruitment of multiple DNA repair factors. Moreover G9a catalytic inhibition using UNC0638 leads to hyperactivation of ATM induced by DNA breaks. This was associated with an increased ATM-dependent “spreading” of pH2AX and MDC1 signals seen at regions of localized DNA breaks induced by UV-laser scissors. These data suggest that G9a activity is required for regulating the extent of ATM activation as well as for efficient recruitment of downstream DNA repair factors. Biochemical data will be presented that explore potential mechanisms for these findings. Overall our data suggests that G9a plays a critical role in the regulation of ATM-dependent signaling during the DNA damage response, and raises the

22 23 Participants Notes

Student Advisor Poster Board # Al-hraishawi, Husam Shridar Ganesan 2 Anderson, Jeremy Li Cai 11 Basu, Urmimala Smita Patel 1 Bhatt, Vrushank Jessie Guo 4 Cai, Na Loren Runnels Oral presenter Gates, Colin Charles Dismukes 6, Oral presenter Giarratana, Anna Janet Alder 12 Grisham, Daniel Vikas Nanda 13 Kalinava, Natallia Sam Gu 16 Keong Foo, Tzeh Bing Xia 3 Khella, Christen Michael Gatza Oral presenter Kogan, Samuel Darren Carpizo Oral presenter Laddha, Saurabh Chang Chan 8 Laureano, Alejandro Kelvin Kwan 15 Morgan, Katherine Sharon Pine Oral presenter Newman, Jenna Andrew Zloza 10 Nguyen, Alexandra Karen Schindler Oral presenter Ojiaku, Christie Reynold Panettieri 14 Pinkerton, Mark Paul Copeland 5 Raduwan, Hamidah Martha Soto 18 Reilly, Eve Mikel Zaratiegui 17 Rodriguez-Colon, Lizahira Shridar Ganesan 19 Stras, Sally Stavroula Sofou 20 Swiatkowski, Przemyslaw Bonnie Firestein 7 Zhou, Anbo Jinchuan Xing 9

24 25 Notes Sponsors

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