Institute For Cancer Research

COMPREHENSIVE CANCER CENTER PROGRAM AT FOX CHASE

MOLECULAR BASIS FOR GAMMA/DELTA T LINEAGE SPECIFICATION

SPORE IN OVARIAN CANCER

IMMUNE MECHANISMS THAT CONTROL ECTROMELIA VIRUS INFECTION

TRAINING PROGRAM IN CANCER RESEARCH

MECHANISM, FUNCTION, AND EXPLOITATION OF INFLUENZA A VIRUS-ACTIVATED CELL DEATH

CANCER PREVENTION-INTERCEPTION TARGETED AGENT DISCOVERY PROGRAM AT FOX CHASE CANCER CENTER - PROJECT SUMMARY - OVERALL HEREDITABLE CANCER-PREDISPOSING MUTATIONS ARE ESTIMATED TO BE AN UNDERLYING CAUSE OF MORE THAN 100,000 ADULT CANCERS IN THE US EACH YEAR. FOR MANY HEREDITARY CANCER SYNDROMES, THE LIFE-TIME RISK OF DEVELOPING CANCER APPROACHES 100%. DESPITE REVOLUTIONARY ADVANCES IN “OMICS” TECHNOLOGIES, OUR UNDERSTANDING OF THE MOLECULAR ALTERATIONS REQUIRED TO SUPPORT THE ESTABLISHMENT OF PRECANCEROUS LESIONS AND PROMOTE EARLY TUMOR DEVELOPMENT REMAINS VERY LIMITED, THUS HINDERING THE DEVELOPMENT OF EFFICACIOUS INTERVENTIONS. A MULTIDISCIPLINARY TEAM OF ACCOMPLISHED INVESTIGATORS AT FOX CHASE CANCER CENTER (FCCC), WITH COMBINED EXPERTISE IN CANCER PREVENTION, HERITABLE CANCER RISK, CANCER BIOLOGY, MOLECULAR MODELING, AND DRUG DISCOVERY HAS BEEN ASSEMBLED TO ADDRESS THIS UNMET IN AN UNPRECEDENTED WAY. THE GOAL OF THE FCCC CAP-IT CENTER IS TO EFFECTIVELY COORDINATE THE DEVELOPMENT OF EFFICACIOUS MOLECULARLY-TARGETED AGENTS FOR PRECISION CANCER PREVENTION AND EARLY INTERCEPTION IN POPULATIONS AT HIGH RISK FOR CANCER. ALL STUDIES ARE FACILITATED BY THE UNIQUE RESOURCES OF THE FCCC RISK ASSESSMENT PROGRAM, WHICH INCLUDES OVER 12,000 FAMILIES AT HIGH RISK FOR CANCER AND 2000 CONFIRMED GERMLINE MUTATION CARRIERS. A COMPREHENSIVE PIPELINE FOR THE DEVELOPMENT OF AGENTS FOR CANCER PREVENTION AND INTERCEPTION IS PROPOSED THAT CONSISTS OF THREE WELL-DEVELOPED RESEARCH DOMAINS: TARGET VALIDATION (AIM 1), AGENT IDENTIFICATION AND SCREENING (AIM 2), AND PILOT IN VIVO EFFICACY STUDIES (AIM 3). EACH DOMAIN WILL BE LED BY A FCCC INVESTIGATOR, WHO IS A NATIONAL LEADER IN THE RESPECTIVE FIELD. TWO HIGHLY INNOVATIVE PROJECTS ARE PROPOSED THAT ILLUSTRATE THE ROBUSTNESS OF THE CAP-IT FRAMEWORK. PROJECT 1 (ENTERING AT TARGET VALIDATION) FOCUSES ON THE DEVELOPMENT OF A NEWLY-IDENTIFIED AGENT THAT REFOLDS MUTANT P53. ITS ABILITY TO TARGET THE TP53 MUTATIONS ASSOCIATED WITH LI- FRAUMENI SYNDROME AND INHIBIT PRECANCEROUS LESIONS IN A SETTING OF MUTANT P53 WILL BE EVALUATED. PROJECT 2 (ENTERING AT AGENT IDENTIFICATION AND SCREENING) UNIQUELY TARGETS THE INITIATED PANCREATIC STROMA AS A STRATEGY FOR EARLY INTERCEPTION IN THE FORMATION OF PANCREATIC CANCER. A NEUTRALIZING ANTIBODY AGAINST THE STROMAL PROTEIN NETRIN G1, THAT CAN REVERT FIBROBLASTS TO A TUMOR-SUPPRESSIVE PHENOTYPE, HAS BEEN DISCOVERED. ANTIBODIES WITH IMPROVED POTENCY WILL BE IDENTIFIED AND TESTED IN VIVO FOR THEIR ABILITY TO INTERCEPT THE PROGRESSION OF PANCREATIC INTRAEPITHELIAL NEOPLASIA. ALL CAP-IT RESEARCH AND TRAINING WILL BE STRONGLY SUPPORTED BY THE LEADERSHIP TEAM AND COORDINATING ACTIVITIES OF THE ADMINISTRATIVE CORE, LED BY DR. CLAPPER. EXPERTISE IN BIOSTATISTICS, BIOINFORMATICS, AND DATA MANAGEMENT WILL BE PROVIDED TO CAP-IT INVESTIGATORS BY AN INFORMATICS CORE, LED BY DR. ROSS. COLLABORATIONS AMONG THE NCI, FCCC AND OTHER CAP-IT CENTERS, AS WELL AS THE SHARING OF DATA AND RESOURCES THROUGH THE DATA AND RESOURCE COORDINATION CENTER, WILL FOSTER PRODUCTIVITY AND INTEGRATION ACROSS THE CAP-IT NETWORK (AIM 4). THE LONG LEGACY OF FCCC IN CLINICAL RISK ASSESSMENT AND PRECLINICAL PREVENTIVE AGENT DEVELOPMENT, WHEN COMBINED WITH EXTENSIVE EXPERTISE IN DRUG DESIGN AND CANCER BIOLOGY, MAKES THIS CENTER UNIQUELY POISED TO BE INSTRUMENTAL IN THE DISCOVERY OF MOLECULARLY-TARGETED AGENTS TO PREVENT OR INTERCEPT EARLY ONCOGENESIS.

STRUCTURAL BIOINFORMATICS OF PROTEINS AND PROTEIN COMPLEXES AND APPLICATIONS TO CANCER BIOLOGY

FOX CHASE CLINICAL EPIDEMIOLOGY AND VALIDATION CENTER

NOVEL REGULATORY MECHANISMS UNDERLYING INSIDE-OUT INTEGRIN ACTIVATION

COMPENSATORY MECHANISMS THAT PROMOTE HOMOLOGOUS RECOMBINATION IN BRCA1 MUTANT CANCERS

REGULATION OF HEMATOPOIESIS BY RIBOSOMAL PROTEIN PARALOGS

THE ROLE OF P21-ACTIVATED KINASES IN MALIGNANT MESOTHELIOMA

INTEGRATION OF RETROVIRAL DNA: ACCESSING HOST TARGET DNA

STRUCTURE AND FUNCTION OF INTEGRASE

MECHANISMS CONTROLLING EPITHELIAL HOMEOSTASIS

P21-ACTIVATED KINASES AS NEW THERAPEUTIC TARGETS IN NEUROFIBROMATOSIS TYPE 1

IMMIGRANT ENCLAVES: CONFERRING HEALTH ADVANTAGES OR CREATING HEALTH DISPARITIES IN CHINESE IMMIGRANTS?

TARGETING RIPK3 IN FLU-ASSOCIATED LUNG INJURY

EVIDENCE-BASED APPROACH TO EMPOWER ASIAN AMERICAN WOMEN IN CERVICAL CANCER SCREENING

A BIOBEHAVIORAL MODEL OF DIABETES RISK IN CHINESE IMMIGRANTS

UNDERSTANDING THE ROLE OF HISTONE DEMETHYLASES AND HETEROCHROMATIN IN CELL CYCLE

RCT OF AN ONLINE MULTIMEDIA PROGRAM TO BOOST COPING & FUNCTION FOR PCA SURVIVORS

ROLE OF ZBP1 IN PATHOGENESIS OF SALMONELLA BIOFILMS - PROJECT SUMMARY INFECTIONS WITH ENTERIC PATHOGENS SUCH AS SALMONELLA, CAMPYLOBACTER, SHIGELLA, OR YERSINIA ARE LEADING CAUSES OF MORBIDITY AND MORTALITY WORLDWIDE. ALTHOUGH IN MOST INDIVIDUALS THE INFECTION RESOLVES, APPROXIMATELY 5% OF PATIENTS SUBSEQUENTLY DEVELOP A PAINFUL CHRONIC INFLAMMATORY CONDITION KNOWN AS REACTIVE ARTHRITIS (REA). HOW SALMONELLA INFECTIONS TRIGGER REA IS NOT WELL UNDERSTOOD. USING SALMONELLA ENTERICA SEROVAR TYPHIMURIUM (STM) AS A MODEL ORGANISM, WE DISCOVERED THAT A SALMONELLA PROTEIN, CURLI, IS A DOMINANT INSTIGATOR OF INFLAMMATION FOLLOWING SALMONELLA INFECTION. CURLI IS A SECRETED PROTEIN AND MAJOR COMPONENT OF THE STM BIOFILM IN THE GASTROINTESTINAL TRACT. CURLI FIBRILS BIND EXTRUDED BACTERIAL DNA WITHIN THE BIOFILM. IT IS THESE CURLI:DNA COMPLEXES, RATHER THAN CURLI ALONE, THAT ARE POTENT TRIGGERS OF TYPE I INTERFERON, IL-17, AND ANTI-DOUBLE STRANDED DNA AUTOANTIBODY PRODUCTION, LEADING TO REA. UNKNOWN, HOWEVER, IS WHY CURLI:DNA COMPLEXES ARE SO INFLAMMATORY. WE REPORT IN THIS PROPOSAL THE REMARKABLE DISCOVERY THAT THE DNA PRESENT WITHIN CURLI:DNA COMPLEXES IS NOT SOLELY B-DNA, THE CLASSIC RIGHT-HANDED (WATSON-CRICK) DOUBLE-HELIX, BUT INCLUDES COPIOUS AMOUNTS OF LEFT-HANDED Z-DNA AS WELL. Z-FORM NUCLEIC ACIDS, SUCH AS Z-DNA AND Z-RNA, WERE THOUGHT NOT TO READILY OCCUR IN NATURE, UNTIL WE SHOWED LAST YEAR THAT Z-RNA IS INDEED PRODUCED DURING VIRUS INFECTIONS AND IS A LIGAND FOR THE NECROPTOSIS-ACTIVATING HOST SENSOR PROTEIN ZBP1. OUR PRELIMINARY RESULTS NOW SHOW THAT THE Z-DNA WITHIN CURLI:DNA COMPLEXES ACTIVATES ZBP1 IN INTESTINAL EPITHELIAL CELLS (IECS) AND FIBROBLASTS, RESULTING IN RIPK3- DEPENDENT NECROPTOSIS OF THESE CELLS. THESE FINDINGS ALLOW US TO PUT FORWARD THE HYPOTHESIS THAT Z-DNA WITHIN CURLI:DNA FIBRILS IN SALMONELLA BIOFILMS ACTIVATES ZBP1 TO INSTIGATE RIPK3-DEPENDENT NECROPTOSIS IN INTESTINAL EPITHELIAL CELLS (IECS) AND OTHER CELL TYPES. NECROPTOSIS, IN TURN, CAUSES CELL LOSS AND DISRUPTS GUT BARRIER INTEGRITY, RELEASING INFLAMMATORY MEDIATORS THAT EVENTUALLY RESULT IN AUTOIMMUNITY AND REA. AS NECROPTOSIS IS A HIGHLY INFLAMMATORY MODE OF CELL DEATH, THESE FINDINGS, AT LONG LAST, SUPPLY A PLAUSIBLE MECHANISM FOR WHY CURLI:DNA COMPLEXES ARE HYPERINFLAMMATORY, AND, THEREFORE, FOR HOW SALMONELLA TRIGGERS REA. THEY ALSO IDENTIFY Z-DNA AS A NEW PAMP, IMPLICATE ZBP1 – UNTIL NOW CONSIDERED AN ANTIVIRAL PROTEIN – AS A SENSOR OF BACTERIAL INFECTIONS, AND POSITION RIPK3 INHIBITORS AS UNANTICIPATED NEW THERAPEUTICS FOR THE TREATMENT OF REA. IN AIM 1, WE WILL DETERMINE HOW Z-DNA FORMS WITHIN CURLI:DNA COMPLEXES, AND HOW Z-DNA ACTIVATES ZBP1. IN AIM 2, WE WILL IDENTIFY THE ZBP1-DRIVEN IMMUNE PATHWAYS THAT PROMOTE CURLI:DNA INDUCED INFLAMMATION AND REA, AND DETERMINE THE CELL TYPES IN WHICH ZBP1 SIGNALING IS IMPORTANT FOR PATHOGENESIS. IN AIM 3, WE WILL EVALUATE WHETHER NECROPTOSIS BLOCKADE WITH RIPK3 KINASE INHIBITORS WILL HAVE PREVENTIVE OR THERAPEUTIC BENEFIT IN REA. A SUCCESSFUL OUTCOME TO THESE STUDIES WILL OUTLINE AN ENTIRELY NEW MECHANISM OF SALMONELLA-TRIGGERED INFLAMMATION. THEY ALSO STAND TO OPEN UP EXCITING NEW THERAPEUTIC AVENUES FOR SALMONELLA-INDUCED REA, WITH POTENTIALLY GAME-CHANGING RAMIFICATIONS FOR THIS CURRENTLY INCURABLE DISEASE.

INVESTIGATING GENETIC ANCESTRY INFLUENCES ON ORAL CAVITY AND LARYNGEAL CANCER SURVIVAL DISPARITIES

EXTENDING A CARIBBEAN BASED COHORT TO PROMOTE US-CARIBBEAN COMPARISONS TO FACILITATE RESEARCH ADDRESSING BLACK HEALTH DISPARITIES

LEGACY: A COHORT OF YOUTH IN FAMILIES FROM THE BREAST CANCER FAMILY REGISTRY

COMPARATIVE EFFECTIVENESS OF VIRTUAL AND OPTICAL COLONOSCOPY FOR CRC SURVEILLANCE

SPECIFICITY OF EFFECTOR ACTIVATION BY RHO FAMILY GTPASES

UNDERSTANDING PSYCHOSOCIAL AND IMMUNOLOGIC RESPONSES IN INDOLENT LYMPHOPROLIFERATIVE DISORDERS

NOVEL ROLE OF THPOK IN MAMMARY CARCINOMA

PANCREATIC CANCER-ASSOCIATED FIBROBLASTS: FUNCTION, DETECTION, AND REGULATION - PROJECT SUMMARY/ABSTRACT PANCREATIC CANCER INDUCES A FIBROUS MICROENVIRONMENT, DESMOPLASIA, WHICH SPANS MOST OF THE TUMOR MASS AND CONTAINS CANCER-ASSOCIATED FIBROBLASTS (CAFS). CAFS SUSTAIN A CANCER HOMEOSTATIC EQUILIBRIUM BY PRODUCING EXTRACELLULAR MATRICES (ECMS) AND SECRETING INFLAMMATORY FACTORS. THE ECM PRODUCED BY CAFS PROMPTS NORMAL FIBROBLASTS TO UNDERGO ACTIVATION AND TRANSITION INTO CAFS, THEREBY PROPAGATING DESMOPLASTIC EXPANSION IN A POSITIVE FEEDBACK LOOP. WHILE THE NORMAL MICROENVIRONMENT SUPPRESSES TUMOR ONSET, DESMOPLASIA CAN EITHER SUPPORT OR AVERT PANCREATIC CANCER. A BETTER UNDERSTANDING OF DESMOPLASTIC EXPANSION AND THE ECM FACTORS THAT CONTROL IT COULD ENABLE US TO FAVOR ITS ANTI-CANCER FUNCTIONS. IN FACT, SEVERAL CLINICAL TRIALS INCLUDING SOME CONDUCTED AT FOX CHASE, AIM AT “NORMALIZING DESMOPLASIA” WITH THE GOAL OF HARNESSING CAF’S ANTI-TUMOR EFFECTS. OF NOTE, WE HAVE DEFINED A SIGNALING AXIS THAT DEPENDS ON CAF-ECM AND INCLUDES ITS MAIN RECEPTORS, INTEGRINS, AND SOME ACTIN BUNDLING, PARTICULAR ENDOCYTIC REGULATORY PROTEINS, AND AN EXTRACELLULARLY TETHERED PRESYNAPTIC PROTEIN KNOWN AS NETRING1. OF NOTE, NETRING1 NECESSITIES CO-RECEPTORS IN CIS AND IN TRANS TO SIGNAL AND WE REVEALED THAT IN RESPONSE TO ECM NETRING1 DRIVES PRO-TUMOR CAF FUNCTION. WE ALSO REPORTED THAT ECM INDUCED PRO-TUMOR CAF ACTIVATION INCLUDES THE ENDOCYTIC LOCALIZATION OF THE ACTIVE CONFORMATION OF AN IMPORTANT ECM RECEPTOR, ACTIVATED A5SS1-INTEGRIN (A-A5), WHICH WE POSIT REGULATES THE PRODUCTION OF TWO UNIQUE EXTRACELLULAR VESICLES. FINALLY, WE SAW THAT THE TRANS CO-RECEPTOR OF NETRING1 IS EXPRESSED IN CAFS AND NEEDED FOR EFFECTIVE FORMATION OF TUMORS WHEN PANCREATIC CANCER CELLS ARE INJECTED INTO THE PANCREATA OF IMMUNE SYSTEM-INTACT MICE. OUR CENTRAL PREMISE PROPOSES THAT CAF PRO-TO-ANTI TUMOR FUNCTION TRANSITION CAN BE ATTAINED VIA BLOCKAGE OF THE ECM-DEPENDENT NETRING1 SIGNALING AXIS, WHICH IS NEEDED TO ACHIEVE THE FUNCTIONAL “DESMOPLASTIC NORMALIZATION” THAT CAN BE DETECTED IN BLOOD. WE PLAN TO TEST THIS HYPOTHESIS IN THREE SPECIFIC AIMS: 1- ASK HOW CAF-ECM REGULATES NETRING1 EXPRESSION AND ENDOCYTIC A-A5 REGULATION AS WELL AS WHAT ARE THE SPECIFIC ECM COMPONENTS THAT ARE RESPONSIBLE FOR NETRING1 EXPRESSION AND CAF’S PRO-TUMOR FUNCTION. 2- INVESTIGATE IF THE UNIQUE EXTRACELLULAR VESICLES GENERATED BY NETRING1 EXPRESSING CAFS COULD BE TRACED SYSTEMICALLY IN PATIENTS’ BLOOD (INCLUDING ARCHIVED SAMPLES AND SAMPLES FROM THE ONGOING TRIAL) AND ASK IF THESE ARE INDICATIVE OF THE TUMOR ASSOCIATED DESMOPLASTIC PRO VS ANTI-PANCREATIC CANCER STATUSES. 3- INQUIRE IF NETRING1’S TRANS RECEPTOR, EXPRESSED IN PRO-TUMORAL FUNCTIONING CAFS, COULD SERVE AS A NEW TARGET. THE STUDY’S ULTIMATE GOAL IS TO CAPITALIZE ON THE NATURAL TUMOR SUPPRESSIVE FUNCTION AND FEATURES OF CAFS AND BLOCK THE TUMOR PROMOTING ONES AS WELL AS TO SYSTEMICALLY INDUCE AND DETECT A PRO-TO-ANTI PANCREATIC CANCER CAF TRANSITION, WHICH COULD BE INDICATIVE OF LOCAL DESMOPLASTIC STATUS, FOR POTENTIAL FUTURE CLINICAL USES.

ADDRESSING SEXUAL CONCERNS IN BREAST CANCER SURVIVORS: RCT OF A NOVEL COUPLE-BASED INTERVENTION

SMALL-MOLECULE EXPLOITATION OF ZBP1-DRIVEN NUCLEAR NECROPTOSIS FOR CANCER IMMUNOTHERAPY - PROJECT SUMMARY/ABSTRACT. IMMUNE CHECKPOINT BLOCKADE (ICB) AND OTHER IMMUNOTHERAPIES HAVE REVOLUTIONIZED CANCER TREATMENT, BUT THE NON-RESPONSIVENESS OF MOST CANCERS TO ICB-BASED MONOTHERAPY REMAINS A SIGNIFICANT PROBLEM. A MAJOR REASON FOR THE NON-RESPONSIVENESS OF THESE SO-CALLED ‘COLD’ TUMORS IS THAT THEY LACK AN IMMUNOGENIC TUMOR MICROENVIRONMENT (TME) AND THUS ESCAPE T-CELL KILLING DESPITE EXPRESSING ICB TARGETS. HOW TO SELECTIVELY INTENSIFY THE IMMUNOGENICITY OF THE TME HAS BEEN AN UNMET CHALLENGE. HERE WE PROPOSE A NEW SMALL-MOLECULE APPROACH THAT ACTIVATES NECROPTOSIS AND TRIGGERS ROBUST INNATE IMMUNE RESPONSES IN THE TME. THIS NEW AVENUE DERIVES FROM OUR WORK ON INFLUENZA A VIRUS (IAV). OUR EARLY FINDINGS SHOWED THAT IAV ACTIVATES NECROPTOSIS IN INFECTED CELLS. NECROPTOSIS KILLS INFECTED CELLS AND IS HIGHLY IMMUNOGENIC. IT IS INITIATED WHEN VIRAL RNAS ACTIVATING THE HOST PROTEIN ZBP1. RECENTLY, AND HIGHLY RELEVANT FOR CANCER IMMUNOTHERAPY, WE FOUND THAT ZBP1 ACTIVATES NECROPTOSIS FROM THE NUCLEUS. SUCH ‘NUCLEAR NECROPTOSIS’ IS SIGNIFICANTLY MORE IMMUNOGENIC THAN CONVENTIONAL (CYTOPLASM-INITIATED) NECROPTOSIS BECAUSE IT RUPTURES THE NUCLEUS AND RELEASES HYPER-INFLAMMATORY NUCLEAR DAMPS INTO THE EXTRACELLULAR SPACE. WE ALSO FOUND THAT THE VIRAL RNAS THAT ACTIVATE ZBP1 ARE Z-RNAS. ALTHOUGH THESE UNIQUE ZBP1 ACTIVATORS SHOULD BE SUPERB ADJUVANTS FOR ICB, Z-RNA IS UNSTABLE AND HARD TO PRODUCE ABSENT VIRUS INFECTION. Z-DNA, HOWEVER, IS STRUCTURALLY ALMOST IDENTICAL TO Z-RNA, BINDS ZBP1 WITH THE SAME AFFINITY, AND CAN BE STABLY PRODUCED IN EUKARYOTIC CELLS BY DISTORTING DNA INTO THE Z-CONFORMATION. THIS SUGGESTED THAT A COMPOUND THAT CAN GENERATE Z-DNA IN CELLS WOULD ACTIVATE ZBP1 AND TRIGGER ON-DEMAND NUCLEAR NECROPTOSIS WITHOUT NEED FOR VIRUS INFECTION. SUCH A COMPOUND WOULD FILL THE LONG-UNMET NEED FOR A NECROPTOSIS AGONIST FOR USE IN CANCER IMMUNOTHERAPY. WE HAVE NOW IDENTIFIED A SMALL MOLECULE, CURAXIN, WHICH INDUCES Z-DNA FORMATION IN LIVE CELLS AND DIRECTLY ACTIVATES ZBP1 TO TRIGGER ‘ON-DEMAND’ NUCLEAR NECROPTOSIS IN CELLS OF THE TME. THESE AND OTHER FINDINGS ALLOW US TO PROPOSE THE HYPOTHESES THAT CURAXIN ALTERS CHROMATIN STRUCTURE AND INDUCES THE FORMATION OF Z-DNA; THAT SUCH Z-DNA RECRUITS ZBP1 TO THE NUCLEUS AND TRIGGERS NUCLEAR NECROPTOSIS; AND THAT CURAXIN-INDUCED NUCLEAR NECROPTOSIS WILL GREATLY IMPROVE ICB TREATMENT OUTCOMES. IN THIS PROPOSAL, WE WILL ASK HOW CURAXIN TRIGGERS Z-DNA FORMATION (AIM 1), HOW Z-DNA ACTIVATES ZBP1 AND NUCLEAR NECROPTOSIS (AIM 2), AND WHETHER INDUCTION OF NUCLEAR NECROPTOSIS BY CURAXIN HAS COMBINATORIAL BENEFIT WITH ICB IN CLINICALLY-RELEVANT MOUSE MODELS OF MELANOMA (AIM 3). THE SUCCESSFUL COMPLETION OF THESE AIMS WILL OUTLINE AN ENTIRELY NEW SMALL- MOLECULE BASED STRATEGY TO ACTIVATE A HIGHLY INFLAMMATORY FORM OF NECROPTOSIS AND POTENTIATE ICB-BASED IMMUNOTHERAPIES, WITH IMPORTANT CLINICAL RAMIFICATIONS.

TREATMENT OF CBS DEFICIENCY WITH PROTEOSTASIS MODULATORS

TARGETING THE BCL2 IMMUNE CHECKPOINT TO ENHANCE THE IMMUNOSTIMULATORY EFFECTS OF RADIATION IN BREAST CANCER - SUMMARY HORMONE RECEPTOR (HR)+ BREAST CANCER (BC) CAUSES THE MAJORITY OF BC-RELATED DEATHS IN THE US, REFLECTING AN UNMET NEED FOR INNOVATIVE THERAPEUTIC APPROACHES. INDEED, RESISTANCE TO STANDARD TREATMENTS AND METASTATIC SPREAD REMAIN MAJOR CHALLENGES, AND NOVEL APPROACHES SUCH AS IMMUNE CHECKPOINT BLOCKERS (ICBS) HAVE SHOWN LIMITED EFFICACY SO FAR. THE LONG-TERM OBJECTIVE OF THIS PROPOSAL IS TO MECHANISTICALLY DISSECT THE IMPACT OF BCL2, AN ANTIAPOPTOTIC PROTEIN THAT FAVORS THE RESISTANCE OF CANCER CELLS TO DEATH IMPOSED BY CHEMOTHERAPY AND RADIATION THERAPY (RT), ON THE IMMUNOLOGICAL CONFIGURATION OF TREATMENT NAÏVE AND IRRADIATED HR+ BCS. SPECIFICALLY, THIS PROJECT WILL TEST THE HIGHLY INNOVATIVE HYPOTHESIS THAT BCL2 MAY REPRESENT A THERAPEUTICALLY ACTIONABLE IMMUNE CHECKPOINT BECAUSE OF ITS ABILITY TO PRESERVE MITOCHONDRIAL INTEGRITY, BASED ON THESE SPECIFIC AIMS: 1) DETERMINING THE INFLUENCE OF BCL2 LEVELS ON THE IMMUNE MICROENVIRONMENT OF TREATMENT-NAÏVE HUMAN AND MOUSE HR+ BCS; 2) DEFINING THE IMPACT OF BCL2 ON THE IMMUNE MICROENVIRONMENT OF HR+ BCS RESPONDING TO RT IN VITRO AND IN VIVO; AND 3) ELUCIDATING THE VALUE OF BCL2 AS A TARGET TO BOOST THE IMMUNOSTIMULATORY EFFECTS OF RT IN MOUSE MODELS OF HR+ BCS, INCLUDING AN INNOVATIVE MODEL THAT MIMICS KEY FEATURES OF HUMAN HR+ BC. BCL2 IS A PARTICULARLY SIGNIFICANT TARGET BECAUSE ~80% OF HR+ BC CASES OVEREXPRESS BCL2, AND THE BCL2 INHIBITOR VENETOCLAX, IS APPROVED FOR CLINICAL USE. TO ACHIEVE OUR GOALS, DIAGNOSTIC BIOPSIES FROM WOMEN WITH HR+ BC WILL BE EVALUATED BY CODEX FOR BCL2 EXPRESSION, TUMOR INFILTRATION BY KEY IMMUNE CELLS THAT REGULATE ANTICANCER IMMUNITY, AND EXPRESSION OF IMMUNOSUPPRESSIVE PROTEINS LIKE MHC CLASS I AND PD-L1. THE IMPACT OF BCL2 ON THE IMMUNOLOGICAL RESPONSE OF HR+ BC CELLS TO RT WILL BE INTERROGATED IN VITRO, BY GENETIC (DELETION, OVEREXPRESSION) AND PHARMACOLOGICAL (E.G., VENETOCLAX ADMINISTRATION) METHODS COUPLED TO FLOW CYTOMETRY, IF MICROSCOPY AND ELISA FOR THE ASSESSMENT OF KEY REGULATORS OF ANTICANCER IMMUNITY. SIMILAR GENETIC AND PHARMACOLOGICAL APPROACHES WILL BE HARNESSED TO ALTER BCL2 COMPETENCE AND DELINEATE THE INFLUENCE OF BCL2 ON THE IMMUNOLOGICAL TME OF TREATMENT-NAÏVE AND IRRADIATED MOUSE HR+ BCS ESTABLISHED IN IMMUNOCOMPETENT HOSTS, BASED ON IHC, FLOW CYTOMETRY AND SINGLE-CELL RNA SEQUENCING. IN VITRO STUDIES BY FLOW CYTOMETRY AND CLONOGENIC ASSAYS, AS WELL AS IN VIVO STUDIES BASED ON MOUSE HR+ BC CELLS GROWING IN IMMUNODEFICIENT VS IMMUNOCOMPETENT MICE, WILL BE EMPLOYED TO DISSECT THE IMPACT OF BCL2 ON INTRINSIC RADIOSENSITIVITY VS IMMUNE-DEPENDENT TUMOR CONTROL. FINALLY, DIFFERENT COMBINATORIAL REGIMENS INVOLVING RT AND VENETOCLAX WILL BE INVESTIGATED FOR EFFICACY (IN BOTH TREATMENT-NAÏVE AND TREATMENT RESISTANCE SETTINGS) AND POTENTIAL MECHANISMS OF RESISTANCE IN AN ENDOGENOUS MOUSE MODEL OF HR+ BCS THAT MIMICS KEY FEATURES OF HUMAN HR+ BC. OUR FINDINGS WILL ELUCIDATE THE IMPACT OF BCL2 ON THE IMMUNE TME OF HR+ BC AND IDENTIFY THE BEST APPROACH TO INFORM THE INITIATION OF CLINICAL TRIALS TESTING RT PLUS VENETOCLAX IN WOMEN WITH HR+ BC, A DEVASTATING DISEASE THAT STILL AFFECTS >200,000 AND KILLS >25,000 NEW WOMEN EVERY YEAR IN THE US.

NEW TOOLS FOR UNDERSTANDING METASTASIS THROUGH TISSUE RESIDENT CELLS: ENABLING AN EXTENSIVE MEDICINE STRATEGY FOR METASTATIC DISEASE

DIVERGENT FUNCTIONS OF ERK SUBSTRATE BINDING DOMAINS IN PATHOGENESIS OF MYELOPROLIFERATIVE NEOPLASMS - PROJECT SUMMARY/ABSTRACT THE RAS/MAPK PATHWAY IS ACTIVATED IN 85% OF HUMAN CANCER. NEVERTHELESS, ATTEMPTS TO TARGET RAS/MAPK SIGNALING HAVE PRODUCED ONLY LIMITED EFFICACY. WE HYPOTHESIZE THAT ONE REASON FOR THE FAILURE TO SUCCESSFULLY TARGET THIS PATHWAY IS THAT THE TARGETING EFFORTS HAVE FOCUSED ON THE ACTIVE SITES OF KINASES IN THIS CASCADE, WHICH HAS FAILED TO PROVIDE LONG-LASTING BENEFIT. WE HYPOTHESIZE THAT THE FAILURE OF THIS APPROACH RESULTS FROM TWO CAUSES: 1) ACTIVE SITE INHIBITORS, WHICH RESEMBLE ADENOSINE TRIPHOSPHATE (ATP), MUST OVERCOME THE EXCEEDINGLY HIGH CYTOSOLIC ATP LEVELS IN CANCER CELLS; AND 2) CRITICAL KINASES IN THIS CASCADE (E.G., ERK1/2) HAVE DISTINCT SUBSTRATE INTERACTIONS DOMAINS THAT CAN PERFORM ANTAGONISTIC ROLES IN REGULATING CANCER PROGRESSION. CONSEQUENTLY, ACTIVE-SITE FOCUSED INHIBITION IS AKIN TO SIMULTANEOUS DEPRESSION OF THE ACCELERATOR AND BRAKE PEDALS OF AN AUTOMOBILE. WE HYPOTHESIZE THAT A MORE SUCCESSFUL APPROACH WILL BE TO DEVELOP INHIBITORS WHICH PRESERVE KINASE ACTIVITY, BUT DIVERT IT EXCLUSIVELY TO “BRAKE PEDAL” SUBSTRATES. IN SUPPORT, WE HAVE DEMONSTRATED THAT THE TWO SUBSTRATE BINDING DOMAINS OF ERK2, TERMED THE D AND DPB DOMAINS, PLAY OPPOSING ROLES IN THE PATHOGENESIS OF JAK2-KINASE DRIVEN MYELOPROLIFERATIVE NEOPLASMS (MPN). INDEED, THE DBP AND D DOMAINS ACT LIKE BRAKE AND ACCELERATOR PEDALS, OPPOSING AND PROMOTING DISEASE PROGRESSION, RESPECTIVELY. CONSEQUENTLY, PHARMACOLOGIC ATTENUATION OF THE ACCELERATOR PEDAL (D-DOMAIN) OR ITS SUBSTRATES SHOULD IMPAIR TUMOR PROGRESSION MORE POTENTLY THAN ACTIVE SITE INHIBITION, BECAUSE IT SELECTIVELY INTERFERES WITH THE DISEASE PROMOTING ACTIVITY OF ERK2, WHILE PRESERVING THE TUMOR SUPPRESSIVE FUNCTION OF THE DBP-DOMAIN. WHILE WE HAVE COMPELLING EVIDENCE FOR THE OPPOSING ROLES OF THE ERK2-D AND DBP DOMAINS, THE MOLECULAR BASIS FOR THEIR ACTION REMAINS UNCLEAR AND THIS IS AN IMPEDIMENT TO DEVELOPING EFFECTIVE, PHARMACOLOGIC INTERVENTIONS FOCUSED ON THE ERK2 D DOMAIN. WE NOW SEEK TO ADDRESS THIS GAP IN KNOWLEDGE ACCORDING TO THE FOLLOWING AIMS. WE WILL: 1) ASSESS THE GENERALITY OF THE OPPOSING FUNCTIONS OF THE ERK2-D AND DBP DOMAINS IN THE PATHOGENESIS OF DISTINCT MPN SUBTYPES; 2) UNDERSTAND THE MECHANISTIC BASIS BY WHICH THE ERK2-D AND DBP DOMAINS EXERT THEIR DISTINCT FUNCTIONS; AND 3) ASSESS THE EFFICACY OF PHARMACOLOGIC TARGETING OF THE ERK2-D DOMAIN AND/OR ITS TARGETS IN INHIBITING CANCER PROGRESSION. THROUGH THESE EFFORTS WE EXPECT TO BRING NEW INSIGHTS INTO THE ROLE OF ERK2 SUBSTRATE BINDING MODULES IN REGULATING CANCER PROGRESSION AND HOW TO EXPLOIT THIS INFORMATION THERAPEUTICALLY. WHILE WE BEGIN WITH MPN, THESE FINDINGS MAY HAVE FAR REACHING IMPLICATIONS FOR OTHER RAS/MAPK DRIVEN CANCERS.

REDUCING URBAN CERVICAL CANCER DISPARITIES USING A TAILORED MHEALTH INTERVENTION TO ENHANCE COLPOSCOPY ATTENDANCE - PROJECT SUMMARY/ABSTRACT CERVICAL CANCER IS ONE OF THE MOST PREVENTABLE CANCERS AND WHEN DIAGNOSED EARLY AND APPROPRIATELY TREATED, THE LIKELIHOOD OF SURVIVAL IS CLOSE TO 100%. HOWEVER, NONATTENDANCE AT ABNORMAL FOLLOW-UP APPOINTMENTS REACHES 63% AMONG URBAN, UNDERSERVED MINORITY WOMEN. CERVICAL CANCER PREVENTION AND TIMELY DIAGNOSIS REQUIRES THAT PATIENTS BE MONITORED OVER TIME. EXISTING INTERVENTION PROTOCOLS TO PROMOTE ATTENDANCE HAVE SIGNIFICANT LIMITATIONS GIVEN A LIMITED FOCUS ON URBAN, UNDERSERVED MINORITY WOMEN AND REDUCED SUSTAINABILITY IN RESOURCE- LIMITED SETTINGS. TO FILL THIS VOID, WE PROPOSE A TAILORED MHEALTH INTERVENTION AVAILABLE IN BOTH ENGLISH AND SPANISH TARGETING FOLLOW-UP ATTENDANCE FOR ABNORMAL TEST FEEDBACK AT 3 URBAN CLINIC SITES SERVING PREDOMINATELY LOW- INCOME MINORITY WOMEN. WE PROPOSE A HYBRID TYPE 1 EFFECTIVENESS-IMPLEMENTATION TRIAL THAT IS THEORETICALLY- GUIDED BY THE COGNITIVE-SOCIAL HEALTH INFORMATION PROCESSING MODEL AND THE EXPLORATION, PLANNING, IMPLEMENTATION AND SUSTAINMENT IMPLEMENTATION FRAMEWORK TO OPERATIONALIZE AND ASSESS THE EFFICACY OF THE HEALTH ENHANCEMENT RESOURCE SYSTEM (HERS) INTERVENTION. HERS AIMS TO INCREASE PATIENT FOLLOW-UP AFTER ABNORMAL TEST RESULTS THROUGH TEXT MESSAGE-BASED BARRIERS COUNSELING FOR WOMEN AND SUPPLEMENTAL TELEPHONE- BASED HEALTH COACHING FOR WOMEN WHO MISS THEIR APPOINTMENT. USING A SEQUENTIAL, MULTIPLE ASSIGNMENT, RANDOMIZED TRIAL (SMART) DESIGN AND STAKEHOLDER-ENGAGED APPROACH OUR AIMS ARE TO: (1) CONDUCT A RANDOMIZED CONTROL TRIAL (RCT) USING THE SMART DESIGN TO EVALUATE THE EFFICACY OF HERS; (2) QUALITATIVELY ASSESS THE CONTEXTUAL FACTORS (PATIENT FACTORS, HEALTHCARE TEAM RESOURCES, AND ORGANIZATIONAL FACTORS) AFFECTING HERS IMPLEMENTATION OUTCOMES AND POTENTIAL FOR SCALABILITY AND SUSTAINABILITY; AND (3) EXPLORE PATIENT-LEVEL MODERATORS OF THE RELATIONSHIP BETWEEN THE HERS INTERVENTION AND ATTENDANCE AT THE COLPOSCOPY APPOINTMENT. WOMEN (N=546) SCHEDULED FOR INITIAL OR REPEAT COLPOSCOPY FOLLOWING AN ABNORMAL TEST RESULT WILL BE RECRUITED AND RANDOMIZED TO ONE OF 2 CONDITIONS (HERS TEXT MESSAGES OR STANDARD OF CARE) AND, THROUGH THE SMART DESIGN, WILL REMAIN IN THEIR ASSIGNED GROUP OR RE-RANDOMIZED TO HERS OR HERS + HEALTH COACHING, DEPENDING ON INITIAL APPOINTMENT ATTENDANCE. THE PRIMARY OUTCOME IS ATTENDANCE AT THE BASELINE COLPOSCOPY AND THE SECONDARY OUTCOME IS LONG-TERM FOLLOW-UP AT 12-MONTHS. ADDITIONAL RESEARCH QUESTIONS WILL EVALUATE THE BEST INITIAL INTERVENTION (E.G., STANDARD OF CARE OR HERS) FOR INCREASING ATTENDANCE AT THE BASELINE AND 12-MONTH FOLLOW-UP APPOINTMENTS. IN-DEPTH INTERVIEWS WITH HEALTHCARE STAKEHOLDERS AND EXIT INTERVIEWS WITH PATIENTS WILL ASSESS THE IMPACT OF TEAM AND HEALTHCARE SYSTEM CONTEXT ON THE HERS IMPLEMENTATION. FINALLY, EXPLORATORY ANALYSES SEEK TO IDENTIFY MODERATORS OF INTERVENTION EFFECT (E.G., RACE/ETHNICITY, SPANISH OR ENGLISH LANGUAGE, HEALTH LITERACY) AT BASELINE AND 12-MONTH FOLLOW-UP APPOINTMENTS TO EVALUATE WHICH PATIENTS SHOULD RECEIVE THE HERS INTERVENTION AS A FIRST-LINE INTERVENTION RATHER THAN STANDARD OF CARE.

MECHANISM TRANSCRIPT ELONGATION IN CHROMATIN

PATHOGENESIS OF MALIGNANT MESOTHELIOMA BY THE HUMAN POLYCOMB COMPLEX BAP1-ASXL

FOLIC ACID SUPPLEMENTATION AND COLITIS-ASSOCIATED COLON CARCINOGENESIS - PROJECT SUMMARY/ABSTRACT PATIENTS WITH ULCERATIVE COLITIS, A FORM OF INFLAMMATORY BOWEL DISEASE, FACE AN INCREASED RISK OF DEVELOPING COLORECTAL CANCER. ALTHOUGH ADVANCES HAVE BEEN MADE IN THE THERAPEUTIC MANAGEMENT OF THIS DISEASE, MUCH LESS ATTENTION HAS BEEN GIVEN TO THE DEVELOPMENT OF CANCER PREVENTIVE STRATEGIES FOR THIS HIGH-RISK POPULATION. ULCERATIVE COLITIS PATIENTS OFTEN DEVELOP FOLATE DEFICIENCIES THAT REQUIRE SUPPLEMENTATION WITH FOLIC ACID (FA), A SYNTHETIC FORM OF FOLATE. THE EFFECT OF FA ON RISK FOR COLORECTAL CANCER REMAINS UNCLEAR AND THE RECENT SUGGESTION THAT FA SUPPLEMENTS MAY BE USEFUL IN PREVENTING COLITIS-ASSOCIATED COLORECTAL CANCER IS OF GREAT CONCERN. PRELIMINARY STUDIES FROM THIS GROUP PROVIDE THE FIRST EVIDENCE THAT FA SUPPLEMENTATION (8 MG/KG DIET) CAUSES A DOSE-DEPENDENT INCREASE IN THE FORMATION OF COLORECTAL TUMORS IN MICE WITH AOM/DSS-INDUCED COLITIS. RESULTS FROM ASSOCIATED RNASEQ AND IN VITRO ANALYSES SUGGEST THAT FA PROMOTES TUMORIGENESIS BY ACTIVATING ERK AND INDUCING NF-B SIGNALING IN COLONIC EPITHELIAL CELLS WITH DYSFUNCTIONAL P53, THE GATEKEEPING EVENT IN THE DEVELOPMENT OF COLITIS-ASSOCIATED CANCERS. THE HYPOTHESIS OF THE PROPOSED STUDIES IS THAT FA SUPPLEMENTATION PROMOTES UC-ASSOCIATED CANCER IN CELLS WITH DYSFUNCTIONAL/MUTANT P53, BUT NOT IN CELLS WITH WILD TYPE P53, VIA AN INFLAMMATORY PATHWAY MEDIATED BY ERK AND NF-B. THE MECHANISM BY WHICH FA INDUCES TUMOR FORMATION WILL BE INVESTIGATED IN AIM 1 USING CRISPR ENGINEERED ISOGENIC HUMAN RKO COLON CARCINOMA CELLS WITH VARYING P53 STATUS (P53+/+, P53-/- AND P53+/MUT). THE IMPACT OF FA AND DYSFUNCTIONAL P53 ON ACTIVATION OF ERK, NF-B SIGNALING, AS WELL AS CELL CYCLE PROGRESSION WILL BE EVALUATED. IN VITRO FINDINGS WILL BE VALIDATED IN AIM 2, WHERE COMPLIMENTARY IN VIVO ANALYSES WILL EXAMINE THE COMBINED EFFECT OF FA AND MUTANT P53 ON DSS-INDUCED COLITIS-ASSOCIATED TUMORIGENESIS AND ASSOCIATED BIOMARKERS IN P53+/+ AND P53+/515A (MUTANT) MICE. IN ADDITION, THE IMPACT OF HIGH DOSE FA GIVEN PRIOR TO THE INDUCTION OF COLITIS WILL BE EXAMINED. TUMOR INCIDENCE AND MULTIPLICITY, AS WELL AS DEGREE OF INTESTINAL INFLAMMATION, WILL SERVE AS PRIMARY ENDPOINTS OF THESE STUDIES. BASED ON THE IMPORTANT CONTRIBUTION OF INTESTINAL MICROBIOTA TO COLITIS AND THEIR ABILITY TO SYNTHESIZE FOLATE DE NOVO, THE IMPACT OF FA ADMINISTRATION ON THE DIVERSITY AND RELATIVE ABUNDANCE OF FECAL AND ADHERENT BACTERIA WITHIN THE INTESTINE OF P53+/515A MICE WITH DSS-INDUCED COLITIS WILL BE EXAMINED IN AIM 3. MICE WILL BE TREATED WITH 5-AMINOSALICYLIC ACID (5-ASA), A COMMON MAINTENANCE THERAPY FOR ULCERATIVE COLITIS, FOR THE DURATION OF FA EXPOSURE TO RECAPITULATE THE CLINICAL THERAPY OF A PATIENT FOLLOWING A DIAGNOSIS OF COLITIS. THE COMPOSITION OF THE FECAL AND COLON-ADHERENT MICROBIOMES, DETERMINED FROM 16S RRNA AND METAGENOMIC SEQUENCING DATA, WILL BE CORRELATED WITH COLONIC INFLAMMATION, BARRIER FUNCTION AND TUMOR INCIDENCE/MULTIPLICITY. THE RESULTS ARE EXPECTED TO PROVIDE SIGNIFICANT INSIGHT INTO THE IMPACT OF FA SUPPLEMENTATION ON COLITIS-ASSOCIATED TUMORIGENESIS AND INFORM THE FIRST GUIDELINES FOR THE USE OF FA SUPPLEMENTS BY PATIENTS WITH ULCERATIVE COLITIS.

BAYESIAN STATISTICS AND ALGORITHMS FOR HOMOLOGY MODELING

NEIGHBORHOOD, SOCIAL CONNECTEDNESS, AND ALLOSTATIC LOAD IN US CHINESE IMMIGRANTS - PROJECT SUMMARY ASIAN AMERICANS ARE THE FASTEST-GROWING RACIAL/ETHNIC GROUP IN THE UNITED STATES (US), AND ASIANS OF CHINESE ORIGIN REPRESENT THE LARGEST SINGLE US ASIAN SUBGROUP. AMONG CHINESE AMERICANS, THE MAJORITY (62%) ARE FOREIGN-BORN. ALTHOUGH CHINESE IMMIGRANTS REPORT BETTER HEALTH THAN THEIR US-BORN COUNTERPARTS, THIS HEALTH AD- VANTAGE DECREASES OVER TIME WITH INCREASING DURATION OF RESIDENCE. THE DOWNWARD HEALTH TRAJECTORY HAS BEEN PRIMARILY ATTRIBUTED TO BEHAVIORAL ACCULTURATION, BUT IMMIGRATION ALSO ENCOMPASSES EXTENSIVE STRESS AND SOCIAL ISOLATION. SOCIAL ISOLATION, IN TURN, MAY INCREASE CHRONIC DISEASE RISK THROUGH DYSREGULATION IN MULTIPLE SYSTEMS – NEUROENDOCRINE, CARDIOVASCULAR, METABOLIC, INFLAMMATORY, IMMUNE – WHICH TOGETHER ARE INDICATIVE OF ALLOSTATIC LOAD (AL). INDEED, STUDIES OF OTHER US IMMIGRANT POPULATIONS (MOSTLY AFRICAN OR LATINX) HAVE NOTED THAT LONGER US RESIDENCE IS ASSOCIATED WITH HIGHER AL. DESPITE THESE FINDINGS, THE QUESTION OF WHETHER IMMIGRANTS’ EXPERI- ENCES OF SOCIAL ISOLATION AFFECT DISEASE RISK AND HEALTH HAS NOT BEEN WELL STUDIED. SOCIAL CONNECTEDNESS, OR THE EXTENT TO WHICH ONE PERCEIVES ONESELF TO BE CLOSELY AND MEANINGFULLY CONNECTED WITH OTHER INDIVIDUALS, GROUPS, AND SOCIETY AS A WHOLE, IS A POSSIBLE STRATEGY TO ADDRESS SOCIAL ISOLATION, BUT THE CONDITIONS AND CONTEXTS THAT FOSTER SOCIAL CONNECTEDNESS ARE NOT WELL UNDERSTOOD. LIVING IN ETHNIC ENCLAVES (I.E. NEIGHBORHOODS WITH A GREATER PROPORTION OF PEOPLE OF THE SAME ETHNICITY) MAY HAVE POSITIVE EFFECTS AMONG CHINESE IMMIGRANTS INCLUDING GREATER SOCIAL SUPPORT AND LESS LONELINESS. IT HAS BEEN SUGGESTED THAT ENCLAVES PROVIDE THE NECESSARY STRUCTURAL CONDITIONS – NAMELY, PHYSICAL AND SOCIAL SPACES – FOR SOCIAL CONNECTEDNESS TO DEVELOP, ALTHOUGH THIS HAS YET TO BE CONFIRMED IN LARGE-SCALE STUDIES. THUS, WE PROPOSE A COMPREHENSIVE INVESTIGATION OF THE FOLLOWING INTERRELATED QUESTIONS: DO POST-MIGRATION EXPERIENCES OF SOCIAL ISOLATION/CONNECTEDNESS HAVE BIOLOGIC CORRELATES AMONG FOREIGN-BORN CHINESE? AND DO ETHNIC ENCLAVES CONTRIBUTE TO SOCIAL CONNECTEDNESS IN THIS POPULATION; IF SO, HOW? TO ADDRESS THESE QUESTIONS, WE WILL RECRUIT A COHORT OF 600 FOREIGN-BORN CHINESE ACROSS THE PHILADELPHIA REGION, INCLUDING RESIDENTS OF ETHNIC ENCLAVES AS WELL AS RESIDENTS OF NEIGHBORHOODS LACKING THE CO-ETHNIC DENSITY AND RESOURCES OF RECOGNIZED ENCLAVES. SPECIFIC AIMS ARE TO: (1) EXAMINE ASSOCIATIONS OF SOCIAL CONNECTEDNESS AND SOCIAL ISOLATION WITH AL IN A COHORT OF US CHINESE IMMIGRANTS; AND (2) EXPLORE WHETHER AND HOW ENCLAVE RESI- DENCE AND ENGAGEMENT WITH ENCLAVE-BASED RESOURCES ARE ASSOCIATED WITH SOCIAL CONNECTEDNESS. DATA COLLECTION WILL INCLUDE QUESTIONNAIRES (E.G., SOCIAL CONNECTEDNESS, ISOLATION, ENGAGEMENT WITH ENCLAVE RESOURCES), BLOOD PRESSURE, ANTHROPOMETRY, AND FASTING BLOOD SAMPLES ANALYZED FOR MARKERS OF AL. ADDRESSES OF RESIDENCES AND LOCATIONS OF ACTIVITIES (E.G., SHOPPING, RELIGIOUS SERVICES) WILL BE GEOCODED. LONGITUDINAL ASSESSMENTS WILL BE OBTAINED AT 2-YEAR FOLLOW-UP TO IDENTIFY CHANGES IN MARKERS OF AL AND CORRELATES OF CHANGES IN THOSE MEASURES. PROJECT FINDINGS WILL IDENTIFY THE MOST VULNERABLE INDIVIDUALS AND NEIGHBORHOODS TO TARGET FOR OUTREACH AND PINPOINT THE CRITICAL COMMUNITY-LEVEL RESOURCES FOR PROMOTING POSITIVE HEALTH TRAJECTORIES IN THIS IMMIGRANT POPULATION.

EXAMINING THE RELATIONSHIP BETWEEN RESIDENTIAL HISTORY AT MIDLIFE AND PROSTATE CANCER OUTCOMES - ABSTRACT PROSTATE CANCER (PCA) IS ONE OF A FEW CANCERS WITH MORE THAN DOUBLE THE MORTALITY FOR BLACK MEN, MAKING THIS ONE OF THE GREATEST RACIAL DISPARITIES IN CANCER. ALTHOUGH THERE ARE DOCUMENTED DISPARITIES IN PCA INCIDENCE AND MORTALITY RELATED TO WHERE PEOPLE LIVE, IT IS UNCLEAR HOW RESIDENTIAL HISTORIES OF PATIENTS CONTRIBUTE TO THEIR PCA OUTCOMES. RESIDENTIAL ENVIRONMENTS VARY GREATLY BY RACE AND SOCIOECONOMICS (SES). STILL LITTLE IS KNOWN ABOUT HOW LONGITUDINAL EXPOSURES TO NEIGHBORHOOD RISK FACTORS AND STRUCTURAL RACISM CAPTURED YEARS BEFORE A CANCER DIAGNOSIS AND INTO SURVIVORSHIP CONTRIBUTE TO PCA DISPARITIES ALONG THE CANCER CARE CONTINUUM. ADDITIONALLY, DISEASE OUTCOMES AND DISPARITIES IN PCA ARE MODERATED BY PATIENT AGE. RESIDENTIAL HISTORY DURING MIDLIFE IS ONE OF THE FACTORS THAT LIKELY INFLUENCES PCA INCIDENCE, PROGRESSION, MORTALITY, AND OVERALL CARE OF SURVIVORS. WE PROPOSE AN INNOVATIVE LINKAGE OF PA CANCER REGISTRY DATA TO HOSPITAL BILLING RECORDS FROM THE PA HEALTHCARE COST CONTAINMENT COUNCIL AND ~30 YEARS OF LEXISNEXIS ADDRESS DATA TO PROVIDE CHARACTERISTICS OF CENSUS TRACTS WHERE PATIENTS LIVE. WE WILL USE PENNSYLVANIA (PA) CANCER REGISTRY DATA (N~20,000 PATIENTS IN SOUTHEASTERN PA) TO DETERMINE THE RELATIONSHIP BETWEEN LONGITUDINAL NEIGHBORHOOD CHARACTERISTICS (POVERTY TRAJECTORIES, HISTORICAL REDLINING, LENDING BIAS, AND GENTRIFICATION) AND PCA OUTCOMES AT CRITICAL POINTS ALONG THE CANCER CARE CONTINUUM IN A DIVERSE AND HISTORIC REGION. THESE VARIOUS CHARACTERISTICS WILL BE USED TO DETERMINE BEST PRACTICES TO EXAMINE RESIDENTIAL HISTORIES IN RISK MODELING FOR PCA OUTCOMES. WE WILL TAKE A NOVEL LIFE COURSE APPROACH TO ADDRESSING THE ROLE OF RESIDENTIAL HISTORY ON PCA DISPARITIES. WE HYPOTHESIZE THAT CUMULATIVE EXPOSURES AS WELL AS EXPOSURES TO NEIGHBORHOOD RISK FACTORS DURING CRITICAL PERIODS IN THE PCA CARE TRAJECTORY INFLUENCE DISEASE CHARACTERISTICS AT DIAGNOSIS AND PCA-MORTALITY. MULTILEVEL REGRESSION MODELS WILL BE CONDUCTED TO EVALUATE INDEPENDENT ASSOCIATIONS OF MULTI-LEVEL FACTORS WITH PCA OUTCOMES. WE WILL ALSO EXAMINE MODIFICATION BY AGE. THE INFORMATION THAT WE LEARN FROM THIS STUDY WILL HELP US TO UNDERSTAND WAYS TO INTEGRATE RESIDENTIAL HISTORY IN CANCER RESEARCH AND STRATEGIZE ABOUT EFFECTIVE INTERVENTIONS TO PROMOTE PROSTATE HEALTH AMONG HIGH-RISK ADULT POPULATIONS WE PROPOSE A LONGITUDINAL, AMBIDIRECTIONAL STUDY TO ADDRESS THE FOLLOWING AIMS: AIM 1: TO EXAMINE THE RELATIONSHIPS BETWEEN PCA DISPARITIES AND RESIDENTIAL CHARACTERISTICS AT DIAGNOSIS; AIM 2: TO WE WILL EMPLOY A LIFE-COURSE FRAMEWORK IN THIS EXAMINE RELATIONSHIPS BETWEEN PCA DISPARITIES AND ACCUMULATED CANCER DISPARITIES RESEARCH (BASED ON ORY, ET AL. RESIDENTIAL HISTORY; AIM 3: TO EXAMINE HOW RESIDENTIAL EXPOSURES 2014, AJPM). DISPARITIES OCCUR WITHIN AN ACCUMULATED SPECIFICALLY DURING MIDLIFE ARE ASSOCIATED WITH PCA ENVIRONMENTAL CONTEXT. RESEARCH FOCUSED ON DISPARITIES; AIM 4: CONDUCT A COMMUNITY NEEDS ASSESSMENT IN PARTICULAR LIFE STAGES PROVIDE UNIQUE OPPORTUNITIES PARTNERSHIP WITH EXPERT CLINICIAN AND COMMUNITY PLANNING STAKEHOLDERS TO INFORM POLICY, PRACTICE, AND THE HEALTH OF THE TO IMPROVE PCA OUTREACH AND CARE COMMUNITY.

PROMOTING EFFECTIVE CLINICAL COMMUNICATION ABOUT SEXUAL HEALTH AFTER GYNECOLOGIC CANCER: A RANDOMIZED CONTROLLED TRIAL OF A PATIENT-FOCUSED INTERVENTION - PROJECT SUMMARY SEXUAL PROBLEMS ARE COMMON, DISTRESSING AND PERSISTENT FOR PATIENTS WITH GYNECOLOGIC CANCER (GC). YET MOST PATIENTS WITH GC WHO EXPERIENCE SEXUAL CONCERNS DO NOT RAISE THEM WITH THEIR CLINICIANS, OFTEN DUE TO A LACK OF PREPARATION FOR HOW TO DO SO EFFECTIVELY. NEGATIVE BELIEFS, SUCH AS LOW SELF-EFFICACY FOR INITIATING DISCUSSIONS OF SEXUAL HEALTH OR EXPECTATIONS FOR THE DISCUSSION, FURTHER LIMIT PATIENTS’ ACTIVE ENGAGEMENT IN THESE DISCUSSIONS. A PATIENT-FOCUSED THEORY-GUIDED INTERVENTION, STARTING THE CONVERSATION (STC), COULD BE IDEALLY SUITED TO ADDRESS THESE CHALLENGES AND EMPOWER PATIENTS TO DRIVE CLINICAL DISCUSSIONS TO MEET THEIR NEEDS. STC WAS DEVELOPED FOR USE WITH BREAST CANCER (BC) PATIENTS AND FOUND EFFECTIVE IN THAT POPULATION. COMPARED TO BC PATIENTS, HOWEVER, GC PATIENTS UNDERGO DIFFERENT TREATMENTS, EXPERIENCE UNIQUE SEXUAL HEALTH CONCERNS, AND HAVE DISTINCT NEEDS FOR A SEXUAL HEALTH COMMUNICATION INTERVENTION. THEREFORE, WE MODIFIED STC TO SUIT THE NEEDS OF WOMEN WITH GC AND CONDUCTED A PILOT TRIAL OF THE NEW INTERVENTION, CALLED STC – GYNECOLOGIC CANCER (STC-GC), FINDING STRONG SUPPORT FOR ITS FEASIBILITY AND ACCEPTABILITY. BEFORE THIS INTERVENTION CAN BE DISSEMINATED, ITS EFFICACY IN THE TARGET POPULATION MUST BE EVALUATED. THE PRIMARY OBJECTIVE OF THE PROPOSED STUDY IS THUS TO EVALUATE THE EFFICACY OF THE STC-GC INTERVENTION AMONG PATIENTS TREATED FOR GC REPORTING SEXUAL CONCERNS. FEMALE PATIENTS WITH ANY STAGE GC (N=200) WILL BE RANDOMIZED TO RECEIVE EITHER THE STC-GC INTERVENTION [VIDEO, WORKBOOK, AND RESOURCE GUIDE] OR TO A CONTROL [USUAL CARE PLUS RESOURCE GUIDE]. IN AIM 1, WE WILL EVALUATE THE EFFICACY OF STC-GC IN FACILITATING PATIENT CLINICAL COMMUNICATION ABOUT SEXUAL HEALTH (PRIMARY), ASSESSED USING RIGOROUS DIALOGUE ANALYSIS OF PATIENTS’ CLINICAL COMMUNICATION ABOUT SEXUAL HEALTH, AND IN IMPROVING PATIENTS’ SEXUAL AND PSYCHOLOGICAL HEALTH OUTCOMES AT POST-INTERVENTION AND 2- AND 6-MONTH FOLLOW-UP (SECONDARY). IN AIM 2, WE WILL EXAMINE WHETHER INTERVENTION-RELATED INCREASES IN PATIENTS’ SELF-EFFICACY AND OUTCOME EXPECTANCIES FOR SEXUAL HEALTH COMMUNICATION MEDIATE EFFECTS OF STC-GC ON PATIENTS’ COMMUNICATION (AIM 2A) AND WHETHER ENHANCED SEXUAL HEALTH COMMUNICATION MEDIATES EFFECTS OF STC-GC ON PATIENTS’ SEXUAL AND PSYCHOLOGICAL HEALTH OUTCOMES (AIM 2B). IN AIM 3, WE WILL CONDUCT IN-DEPTH QUALITATIVE INTERVIEWS WITH A PURPOSIVE SAMPLE OF PATIENTS IN STC-GC AND WITH CLINICIANS OF GC PATIENTS TO PROVIDE INFORMATION FROM MULTIPLE PERSPECTIVES TO CONTEXTUALIZE AND INTERPRET THE QUANTITATIVE FINDINGS OF THE TRIAL. AS THE FIRST EFFICACY TRIAL OF A SEXUAL HEALTH COMMUNICATION INTERVENTION FOR WOMEN WITH GC, FINDINGS FROM THIS STUDY WILL BE INSTRUMENTAL IN ADVANCING EFFORTS TO INTEGRATE SEXUAL HEALTH INTO ROUTINE CANCER CARE. FURTHER, THE PROPOSED STUDY HAS A NUMBER OF UNIQUE FEATURES, INCLUDING A QUALITATIVE INVESTIGATION OF MULTIPLE PERSPECTIVES, NOVEL APPLICATION OF DIALOGUE ANALYSIS, ANALYSIS OF MULTIPLE INTERVENTION MEDIATORS, AND A MEDICALLY INCLUSIVE PATIENT POPULATION, WHICH HEIGHTEN STUDY IMPACT AND INNOVATION. DATA FROM THIS STUDY WILL SERVE AS THE PLATFORM FOR A FUTURE DISSEMINATION TRIAL OF STC-GC IN MULTIPLE SETTINGS.

WERNER SYNDROME PROTEIN, DNA END PROCESSING, AND DOUBLE-STRAND BREAK REPAIR

LUNG CANCER IN NEVER-SMOKERS: ROLE OF ESTROGEN AND ITS METABOLITES

INVESTIGATING THE IL-1R PATHWAY IN ANAPLASTIC LARGE CELL LYMPHOMA FOR TARGETED THERAPY - PROJECT SUMMARY ANAPLASTIC LARGE CELL LYMPHOMA (ALCL) COMPRISES A COLLECTION OF MATURE T-CELL NEOPLASMS THAT SHARE ELEVATED EXPRESSION OF CD30 AND ANAPLASTIC CYTOLOGY. ALCL SUBTYPES ARE DIVIDED INTO TWO CLASSES BASED ON THE STATUS OF ANAPLASTIC LYMPHOMA KINASE (ALK), ALK+ AND ALK-. WHILE ALK+ ALCL IS RELATIVELY HOMOGENEOUS, ALK- ALCL REPRESENTS A HETEROGENEOUS GROUP COMPRISING SYSTEMIC ALK NEGATIVE AND PRIMARY CUTANEOUS ALCL (PC-ALCL). THE RECENTLY RECOGNIZED BREAST IMPLANT-ASSOCIATED (BIA) ALCL, WHICH ARISES IN THE SEROMA CAVITY SURROUNDING BREAST IMPLANTS, WAS ACKNOWLEDGED AS A DISTINCT CLINICAL AND PATHOLOGICAL ENTITY THAT SHARES MORPHOLOGIC FEATURES WITH ALK- ALCL. CURRENT THERAPEUTIC STRATEGIES FOR ALCL ARE LARGELY BASED ON AGGRESSIVE B-CELL LYMPHOMA REGIMENS. HOWEVER, THE OUTCOMES ARE GENERALLY MUCH WORSE IN PATIENTS WITH ALK- ALCL THAN IN THOSE WITH ALK+ ALCL. THUS, THERE IS A NEED TO DEVELOP NOVEL, PREFERABLY SMALL MOLECULE-BASED TARGETED THERAPIES FOR THESE LYMPHOID MALIGNANCIES, ESPECIALLY IN ALK- AND BIA ALCL CASES. A MAJOR BARRIER TO THIS GOAL IS THE LACK OF A SYSTEMATIC AND COMPREHENSIVE UNDERSTANDING OF THE DEEP MOLECULAR CHARACTERISTICS OF ALK- AND BIA ALCL PATHOLOGY, WHICH IS CLEARLY NEEDED IN ORDER TO IDENTIFY CRITICAL THERAPEUTIC VULNERABILITIES. TO ADDRESS THE GAPS IN KNOWLEDGE, WE APPLIED AN UNBIASED HIGH THROUGHPUT CRISPR SCREENING IN ALCL, AND IDENTIFIED AN UNEXPECTED ROLE OF THE IL-1R-MYD88 PATHWAY IN SUPPORTING ALK- AND BIA ALCL. THE IL-1R SIGNALING PATHWAY IS A KEY MEDIATOR OF IMMUNITY AND INFLAMMATION AND HAS BEEN SHOWN TO PLAY A CRITICAL ROLE IN MANY SOLID TUMORS; HOWEVER, ITS ROLE IN LYMPHOID MALIGNANCIES HAS NOT BEEN ESTABLISHED. INDEED, OUR PRELIMINARY STUDIES PROVIDE THE FIRST UNEQUIVOCAL EVIDENCE THAT IL-1R1 PATHWAY PLAYS AN ESSENTIAL ROLE IN SUPPORTING ALK- AND BIA ALCL CELL SURVIVAL. CLINICALLY, WE FOUND THAT IL-1 RECEPTOR AND IL-1A EXPRESSION ARE CONSISTENTLY ELEVATED IN PRIMARY ALK- CASES, AND THIS IS CORRELATED WITH IL-1R SIGNALING ACTIVATION (P-IRAK4 LEVEL) IN PRIMARY SAMPLES. MOREOVER, USING RNA-SEQ ANALYSIS, WE IDENTIFIED A SET OF IL-1R PATHWAY REGULATED GENES IN ALK- ALCL THAT OVERLAPPED SIGNIFICANTLY WITH SIGNATURES REFLECTING JAK-STAT3 ACTIVITY AND TH17/TH1 PHENOTYPING. FINALLY, A HIGHLY SPECIFIC IRAK4 INHIBITOR SHOWS PROMISING ACTIVITY AGAINST ALK- AND BIA ALCL IN VITRO AND IN A MOUSE XENOGRAFT MODEL. ALTOGETHER, THESE FINDINGS PROVIDE STRONG SUPPORT FOR OUR HYPOTHESIS THAT THE IL-1R PATHWAY PROMOTES ALK- AND BIA ALCL PATHOGENESIS, AND THAT TARGETING THIS PATHWAY COULD BE A NOVEL THERAPEUTIC STRATEGY IN THESE DISEASES. IN THIS STUDY, WE WILL TEST OUR HYPOTHESIS THROUGH THE FOLLOWING AIMS: 1) ELUCIDATION OF THE EXACT ROLE OF IL-1R PATHWAY IN ALK- AND BIA ALCL, 2) UNDERSTANDING OF MECHANISMS REGULATING THIS PATHWAY AND ITS RELATIONSHIP TO RECURRENT GENETIC LESIONS IN ALCL, AND 3) VALIDATION OF THE IL-1R PATHWAY AS A NOVEL THERAPEUTIC TARGET IN THESE MALIGNANCIES. THE PROPOSED STUDIES SHOULD PROVIDE CRITICAL INSIGHTS INTO THE MOLECULAR CIRCUITRY THAT DRIVES THESE TYPES OF ALCL AND, CONSEQUENTLY, RESULT IN THE DEVELOPMENT OF NOVEL TARGETED THERAPEUTIC STRATEGIES FOR THESE DISTINCT LYMPHOPROLIFERATIVE DISORDERS.

TARGETING THE RAC1 SIGNALING PATHWAY IN MALIGNANT MELANOMA

DESIGNING SELECTIVE KINASE INHIBITORS VIA DEEP LEARNING - PROJECT SUMMARY/ABSTRACT MODERN CANCER BIOLOGY LEANS HEAVILY ON KINASE INHIBITORS AS A MEANS TO PROBE THE CONSEQUENCES OF DEACTIVATING A PARTICULAR KINASE, BUT THE MAJORITY OF COMMONLY-USED CHEMICAL PROBES ARE NOT SUFFICIENTLY TARGET- SELECTIVE FOR ROBUST INTERPRETATION OF THE OBSERVED PHENOTYPES. BY ASSEMBLING LARGE PANELS OF KINASES (CORRESPONDING TO MUCH OF THE HUMAN KINOME), IT HAS BECOME POSSIBLE TO DETERMINE THE SELECTIVITY FOR A GIVEN PROBE: HOWEVER, THESE EXPERIMENTS ARE EXPENSIVE AND IMPRACTICAL TO PERFORM AT HIGH THROUGHPUT. WE HAVE RECENTLY DEVELOPED A NEW COMPUTATIONAL APPROACH FOR RAPIDLY AND ACCURATELY BUILDING 3D STRUCTURAL MODELS OF INDIVIDUAL INHIBITOR/KINASE COMPLEXES. AIM 1 OF THIS PROJECT ENTAILS APPLYING DEEP LEARNING TO BUILD MODELS FOR PREDICTING THE BINDING AFFINITY OF INDIVIDUAL INHIBITOR/KINASE PAIRS, USING 3D STRUCTURAL DESCRIPTORS DERIVED FROM THE CORRESPONDING INHIBITOR/KINASE COMPLEXES. AIM 2 OF THIS PROJECT WILL BUILD VERY LARGE COMPUTATIONAL LIBRARIES OF NOVEL CHEMICAL MATTER, ENRICHED IN COMPOUNDS WITH 3D PROPERTIES THAT COMPLEMENT KINASE BINDING SITES. WE WILL FIRST USE THE TOOLS DEVELOPED IN AIM 1 TO RE-EVALUATE THE SELECTIVITY OF CHEMICAL PROBES THAT ARE WIDELY USED BY CELL BIOLOGISTS, THUS INFORMING ON WHICH ONES ARE USEFUL TOOLS AND WHICH ONES SHOULD BE DEPRECATED. TO PROVIDE A REPLACEMENT FOR THE OUTDATED CHEMICAL PROBES, WE WILL COMPUTATIONALLY SCREEN THE LIBRARIES OF AIM 2 FOR MORE SELECTIVE COMPOUNDS, FOCUSING FIRST ON CDK KINASES AND SEVERAL KINASES THAT REPRESENT THERAPEUTIC VULNERABILITIES IN GIST. WE WILL SYNTHESIZE THE TOP-SCORING COMPUTATIONAL HITS, AND CHARACTERIZE THEM USING AN ESCALATION OF BIOCHEMICAL ASSAYS, PROTEOMIC KINOME PROFILING, STRUCTURAL BIOLOGY, AND CELLULAR ASSAYS. IF SUCCESSFUL, THIS PROJECT WILL DELIVER NEW CHEMICAL PROBES FOR SEVERAL HITHERTO UNADDRESSED (“ORPHAN”) KINASES, TO SERVE AS CHEMICAL TOOLS AND AS STARTING POINT FOR DRUG DEVELOPMENT. EQUALLY IMPORTANTLY THOUGH, COMPLETION OF THIS PROJECT WILL PROVIDE A ROBUST AND VALIDATED APPROACH FOR DESIGNING POTENT AND SELECTIVE KINASE INHIBITORS, TO BE SUBSEQUENTLY APPLIED FOR DEVELOPING NEW HIGH-QUALITY PROBES AGAINST EACH OF THE 500 HUMAN KINASES.

DECIPHERING NETWORKS CONTROLLING DNA AMPLIFICATION - PROJECT SUMMARY DNA AMPLIFICATION IS ASSOCIATED WITH PATHOLOGICAL STATES SUCH AS NEUROLOGICAL DISORDERS, CARDIAC DISEASE AND CANCER. AT LEAST 50% OF THE AMPLIFICATIONS IN CANCER ARE TRANSIENT EXTRACHROMOSOMAL DNA (ECDNA). THE TRANSIENT BEHAVIOR CONTRIBUTES TO COPY NUMBER PLASTICITY, RESULTS IN HETEROGENEOUS ONCOGENE EXPRESSION AND ALTERS THERAPEUTIC RESPONSE. THE UNANSWERED QUESTION REMAINS AS TO WHETHER DISTINCT MECHANISMS CONTROL ECDNA COPY GAINS WITHIN CELLS AND HOW THEY IMPACT COPY GAIN EVENTS ASSOCIATED WITH DISEASE. MY OVERALL GOAL IS TO DEFINE THE PRINCIPLES REGULATING SELECTIVE DNA COPY GAINS AND THE ASSOCIATED PLASTICITY, SO WE MAY CONTROL THESE EVENTS. MY LABORATORY WAS THE FIRST TO DISCOVER A MOLECULAR BASIS FOR EXTRACHROMOSOMAL TRANSIENT SITE-SPECIFIC DNA COPY GAINS (TSSGS) IN THE HUMAN GENOME. SPECIFICALLY, WE IDENTIFIED THE FIRST ENZYME CAPABLE OF DRIVING SITE-SPECIFIC ECDNA AMPLIFICATION [THE HISTONE 3 LYSINE 9 AND 36 TRI-DEMETHYLASE (H3K9/36ME3) KDM4A] AND DEMONSTRATED A FUNDAMENTAL ROLE FOR EPIGENETIC STATES IN CONTROLLING THE PREDILECTION OF SPECIFIC DNA REGIONS TO REREPLICATE AND AMPLIFY. WE DISCOVERED SEVEN MORE CHROMATIN ENZYMES- LYSINE METHYLTRANSFERASES (KMTS) AND DEMETHYLASES (KDMS)- THAT FUNCTION IN CONCERT TO CONTROL SITE-SPECIFIC AMPLIFICATION IN BOTH NON-CANCER AND CANCER CELLS. THESE STUDIES ESTABLISHED A CRITICAL ROLE FOR CHROMATIN FACTORS AND THEIR ASSOCIATED STATES IN REGULATING DNA AMPLIFICATIONS. WITH THIS NIGMS R35, MY LABORATORY WILL EXPAND OUR STUDIES IN ORDER TO ELUCIDATE: 1) THE FUNDAMENTAL MECHANISMS CONTROLLING DNA AMPLIFICATION; 2) THE MOLECULAR PROCESSES AND CHARACTERISTICS PROMOTING OR PREVENTING DNA AMPLIFICATION; AND 3) THE RELATIONSHIP BETWEEN ECDNA GENERATION AND THE ASSOCIATED RNA HETEROGENEITY/DNA MUTATION BURDEN. WE WILL ADDRESS THESE POINTS BY LEVERAGING MICROSCOPY- BASED SCREENS USING GENETIC AND CHEMICAL TOOLS IN ORDER TO IDENTIFY KEY AMPLIFIERS, AND IN TURN, GENERATE EPIGENOME PROFILES COUPLED TO GENOME ORGANIZATION MAPS ASSOCIATED WITH THESE PATHWAYS SO THAT MOLECULAR FEATURES CONTROLLING DNA AMPLIFICATION ARE RESOLVED. THESE STUDIES WILL ALSO BE COUPLED TO STATE-OF-THE-ART LONG READ SEQUENCING AND SINGLE CELL (DNA AND RNA) SEQUENCING STRATEGIES SO THAT THE ASSOCIATED HETEROGENEITY WITHIN THE CELL POPULATION AND INDIVIDUAL CELLS CAN BE CORRELATED WITH THE EFFECT OF THE AMPLIFIER ON TSSGS. THESE STUDIES ARE BEING CONDUCTED IN NON-TRANSFORMED CELLS THAT HAVE A NEARLY DIPLOID GENOME SO THAT ADDITIONAL GENOMIC ANOMALIES AND MUTATIONS DO NOT IMPACT THESE STUDIES. COLLECTIVELY, THE DATA GENERATED FROM THESE STUDIES WILL INCREASE OUR KNOWLEDGE ABOUT THE MOLECULAR FEATURES GOVERNING DNA COPY GAINS AND THE ASSOCIATED HETEROGENEITY, WHICH WILL RESOLVE NOVEL BIOMARKERS AND THERAPEUTIC TARGETS IN ORDER TO CONTROL COPY NUMBER- ASSOCIATED DISEASES IN THE YEARS AHEAD.

3D-ADHESION STROMAGENESIS IN CANCER PERMISSIVENESS

ASSESSING DNA POLYMERASE THETA AS A THERAPEUTIC TARGET IN BRCA1 MUTANT CANCER - PROJECT SUMMARY GENETIC DISRUPTION OF DNA POLYMERASE THETA (POL) ACTIVITY HAS BEEN SHOWN TO EFFECTIVELY TARGET BRCA1 MUTATED CELLS, WHILE LEAVING BRCA1 WILD-TYPE (WT) CELLS INTACT. POL FACILITATES THETA-MEDIATED DNA END JOINING (TMEJ) REPAIR BY PROMOTING DNA SYNAPSIS AND REPAIR SYNTHESIS AT BREAK SITES CONTAINING 3' SINGLE STRANDED (SS)DNA OVERHANGS. ALTHOUGH SMALL MOLECULE INHIBITORS OF POL ACTIVITY ARE CURRENTLY UNDER DEVELOPMENT FOR THE TREATMENT OF BRCA1 MUTANT CANCERS, VERY LITTLE IS KNOWN REGARDING THE MECHANISMS THAT ACTIVATE TMEJ AND RESULT IN POL- DEPENDENCY IN BRCA1 MUTANT CELLS. MOREOVER, THE CURRENT PARADIGM ASSUMES THAT HOMOLOGOUS RECOMBINATION (HR)-DEFICIENCY CONFERS POLI SENSITIVITY, THEREFORE PARPI RESPONSIVENESS IS EXPECTED TO BE A BIOMARKER FOR POL INHIBITOR (POLI) SENSITIVITY. IN OUR PRELIMINARY DATA, WE UNEXPECTEDLY IDENTIFIED COMMONLY USED BRCA1 MUTANT CELLS THAT GROW RELATIVELY UNPERTURBED WITH GENETIC POLQ (POL) KNOCKOUT (KO), INDICATING THAT POLI AND PARPI SENSITIVITY MAY NOT NECESSARILY CORRELATE. IN THIS PROPOSAL, WE WILL ELUCIDATE THE MOLECULAR REQUIREMENTS FOR TMEJ ACTIVATION AND IDENTIFY BIOLOGICAL FACTORS THAT DISTINGUISH PARPI AND POLI SENSITIVITY. WE WILL ADDRESS THE FOLLOWING SPECIFIC AIMS: 1) REVEAL THE MOLECULAR BASIS OF TMEJ ACTIVATION IN BRCA1 MUTANT CELLS; 2) UNCOVER GENETIC POL- DEPENDENCIES IN BRCA1 MUTANT CELLS; AND 3) EXAMINE PHARMACOLOGIC POL INHIBITION IN BRCA1 MUTANT CELLS. COLLECTIVELY, THESE STUDIES WILL BE INFORMATIVE FOR FUTURE CLINICAL STUDIES EMPLOYING POLI.

LY-1 B CELLS: DEVELOPMENTAL ORIGINS AND V GENE BIASES

TARGETED CHEMOPREVENTION OF FLAT AND POLYPOID COLITIS-ASSOCIATED DYSPLASIAS

THE MED1 PROTEIN IN DNA DAMAGE RESPONSE AND REPAIR

KINETICS OF EARLY EVENTS IN PROTEIN FOLDING

DEVELOPMENT AND FUNCTION OF NATURAL AUTOREACTIVE B CELLS

INTRA- AND INTER-NEURONAL VIRAL TRAFFICKING

CONTROL OF ALPHA-BETA/GAMMA-DELTA T LINEAGE COMMITMENT

TELOMERASE RNP PRISONBREAKS FROM PHASE-SEPARATED NUCLEAR BODY - PROJECT SUMMARY OVERVIEW: THE RIBONUCLEOPROTEIN ENZYME TELOMERASE MAINTAINS TELOMERE LENGTH HOMEOSTASIS – A SHARED HALLMARK BETWEEN AGING AND CARCINOGENESIS. INSUFFICIENT TELOMERASE LEADS TO TELOMERE DYSFUNCTIONS AND REPLICATIVE SENESCENCE IN STEM CELLS, PRECIPITATING SHORT-TELOMERE DISEASES. CONVERSELY, TELOMERASE IS EXPLOITED BY ~90% OF CANCERS FOR GROWTH IMMORTALITY. ACTIVATING PROMOTER MUTATIONS IN THE REVERSE TRANSCRIPTASE (TERT) GENE RANKS THE MOST FREQUENT NON-CODING DRIVER MUTATIONS. WE HAVE MADE CONTRIBUTIONS TO AN UNDERSTANDING OF HOW TELOMERASE AND TELOMERE CAN BE MODULATED. 1) WE UNCOVERED THAT TCAB1, A NON-CATALYTIC SUBUNIT OF TELOMERASE AND A CAJAL BODY (CB) TRAFFICKING PROTEIN, FUNCTIONS AS AN ACTIVITY SWITCH DURING TELOMERASE CATALYSIS. USING NEXT-GEN RNA STRUCTURAL PROFILING, WE FOUND THAT TCAB1-BOUND RNPS ARE ENDOWED WITH AN RNA CONFORMATION FAVORABLE FOR TERT-TR ENGAGEMENT, LINKING AN RNA QUALITY-CONTROL WITH RNP TRAFFICKING AND CATALYSIS; 2) WE SHOWED THAT THE 5’ TR CAP HYPERMETHYLATION PLAYS A NEGATIVE ROLE IN TELOMERASE RNA ACCUMULATION AND ACTIVITY. WE CAN INDUCE ROBUST TELOMERE ELONGATION BY GENETIC INACTIVATION AND CHEMICAL INHIBITION OF THE CAP HYPERMETHYLASE TGS1; 3) WE ALSO DISCOVERED A CROSSTALK BETWEEN SNRNA 5’ AND 3’ PTM CRITICAL FOR GLOBAL SPLICING FIDELITY AND MOTOR NEURON VIABILITY IN MULTIPLE ORGANISMS. 4) WE UNCOVERED A TOXIC TELOMERASE RNP THAT PROVOKES ACUTE AND SELECTIVE CANCER GENOTOXICITY AT TELOMERES, UNLIKE THE CONVENTIONAL DELAYED KILLING BY DIRECT TELOMERASE INHIBITION. GOALS: WE WILL TEST A MODEL THAT RNP ASSEMBLY AND/OR ACTIVITY CAN BE LIMITED BY PHASE-SEPARATED CB. WE HAVE FOUND THAT DISMANTLEMENT OF THE RNA AND PROTEIN COMPONENTS OF CB BOTH LED TO GOF OF TELOMERASE. WE ARE ADDRESSING: 1) CAN CB CONTRIBUTE TO THE MOLECULAR DETERMINANT OF TELOMERE LENGTH SET POINTS? WE ARE TESTING THIS WITH A NOVEL OPTOGENETIC PIPELINE TO MANIPULATE PHASE SEPARATION OF A SUBSET OF CELLULAR CBS AND MONITOR A SINGLE TELOMERE ELONGATION; 2) WHAT IS THE RNA BASIS FOR TELOMERASE PHASE SEPARATION AT CB, AT TELOMERES, OR WHEN MISLOCALIZED TO NUCLEOLI? WE WILL IMPROVE THE CURRENT ICSHAPE-SEQ TO DETERMINE RNA STRUCTURE AT SUBCELLULAR LOCATIONS; 3) WE AIM TO ELUCIDATE THE MECHANISM BY WHICH PHASE SEPARATION SEQUESTERS TELOMERASE RNPS, FOCUSING ON THE DYNAMIC INTERPLAY BETWEEN TCAB1 AND COILIN; 4) WE AIM TO UNDERSTAND THE GENOTOXIC MECHANISM UNDERLY THE TOXIC TERT. WE ALSO USE THIS AS A TRACTABLE SYSTEM TO IDENTIFY SUPPRESSORS AS POTENTIAL NEW FACTORS IN RNP ASSEMBLY AND TARGETING. VISION: WE WILL ENGINEER TOOLS TO STUDY STRUCTURE-FUNCTION OF RNP WITHIN PHASE-SEPARATED BODIES. WE WILL IDENTIFY ADDITIONAL TELOMERASE-LIKE RNPS THAT ARE SIMILARLY GOVERNED BY PHASE-SEPARATION, RNA QC, AND RNA PTMS. OUR LONG-TERM GOAL IS TO DEVELOP NOVEL CHEMICAL MATTERS THAT CAN BOOST TELOMERASE TO IMPROVE CELL THERAPY, SUCH AS MAKING EXHAUSTION-RESISTANT CAR-T; WE AIM TO FURTHER DEVELOP OUR BIFUNCTIONAL TELOMERASE-TARGETING MOLECULE THAT INDUCES RAPID AND SELECTIVE CANCER CYTOTOXICITY INTO A PAN-CANCER DRUG.

RIP1/3 KINASES AS NEW TARGETS IN MALIGNANT MESOTHELIOMA

ANALYSIS AND THERAPEUTIC TARGETING OF THE LINEAR-UBIQUITINATION PATHWAY IN HODGKIN LYMPHOMA - PROJECT SUMMARY HODGKIN LYMPHOMA (HL) IS THE MOST COMMON (6,000 TO 7,000 NEW CASES PER YEAR) LYMPHOMA SUBTYPE IN YOUNG ADULTHOOD. ALTHOUGH THERE HAS BEEN GREAT PROGRESS DURING THE LAST FEW DECADES, THE SURVIVAL RATE FOR PATIENTS DIAGNOSED AT AN ADVANCED STAGE OR WITH RELAPSED/REFRACTORY DISEASE REMAINS LOW. THE CURRENT UNDERSTANDING OF THE BIOLOGY OF THE DISEASE HAS BEEN TRANSLATED INTO THE DEVELOPMENT AND APPROVAL OF THERAPEUTIC AGENTS THAT TARGET HL-SPECIFIC ANTIGENS OR IMMUNE CHECKPOINT PATHWAYS. HOWEVER, THE NUMBER OF PATIENTS IN COMPLETE REMISSION HAS BEEN LOW, AND RELAPSE FREQUENTLY DEVELOPS, LEADING TO POOR OUTCOMES. THUS, A CLEARER UNDERSTANDING OF THE MOLECULAR PATHOLOGY OF HL IS NECESSARY TO DEVELOP NEW TREATMENT STRATEGIES. HL IS CHARACTERIZED BY A MINORITY POPULATION OF MALIGNANT HODGKIN AND REED/STERNBERG (HRS) CELLS IN A BACKGROUND OF DENSE INFLAMMATORY CELLS. HRS CELLS HAVE LOST THEIR B CELL PHENOTYPE, HOWEVER, AND ESCAPED FROM BCR- MEDIATED APOPTOSIS AND IMMUNE ELIMINATION. THEREFORE, TWO MAJOR QUESTIONS REMAIN: (A), HOW DO HRS CELLS ESCAPE THE CONTROL OF THE IMMUNE SYSTEM; (B), HOW DO THEY SURVIVE DESPITE THE ABSENCE OF BCR EXPRESSION? TO ADDRESS THESE GAPS IN KNOWLEDGE, WE APPLIED AN UNBIASED HIGH THROUGHPUT CRISPR SCREENING, AND IDENTIFIED AN ESSENTIAL ROLE FOR THE LINEAR UBIQUITIN CHAIN ASSEMBLY COMPLEX (LUBAC) IN HL PATHOGENESIS. OUR PRELIMINARY STUDIES DEMONSTRATED THAT LUBAC ACTIVITY PROMOTES HRS CELL SURVIVAL AND IMMUNE ESCAPE, WHICH SIGNIFICANTLY OVERLAPS WITH MUTATION STATUS OF THE MOST RECURRENT GENETICALLY ALTERED GENE IN HL, A20. CLINICALLY, LUBAC ACTIVITY IS CONSISTENTLY ELEVATED IN MOST PRIMARY HL CASES, AND THIS IS CORRELATED WITH LOW A20 EXPRESSION. MOREOVER, USING RNA-SEQ ANALYSIS, WE IDENTIFIED A SET OF LUBAC-REGULATED GENES IN HL THAT OVERLAPPED SIGNIFICANTLY WITH SIGNATURES REFLECTING NF-B AND JAK-STAT ACTIVITIES, AS WELL AS TH2 CYTOKINES AND CELL SURFACE IMMUNOSUPPRESSIVE MOLECULES. UNEXPECTEDLY, OUR BIOID PROTEOMIC SCREENING REVEALS A CD30-LUBAC COMPLEX IN HL, SUGGESTING THE ROLE OF LUBAC-A20 AXIS IN THE CD30 MEDIATED NF-B SIGNALING, TH2 CYTOKINE PRODUCTION, AND STAT6 ACTIVATION. FINALLY, A HIGHLY SPECIFIC LUBAC SMALL MOLECULAR INHIBITOR SHOWS PROMISING ACTIVITY AGAINST HL IN VITRO AND IN A MOUSE XENOGRAFT MODEL. ALTOGETHER, THESE FINDINGS PROVIDE STRONG SUPPORT FOR OUR HYPOTHESIS THAT THE LUBAC-A20 AXIS REGULATES HL PATHOGENESIS, AND THAT TARGETING LUBAC COULD BE A NOVEL THERAPEUTIC STRATEGY IN THIS DISEASE. IN THIS STUDY, WE WILL: 1) INVESTIGATE THE MECHANISTIC BASIS BY WHICH THE LUBAC-A20 AXIS SUPPORTS HRS SURVIVAL AND PROLIFERATION; 2) EVALUATE HOW LINEAR-UBIQUITIN-DEPENDENT SIGNALING REGULATES THE MOLECULAR CIRCUITRY THAT DRIVES TUMOR IMMUNE ESCAPE OF HL; AND 3) EXPLOIT THE THERAPEUTIC POTENTIAL OF TARGETING LUBAC TO PROVIDE NOVEL INTERVENTION STRATEGIES FOR BOTH TARGETED AND IMMUNE THERAPIES IN HL. THESE STUDIES PROMISE TO REVEAL CRITICAL INSIGHTS INTO THE MOLECULAR CIRCUITRY THAT DRIVES THIS LYMPHOID CANCER, AS WELL AS PROVIDE UNIQUE OPPORTUNITIES FOR THE DEVELOPMENT OF NOVEL STRATEGIES FOR BOTH TARGETED AND IMMUNE THERAPIES TO TREAT HL.

MTAP, 5'-DEOXY-5'-METHYLTHIOADENOSINE, AND THE DYSREGULATION OF SYMMETRIC DIMETHYLARGININE IN CANCER

EXPLOITING VULNERABILITIES IN GIST USING NOVEL COMBINATION THERAPIES

TARGETING THE KINOME IN K-RAS DRIVEN COLORECTAL CANCERS

BASIS FOR LYMPHOMAGENESIS IN AKT2 TRANSGENIC MICE

INTERACTION OF PROTEIN-TARGETED THERAPEUTICS AND CILIARY DYNAMICS

MECHANISMS REGULATING THE B LYMPHOPOIESIS FETAL/ADULT SWITCH

REGULATION OF HEMATOPOIESIS BY RIBOSOMAL PROTEIN PARALOGS

HEF1 FUNCTIONS IN CELL DIVISION-RELATED SIGNALING

OPTIMIZATION OF URINARY DNA DEEP SEQUENCING TESTS TO ENHANCE CLINICAL STAGING OF BLADDER CANCER PATIENTS - PROJECT SUMMARY/ABSTRACT MUSCLE-INVASIVE BLADDER CANCER (MIBC) IS OPTIMALLY TREATED WITH NEOADJUVANT CHEMOTHERAPY FOLLOWED BY RADICAL CYSTECTOMY (RC), WHEREBY ~35% OF PATIENTS WILL HAVE A PATHOLOGIC COMPLETE RESPONSE (PCR). GIVEN THE MORBID, COMPLICATED, AND EXPENSIVE NATURE OF RC AND THE WELL-ESTABLISHED PCR RATE, THERE IS A GROUNDSWELL OF INTEREST IN RC AVOIDANCE FOR PATIENTS ACHIEVING PCR. HOWEVER, IDENTIFYING PCR CLINICALLY (AS OPPOSED TO PATHOLOGICALLY) IS AN INACCURATE PROCESS. IN PUBLISHED STUDIES, PATIENTS WHO AVOID RC AFTER BEING DEEMED CLINICAL COMPLETE RESPONDERS HAVE A 25-60% LIKELIHOOD OF RECURRENCE, METASTASIS, OR BLADDER CANCER MORTALITY. BETTER TOOLS TO ASSESS RESIDUAL DISEASE STATUS ARE NEEDED. TO ADDRESS THIS NEED, WE DEVELOPED A URINE BIOPSY TEST WHICH WE CALL UTERD (URINE TEST FOR RESIDUAL DISEASE). IN UTERD, DNA IS ISOLATED FROM URINE AND SUBJECTED TO NEXT GENERATION SEQUENCING TO DETECT POINT MUTATIONS IN A TARGETED PANEL OF GENES. USING UTERD, MOST MUTATIONS IN TUMOR TISSUE ARE DETECTABLE AS MUTATIONS IN URINE. FURTHER, PRESENCE OR ABSENCE OF RESIDUAL MU AFTER COMPLETION OF CHEMOTHERAPY STRONGLY ASSOCIATES WITH RESIDUAL DISEASE OR PCR AT THE TIME OF RC, RESPECTIVELY. THEREFORE, UTERD COULD BE USED AFTER NEOADJUVANT THERAPY TO BETTER IDENTIFY PATIENTS FOR RC AVOIDANCE. ALTHOUGH UTERD PERFORMS WELL IN DISTINGUISHING PATIENTS WITH PCR FROM RESIDUAL DISEASE, THE NEGATIVE PREDICTIVE VALUE (NPV) OF UTERD IS ONLY 76%, SOME URINE SAMPLES WERE NONDIAGNOSTIC, AND A URINARY DNA PRESERVATION PROTOCOL NEEDS TO BE DEVELOPED IN ORDER FOR THE TEST TO BE WIDELY ADOPTED. PRE-ANALYTICAL FACTORS AND METHODOLOGY IMPROVEMENTS WHICH WE BELIEVE WILL INCREASE THE NPV AND DECREASE NONDIAGNOSTIC RATES WILL BE STUDIED IN AIM 1. IN AIM 2, WE WILL DETERMINE IF URINE PRESERVATIVES CAN BE USED TO FACILITATE SHIPPING TO A CENTRALIZED LAB WITHOUT LOSS OF FIDELITY OF THE TEST. LASTLY, IN AIM 3, WE WILL DETERMINE IF THE ABSENCE OF MUTATIONS FROM A URINE BIOPSY IS ASSOCIATED WITH PCR REGARDLESS OF THE PRE-SURGICAL THERAPY. TO ANSWER THIS QUESTION, SAMPLES OBTAINED ON 5 PROSPECTIVE MIBC CLINICAL TRIALS FROM MULTIPLE INSTITUTIONS WILL BE STUDIED USING THE OPTIMIZED PROTOCOLS IDENTIFIED THROUGH THIS RESEARCH. THE RESEARCH TEAM IS COMPRISED OF A UROLOGIST, MEDICAL ONCOLOGISTS, A RADIATION ONCOLOGIST, A STATISTICIAN, A COMPUTATIONAL BIOLOGIST WHO ARE EXPERTS IN THEIR FIELDS. THE SKILLS AND CONTRIBUTIONS OF THE TEAM ARE COMPLIMENTARY AND WILL CULMINATE IN THE DEVELOPMENT OF A UNIQUE AND ROBUST BIOMARKER THAT ADDRESSES A SIGNIFICANT CLINICAL NEED USING A ONE-OF-A-KIND SAMPLE COHORT. UTERD MAY ENHANCE THE ABILITY OF A BLADDER CANCER CLINICIAN TO ANSWER HIGHLY RELEVANT CLINICAL QUESTION, NAMELY, “DOES THIS PATIENT HAVE RESIDUAL DISEASE AFTER PRE- SURGICAL THERAPY, AND THEREFORE, WILL HE/SHE BENEFIT FROM RC?”

TARGETING THE ONCOGENIC MUTANT P53 SIGNALING IN COLORECTAL CANCER THERAPY

TRANSCRIPTIONAL CONTROL OF TH-POK, A KEY REGULATOR OF LINEAGE CONTROL

PEMBROLIZUMAB MAINTENANCE AFTER ENFORTUMAB VEDOTIN/PEMBROLIZUMAB INDUCTION IN FRONT-LINE METASTATIC UROTHELIAL CARCINOMA.

A NEW VIEW OF PAH ALLOSTERY - CORRELATION WITH DISEASE-ASSOCIATED ALLELES

CONTROL OF LINEAGE COMMITMENT IN DEVELOPING THYMOCYTES

TARGETING DHX9 TO TRIGGER VIRAL MIMICRY AND IMMUNOTHERAPY RESPONSIVENESS IN SMALL CELL LUNG CANCER (SCLC) - PROJECT SUMMARY / ABSTRACT DESPITE THE IMPRESSIVE CLINICAL SUCCESS OF IMMUNE CHECKPOINT BLOCKADE (ICB) THERAPY IN CANCER, THERAPY RESISTANCE IS COMMON AND ONLY A SMALL SUBSET OF PATIENTS MOUNTS LASTING ANTITUMOR RESPONSES, HIGHLIGHTING THE URGENT NEED TO IDENTIFY STRATEGIES TO OVERCOME RESISTANCE AND IMPROVE RESPONSIVENESS TO IMMUNOTHERAPY. SUCH RESISTANCE IS RELATED WITH THE FACT THAT MANY TUMORS ARE IMMUNOLOGICALLY ‘COLD’. ACTIVATING INNATE IMMUNITY IN TUMOR CELLS IS A POTENT MEANS BY WHICH ‘COLD’ TUMORS CAN BE TURNED ‘HOT’. ONE PROMISING STRATEGY TO TRIGGER AN INNATE IMMUNE RESPONSE WITHIN TUMORS IS BY INDUCING THE INTRACELLULAR ACCUMULATION OF ENDOGENOUS ‘VIRUS-MIMETIC’ NUCLEIC ACIDS IN CANCER CELLS. OUR PRELIMINARY DATA DEMONSTRATE THAT TARGETING THE RNA/DNA HELICASE DHX9 IS A PROMISING AND UNEXPLORED STRATEGY BY WHICH ‘VIRAL MIMICRY’ CAN BE TRIGGERED IN TUMORS. DHX9 IS AN ABUNDANT RNA/DNA HELICASE CAPABLE OF UNWINDING BOTH RNA AND DNA DUPLEXES, AS WELL AS MORE COMPLEX NUCLEIC ACID STRUCTURES. ITS FUNCTIONS INCLUDE REGULATION OF DNA REPLICATION AND TRANSCRIPTION, RNA PROCESSING AND TRANSPORT, AND MAINTENANCE OF GENOMIC STABILITY. HERE, WE PROVIDE DATA THAT ABLATING DHX9 INDUCES THE FORMATION OF DOUBLE- STRANDED RNAS (DSRNAS) DERIVED FROM ENDOGENOUS RETROVIRAL ELEMENTS (ERES), PROVOKING AN ANTITUMOR IMMUNE RESPONSE IN ‘COLD’ TUMORS. INTRIGUINGLY, ELIMINATING DHX9 ALSO INDUCED THE ACCUMULATION OF RNA-DNA HYBRIDS (R- LOOPS), LEADING NOT ONLY TO AN ANTIVIRAL IMMUNE RESPONSE BUT ALSO TO DNA REPLICATION STRESS AND DNA DAMAGE IN SMALL CELL LUNG CANCER (SCLC) CELLS. IN VIVO, ELIMINATING DHX9 CAUSES A SIGNIFICANT DECREASE IN TUMOR GROWTH WHILE INDUCING A MORE IMMUNOGENIC TUMOR MICROENVIRONMENT (TME) IN SCLC MOUSE MODELS, DRAMATICALLY ENHANCING RESPONSIVENESS TO ICB. TO OUR KNOWLEDGE, THIS IS THE FIRST DESCRIPTION OF THE ROLE OF DHX9 ON TUMOR IMMUNITY AND GENOMIC INSTABILITY AND THE IDENTIFICATION OF A NOVEL VIRAL MIMICRY-INDUCING STRATEGY TO ENHANCE ANTITUMOR IMMUNITY AND BOOST CANCER IMMUNOTHERAPY. EXCITINGLY, WE NOW PRESENT A FIRST-IN-CLASS, ORALLY BIOAVAILABLE SMALL MOLECULE INHIBITOR OF DHX9, WHICH WILL ALLOW US TO EVALUATE THE TRANSLATIONAL RELEVANCE OF TARGETING DHX9 IN SCLC AND IN IMMUNOTHERAPY SETTINGS. OUR OVERARCHING HYPOTHESIS IS THAT TARGETING DHX9 INDUCES DSRNA ACCUMULATION, CAUSING ANTIVIRAL SIGNALING, WHILE CONCURRENTLY TRIGGERING THE FORMATION OF R-LOOPS, COMPROMISING GENOME STABILITY, AND TRIGGERING THESE TUMOR-INTRINSIC EVENTS GREATLY IMPROVES ICB. IN AIM 1, WE WILL DETERMINE WHICH DSRNAS ARE SUBSTRATES OF DHX9 AND WHETHER THEY ARE IMMUNOGENIC, AS WELL AS HOW DHX9 SENSES AND SUPPRESSES R-LOOPS. WE WILL ALSO DELINEATE THE MECHANISM BY WHICH DHX9 LOSS TRIGGERS CELL DEATH IN SCLCS. IN AIM 2, WE WILL DISSECT THE IMPACT OF DHX9 LOSS OR INHIBITION ON THE TME AT A SINGLE CELL RESOLUTION, AND WE WILL EVALUATE WHETHER DHX9 DEPLETION OR INHIBITION INDUCES A ROBUST ANTITUMOR IMMUNITY ABLE TO BOOST CANCER IMMUNOTHERAPY USING MURINE IMMUNOCOMPETENT SCLC MODELS AND A SCLC GEMM. THE SUCCESSFUL COMPLETION OF THESE AIMS WILL OUTLINE AN ENTIRELY NEW VIRAL MIMICRY-INDUCING STRATEGY WITH WIDESPREAD APPLICATION IN CANCER TREATMENT, AS STAND-ALONE ANTI-CANCER THERAPY TO IMPROVE RESPONSIVENESS TO IMMUNOTHERAPY.

NEW METHODS FOR HIGH-RESOLUTION COMPARATIVE MODELING

DISSECTING BRCA1-PALB2 ACTIVITY IN DNA REPAIR AND DEVELOPMENT

TARGETING THE SRPK1-AKT SIGNALING AXIS IN ENDOMETRIAL CANCER

SYNERGISTIC TARGETING OF CHOLESTEROL METABOLISM AND EGFR SIGNALING IN CANCER

LEUKOTRIENE-INDUCED NESTIN EXPRESSION PROMOTES MEDULLOBLASTOMA TUMORIGENESIS

INTERFERON ACTIVATED NECROPTOSIS AS A NEW THERAPEUTIC AVENUE FOR KIDNEY CANCER

THE ROLE OF MICROHOMOLOGY-MEDIATED END JOINING IN FANCONI ANEMIA PATHOGENESIS

HEPATITIS B VIRUS CCCDNA

NEGATIVE SIGNALLING BY KILLER IG-LIKE RECEPTORS

THE ROLE OF METHYLTHIOADENOSINE PHOSPHORYLASE LOSS IN TUMORIGENESIS

ORIGIN OF CD5+ B CELL LYMPHOMA/LEUKEMIA IN MICE

A TAILORED INTERNET INTERVENTION FOR SKIN CANCER RISK REDUCTION IN YOUNG ADULTS

MHC CLASS I ANTIGEN PRESENTATION IN VIRAL INFECTIONS

ELUCIDATING THE CRITICAL ROLE OF WEE1 IN GIST - PROJECT SUMMARY MANAGEMENT OF GASTROINTESTINAL STROMAL TUMOR (GIST) TREATMENT HAS BEEN REVOLUTIONIZED BY THE IDENTIFICATION OF ACTIVATING MUTATIONS IN KIT AND PDGFRA AND CLINICAL APPLICATION OF TYROSINE KINASE INHIBITORS (TKIS) IN ADVANCED DISEASE. HOWEVER, RESISTANCE TO ALL APPROVED LINES OF TKIS IS A LIFE-THREATENING CLINICAL OBSTACLE IN METASTATIC GIST PATIENTS, WHO HAVE POLYCLONAL TUMORS COMPRISED OF A VARIETY OF RESISTANCE MUTATIONS IN KIT/PDGFRA. DEVELOPMENT OF EFFECTIVE TREATMENT STRATEGIES FOR REFRACTORY GIST REQUIRES IDENTIFICATION OF NOVEL TARGETS. USING KINOME PROFILING AND LOSS-OF FUNCTION ASSAYS, WE FOUND THAT GIST ARE EXQUISITELY DEPENDENT ON WEE1 ACTIVITY. WEE1 HAS LONG BEEN KNOWN AS A CRITICAL G2/M CELL CYCLE CHECKPOINT GATEKEEPER CONTROLLING GENOMIC INTEGRITY AND REGULATING PROLIFERATION. HOWEVER, RECENT STUDIES HAVE IMPLICATED WEE1, BOTH DIRECTLY AND INDIRECTLY, IN OTHER CELLULAR FUNCTIONS, INCLUDING RESTORATION OF STALLED REPLICATION FORKS AND CHROMATIN REMODELING. TRANSCRIPTOME PROFILING OF TKI-SENSITIVE GIST CELL LINES HIGHLIGHTED A ROLE FOR ONCOGENIC KIT/PDGFRA IN DNA DAMAGE RESPONSE (DDR) AND REPLICATION STRESS. OUR IN VITRO AND IN VIVO STUDIES REVEALED SIGNIFICANT EFFICACY OF ADAVOSERTIB (WEE1 INHIBITOR) IN COMBINATION WITH AVAPRITINIB (KIT/PDGFRA INHIBITOR) IN TKI-SENSITIVE KIT AND PDGFRA-MUTANT GIST LINES AND IN A PATIENT-DERIVED XENOGRAFT (PDX) MODEL. FURTHERMORE, OUR PRELIMINARY DATA IN THE TKI-REFRACTORY SETTING DEMONSTRATED THERAPEUTIC SYNERGIES BETWEEN WEE1 INHIBITION AND THE TOPOISOMERASE II INHIBITOR, DOXORUBICIN, AT LOW NANOMOLAR CONCENTRATIONS IN A PANEL OF TKI-RESISTANT GIST CELL LINES, SUGGESTING WEE1 INHIBITION SENSITIZES REFRACTORY GIST TO DOXORUBICIN, PROVIDING VIABLE TARGETS BEYOND KIT AND PDGFRA. WE HYPOTHESIZE THAT ONCOGENIC KIT/PDGFRA ACTIVATES DDR PROTEINS TO INHIBIT REPLICATIVE STRESS AND DNA DAMAGE AND MAINTAIN GENOMIC STABILITY IN GIST LEADING TO RESISTANCE TO DNA DAMAGING AGENTS. OUR PRELIMINARY FINDINGS PROVIDE A STRONG PREMISE THAT WEE1 IS A CRITICAL MEDIATOR OF THIS PROCESS AND THAT ITS INHIBITION HAS POTENTIAL IN THE TREATMENT OF GIST TUMORS. STUDIES INTERROGATING MECHANISMS OF WEE1 AND KIT/PDGFRA COOPERATIVITY IN RESPONSE TO DNA DAMAGE AND REPLICATION STRESS IN GIST ARE WARRANTED TO UNDERSTAND THIS CRITICAL CELL-PROTECTIVE MECHANISM IN GIST, WHICH MAY REPRESENT A NOVEL THERAPEUTIC VULNERABILITY. ULTIMATELY, THIS PROPOSAL SEEKS TO TEST THE HYPOTHESIS THAT WEE1 INHIBITION WILL BE A VALUABLE ADDITION TO CURRENT TREATMENTS FOR GIST PATIENTS WITH TKI-SENSITIVE OR -RESISTANT DISEASE. WE BELIEVE THAT THE STUDIES OUTLINED IN THIS PROPOSAL WILL PROVIDE NOVEL INSIGHTS INTO THE ROLE OF WEE1 IN MAINTAINING GENOMIC INTEGRITY AS WELL AS PRECLINICAL DATA TO SUPPORT CLINICAL TRIALS IN GIST.

ENDOCYTIC CONTROL OF NOTCH-MEDIATED CELL FATE DECISIONS IN NEUROGENESIS

ROLE OF RPL22 IN THYMOCYTE DEVELOPMENT

HEPATIC TISSUE INTEGRITY AND CLONAL FITNESS: KEY FACTORS IN CONTROLLING Β-CATENIN INDUCED ONCOGENESIS - PROJECT SUMMARY GIVEN THE IMPORTANCE OF MUTATIONS IN ONCOGENES AND TUMOR SUPPRESSOR GENES, IT HAS BEEN WIDELY ASSUMED THAT THE MERE ACCUMULATION OF MUTATIONS IS THE PRIMARY PROCESS TO EXPLAIN CANCER INCIDENCE. HOWEVER, CANCER IS PREDOMINANTLY A DISEASE OF AGING, WITH ITS INCIDENCE REMAINING LOW UNTIL THE FOURTH DECADE OF LIFE, UNDERGOING EXPONENTIAL GROWTH THEREAFTER. FURTHERMORE, CELLS CARRYING WELL-CHARACTERIZED ONCOGENIC MUTATIONS CAN BE FOUND ACROSS NORMAL HUMAN TISSUES, AND CAN PERSIST FOR DECADES WITHOUT EVER DEVELOPING CANCER. OUR CURRENT UNDERSTANDING OF WHAT FACTORS GOVERN THIS DECADES-LONG LATENCY AND EVENTUAL FAILURE IN AGED TISSUES ARE EXTREMELY LIMITED. A COMPELLING ARGUMENT TO DESCRIBE THIS IS TISSUE INTEGRITY IN TERMS OF ITS STRUCTURE AND FUNCTION, BOTH OF WHICH DECLINE WITH AGE, AND COULD EXPLAIN DIFFERENTIAL FITNESS FOR CELLS HARBORING ONCOGENIC MUTATIONS. OUR IGNORANCE OF THESE TISSUE DYNAMIC PROCESSES STEMS FROM OUR INABILITY TO PERFORM IN VIVO ANALYSIS OVER SUCH LONG- TIME FRAMES IN RELEVANT MOUSE MODELS. WE HYPOTHESIZE THAT CHRONIC LIVER DISEASE (CLD) CAN BE UNDERSTOOD AS AN ACCELERATED AGING OF THE LIVER THAT SIMILARLY ALTERS THE FITNESS LANDSCAPE, PROMOTING THE SELECTION OF MUTATED CELLS THAT PROGRESS TOWARDS HEPATOCELLULAR CARCINOMA (HCC). WE FOCUSED ON CTNNB1 ENCODING FOR Β-CATENIN, AS IT IS THE MOST FREQUENTLY MUTATED ONCOGENE IN HUMAN HCC, WITH ~30% OF PATIENTS HAVING ALTERATIONS THAT RENDER Β-CATENIN CONSTITUTIVELY ACTIVE. HOWEVER, THE PRECISE MECHANISMS BY WHICH Β-CATENIN MUTATIONS DRIVE HCC PROGRESSION REMAIN UNKNOWN. TO ADDRESS THIS KNOWLEDGE GAP, WE HAVE PERFORMED A LONG-TERM CLONAL LINEAGE TRACING OF HEPATOCYTES BEARING CTNNB1 ACTIVATING MUTATIONS IN BOTH THE NORMAL AND IN THE CHRONICALLY INJURED LIVER. BY COUPLING THIS TRACING SYSTEM WITH SINGLE CELL RNASEQ, WE DISCOVERED THAT IN THE NORMAL LIVER, Β- CATENIN MUTATED HEPATOCYTES ARE INCAPABLE OF UNDERTAKING A SINGLE CELL DIVISION, BUT INSTEAD LAST FOR MONTHS IN THE TISSUE THROUGH A LONG PROCESS OF CELLULAR ATTRITION AND ELIMINATION, WHICH WE HYPOTHESIZE IS PRIMARILY ATTRIBUTED TO ER STRESS AND MALADAPTIVE UPR. STRIKINGLY, IN THE CONTEXT OF CLD, WE FOUND THAT TISSUE INJURY UNLEASHED THE POTENTIAL OF Β-CATENIN MUTATED HEPATOCYTES TO CLONALLY EXPAND AND DRIVE THE DEVELOPMENT OF HCC TUMORS, SOLVING A LONGSTANDING CONUNDRUM IN THE FIELD. IMPORTANTLY, USING THE SAME LINEAGE TRACING SYSTEM, WE FOUND THAT Β- CATENIN MUTATED HEPATOCYTES IN NORMAL LIVERS OF AGED MICE CAN SIMILARLY UNDERGO CLONAL EXPANSION AS OBSERVED IN CLD. IN THIS PROPOSAL, WE WILL INVESTIGATE THE SPECIFIC MOLECULAR MECHANISMS THAT RESULT IN DIMINISHED CELLULAR FITNESS OF Β-CATENIN MUTATED HEPATOCYTES IN THE NORMAL LIVER AND CONVERSELY, WHAT MECHANISMS ARE BEHIND THE INCREASE IN CELLULAR FITNESS OF Β-CATENIN MUTATED HEPATOCYTES DURING CHRONIC LIVER DAMAGE. BY FOCUSING ON THESE MECHANISMS, WE EXPECT TO LAY THE GROUNDWORK FOR EXPLOITING THE VULNERABILITIES OF Β-CATENIN MUTATED HEPATOCYTES FOUND IN THE NORMAL LIVER WHILE BLOCKING THE STRENGTHS THEY ACQUIRE DURING CLD TO TACKLE THIS DEVASTATING DISEASE.

MECHANISM OF MITOTIC CHECKPOINT IN MAMMALIAN CELLS

STRUCTURAL PLASTICITY AND FUNCTIONAL INTERACTIONS OF THE SIGNALING ADAPTER NHERF

FIBROBLASTS SUPPORT THE GROWTH OF BRAIN METASTASIS BY RENDERING CANCER CELLS RESISTANT TO CHEMOTHERAPY AND INDUCING IMMUNOSUPPRESSION IN TUMOR MICROENVIRONMENT - PROJECT SUMMARY/ABSTRACT BRAIN METASTASIS (BRM) IS THE MOST COMMON INTRACRANIAL TUMOR IN ADULTS. DESPITE ADVANCED THERAPIES, BRM REMAINS A MAJOR CAUSE OF MORBIDITY AND MORTALITY IN PATIENTS WITH LUNG CANCER. THE MECHANISMS UNDERLYING BRM PROGRESSION AND IMMUNE EVASION REMAIN POORLY UNDERSTOOD. FIBROBLASTS ARE ABUNDANT IN THE LUNG CANCERS THAT HAVE METASTASIZED TO THE BRAIN, BUT FUNCTIONS OF FIBROBLASTS IN BRM ARE STILL NOT KNOWN. IN OUR PRELIMINARY STUDIES, METASTASIS-ASSOCIATED FIBROBLASTS (MAFS) PROMOTE BRM GROWTH THROUGH A SOLUBLE FORM OF PLACENTAL GROWTH FACTOR (PGF). MAF-DERIVED PGF PROTECT CANCER CELLS FROM TREATMENT WITH TYROSINE KINASE INHIBITORS (TKIS) AND INDUCE IMMUNOSUPPRESSIVE ENVIRONMENT IN BRM. BASED ON THESE OBSERVATIONS, WE PROPOSE THAT MAFS-DERIVED PGF SUPPORTS BRM GROWTH IN TWO WAYS: 1) DIRECTLY BY STIMULATING THE PROLIFERATION AND CHEMORESISTANCE OF CANCER CELLS; 2) INDIRECTLY BY INDUCING AN IMMUNOSUPPRESSIVE TUMOR MICROENVIRONMENT. THIS HYPOTHESIS WILL BE TESTED IN TWO SPECIFIC AIMS: 1) DETERMINE HOW MAF-DERIVED PGF DIRECTLY REGULATES THE PROLIFERATION AND TKI RESISTANCE OF CANCER CELLS IN BRM. 2) DETERMINE HOW MAF-DERIVED PGF CAUSES IMMUNOSUPPRESSION IN BRM. OUR STUDIES WILL ESTABLISH THE IMPORTANCE OF MAF-DERIVED PGF IN INDUCING TKI RESISTANCE AND IMMUNOSUPPRESSION IN BRM. PGF NEUTRALIZING ANTIBODIES EFFICIENTLY PENETRATE THE BRAIN, AND ALREADY SHOW PROMISE IN TREATING PRIMARY BRAIN TUMORS, BOTH IN PRECLINICAL STUDIES AND IN ONGOING CLINICAL TRIALS. OUR STUDIES WILL PROVIDE STRONG MECHANISTIC RATIONALE AND PAVE THE WAY FOR THERAPEUTIC USE OF PGF ANTIBODIES IN TREATING BRM.

INTERROGATING TYPE I INTERFERON SIGNALING IN BREAST CANCER BRAIN METASTASIS - PROJECT SUMMARY THE BRAIN IS ONE OF THE COMMON ORGANS FOR BREAST CANCER RECURRENCE. BREAST CANCER BRAIN METASTASIS IS INCREASINGLY BECOMING A SIGNIFICANT CLINICAL PROBLEM DUE TO ITS RISING INCIDENCE AND LIMITED EFFICACY OF EXISTING SYSTEMIC THERAPIES. METASTASIS IS THE CONSEQUENCE OF FAVORABLE INTERACTIONS BETWEEN THE INVADED CANCER CELLS AND THE MICROENVIRONMENT IN THE DISTAL ORGAN. TO CANCER CELLS, THE BRAIN HAS THE MOST UNIQUE MICROENVIRONMENT SINCE THE STROMAL CELLS IN THE BRAIN DO NOT EXIST IN ANY OTHER ORGANS. THIS EXPLAINS WHY THERAPEUTIC STRATEGIES, WHICH EFFICIENTLY DIMINISH PRIMARY AND NON-BRAIN METASTATIC BREAST TUMORS, ARE INEFFECTIVE IN CONTROLLING THE ESTABLISHED BRAIN LESIONS. OUR CURRENT WORK AIMS TO UNDERSTAND THE UNIQUE BRAIN METASTASIS MICROENVIRONMENT AND DELINEATE HOW IT FACILITATES METASTATIC OUTGROWTH. TYPE I INTERFERON (IFN) SIGNALING IS A WELL-RECOGNIZED ANTI-TUMOR PATHWAY. HOWEVER, EXPERIMENTS FROM OUR ANIMAL MODELS SHOW THAT TYPE I RESPONSE IN ASTROCYTES, THE UNIQUE BRAIN STROMAL CELLS, HAS A PRO-METASTATIC EFFECT IN THE BRAIN. BASED ON THESE FINDINGS, WE WILL FURTHER ADDRESS THE FOLLOWING QUESTIONS: 1) DEFINE THE UNDERLYING MECHANISMS IN HOW THE TYPE I IFN RESPONSE IN ASTROCYTES MEDIATES BRAIN METASTASIS. WE WILL TEST THE HYPOTHESIS THAT THE ACTIVATED IFN RESPONSE IN ASTROCYTES HELPS THE RECRUITMENT OF SPECIFIC IMMUNE CELLS INTO THE BRAIN LESIONS. 2) VALIDATE THE TYPE I IFN ACTIVATION AT DIFFERENT STAGES OF BRAIN METASTASIS. WE WILL APPLY THE TOP-NOTCH IMAGING TECHNIQUE IN OUR MOUSE MODELS TO DIRECTLY VISUALIZE CELLULAR AND MOLECULAR CHANGES AS THEY OCCUR IN REAL-TIME, AND VALIDATE THESE OBSERVATIONS IN CLINICAL SAMPLES. 3) INVESTIGATE THE THERAPEUTIC EFFECT OF INHIBITION OF IMMUNE CELL RECRUITMENT ON BRAIN METASTASIS. WE WILL NOT ONLY IDENTIFY THE DRUGGABLE TARGETS, BUT ALSO OPTIMIZE THE THERAPEUTIC WINDOWS IN OUR PRE-CLINICAL MOUSE MODELS. OVERALL, OUR IDEA IS THAT ONCE WE KNOW HOW THE BRAIN MICROENVIRONMENT HELPS CANCER GROWTH IN THE BRAIN, WE CAN FOCUS OUR EFFORTS ON STOPPING IT. OUR RESEARCH PROPOSAL WILL YIELD REAL AND ACTIONABLE TARGETS ON BRAIN MICROENVIRONMENT, INSTEAD OF ON CANCER CELLS, TO TREAT BRAIN METASTASIS. MORE IMPORTANTLY, OUR STUDIES ON TRACKING THE DYNAMIC CHANGES DURING BRAIN METASTATIC PROCESS WILL HELP IDENTIFY THE OPTIMAL THERAPEUTIC STRATEGIES TO EFFECTIVELY TREAT BRAIN METASTASIS AND MINIMIZE POTENTIAL SIDE EFFECT.

THERAPEUTICS OF XIAP DEGRADATION BY ZINC CHELATORS

THE ROLE OF HEF1 IN OVARIAN CANCER DEVELOPMENT, PROGRESSION, AND METASTASIS

IDENTIFYING STABILIZERS OF P53 USING POCKET COMPLEMENTARITY

POLY ADP-RIBOSE POLYMERASE IN CHROMATIN AND TRANSCRIPTIONAL REGULATION

INTERROGATING MRCK PROTEIN KINASES IN OVARIAN CANCER - THE MAJORITY OF RECURRENT OVARIAN CANCERS SPREAD TO THE PERITONEAL CAVITY IN THE FORM OF ASCITES, WHERE TUMOR CELLS GROW AS SPHEROIDS, AND METASTASIZE TO OTHER ORGANS CAUSING MORBIDITY AND DEATH. THE OVERALL GOAL OF THIS PROPOSAL IS TO DEFINE THE MECHANISMS BY WHICH PROTEIN KINASES CONTROL SPHEROID GROWTH AND METASTASIS OF OVARIAN CANCER CELLS, AND USE THIS INFORMATION TO DEVELOP KINASE INHIBITOR THERAPIES FOR THE TREATMENT OF RECURRENT OVARIAN CANCER. THE CDC42 DOWNSTREAM EFFECTOR PROTEIN KINASES MRCKΑ AND MRCKΒ (MRCKS) ARE HIGHLY EXPRESSED IN OVARIAN CANCER AND HAVE BEEN IMPLICATED IN CELL MIGRATION, INVASION AND METASTASIS. STRIKINGLY, WE RECENTLY DISCOVERED THAT INHIBITION OF MRCK IMPAIRED ACTIN CYTOSKELETON REMODELING AND FOCAL ADHESION ASSEMBLY BLOCKING CELL MIGRATION AND SPHEROID GROWTH AND INVASION OF OVARIAN CANCER CELLS, REVEALING MRCK AS A NEW AND UNTAPPED TARGET FOR THE TREATMENT OF RECURRENT OVARIAN CANCER. MOREOVER, OUR MOST RECENT FINDINGS SHOWED INHIBITION OF MRCK BLOCKED TUMOR GROWTH AND INDUCED TUMOR APOPTOSIS IN OVARIAN CANCER XENOGRAFTS AND ASCITES MODELS. NEVERTHELESS, THE MECHANISTIC BASIS FOR MRCK SUPPORT OF OVARIAN CANCER PATHOGENESIS REMAINS POORLY UNDERSTOOD. OUR OVERALL HYPOTHESIS IS THAT MRCKS CONTROL SPHEROID GROWTH AND INVASION OF OVARIAN CANCER CELLS THROUGH THE REGULATION OF ACTIN CYTOSKELETON REMODELING THAT INVOLVES THE PHOSPHORYLATION AND/OR INTERACTION WITH PROTEINS ASSOCIATED WITH ACTIN AND MYOSIN SIGNALING. TO TEST THIS HYPOTHESIS, WE HAVE DESIGNED TWO SPECIFIC AIMS, AIM 1: IDENTIFY MRCK PROTEIN INTERACTORS/SUBSTRATES THAT CONTRIBUTE TO OVARIAN CANCER USING PROTEOMICS STRATEGIES AND AIM 2: DETERMINE THE EFFECT OF MRCK INHIBITION ON SPHEROID VIABILITY AND INVASION USING IN VITRO AND IN VIVO OVARIAN CANCER MODELS. IN AIM 1, WE WILL PERFORM A FOCUSED ANALYSIS OF OUR CURRENT MRCK SUBSTRATE CANDIDATES USING PHOSPHOANTIBODIES AND MASS SPECTROMETRY IN 2D AND 3D CULTURES, AND WILL DECIPHER THE FUNCTION OF MRCK PHOSPHORYLATION EVENTS USING SITE-DIRECTED MUTAGENESIS. NEXT, WE WILL APPLY UNBIASED PROTEOMICS METHODS TO DEFINE ADDITIONAL INTERACTING PARTNERS, SUBSTRATES AND SIGNALING PATHWAYS CONTROLLED BY MRCK. TOGETHER, WE WILL ESTABLISH BONA FIDE MRCK SUBSTRATES AND WILL DEFINE THE MECHANISMS BY WHICH MRCK PROMOTE SPHEROID PROLIFERATION, SURVIVAL AND INVASION IN OVARIAN CANCER. IN AIM 2, WE WILL INHIBIT MRCK AND MONITOR VIABILITY, INVASION AND ACTIN REMODELING OF OVARIAN CANCER SPHEROIDS, ORGANOIDS AND ASCITES ISOLATED FROM PATIENTS WITH METASTATIC DISEASE. NEXT, USING A PANEL OF ORTHOTOPIC OVARIAN CANCER PATIENT-DERIVED XENOGRAFTS, WE WILL INHIBIT MRCK AND MEASURE IN VIVO TUMOR GROWTH, METASTASIS AND ASCITES. TOGETHER, THE WORK PROPOSED HERE WILL DEFINE THE MECHANISMS BY WHICH MRCKS PROMOTE OVARIAN CANCER GROWTH AND METASTASIS AND ESTABLISH MRCK AS A NEW TARGET IN RECURRENT OVARIAN CANCER.

ROBUST RATIONAL DESIGN OF CHEMICAL TOOLS TO INHIBIT RNA-BINDING PROTEINS

HYPERHOMOCYSTEINEMIA, S-ADENOSYLHOMOCYSTEINE ACCUMULATION, AND EPIGENETICS

IDENTIFYING INHIBITORS OF PROTEIN INTERACTIONS USING POCKET OPTIMIZATION

INTERPLAY BETWEEN DNA BASE EXCISION REPAIR AND TRANSCRIPTIONAL REGULATION - PROJECT SUMMARY GUANINE-RICH G-QUADRUPLEX (G4) FORMING SEQUENCES ARE ENRICHED AT PROMOTER PROXIMAL REGIONS OF THE GENOME, IN PARTICULAR THOSE OF CANCER AND DNA REPAIR-RELATED GENES. THESE REGIONS ARE HOT SPOTS FOR OXIDATIVE LESIONS SUCH AS 8OXOG, COUPLING THEIR REPAIR VIA THE BASE EXCISION REPAIR (BER) PATHWAY TO TRANSCRIPTIONAL REGULATION. UNFORTUNATELY, THE MOLECULAR LEVEL INTERACTIONS AND MECHANISTIC DETAILS OF THE COUPLED REPAIR AND GENE REGULATION ARE NOT WELL UNDERSTOOD, INCLUDING THE ROLE OF DNA STRUCTURAL DYNAMICS, THE PRECISE MECHANISMS OF REPAIR AND GENE ACTIVATION, THE ROLE OF THE N-TERMINAL INTRINSICALLY DISORDERED REGION AND REDOX MECHANISM OF BER PROTEIN APURINIC/APYRIMIDINIC ENDONUCLEASE 1 (APE1). MY GOAL AS THE LEADER OF MY INDEPENDENT RESEARCH PROGRAM AT FOX CHASE OVER THE NEXT FIVE YEARS IS TO EMPOWER AND SUPPORT A DIVERSE TEAM OF YOUNG SCIENTISTS TO CHARACTERIZE THE MOLECULAR-LEVEL INTERACTIONS AND COORDINATION EVENTS COUPLING THE REPAIR OF OXIDATIVE DNA DAMAGE AND GENE ENHANCEMENT AT G4 PROMOTERS IN RESPONSE TO OXIDATIVE DNA DAMAGE. THIS WILL INVOLVE IMPLEMENTING A MULTI-DISCIPLINARY APPROACH OF TECHNIQUES RANGING FROM STRUCTURAL BIOLOGY AND SINGLE-MOLECULE FLUORESCENCE TO CELL-BASED ASSAYS. BY FILLING THE CURRENT GAPS IN KNOWLEDGE I WILL POSITION MY RESEARCH PROGRAM TOWARD OUR LONG-TERM VISION OF DEVELOPING NOVEL THERAPEUTICS THAT CAN MODULATE TRANSCRIPTION OF KEY DISEASE-ASSOCIATED GENES THROUGH INTERFERING WITH THE KEY REGULATORY PROTEIN:PROTEIN AND/OR PROTEIN:DNA INTERACTIONS.

MECHANISTIC STUDIES OF GENOME FOLDING - PROJECT SUMMARY OVERVIEW: DURING INTERPHASE, THE COHESIN COMPLEX EXTRUDES CHROMATIN LOOPS TO MEDIATE THE FORMATION OF CHROMATIN DOMAINS AND LOOPS, WHICH ARE ELEMENTARY 3D STRUCTURES OF THE HUMAN GENOME AND GUIDE ENHANCER- PROMOTER INTERACTIONS. DISRUPTION TO THESE STRUCTURES CAN LEAD TO MANY DISEASES INCLUDING CANCER. OUR RESEARCH HAS SIGNIFICANTLY ADVANCED OUR UNDERSTANDING OF HOW COHESIN ACTIVELY EXTRUDE NATIVE CHROMATIN LOOPS. SPECIFICALLY, WE HAVE ACHIEVED THE FOLLOWING MILESTONES: 1) ESTABLISHED A SIMPLE YET VERY POWERFUL SYSTEM ENABLING MECHANISTIC STUDIES OF LOOP EXTRUSION IN NEAR-NATIVE NUCLEI UNDER HIGHLY CONTROLLED MANNERS. 2) UNCOVERED THAT COHESIN ENGAGES WITH CHROMATIN IN DISTINCT WAYS DEPENDENT ON THE STAGES OF LOOP EXTRUSION. 3) DISCOVERED DISTINCT BIOCHEMICAL AND CONFORMATION STATES OF COHESIN DURING LOOP EXTRUSION. GOALS: OUR PRELIMINARY RESULTS REVEALED A CORRELATION BETWEEN COHESIN’S BIOCHEMICAL STATES AND ITS ROLE IN GENOME FOLDING, AND ALSO DEMONSTRATED THE POWER OF OUR SEMI-IN VITRO SYSTEMS TO STUDY GENOME FOLDING. WE AIM TO USE THIS SYSTEM TO CAPTURE AND ANALYZE DISTINCT STATES OF COHESIN DURING THE HIGHLY DYNAMIC LOOP EXTRUSION PROCESS. OUR INNOVATIVE APPROACH ALSO AFFORDS US THE ABILITY TO ANALYZE ADDITIONAL COHESIN-DEPENDENT ACTIVITIES SUCH AS TRANSCRIPTION. WE PLAN TO ADDRESS FOUR MAJOR GAPS IN OUR UNDERSTANDING OF GENOME FOLDING AND ITS RELEVANCE IN CANCER. 1) HOW DOSE COHESIN ENGAGE WITH CHROMATIN? WE WILL USE SYNTHETIC VARIANTS OF COHESIN AND CTCF TO PROBE THE MOLECULAR CONNECTION BETWEEN CTCF BINDING AND COHESIN-CHROMATIN INTERACTIONS. 2) WHAT CHANGES OCCUR IN COHESIN'S COMPOSITION AND CONFORMATION DURING THE LOOP EXTRUSION PROCESS? WE WILL ESTABLISH A NOVEL ANALYTIC FRAMEWORK TO SYSTEMATICALLY EXPLORE DYNAMIC CHANGES OF COHESIN AND IDENTIFY NOVEL REGULATORS OF COHESIN. 3) HOW DOES COHESIN INTERPLAY WITH TRANSCRIPTION MACHINERY? WE WILL EMPLOY OUR METHODS TO ANALYZE COHESIN’S STATES DURING TRANSCRIPTION AND PROBE THE INTERPLAY BETWEEN GENOME FOLDING AND TRANSCRIPTION. 4) HOW DO CANCER-ASSOCIATED MUTATIONS WITHIN COHESIN AFFECT GENOME FOLDING AND FUNCTIONS. COHESIN MUTATIONS ARE STRONGLY ASSOCIATED WITH CANCER, BUT THEIR MECHANISMS OF ACTION REMAIN LARGELY UNCLEAR. WE WILL INTEGRATE OUR ANALYSES WITH ALPHAFOLD TO CONSTRUCT A PREDICTIVE MODEL AND ASSESS THE IMPACT OF CLINICALLY RELEVANT MUTATIONS WITHIN COHESIN ON GENOME FOLDING AND TRANSCRIPTION. VISION: OUR INNOVATIVE METHODOLOGIES NOT ONLY ENABLE THE FUNCTIONAL ANALYSIS OF COHESIN'S BIOCHEMICAL STATES (SUBUNIT COMPOSITION AND CONFORMATION SUCH AS ITS RING-LIKE STRUCTURE) DURING HIGHLY DYNAMIC ACTIVITIES LIKE LOOP EXTRUSION AND TRANSCRIPTION, BUT ALSO AFFORD A COMPREHENSIVE UNDERSTANDING OF GENOME FOLDING AND REGULATION, PARTICULARLY IN THE CONTEXT OF CANCER.

IMPACT OF SOCIAL DETERMINANTS OF HEALTH ON QUALITY OF LIFE AND TREATMENT-RELATED DECISION-MAKING IN ADVANCED PROSTATE CANCER

OVERCOMING RESISTANCE TO EGFR INHIBITORS IN ADVANCED HEAD AND NECK CANCERS

DELINEATING THE ROLE OF THE ACETYL-COA PATHWAY IN THE RESISTANCE TO ANTI-ANDROGEN THERAPY

THE PORPHOBILINOGEN SYNTHASE FAMILY

ASIAN AMERICAN COMMUNITY COHORT AND ENGAGEMENT STUDY (ACCESS) - BETWEEN 2000 AND 2020, ASIAN AMERICANS WERE THE FASTEST GROWING RACIAL GROUP IN THE US, INCREASING FROM 10.5 MILLION TO 24 MILLION INDIVIDUALS. STUDIES HAVE DOCUMENTED THAT ASIAN AMERICANS (AAS) EXPERIENCE CHRONIC DISEASE RATES THAT CONVERGE WITH OR EXCEED THOSE OF THE GENERAL US POPULATION; NOTABLY, AAS ARE AT HIGHER RISK FOR SEVERAL CARDIOMETABOLIC DISORDERS DESPITE HAVING LOWER RATES OF OBESITY. HOWEVER, DUE TO LIMITED DATA AND THE COMMON PRACTICE OF REPORTING AGGREGATED DATA ACROSS AA POPULATIONS, THE TRUE EXTENT AND NATURE OF THE HEALTH RISKS THAT EXIST ARE NOT WELL UNDERSTOOD. THUS, TO ADDRESS IMPORTANT GAPS IN THE FIELD, WE PROPOSE TO ESTABLISH THE ASIAN AMERICAN COMMUNITY COHORT AND ENGAGEMENT STUDY (ACCESS), WHICH WILL ENROLL OVER 2,000 ASIAN AMERICAN MEN AND WOMEN AGES 25-64 RECRUITED FROM ACROSS THE GREATER PHILADELPHIA-NEW JERSEY-NEW YORK CITY REGION. OUR MULTIDISCIPLINARY TEAM WILL LEVERAGE OUR 22-YEAR ESTABLISHED PA-NJ-NYC REGIONAL NETWORK OF COLLABORATIVE COMMUNITY-BASED ORGANIZATION PARTNERS, CLINICAL PROVIDERS, CITY HEALTH DEPARTMENTS, AND ACADEMIC INVESTIGATORS TO SUPPORT THE COHORT’S INFRASTRUCTURE, THE RECRUITMENT OF RESEARCH PARTICIPANTS, AND DATA COLLECTION ACTIVITIES. OUR TEAM HAS A STRONG AND SUCCESSFUL RECORD OF SCIENTIFIC PRODUCTIVITY AND EXPERTISE IN: 1) THE CONDUCT OF LONGITUDINAL COHORT STUDIES; 2) RIGOROUS ASSESSMENT OF DIETARY INTAKE AND OTHER HEALTH BEHAVIORS; 3) STANDARDIZED MEASURES OF PSYCHOSOCIAL FUNCTIONING, LIFESTYLE FACTORS, AND NEIGHBORHOOD ENVIRONMENT; 4) COLLECTION OF HIGH-QUALITY BIOSPECIMENS FOR ANALYSIS OF BIOLOGIC MARKERS; AND 5) ASSESSMENT OF CARDIOMETABOLIC OUTCOMES (E.G., HYPERTENSION, TYPE 2 DIABETES, CARDIOVASCULAR DISEASE). THE OVERALL OBJECTIVES OF THIS APPLICATION ARE TO ESTABLISH A RIGOROUS INFRASTRUCTURE OF ACCESS INCLUDING FORMALIZING CLINICAL/COMMUNITY PARTNERSHIPS, DEVELOPING COHORT INFRASTRUCTURE, AND ESTABLISHING STUDY PROTOCOLS TO SUPPORT THE STANDARDIZED COLLECTION OF COMPREHENSIVE PSYCHOSOCIAL, BEHAVIORAL, AND NEIGHBORHOOD-LEVEL DATA, ALONG WITH BIOSPECIMENS AND OTHER CLINICAL EXAMS. THE PROPOSED ACTIVITIES ARE CLOSELY ALIGNED WITH NHLBI’S STRATEGIC VISION AND WILL ADDRESS KEY RESEARCH QUESTIONS REGARDING HOW THE PREVALENCE OF CARDIOMETABOLIC DISORDERS VARIES ACROSS POPULATIONS AND THE IDENTIFICATION OF BEHAVIORAL AND BIOLOGIC PATHWAYS THAT MAY ACCOUNT FOR INDIVIDUAL OR GROUP DIFFERENCES IN DISEASE RISK. THIS SYNERGISTIC MULTIDISCIPLINARY PLAN TO ESTABLISH A PROSPECTIVE COMPREHENSIVE COHORT WILL YIELD A RICH RESOURCE TO SUPPORT RIGOROUS RESEARCH ON MULTI-LEVEL PATHWAYS CONTRIBUTING TO CARDIOMETABOLIC DISEASE RISK AND HEALTH OUTCOMES. STUDY FINDINGS WILL INFORM CLINICAL PRACTICE BY ILLUMINATING NOVEL RISK FACTORS AND WILL SUPPORT THE DEVELOPMENT OF MORE DATA-DRIVEN SCREENING, PREVENTION, AND INTERVENTION GUIDELINES THAT BENEFIT THE BROADER POPULATION.

DISSECTING THE ROLE OF THPOK IN THYMIC DEVELOPMENT AND T CELL DIFFERENTIATION

VALIDATION OF BLOOD-BASED PREDICTIVE BIOMARKERS OF THERAPEUTIC RESPONSE TO NEOADJUVANT CHEMORADIATION THERAPY IN PATIENTS WITH LOCALLY ADVANCED RECTAL CANCER - PROJECT SUMMARY/ABSTRACT NEOADJUVANT CHEMORADIATION THERAPY (NCRT) FOLLOWED BY SURGERY IS THE STANDARD OF CARE FOR PATIENTS WITH LOCALLY ADVANCED RECTAL CANCER (LARC), WHICH ACCOUNTS FOR ~60% OF NEWLY DIAGNOSED RECTAL CANCER CASES. ALTHOUGH NCRT BENEFITS MANY PATIENTS, IT IS CURRENTLY NOT KNOWN WHO WILL OR WILL NOT RESPOND FAVORABLY. ABOUT 20% PATIENTS THAT RECEIVE NCRT WILL EXPERIENCE A PATHOLOGIC COMPLETE RESPONSE (PCR), WHILE ~25% PATIENTS WILL EXHIBIT NO RESPONSE. RECENTLY, SEVERAL CLINICAL TRIALS HAVE ASSESSED NEW TREATMENT PARADIGMS, AND THEIR RESULTS PRESENT NEW TREATMENT STRATEGIES WHICH WERE PREVIOUSLY NOT AVAILABLE FOR LARC PATIENTS. WITH THE AVAILABILITY OF THESE NEW STRATEGIES, IT IS CRUCIAL TO BE ABLE TO A PRIORI IDENTIFY LARC PATIENTS, VIA A PREDICTIVE BIOMARKER, WHO HAVE A HIGHER LIKELIHOOD OF RESPONDING OR NOT RESPONDING TO NCRT. OUR GOAL IS TO OPTIMIZE AND VALIDATE AN EFFICIENT ASSAY THAT IS ACCURATE, PRECISE, AND MINIMALLY INVASIVE TO ASSESS BIOMARKER(S) THAT WILL PREDICT RESPONSE TO NCRT IN THE SETTING OF LARC. THE ASSAY THAT WILL BE VALIDATED IN THIS PROPOSAL IS A LUMINEX MULTIPLEXED ASSAY THAT USES THE XMAP TECHNOLOGY. WE HAVE DEFINED SIX CANDIDATE BIOMARKERS THAT WILL BE VALIDATED IN THIS STUDY. HERE, USING THE OPTIMIZED AND VALIDATED ASSAY WE WILL THEN ACHIEVE THE CLINICAL VALIDATION OF THE CANDIDATE BIOMARKER(S) IN A REAL-WORLD CLINICAL LABORATORY SETTING USING LARC PATIENT SPECIMENS. AT THE END OF THIS STUDY, WE WILL ACHIEVE A MINIMALLY INVASIVE, BLOOD-BASED ASSAY FOR PATIENT TREATMENT STRATIFICATION WHICH WILL BE OF TREMENDOUS BENEFIT TO LARC PATIENT(S) AND THE HEALTHCARE SYSTEM. USING THE XMAP ASSAY, WE ARE DETECTING CANDIDATE BIOMARKERS OF DNA DAMAGE RESPONSE (DDR) SIGNALING IN CELL LYSATES FROM CRYOPRESERVED PERIPHERAL BLOOD MONOCYTES (PBMCS) OF LARC PATIENTS. IN OUR PRELIMINARY WORK, THE CHANGE IN THE EXPRESSION OF THESE BIOMARKERS SIGNIFICANTLY ASSOCIATED WITH RESPONSE TO NCRT IN LARC PATIENTS. THESE CANDIDATE BIOMARKERS WERE IDENTIFIED THROUGH OUR RECENT HYPOTHESIS-DRIVEN TRANSLATIONAL STUDY FUNDED BY THE DOD. THIS PROPOSAL WAS DEVELOPED THROUGH A COLLABORATION BETWEEN THE TWO PRIMARY INVESTIGATORS BRINGING TOGETHER COMPLEMENTARY EXPERTISE. THE ASSEMBLED MULTI-DISCIPLINARY TEAM BRINGS TOGETHER EXPERTISE IN CLINICAL AND BASIC SCIENCE, ASSAY DEVELOPMENT/VALIDATION, AND THEIR CLINICAL DEPLOYMENT. HERE, WE WILL ANALYTICALLY VALIDATE OUR ASSAY (UH2 PHASE) AND THEN ESTABLISH THE CLINICAL VALIDITY BY USING BIOSPECIMENS FROM LARC PATIENTS (UH3 PHASE). THE BIOSPECIMENS USED ARE FROM LARC PATIENTS AND HEALTHY CONTROLS FROM THE FOX CHASE BIOSAMPLE REPOSITORY FACILITY, AND FROM LARC CLINICAL STUDIES/TRIALS EVALUATING THERAPEUTIC RESPONSE. IN THE UH2 PHASE WE WILL PERFORM PRE-ANALYTICAL (BIOSPECIMEN VARIABILITY) AND ANALYTICAL (E.G., PRECISION, ACCURACY) VALIDATION. IN THE UH3 PHASE, WE WILL ESTABLISH CLINICAL VALIDITY BY EVALUATING CLINICAL UTILITY PARAMETERS (E.G., SENSITIVITY/SPECIFICITY, OPTIMAL CUT-OFFS) AND COMPARE WITH NCRT RESPONSE STATUS. SUCCESSFUL COMPLETION WILL YIELD VALIDATED BIOMARKERS/ASSAYS FOR USE AS INVESTIGATIONAL ASSAYS IN CLINICAL TRIALS/STUDIES. OVER THE LONG-TERM, THIS WORK MAY IMPROVE PATIENT STRATIFICATION FOR TREATMENT IN LARC PATIENTS.

MECHANISM OF YFACT ACTION DURING CHROMATIN TRANSCRIPTION

IDENTIFYING DETERMINANTS OF PARP INHIBITOR SENSITIVITY IN OVARIAN CANCER

TARGETING ANOCTAMIN 6 TO DISRUPT TROGOCYTOSIS OF CANCER-ASSOCIATED FIBROBLASTS - PROJECT SUMMARY THE FIBROBLASTIC STROMA COMPRISES MOST OF PANCREATIC ADENOCARCINOMA MASS AND IS REMARKABLY DEVOID OF FUNCTIONAL BLOOD VESSELS. IT HAS BEEN ASSUMED THAT THE PANCREATIC CANCER CELLS OBTAIN THEIR ESSENTIAL METABOLITES, SUCH AS LIPIDS, DIRECTLY FROM THE INTERSTITIAL FLUID, BUT WE HAVE FOUND THAT THIS IS NOT THE CASE. INSTEAD, WE PRESENT EVIDENCE FROM OUR INTRAVITAL FLUORESCENT LDL PARTICLES TRACING EXPERIMENTS THAT PDAC TUMOR CELLS DERIVE THEIR LIPIDS DIRECTLY FROM CANCER-ASSOCIATED FIBROBLASTS (CAFS). WE HAVE DISCOVERED THAT CAFS FEED TUMOR CELLS LIPIDS VIA DIRECT TRANSFER OF MEMBRANES IN A PROCESS CALLED TROGOCYTOSIS (TROGO = ‘TO GNAW’ OR ‘NIBBLE’). WE HAVE ALSO FOUND THAT ANOCTAMIN 6 (ANO6) IS A UNIQUE PHOSPHOLIPID SCRAMBLASE EXPRESSED IN CAFS IN BOTH HUMAN AND MURINE PDAC WHICH IS CRITICAL FOR TROGOCYTOSIS AND FOR CANCER CELL SURVIVAL. TROGOCYTOSIS IS EXECUTED WHEN CANCER CELLS AND CAFS FORM SYNAPSE-LIKE PLASMA MEMBRANES CONTACTS (ONCOSYNAPSES). WITHIN THE ONCOSYNAPSE, PDAC CELLS INDUCE CYTOSOLIC CALCIUM INFLUX VIA ORAI CHANNELS (GREEK, ORAI, GATEKEEPERS) RESULTING IN PTDSER EXPOSURE ON CAFS. FINALLY, WE HAVE DISCOVERED THAT ANO6 IS CRITICAL FOR CAF MEMBRANE TROGOCYTOSIS BY CYTOTOXIC T CELLS (CTLS) AND IS HIGHLY IMMUNOSUPPRESSIVE. HERE, WE WILL TEST OUR CENTRAL HYPOTHESIS THAT ANO6 IS A SAFE AND EFFECTIVE TARGET IN PDAC TO DISRUPT DELIVERY OF EXOGENOUS LIPIDS TO CANCER CELLS AND REVERSE RESISTANCE TO IMMUNOTHERAPY IN THREE AIMS: AIM 1. HOW ANO6 ACTIVITY IS REGULATED IN CAF-CANCER CELL ONCOSYNAPSE? WE WILL FOCUS ON DELINEATING THE SIGNALING MECHANISM BY WHICH CANCER CELLS INDUCE INFLUX OF CALCIUM VIA ORAI CHANNELS TO THE CAF CYTOSOL AND ACTIVATE ANO6 LIPID SCRAMBLING, RESULTING IN PTDSER EXPOSURE AND TROGOCYTOSIS. AIM 2. HOW DOES BLOCKADE OF ANO6 PREVENT CAF TROGOCYTOSIS AND ANTAGONIZE CANCER GROWTH? IN THIS AIM, WE WILL ADDRESS THE MECHANISM BY WHICH ANO6 FUNCTIONS TO PROMOTE TROGOCYTOSIS. SUB-AIM 2.1 WILL TEST HOW ANO6 STRUCTURE REGULATES TROGOCYTOSIS IN CAFS AND SENSITIVITY TO ANO6 INHIBITORS. IN SUB-AIM 2.2, WE WILL TEST BLOCKADE OF ANO6 IN CAFS AS A THERAPEUTIC STRATEGY TO ANTAGONIZE CANCER GROWTH. AIM 3. DOES BLOCKING ANO6 ENHANCE ANTI-PDAC IMMUNITY? WE WILL DELINEATE THE ROLE OF ANO6 IN CAFS AS A REGULATOR OF CTL TROGOCYTOSIS IN CAF-IMPOSED IMMUNOSUPPRESSION. INTERFERENCE WITH THIS PATHWAY SHOULD INCREASE THE EFFICACY OF ANTI-CANCER IMMUNOTHERAPIES BY BLOCKING CHOLESTEROL TRANSFER FROM CAFS TO CTLS. WE HAVE ASSEMBLED A TEAM OF EXPERTS IN CANCER BIOLOGY AND LIPID METABOLISM (ASTSATUROV), CALCIUM SIGNALING (SOBOLOFF), AND IMMUNITY (FUCHS) TO EXECUTE THESE STUDIES. A SUCCESSFUL OUTCOME TO THESE STUDIES WILL DEFINE A PARADIGM OF COMBINED TARGETING OF ANO6, AND MEMBRANE LIPIDS DONATION TO REINVIGORATE CTLS, SUPPRESS GROWTH OF PDAC TUMORS AND INCREASE THEIR RESPONSES TO IMMUNOTHERAPY WITH GROUNDBREAKING RAMIFICATIONS FOR THE TREATMENT OF THIS INTRACTABLE MALIGNANCY.

EVALUATION OF IN VIVO OPTICAL IMAGING IN PANCREATIC AND OVARIAN CANCER PATIENTS

TARGETING P2X7 RECEPTOR IN RENAL CELL CARCINOMA

ASIAN AMERICAN COMMUNITY COHORT AND EQUITY STUDY (ACCESS) - PROJECT SUMMARY BETWEEN 2000 AND 2020, ASIAN AMERICANS WERE THE FASTEST GROWING RACIAL GROUP IN THE US, INCREASING FROM 10.5 MILLION TO 24 MILLION INDIVIDUALS. BY 2060, THE NUMBER OF US ASIANS IS PROJECTED TO RISE TO 46 MILLION, MORE THAN TRIPLE THEIR 2000 POPULATION. ALTHOUGH ASIAN AMERICANS (AAS) ARE COMMONLY VIEWED AS A 'MODEL MINORITY' BASED ON SOCIOECONOMIC AND HEALTH INDICATORS, AAS ACTUALLY HAVE CHRONIC DISEASE RATES THAT CONVERGE WITH OR EXCEED THOSE OF US WHITES AND ARE AT HIGHER RISK FOR SEVERAL CARDIOMETABOLIC DISORDERS DESPITE HAVING LOWER RATES OF OBESITY. HOWEVER, DUE TO LIMITED DATA AND THE COMMON PRACTICE OF REPORTING AGGREGATED DATA ACROSS MULTIPLE AA SUBGROUPS, THE TRUE EXTENT AND NATURE OF THE DISPARITIES THAT EXIST IS NOT WELL UNDERSTOOD. THUS, TO ADDRESS IMPORTANT GAPS IN THE FIELD, WE PROPOSE TO ESTABLISH THE ASIAN AMERICAN COMMUNITY COHORT AND EQUITY STUDY (ACCESS) SPANNING ACROSS THE GREATER PHILADELPHIA-NEW JERSEY-NEW YORK CITY REGION, WHICH WILL INCLUDE 2,400 MEN AND WOMEN AGES 25-64 DRAWN FROM 3 US ASIAN SUBGROUPS: CHINESE (N=800), VIETNAMESE (N=800), AND FILIPINO (N=800). OUR MULTIDISCIPLINARY TEAM WILL LEVERAGE OUR 22-YEAR ESTABLISHED PA-NJ-NYC REGIONAL NETWORK OF COLLABORATIVE COMMUNITY-BASED ORGANIZATION PARTNERS, CLINICAL PROVIDERS, CITY HEALTH DEPARTMENTS, AND ACADEMIC INVESTIGATORS TO SUPPORT THE COHORT’S INFRASTRUCTURE AND THE RECRUITMENT OF DIVERSE RESEARCH PARTICIPANTS WITH RESPECT TO NATIVITY, LANGUAGE, AND GENERATIONAL STATUS. WITH COLLABORATION FROM OUR ESTEEMED COMMUNITY ADVISORY BOARD AND SCIENTIFIC ADVISORY BOARD MEMBERS, OUR TEAM HAS A STRONG AND SUCCESSFUL RECORD OF SCIENTIFIC PRODUCTIVITY AND EXPERTISE IN: 1) THE CONDUCT OF COMMUNITY-ENGAGED LONGITUDINAL COHORT STUDIES WITH AA POPULATIONS; 2) RIGOROUS ASSESSMENT OF DIETARY INTAKE AND OTHER HEALTH BEHAVIORS AND LIFESTYLE FACTORS; 3) STANDARDIZED MEASURES OF SOCIAL DETERMINANTS OF HEALTH (SDOH) AND NEIGHBORHOOD-LEVEL EXPOSURES; 4) COLLECTION OF HIGH-QUALITY BIOSPECIMENS FOR ANALYSIS OF BIOLOGIC MARKERS; AND 5) ASSESSMENT OF CARDIOMETABOLIC OUTCOMES (E.G., HYPERTENSION, TYPE 2 DIABETES, CARDIOVASCULAR DISEASE). THE OVERALL OBJECTIVES OF THIS APPLICATION ARE TO ESTABLISH A RIGOROUS INFRASTRUCTURE OF ACCESS INCLUDING FORMALIZING CLINICAL/COMMUNITY PARTNERSHIPS, DEVELOPING COHORT INFRASTRUCTURE, AND ESTABLISHING STUDY PROTOCOLS TO SUPPORT THE STANDARDIZED COLLECTION OF COMPREHENSIVE PSYCHOSOCIAL, BEHAVIORAL, AND NEIGHBORHOOD-LEVEL DATA, ALONG WITH BIOSPECIMENS AND OTHER CLINICAL EXAMS. THE PROPOSED ACTIVITIES ARE CLOSELY ALIGNED WITH NHLBI’S STRATEGIC VISION AND WILL ADDRESS KEY RESEARCH QUESTIONS REGARDING HOW THE PREVALENCE OF CARDIOMETABOLIC DISORDERS VARIES ACROSS ASIAN ETHNIC SUBPOPULATIONS, HOW SDOH RELATES TO DISEASE RISK IN SPECIFIC SUBPOPULATIONS, AND THE IDENTIFICATION OF BEHAVIORAL AND BIOLOGIC PATHWAYS THAT MAY ACCOUNT FOR INDIVIDUAL OR GROUP DIFFERENCES IN DISEASE RISK. THIS SYNERGISTIC MULTIDISCIPLINARY PLAN TO ESTABLISH A PROSPECTIVE COMPREHENSIVE COHORT THAT INCLUDES 3 LARGE AA SUBGROUPS WILL YIELD A RICH RESOURCE TO SUPPORT RIGOROUS RESEARCH ON MULTI-LEVEL PATHWAYS CONTRIBUTING TO CARDIOMETABOLIC DISEASE RISK AND HEALTH OUTCOMES IN THESE LARGE AND GROWING, BUT UNDERSTUDIED POPULATIONS THAT EXPERIENCE SIGNIFICANT DISPARITIES.

CAS PROTEIN REGULATION OF EMT IN CANCER

ELIMINATING METASTATIC TRIPLE-NEGATIVE BREAST CANCER THROUGH FERROPTOSIS

DISCOVERY OF EPIGENETIC MARKS IN HUMAN CELLS BY HIGH THROUGHPUT SIRNA SCREENING

INHIBITION OF THE INTERFERON RESPONSE BY WEST NILE VIRUS

RESTORING PALB2 FUNCTION AS A MECHANISM OF PARPI RESISTANCE IN BRCA1-MUTANT EOC

HEPADNAVIRUS INFECTIONS AND LIVER CANCER

SIGNALING BY P21-ACTIVATED PROTEIN KINASES

COLLABORATIVE RESEARCH: EARLY STAGES OF PROTEIN FOLDING EXPLORED BY EXPERIMENTAL AND COMPUTATIONAL APPROACHES

THYROID HORMONE INHIBITS MEDULLOBLASTOMA GROWTH BY INDUCING TUMOR CELL DIFFERENTIATION - PROJECT SUMMARY/ABSTRACT MEDULLOBLASTOMA (MB) IS THE MOST COMMON MALIGNANT BRAIN TUMOR IN CHILDREN. DESPITE CONVENTIONAL TREATMENT INCLUDING SURGERY, CHEMOTHERAPY AND RADIATION, A SIGNIFICANT PROPORTION OF MB PATIENTS STILL SUCCUMBS TO THIS DISEASE. MOREOVER, ALMOST ALL PATIENTS SUFFER LONG-TERM SIDE EFFECTS OF THE AGGRESSIVE TREATMENT, SUCH AS HEARING LOSS AND COGNITIVE DEFICIT. IMPROVED STRATEGIES TO TREAT MB ARE URGENTLY NEEDED. THYROID HORMONE (TH) PLAYS AN IMPORTANT ROLE IN NORMAL BRAIN DEVELOPMENT, BUT THE POSSIBLE FUNCTION OF TH IN MB PATHOGENESIS IS STILL UNKNOWN. OUR RECENT STUDIES REVEALED AN UNANTICIPATED LINK BETWEEN TH SIGNALING AND MB PATHOGENESIS, WITH EXCITING THERAPEUTIC IMPLICATIONS FOR MB TREATMENT. IN OUR PRELIMINARY STUDIES, WE FOUND THAT TH INDUCES THE EXPRESSION OF NEUROD1, A HELIX-LOOP-HELIX TRANSCRIPTION FACTOR IN MB CELLS AND STIMULATES THE TERMINAL DIFFERENTIATION OF TUMOR CELLS. UPON THEIR DIFFERENTIATION, MB CELLS LOSE THEIR TUMORIGENIC POTENTIAL AND SECRETE GLUTAMATE INTERFERING WITH THE SURVIVAL OF SURROUNDING MB CELLS. TH-INDUCED DIFFERENTIATION INHIBITS MB CELL PROLIFERATION, AND REPRESSES MB GROWTH IN VIVO. BASED ON THESE OBSERVATIONS, WE HYPOTHESIZE THAT TH SUPPRESSES MB PATHOGENESIS THROUGH INDUCING TUMOR CELL DIFFERENTIATION. THIS HYPOTHESIS WILL BE TESTED IN THREE SPECIFIC AIMS: 1) EXAMINE HOW TH PROMOTES MB CELL DIFFERENTIATION; 2) EXAMINE HOW TUMOR CELL DIFFERENTIATION REPRESSES MB PATHOGENICITY; 3) TEST IF TH SIGNALING CAN BE EXPLOITED FOR MB THERAPY. OUR STUDIES WILL ELUCIDATE THE MECHANISMS UNDERLYING TERMINAL DIFFERENTIATION OF MB CELLS, AND ESTABLISH AN UNPRECEDENTED ASSOCIATION BETWEEN TH AND MB PROGRESSION, WHICH WILL PAVE THE WAY FOR TH AS A NEW THERAPEUTIC MODALITY FOR MB.

EXAMINING THE RELATIONSHIP BETWEEN COMMUNITY HISTORY AND PROSTATE CANCER DISPARITIES

PRE-BCR FUNCTION SELECTING NOVEL B CELL RECEPTORS IN CHRONIC LYMPHOCYTIC LEUKEMIA

TRAINING GRANT IN PRECISION CANCER CONTROL - PROJECT SUMMARY IN THE UNITED STATES, MORE THAN 40 PERCENT OF NEW CANCER CASES CAN BE ATTRIBUTED TO MODIFIABLE FACTORS. YET, DESPITE ADVANCES IN KNOWLEDGE REGARDING THE MULTILEVEL FACTORS ASSOCIATED WITH CANCER RISK, THE ANNUAL NUMBER OF CANCER CASES IS PREDICTED TO INCREASE NEARLY 50%, FROM 1.5 MILLION NEW CASES IN 2015 TO APPROXIMATELY 2.3 MILLION IN 2050. THUS, A GREATER EMPHASIS ON CANCER RISK REDUCTION AND CANCER CONTROL – ALONG WITH A HIGHLY TRAINED WORKFORCE IN THIS DOMAIN -- IS NEEDED TO COUNTER THIS PROJECTED INCREASE. RECENT ADVANCES IN PRECISION MEDICINE HAVE RESULTED IN GREAT OPTIMISM FOR POTENTIAL THERAPEUTIC OPTIONS AND MAY PROVIDE A ‘MODEL’ FOR HOW TO EVOLVE THE FIELD OF CANCER CONTROL. TO REALIZE THE FULL POTENTIAL OF PRECISION CANCER CONTROL, IT WILL BE IMPERATIVE TO NOT ONLY ASSESS BIOLOGIC PROPERTIES, BUT TO ALSO CONSIDER INDIVIDUAL VARIABILITIES IN BEHAVIORAL, LIFESTYLE, AND ENVIRONMENTAL FACTORS. AS A RESULT, PRECISION CANCER CONTROL RESEARCH REQUIRES MULTIDISCIPLINARY APPROACHES THAT ENABLE SEAMLESS INTEGRATION AND COLLABORATION TO INFORM OUR UNDERSTANDING OF HOW TO IDENTIFY THOSE INDIVIDUALS WHO ARE AT ELEVATED RISK OR WHO MIGHT BENEFIT FROM SPECIFIC, EFFECTIVE, AND IMPLEMENTABLE INTERVENTIONS. THUS, THERE IS A SIGNIFICANT NEED TO EQUIP THE NEXT GENERATION OF CANCER CONTROL SCIENTISTS WITH SKILLS REQUIRED TO: (1) PRECISELY CHARACTERIZE THE POPULATIONS AT INCREASED RISK FOR CANCER OR POOR OUTCOMES; (2) IDENTIFY THE MULTILEVEL FACTORS CONTRIBUTING TO ELEVATED RISK OR NEGATIVE OUTCOMES; AND (3) DEVELOP AND IMPLEMENT APPROPRIATE INTERVENTIONS TO EFFECTIVELY ADDRESS THOSE FACTORS. THIS APPLICATION FOR A NEW T32 POSTDOCTORAL TRAINING PROGRAM AT FOX CHASE CANCER CENTER IS DESIGNED TO PREPARE PHD AND MD POSTDOCTORAL FELLOWS TO CONDUCT INNOVATIVE RESEARCH IN PRECISION CANCER CONTROL WITH DIVERSE POPULATIONS. THE TRANSDISCIPLINARY TRAINING INCLUDES A COMPLEMENTARY PROGRAM OF DIDACTIC ACTIVITIES AND INTENSIVE MENTORED RESEARCH EXPERIENCES, WHICH WILL EQUIP TRAINEES TO LEAD INDEPENDENT CAREERS IN PRECISION CANCER CONTROL. THE PROGRAM FACULTY INCLUDE 25 MENTORS, ALL OF WHOM HAVE ESTABLISHED TRACK RECORDS OF OBTAINING PEER-REVIEWED FUNDING. WE PROPOSE TO ENROLL 2 POSTDOCTORAL FELLOWS EACH YEAR (FOR TWO-YEAR TERMS) OVER THE FIVE-YEAR AWARD. ALL FELLOWS WILL RECEIVE RIGOROUS TRAINING IN THE PRINCIPLES OF PRECISION CANCER CONTROL, RESEARCH DESIGN AND METHODOLOGY, GRANT-WRITING, RESPONSIBLE CONDUCT OF RESEARCH, AND CAREER/PROFESSIONAL SKILLS DEVELOPMENT. T32 MENTORS ARE DRAWN FROM A BROAD BASE OF EXCEPTIONAL CANCER CENTER FACULTY WITH A BREADTH OF EXPERTISE RANGING FROM MOLECULAR BIOLOGY, GENETICS, EPIDEMIOLOGY, BIOSTATISTICS, GEOSPATIAL TECHNOLOGY, PSYCHOLOGY, PUBLIC HEALTH, AND IMPLEMENTATION SCIENCE. THE RICH RESOURCES AVAILABLE AT FOX CHASE CANCER CENTER (FCCC) INCLUDE COMPREHENSIVE GENOMIC, BIOLOGIC, SOCIOCULTURAL, BEHAVIORAL, AND ENVIRONMENTAL-LEVEL DATA COMBINED WITH ADVANCED GEOSPATIAL AND STATISTICAL TOOLS THAT WILL ENABLE OUR FACULTY AND THEIR TRAINEES TO APPLY PRECISION CANCER CONTROL METHODS IN STRATEGIC EFFORTS TOWARD REDUCING CANCER RISK AND MORTALITY ACROSS DIVERSE POPULATIONS.

A MOUSE MODEL OF EPIGENETIC EVENTS IN MELANOMAGENESIS

DECIPHERING BRAIN STROMA-REGULATED IMMUNE MICROENVIRONMENT IN MELANOMA BRAIN METASTASIS MOD P00001 INCORPORATED TRANSFER OF AWARD TO INSTITUTE FOR CANCER RESEARCH AND DE-OB FUNDS OF $1,399.04

MOLECULAR TRIGGERS OF T HELPER LINEAGE CHOICE

HARNESSING ZBP1-DRIVEN CELL DEATH TO IMPROVE INFLUENZA VACCINE EFFICACY - PROJECT SUMMARY VACCINATION REPRESENTS THE MOST EFFECTIVE MEANS OF PREVENTING INFLUENZA A VIRUS (IAV) INFECTIONS. CURRENT APPROACHES TO IAV VACCINES PRIMARILY TARGET THE HA PROTEIN, BUT HA UNDERGOES SIGNIFICANT ANTIGENIC DRIFT AND IS THUS A POOR TARGET FOR LASTING HUMORAL IMMUNITY. AN ALTERNATIVE APPROACH TO DEVELOPING A UNIVERSAL IAV VACCINE IS TO TARGET INTERNAL VIRAL PROTEINS (SUCH AS THE NUCLEOPROTEIN), WHICH ARE ALSO HIGHLY CONSERVED BETWEEN MOST IAV STRAINS. A MAJOR ROADBLOCK TO THIS APPROACH, HOWEVER, IS A LACK OF ADJUVANTS THAT TRIGGER THE RIGHT KIND OF IMMUNE RESPONSE - A ‘TYPE I’ (OR TH1/CD8+ T-CELL DRIVEN) RESPONSE - TO THESE INTERNAL ANTIGENS. IN THIS PROPOSAL, WE OUTLINE A NEW STRATEGY THAT SEEKS TO HARNESS IMMUNOGENIC CELL DEATH AS A MEANS OF ACTIVATING TYPE I IMMUNITY TO IAV VACCINES. WE HAVE IDENTIFIED A HOST SIGNALING PATHWAY WHICH ACCOUNTS FOR ALMOST ALL IAV-ACTIVATED IMMUNOGENIC DEATH IN INFECTED CELLS, INCLUDING PRIMARY AIRWAY EPITHELIAL CELLS, MACROPHAGES AND DCS. THIS CELL DEATH PATHWAY IS INITIATED WHEN THE HOST SENSOR PROTEIN ZBP1 DETECTS IAV GENOMIC RNA AND ACTIVATES PARALLEL PATHWAYS OF PROGRAMMED NECROSIS (NECROPTOSIS) AND APOPTOSIS TO KILL THE INFECTED CELL AND INSTIGATE CD8+ T CELL-MEDIATED ADAPTIVE IMMUNE RESPONSES. ADDING TO THE ATTRACTIVENESS OF ZBP1-INITIATED CELL DEATH AS A VACCINE APPROACH ARE OUR DISCOVERIES, FIRST, THAT IAV PRODUCES A NEW FORM OF DOUBLE-STRANDED RNA - TERMED Z-RNA - TO ACTIVATE ZBP1. Z-RNA IS THUS A NEW PAMP, AND CAN BE READILY HARNESSED TO TRIGGER IMMUNOGENIC CELL DEATH AND ADJUVANT IAV VACCINES. SECOND, ZBP1 INITIATES NECROPTOSIS FROM THE NUCLEUS, RESULTING IN NUCLEAR ENVELOPE RUPTURE AND RELEASE OF HIGHLY-IMMUNOGENIC NUCLEAR DAMPS AND IAV ANTIGENS. NUCLEAR NECROPTOSIS IS EVEN MORE IMMUNOGENIC THAN CONVENTIONAL (CYTOPLASM-INITIATED) NECROPTOSIS. AS ZBP1-DRIVEN IMMUNOGENIC CELL DEATH (BOTH APOPTOSIS AND NUCLEAR NECROPTOSIS) IS IMPORTANT FOR EFFECTIVE ANTI-IAV CYTOTOXIC T CELL RESPONSES, OUR DISCOVERIES ALLOW US TO PROPOSE THAT Z-RNAS ARE POTENT NEW ADJUVANTS FOR ACTIVATING TYPE I IMMUNE RESPONSES TO IAV, AND THAT RECOMBINANT IAVS ENGINEERED TO PRODUCE Z-RNAS REPRESENT NEW TYPE I IMMUNITY-ACTIVATING VACCINES. IN THIS PROPOSAL, THREE LABS WITH STRONG EXPERTISE IN IAV CELL DEATH SIGNALING (BALACHANDRAN), RECOMBINANT IAV TECHNOLOGY (LANGLOIS), AND PATHOGENESIS/VACCINE STRATEGIES (LOPEZ) WILL UNITE TO IDENTIFY IAV-GENERATED Z-RNAS THAT ACTIVATE ZBP1 (AIM 1); DETERMINE WHICH STROMAL AND IMMUNE CELL TYPES DIE BY ZBP1-MEDIATED MECHANISMS TO INITIATE AND REGULATE EFFECTIVE ADAPTIVE IMMUNE RESPONSES (AIM 2); AND TEST IF TRIGGERING ZBP1-MEDIATED CELL DEATH WITH SYNTHETIC AND VIRUS-GENERATED Z-RNAS CAN BE LEVERAGED TO INFORM AND SUPPLY NEXT-GENERATION VACCINES CAPABLE OF PROVIDING EFFECTIVE CROSS-PROTECTIVE IMMUNITY TO IAV (AIM 3).

INVESTIGATING PALB2 MUTANT BREAST CANCER

IDENTIFYING REGULATORS OF PALB2 FUNCTION AND PARP INHIBITOR RESISTANCE IN TNBC

HARNESSING ZBP1-TRIGGERED CELL DEATH TO ENHANCE INFLUENZA VACCINE RESPONSIVENESS - PROJECT SUMMARY/ABSTRACT VACCINATION REPRESENTS THE MOST EFFECTIVE MEANS OF PREVENTING INFLUENZA A VIRUS (IAV) INFECTIONS. CURRENT APPROACHES TO IAV VACCINES PRIMARILY TARGET THE HA PROTEIN, BUT HA UNDERGOES SIGNIFICANT ANTIGENIC DRIFT AND IS THUS A POOR TARGET FOR LASTING HUMORAL IMMUNITY. AN ALTERNATIVE APPROACH TO DEVELOPING A UNIVERSAL IAV VACCINE IS TO TARGET INTERNAL VIRAL PROTEINS (SUCH AS THE NUCLEOPROTEIN), WHICH ARE ALSO HIGHLY CONSERVED BETWEEN MOST IAV STRAINS. A MAJOR ROADBLOCK TO THIS APPROACH, HOWEVER, IS A LACK OF ADJUVANTS THAT TRIGGER THE RIGHT KIND OF IMMUNE RESPONSE - A ‘TYPE I’ (OR TH1/CD8+ T-CELL DRIVEN) RESPONSE - TO THESE INTERNAL ANTIGENS. IN THIS PROPOSAL, WE OUTLINE A NEW STRATEGY THAT SEEKS TO HARNESS IMMUNOGENIC CELL DEATH AS A MEANS OF ACTIVATING TYPE I IMMUNITY TO IAV VACCINES. WE HAVE IDENTIFIED A HOST SIGNALING PATHWAY WHICH ACCOUNTS FOR ALMOST ALL IAV-ACTIVATED IMMUNOGENIC DEATH IN INFECTED CELLS, INCLUDING PRIMARY AIRWAY EPITHELIAL CELLS, MACROPHAGES AND DCS. THIS CELL DEATH PATHWAY IS INITIATED WHEN THE HOST SENSOR PROTEIN ZBP1 DETECTS IAV GENOMIC RNA AND ACTIVATES PARALLEL PATHWAYS OF PROGRAMMED NECROSIS (NECROPTOSIS) AND APOPTOSIS TO KILL THE INFECTED CELL AND INSTIGATE CD8+ T CELL-MEDIATED ADAPTIVE IMMUNE RESPONSES. ADDING TO THE ATTRACTIVENESS OF ZBP1-INITIATED CELL DEATH AS A VACCINE APPROACH ARE OUR DISCOVERIES, FIRST, THAT IAV PRODUCES A NEW FORM OF DOUBLE-STRANDED RNA - TERMED Z-RNA - TO ACTIVATE ZBP1. Z-RNA IS THUS A NEW PAMP, AND CAN BE READILY HARNESSED TO TRIGGER IMMUNOGENIC CELL DEATH AND ADJUVANT IAV VACCINES. SECOND, ZBP1 INITIATES NECROPTOSIS FROM THE NUCLEUS, RESULTING IN NUCLEAR ENVELOPE RUPTURE AND RELEASE OF HIGHLY-IMMUNOGENIC NUCLEAR DAMPS AND IAV ANTIGENS. NUCLEAR NECROPTOSIS IS EVEN MORE IMMUNOGENIC THAN CONVENTIONAL (CYTOPLASM-INITIATED) NECROPTOSIS. AS ZBP1-DRIVEN IMMUNOGENIC CELL DEATH (BOTH APOPTOSIS AND NUCLEAR NECROPTOSIS) IS IMPORTANT FOR EFFECTIVE ANTI-IAV CYTOTOXIC T CELL RESPONSES, OUR DISCOVERIES ALLOW US TO PROPOSE THAT Z-RNAS ARE POTENT NEW ADJUVANTS FOR ACTIVATING TYPE I IMMUNE RESPONSES TO IAV, AND THAT RECOMBINANT IAVS ENGINEERED TO PRODUCE Z-RNAS REPRESENT NEW TYPE I IMMUNITY-ACTIVATING VACCINES. IN THIS PROPOSAL, THREE LABS WITH STRONG EXPERTISE IN IAV CELL DEATH SIGNALING (BALACHANDRAN), RECOMBINANT IAV TECHNOLOGY (LANGLOIS), AND PATHOGENESIS/VACCINE STRATEGIES (LOPEZ) WILL UNITE TO IDENTIFY IAV-GENERATED Z-RNAS THAT ACTIVATE ZBP1 (AIM 1); DETERMINE WHICH STROMAL AND IMMUNE CELL TYPES DIE BY ZBP1-MEDIATED MECHANISMS TO INITIATE AND REGULATE EFFECTIVE ADAPTIVE IMMUNE RESPONSES (AIM 2); AND TEST IF TRIGGERING ZBP1-MEDIATED CELL DEATH WITH SYNTHETIC AND VIRUS-GENERATED Z-RNAS CAN BE LEVERAGED TO INFORM AND SUPPLY NEXT-GENERATION VACCINES CAPABLE OF PROVIDING EFFECTIVE CROSS-PROTECTIVE IMMUNITY TO IAV (AIM 3).

THE ROLE OF CDON IN OVARIAN CARCINOMA

A NOVEL ALLELE-SPECIFIC RNA-ISH FOR DIFFERENTIAL ALLELE-SPECIFIC EXPRESSION

INTRATUMOR HETEROGENEITY AS A CORRELATE OF CLINICAL OUTCOME IN PATIENTS AVOIDING RADICAL CYSTECTOMY - PROJECT SUMMARY/ABSTRACT IN 2025, PATIENTS AND PHYSICIANS ARE SEEKING TO AVOID RADICAL CYSTECTOMY - A LIFE ALTERING, COMPLICATED, AND EXPENSIVE SURGERY THAT IS OFTEN EMPLOYED IN THE EFFORT TO CURE BLADDER CANCER - IN SITUATIONS WHERE COMPLETE RESPONSE TO NEOADJUVANT THERAPY HAS BEEN ACHIEVED. TO ADDRESS THIS DESIRE, TWO CLINICAL TRIALS TESTING APPROACHES TO SELECT PATIENTS FOR CYSTECTOMY AVOIDANCE HAVE NOW BEEN COMPLETED AT FOX CHASE. UNFORTUNATELY, MANY SUBJECTS WHO WERE DEEMED TO HAVE HAD COMPLETE CLINICAL RESPONSE EXPERIENCED SIGNIFICANT LOCAL OR DISTANT RECURRENCES THOUGH. BETTER TOOLS FOR SELECTION OF PATIENTS AND FOR SURVEILLANCE OF PATIENTS WHO AVOID RADICAL CYSTECTOMY ARE NEEDED. TO THIS END, THE GENETIC EVOLUTION OF CANCERS PRIOR TO AND DURING CHEMOTHERAPY LIKELY IMPACTS PATIENT CLINICAL OUTCOME/RECURRENCE RISK. WE AND OTHERS HAVE MOLECULAR SIGNATURES OF ENDOGENOUS AND EXOGENOUS MUTAGENIC PROCESSES SHAPE THE BLADDER CANCER GENOME. APOBEC3 IS A HUMAN PROTEIN WHOSE FUNCTION IS TO ENHANCE IMMUNITY THROUGH ITS MUTAGENIC FUNCION. THE UNINTENDED CONSEQUENCE OF THIS PROTECTIVE FUNCTION IS THE MOST PREVALENT ENDOGENOUS MUTAGENIC PROCESS THAT CAUSES BLADDER CANCER. SIMILARLY, CISPLATIN IS KNOWN TO CAUSE DNA DAMAGE AND RESULT IN MUTAGENESIS, AND THIS EXOGENOUS PROCESS ALSO RESULTS IN WIDESPREAD DNA ALTERATION. THE MOLECULAR SIGNATURES THAT RESULT FROM THESE TWO PROCESSES WILL BE STUDIED IN DETAIL DURING THIS PROPOSAL AND USED TO INFER THE ORIGIN OF LOCAL RECURRENCE IN PATIENTS WITH CLINICAL COMPLETE RESPONSE TO CHEMOTHERAPY (IN AIM 1) AND TO DEVELOP BIOMARKERS THAT ARE POSITIONED TO TRANSLATE THESE EXPERIMENTS INTO CLINICAL REALITY (IN AIM 2). THE SCIENTIFIC HYPOTHESIS THAT UNDERGIRDS THIS PROJECT IS THAT THESE MUTAGENIC PROCESSES RESULT IN INCREASED GENETIC HETEROGENEITY PROMOTING RECURRENCE, CHEMORESISTANCE, AND METASTASIS. THE GOAL OF THIS PROJECT IS THEREFORE TO QUANTIFY THESE TWO MUTAGENIC SIGNATURES OVER THE LIFETIME OF SUBJECTS ENROLLED IN CYSTECTOMY AVOIDANCE CLINICAL TRIALS TO DETERMINE THE GENETIC ORIGIN OF RECURRENCES AND TO DEVELOP URINARY BIOMARKERS OF RECURRENCE. RECURRENCES MAY ORIGINATE FROM SUBCLINICAL RESIDUAL DISEASE OR FROM NEW PRIMARIES THAT ARISE AT REMOTE LOCATIONS WITHIN THE BLADDER, AND WE WILL USE DEEP WHOLE GENOME SEQUENCING TO DISTINGUISH THESE ORIGIN STORIES. WE WILL USE THE SAME APPROACH TO DEVELOP URINE BIOMARKERS THAT QUANTITATE RELEVANT MUTAGENIC PROCESSES AND GENETIC HETEROGENEITY AND THEN MEASURE ASSOCIATIONS BETWEEN HETEROGENEITY AND CLINICAL OUTCOME WITH THE INTENT TO TRANSLATE THIS KNOWLEDGE TO THE NEXT ITERATION OF CLINICAL TRIALS EVALUATING NEW CYSTECTOMY AVOIDANCE APPROACHES.

REPAIR OF OXIDATIVE DAMAGE IN G-QUADRUPLEX PROMOTER DNA - PROJECT SUMMARY/ABSTRACT ENVIRONMENTAL EXPOSURES AND LIFESTYLE CHOICES CAN RESULT IN CELLULAR OXIDATIVE STRESS, CHARACTERIZED BY THE GENERATION OF AN ABUNDANCE OF REACTIVE OXYGEN SPECIES (ROS). ROS WREAK HAVOC ON THE STRUCTURE OF DNA BASES, WITH GUANINE MODIFICATION YIELDING THE LESION 8-OXO-7,8- DIHYDROGUANINE (8OXOG) BEING PARTICULARLY PREVALENT. IF NOT REPAIRED, 8OXOG IS MUTAGENIC, CAUSING G TO T TRANSVERSION MUTATIONS THAT CAN INITIATE AND PROMOTE HUMAN DISEASE. GUANINE-RICH G- QUADRUPLEX (G4) FORMING SEQUENCES ARE ENRICHED AT PROMOTER PROXIMAL REGIONS OF THE GENOME, MAKING THESE REGIONS HOT SPOTS FOR 8OXOG LESIONS. THE REPAIR OF 8OXOG BY THE BASE EXCISION REPAIR (BER) PATHWAY ON G4 PROMOTER SEQUENCES (I.E., VEGF) CAN MODULATE TRANSCRIPTION, HOWEVER THE MOLECULAR LEVEL INTERACTIONS AND MECHANISTIC DETAILS OF THE REPAIR ACTIVITY WITHIN THE G4 PROMOTER CONTEXT ARE NOT WELL UNDERSTOOD. THE OVERALL GOAL OF THE PROPOSED RESEARCH IS TO CHARACTERIZE THE MOLECULAR LEVEL INTERACTIONS AND COORDINATION EVENTS COUPLING THE REPAIR OF 8OXOG AND GENE ENHANCEMENT AT THE VEGF PROMOTER IN RESPONSE TO OXIDATIVE STRESS. THE EXPERIMENTS PROPOSED TO ADDRESS THIS WILL BE CONDUCTED IN TWO PHASES. DURING THE INITIAL MENTORED K99 PHASE, X-RAY CRYSTALLOGRAPHY, ADVANCED NUCLEIC ACID KINETICS, SINGLE-MOLECULE FLUORESCENCE, AND A HUMAN CELL- BASED TRANSCRIPTION ASSAYS WILL BE UTILIZED TO CHARACTERIZE THE ACTIVITIES OF APE1 AND POLSS ON THE VEGF G4 PROMOTER (AIM 1). WHILE IN THE MENTORED PHASE, THE CANDIDATE WILL ALSO TAKE ADVANTAGE OF THE RESOURCES AVAILABLE AT UNIVERSITY OF KANSAS MEDICAL CENTER FOR PROFESSIONAL DEVELOPMENT AND WILL CONTINUOUSLY APPLY THESE SKILLS THROUGH STRUCTURED TEACHING, MENTORING, DATA PRESENTATION, AND WRITING OPPORTUNITIES. DURING THE NON-MENTORED PHASE (R00) OF THE PROJECT, TECHNICAL SKILLS THE CANDIDATE HAS GAINED WILL BE USED TO ELUCIDATE A MODEL FOR THE RECRUITMENT OF TRANSCRIPTION FACTORS TO THE VEGF G4 PROMOTER SEQUENCE (AIM 2). ALSO, DURING THE R00 PHASE THE CANDIDATE WILL EXTEND THESE APPROACHES TO INTERROGATE HOW BER IS COMPLETED ON THE UNIQUE G4 SUBSTRATE AND ELUCIDATE THE EXTENT OF COUPLING BETWEEN REPAIR AND TRANSCRIPTION (AIM 3). THESE EXPERIMENTS WILL PROVIDE THE CANDIDATE WITH THE DATA REQUIRED FOR AN EARLY INDEPENDENT PUBLICATION AND PRELIMINARY DATA FOR R-SERIES GRANTS. IMPORTANTLY, DURING THE R00 PHASE THE CANDIDATE WILL DEVELOP INDEPENDENCE FROM THEIR MENTOR BY FOCUSING ON THE INTERPLAY BETWEEN DNA REPAIR AND TRANSCRIPTION REGULATION AND SHIFTING THEIR WORK TO STUDY THE EPIGENETIC-LIKE ROLE OF OXIDATIVE DNA LESIONS AS TRANSCRIPTION MODULATORS THROUGH DNA REPAIR.

INVESTIGATING THERAPEUTIC RESPONSE DISPARITIES IN LOCALLY ADVANCED RECTAL CANCER

NF130108: TESTING THE ROLE OF P21 ACTIVATED KINASES IN SCHWANNOMA FORMATION USING A NOVEL GENETICALLY ENGINEERED MURINE MODEL THAT CLOSELY PHENOCOPIE

EMPOWERING THE NEXT GENERATION OF CANCER PROFESSIONALS: THE FOX CHASE CANCER CENTER-UNIVERSITY OF DELAWARE PARTNERSHIP FOR UNDERGRADUATE RESEARCH AND CAREER DEVELOPMENT - PROJECT SUMMARY THE NUMBER OF CANCER HEALTHCARE PROVIDERS AND RESEARCHERS IS NOT EXPECTED TO KEEP PACE WITH THE AGING POPULATION OF THE UNITED STATES, CREATING AN IMPERATIVE TO EDUCATE AND MOTIVATE THE NEXT GENERATION OF CANCER PROFESSIONALS. EXPERIENTIAL RESEARCH LABORATORY INTERNSHIPS HAVE BEEN SHOWN TO BE AN IMPACTFUL WAY TO INCENTIVIZE STUDENTS TOWARD CAREERS IN CANCER RESEARCH, BUT OFTEN SUCH PROGRAMS ARE LIMITED IN NUMBER AND SCOPE, THUS IMPEDING THEIR POTENTIAL TO INFLUENCE UNDERGRADUATE COURSE SELECTION AND LONG-TERM CAREER GOALS. MOREOVER, SUCH EXPERIENCES DO NOT EMPHASIZE CRITICAL ANCILLARY SKILLS, SUCH AS SCIENTIFIC LITERACY, DESIGNING AND PRESENTING POSTERS AND SEMINARS, AND NETWORKING. THE FOX CHASE CANCER CENTER-UNIVERSITY OF DELAWARE SUMMER FELLOWSHIP PROGRAM SEEKS TO PROVIDE TWELVE UNDERCLASSMEN WITH A RESIDENTIAL, INTENSIVE 10-WEEK SUMMER INTERNSHIP FOCUSED ON BASIC LABORATORY SKILL ACQUISITION, A CANCER RESEARCH EXPERIENCE TAILORED TO THE STUDENT'S INTERESTS, AND COMPLEMENTARY TRAINING AND GUIDANCE IN PROFESSIONAL DEVELOPMENT. STUDENTS WILL BE RECRUITED TO THIS PROGRAM VIA AN INTRODUCTORY, DAY-LONG EXPOSURE TO THE CENTER, WHICH WILL INCLUDE BRIEF RESEARCH LABORATORY ROTATIONS AND DISCUSSION OF CANCER-FOCUSED, STEM-BASED CAREERS; THIS INTRODUCTORY VISIT IS OPEN TO ALL UNIVERSITY OF DELAWARE STUDENTS IN THE COLLEGE OF ARTS AND SCIENCES. METRICS OF PROGRAMMATIC SUCCESS WILL BE OBTAINED THROUGH WEEKLY MEETINGS WITH MENTORS AND STUDENTS, PRE- AND POST-INTERNSHIP EVALUATIONS, AND LONG- TERM TRACKING OF STUDENT CAREER DECISIONS. THROUGH THIS PROGRAM, WE AIM TO INCORPORATE STUDENTS INTO THE CANCER RESEARCH COMMUNITY, INSPIRE THEM TO PURSUE CAREERS THAT ARE CRITICAL IN THE ONGOING BATTLE AGAINST CANCER, AND EQUIP THEM WITH THE TOOLS REQUIRED TO SUCCEED AS PROFESSIONALS.

POSITIVE ACTIVITIES FOR ASIAN AMERICAN CANCER PATIENTS AND CAREGIVERS - PROJECT SUMMARY/ABSTRACT ASIAN AMERICANS (AAS) ARE THE FASTEST GROWING MINORITY GROUP IN THE U.S., AND CANCER IS THE LEADING CAUSE OF DEATH AMONG THIS GROUP. ALTHOUGH AA WHO ARE DIAGNOSED WITH CANCER COMMONLY REPORT FEAR, DISTRESS, AND DEPRESSION, THEY HAVE BEEN FOUND TO UTILIZE MENTAL HEALTH SERVICES AT LOWER RATES THAN OTHER GROUPS AND THIS MAY BE DUE TO A DEARTH OF CULTURALLY-COMPETENT SERVICES. PRIOR RESEARCH ON THESE CANCER PATIENTS’ LIVES HAS FOCUSED ON BARRIERS ASSOCIATED WITH HEALTH LITERACY AND LANGUAGE PROFICIENCY BUT HAS IGNORED UNIQUE CULTURE- RELATED CHALLENGES THAT CONTRIBUTE TO THEIR POOR EMOTIONAL OUTCOMES. AAS ARE MEMBERS OF COLLECTIVIST CULTURES WHO VIEW THEMSELVES AS CONNECTED, RELATIONAL, AND BELONGING TO A LARGER SOCIAL GROUP. FOLLOWING CHANGES IN PHYSICAL FUNCTION AND SOCIAL ROLES AND RESPONSIBILITIES (E.G., JOB LOSS) AFTER A CANCER DIAGNOSIS, INDIVIDUALS MAY SELF-PERCEIVE THAT THEY ARE A BURDEN ON THEIR FAMILY MEMBERS/CAREGIVERS. THEREFORE, THE OVERARCHING GOAL OF THE CURRENT PROPOSAL IS TO REDUCE THE BURDEN AA PATIENTS MAY FEEL THEY ARE ON THEIR CAREGIVERS BY DESIGNING AND TESTING THE FEASIBILITY OF TWO POSITIVE ACTIVITY INTERVENTIONS. WE EXPECT THAT CONTRIBUTING TO ONE’S HOUSEHOLD AND OUTSIDE ONE’S HOME WILL INCREASE HEALTH-RELATED QUALITY OF LIFE (HRQOL) IN AA CANCER PATIENTS BY INCREASING A SENSE OF RELATEDNESS, AUTONOMY, AND COMPETENCE (MEDIATORS). IN THE K99 PHASE, 30 AAS AGES 25-70 AND WITHIN 1 YEAR OF ANY CANCER DIAGNOSIS WILL ENGAGE IN EITHER: 1) HOUSEHOLD CONTRIBUTION; 2) OUTSIDE CONTRIBUTION; OR 3) CONTROL ACTIVITIES. QUANTITATIVE AND QUALITATIVE (E.G., SEMI-STRUCTURED INTERVIEW, PROJECT PERSONNEL WORK LOGS) DATA ABOUT THE SUCCESSFUL ELEMENTS OF THE INTERVENTIONS WILL BE COLLECTED. IN COLLABORATION WITH THE MENTORSHIP TEAM, AA COMMUNITY MEMBERS, AND CLINICIANS, A PROTOTYPE OF ONE OR BOTH POSITIVE ACTIVITY INTERVENTIONS (HOUSEHOLD OR OUTSIDE CONTRIBUTION) WILL BE DEVELOPED FOR AA CANCER PATIENTS. IN THE R00 PHASE, 118 PATIENTS (SAME INCLUSION CRITERIA AS K99 PHASE) WILL BE RANDOMIZED TO EITHER THE CONTRIBUTION OR CONTROL GROUP. THEY WILL ENGAGE IN THE POSITIVE OR CONTROL ACTIVITY ONCE PER WEEK FOR 3 MONTHS, AND OUTCOMES AND MEDIATORS WILL BE ASSESSED AT BASELINE, 1.5 MONTHS (MIDPOINT), 3 MONTHS (POST-TEST), AND 6 MONTHS (FOLLOW-UP). THE TRIAL WILL: 1) ASSESS THE FEASIBILITY AND ACCEPTABILITY OF THE HOUSEHOLD AND OUTSIDE CONTRIBUTION POSITIVE ACTIVITIES, 2) DEVELOP A PROTOTYPE OF A POSITIVE ACTIVITY INTERVENTION (HOUSEHOLD OR OUTSIDE CONTRIBUTION) FOR AA CANCER PATIENTS, 3) ASSESS CHANGES IN HRQOL COMPARING INTERVENTION TO CONTROL PATIENTS, AND 4) ASSESS MEDIATORS OF THE INTERVENTION EFFECTS. THIS PROPOSAL INTRODUCES A NOVEL, LOW COST, NOT STIGMATIZING, EASY TO IMPLEMENT, AND HIGHLY SCALABLE APPROACH NOT PREVIOUSLY TESTED IN AA CANCER PATIENTS: ENGAGING IN POSITIVE ACTIVITIES. IF FOUND TO BE SUCCESSFUL, THIS FRAMEWORK FOR UNDERSTANDING PATIENT-CAREGIVER RELATIONSHIPS IN AAS CAN BE USED TO DEVELOP OTHER POSITIVE ACTIVITIES THAT WILL IMPROVE AND EXTEND THE LIVES OF CANCER PATIENTS FROM OTHER COLLECTIVIST CULTURES. THE PROPOSED TRAINING PLAN WILL BE CRITICAL IN EXPEDITING THE CANDIDATE’S TRANSITION INTO AN INDEPENDENT INVESTIGATOR WITH FOCUSED EXPERTISE IN DEVELOPING POSITIVE ACTIVITIES TO ELIMINATE CANCER CARE DISPARITIES IN AAS.

DEFINING THE MOLECULAR BASIS CONTROLLING HEMATOPOIETIC STEM CELL SYMMETRIC AND ASYMMETRIC DIVISIONS - PROJECT SUMMARY AND ABSTRACT HEMATOPOIETIC STEM CELLS (HSCS) MAINTAIN BLOOD HOMEOSTASIS THROUGH A DELICATE BALANCE IN FATE CHOICES OF SELF-RENEWAL AND COMMITMENT TO DIFFERENTIATION. AN IMBALANCE IN HSC FATE CHOICES IS THE KEY CONTRIBUTOR TO HEMATOLOGIC DISEASES THAT AFFECT MILLIONS OF PEOPLE. HSC FATE CHOICES IS MAINTAINED BY COORDINATED SYMMETRIC SELF-RENEWAL, SYMMETRIC COMMITMENT AND ASYMMETRIC DIVISIONS. THUS, UNDERSTANDING THE CONTROL OF HSC DIVISION CHOICES HOLDS THERAPEUTIC POTENTIAL FOR HEMATOPOIETIC DISEASES. HOWEVER, OUR KNOWLEDGE ON THE CONTROL OF HSC DIVISIONS IS STILL LACKING. HERE, I AIM TO FILL THE GAP BY IMPLEMENTING NOVEL SYSTEMS AND HIGH-THROUGHPUT ASSAYS TO INTERROGATE HSC FATE CHOICES. WE RECENTLY REVEALED A UNIQUE ROLE OF M6A RNA METHYLATION THAT IS ESSENTIAL FOR HSC SYMMETRIC COMMITMENT, THE DIVISION CHOICE THAT IS CRITICAL FOR THE RAPID REPLENISHMENT OF MATURE BLOOD CELLS UPON STRESS. HENCE, I PROPOSE TO LEVERAGE THE M6A DEFICIENT HSCS AS A NOVEL SYSTEM TO ELUCIDATE THE M6A-ASSOCIATED MOLECULAR PROGRAMS IN CONTROLLING HSC SYMMETRIC COMMITMENT. TO UNCOVER NOVEL REGULATORS IN HSC FATE CHOICES, I AIM TO DEFINE THE ROLE OF THE UNDERSTUDIED RBP NYNRIN, WHICH IS A STEMNESS FACTOR IDENTIFIED FROM MY PRELIMINARY DATA AND OUR RECENT AML-IPSC STUDY, IN CONTROLLING HSC DIVISIONS. I ALSO AIM TO IMPLEMENT FATE-SEQ, A NOVEL METHOD INVOLVES HSC BARCODING FOLLOWED BY IN VITRO DIVISION AND SINGLE CELL RNASEQ THAT ALLOWS FOR A GLOBAL ASSESSMENT OF HSC DIVISIONS. FATE-SEQ AS AN ORTHOGONAL SYSTEM WILL IDENTIFY NOVEL REGULATORS OF HSC FATE CHOICES. THE SPECIFIC AIMS ARE: (1): CHARACTERIZE THE HSC-LIKE INTERMEDIATE STATE CONTROLLED BY M6A RNA METHYLATION. (2): DETERMINE THE MOLECULAR PROGRAMS DRIVEN BY M6A RNA METHYLATION IN CONTROLLING HSC SYMMETRIC COMMITMENT. (3): UNCOVER NOVEL REGULATORS IN HSC SYMMETRIC AND ASYMMETRIC FATE DECISIONS. SUCCESS OF THIS WORK WILL DEFINE THE NOVEL REGULATORS OF HSC FATE CONTROL AND PROVIDE NOVEL THERAPEUTIC OPPORTUNITIES FOR HEMATOLOGICAL DISEASES AND STEM CELL EXPANSION. DR. HANZHI LUO IS CURRENTLY A POSTDOC FELLOW IN THE MOLECULAR PHARMACOLOGY PROGRAM AT THE MEMORIAL SLOAN KETTERING CANCER CENTER. HER INITIAL ACHIEVEMENTS INCLUDE UNCOVERING M6A'S ROLE IN HSC SYMMETRIC COMMITMENT, AS WELL AS REVEALING THE RUNX1 DEPENDENCY IN LEUKEMIA STEM CELLS WITH THE AML-IPSC MODEL. BOTH STUDIES WERE RECENTLY PUBLISHED IN CELL REPORTS. HER LONG-TERM GOAL IS TO ESTABLISH A RESEARCH TEAM WITH AN EMPHASIS ON MOLECULAR MECHANISMS OF HSC FATE CHOICES WITH A STRONG COMMITMENT TO TRANSLATE BASIC SDISCOVERIES INTO THE CLINIC. THE PROPOSED RESEARCH WILL PROVIDE NEW TRAINING FOR DR. LUO IN HEMATOPOIESIS AND RNA REGULATORS. THIS WORK WILL BE PERFORMED AT THE MSKCC, AN EXCITING RESEARCH ENVIRONMENT WITH CUTTING- EDGE FACILITIES. DR. LUO WILL BE MENTORED BY DR. MICHAEL KHARAS, A LEADING EXPERT IN STUDYING RNA REGULATORS IN NORMAL AND MALIGNANT STEM CELLS, AND A DEDICATED SUPPORTER FOR YOUNG TRAINEES. TOGETHER, THIS CAREER DEVELOPMENT PLAN WILL HELP DR. LUO ESTABLISH HER INDEPENDENT RESEARCH LAB AT A RESEARCH-ORIENTED ACADEMIC INSTITUTE AND BECOME A LEADER IN THE FIELD OF HEMATOPOIESIS.

THE ROLE OF MER/PROS1 IN PROMOTING STROMAL INDUCED EMERGENCE FROM METASTATIC MELANOMA DORMANCY - PROJECT SUMMARY THE GOALS OF THIS PATHWAY TO INDEPENDENCE CAREER DEVELOPMENT PROPOSAL ARE TO REQUEST SUPPORT FOR DR. FANE TO DEVELOP TRAINING IN TUMOR DORMANCY AND UNDERLYING CANCER IMMUNOLOGY AND BIOINFORMATICS TECHNIQUES TO INVESTIGATE HOW DORMANT MELANOMA CELLS LOCATED WITHIN METASTATIC TISSUES CAN REGULATE STROMAL CELLS TO FACILITATE METASTATIC OUTGROWTH AND RESISTANCE TO THERAPY. THE TRAINING PLAN OUTLINED IN THIS PROPOSAL WILL TAKE ADVANTAGE OF THE EXTENSIVE RESOURCES AND CAREER DEVELOPMENT PROGRAMS AVAILABLE AT JOHNS HOPKINS. DR. FANE HAS ASSEMBLED A TEAM OF LEADERS IN THE FIELD OF MELANOMA, DORMANCY, IMMUNOLOGY, AND BIOINFORMATICS WHO WILL GUIDE HIS TRAINING. METASTASIS IS THE LARGEST CAUSE OF MELANOMA DEATHS, WITH TREATMENTS FAILING TO PROVIDE A DURABLE RESPONSE. WHILE A SUBSET OF PATIENTS SHOW-REMARKABLE RESPONSES INITIALLY TO THERAPY, MOST OF THEM WILL HAVE TUMOR CELLS LYING DORMANT IN DISTAL ORGANS THAT PERSIST DURING THERAPY BUT ARE CLINICALLY UNDETECTABLE. EVENTUALLY, THESE CELLS WILL ‘REACTIVATE’ FROM DORMANCY TO FORM METASTATIC COLONIES, NOW RESISTANT TO THERAPY. THERE ARE FEW LABS THAT FOCUS ON MELANOMA DORMANCY AND AS SUCH, THERE ARE NO CURRENT TREATMENTS OR DIAGNOSTIC TOOLS TO IDENTIFY AND TARGET DORMANT CELLS. THE PROPOSED STUDIES ARE BASED ON DR. FANES NOVEL FINDINGS THAT UPREGULATION OF THE TYROSINE KINASE RECEPTOR MER PROMOTES CANCER GROWTH, WHICH ALLOWS ‘REACTIVATION’ OF DORMANT MELANOMA CELLS WITHIN THE LUNG. IT ISN’T KNOWN HOW ‘REACTIVATED’ CELLS OVERCOME TARGETING BY THE IMMUNE SYSTEM, GROWTH RESTRICTIVE CUES FROM LUNG FIBROBLASTS, OR HOW THEY BECOME RESISTANT TO THERAPY. DR. FANES PRELIMINARY DATA FIRST SHOWS THAT MERHIGH MELANOMA CELLS REGULATE LUNG FIBROBLASTS TO ALTER SECRETION OF THE EXTRACELLULAR MATRIX, CHANGING IT FROM BEING DORMANCY PROMOTING TO ALLOWING MELANOMA OUTGROWTH. DR FANE HAS ALSO SHOWN THAT FOLLOWING ‘REACTIVATION’ OF MELANOMA WITHIN THE LUNG, THERE IS AN INCREASE IN MYELOID DERIVED SUPPRESSOR CELLS (MDSCS) AND T-REGULATORY (TREGS) CELLS WHICH INHIBIT THE IMMUNE SYSTEM FROM TARGETING CANCER CELLS FOR DESTRUCTION AND ARE OFTEN A COMMON FEATURE IN PATIENTS RESISTANT TO IMMUNOTHERAPY. FINALLY, DR. FANE HAS SHOWN THAT ‘REACTIVATED’ MELANOMA CELLS SECRETE HIGH LEVELS OF THE SOLUBLE PROTEIN PROS1, WHICH IS KNOWN TO BE INVOLVED IN REGULATING THE ACTIVITY OF MDSCS, TREGS, AND LUNG FIBROBLASTS WITHIN OTHER DISEASE STATES, BUT HAS NOT BEEN INVESTIGATED IN METASTATIC DORMANCY. DR. FANE WILL EXPLORE THE FOLLOWING SCIENTIFIC AIMS: 1) DETERMINE WHETHER MER INDUCED SECRETION OF PROS1 REGULATES LUNG FIBROBLAST TO PROMOTE OUTGROWTH AND THERAPY RESISTANCE AND 2) INVESTIGATE THE MECHANISM BY WHICH MER INDUCED SECRETION OF PROS1 BY MELANOMA CELLS IN THE LUNG REGULATES IMMUNE CELLS AND RESPONSE TO A-PD1. THE COMPLETION OF THE SCIENTIFIC AIMS IN THIS PROPOSAL WILL DEVELOP DR. FANES SCIENTIFIC AND PROFESSIONAL SKILLS THAT ARE REQUIRED TO BE AN INDEPENDENT INVESTIGATOR INTO THE FIELD OF DORMANCY AND IMPORTANTLY, WILL PROVIDE NOVEL INSIGHT INTO HOW CANCER CELLS OVERCOME TARGETED AND IMMUNOTHERAPIES IN DORMANT, METASTATIC DISEASE.

DEVELOPMENT OF MOSAIC MOUSE MODELS OF HCC FOR GENETIC INTERSPECIES INFERENCE

MYHEALTHPORTAL: USING AN ELECTRONIC PORTAL TO EMPOWER PATIENTS WITH BREAST CANCER

ZNF-MEDIATED RESISTANCE TO IMATINIB MESYLATE IN GASTROINTESTINAL STROMAL TUMOR

THE ROLE OF INTERLEUKIN 23 IN COLITIS ASSOCIATED CANCER

TARGETING NUCLEAR NECROPTOSIS PATHWAY IN PANCREATIC CANCER MICROENVIRONMENT

TARGETING NUCLEAR NECROPTOSIS PATHWAY IN PANCREATIC CANCER MICROENVIRONMENT

DEVELOPMENT OF METHODS FOR ANTIBODY COMPUTATIONAL DESIGN

CANCER-ASSOCIATED MACROPHAGELIKE (CAML) CELLS TO ENHANCE DETECTION OF EARLY-STAGE LUNG CANCER AND RELAPSE AFTER DEFINITIVE TREATMENT

IMMUNOLOGIC AND MICROBIAL CORRELATES AND MECHANISMS OF COMPLETE RESPONSE TO NEOADJUVANT CHEMOTHERAPY IN MUSCLE-INVASIVE BLADDER CANCER

DEVELOPING BIOMARKERS OF RESPONSE TO CHEMORADIATION THERAPY IN RECTAL CARCINOMA: TOWARD PRECISION MEDICINE

ENHANCING IMMUNE CHECKPOINT BLOCKADE BY REPROGRAMMING THE METHYLOME WITH NOVEL EPIGENETIC MODULATORS THAT INDUCE A PROINFLAMMATORY RESPONSE

STRUCTURE AND REPLICATION OF HEPATITIS DELTA VIRUS

FOXO TRANSCRIPTION FACTORS ARE REQUIRED FOR MAINTENANCE OF ACUTE MYELOID LEUKEMIA

MARGRET B. EINARSON, PH.D., MANAGER, HIGH THROUGHPUT SCREENING FACILITY, FOX CHASE CANCER CENTER

THYMINE DNA GLYCOSYLASE AS A NOVEL TARGET FOR LUNG CANCER

MODELING OF PROTEIN COMPLEXES AND MISSENSE MUTATIONS

EARLY STAGES OF APOMYOGOBIN FOLDING

MULTIPHOTON MICROSCOPY SYSTEM

TOWARDS PRECISION PREVENTION: TESTING A NOVEL RISK PREDICTION ALGORITHM IN PANCREATIC CANCER

ANALYSIS AND THERAPEUTIC TARGETING NON-PROTEOLYTIC PROTEIN UBIQUITINATION IN DIFFUSE LARGE B CELL LYMPHOMA

HISTONE-DEPENDENT PARP-1 INHIBITORS: A NOVEL THERAPEUTIC MODALITY FOR THE TREATMENT OF RENAL CELL CARCINOMA

INCREASE CLINICAL TRIAL ENROLLMENT OF UNDERREPRESENTED KIDNEY CANCER PATIENTS BY IMPROVING ACCESS TO PARTICIPATION

PLANNING FOR A SUSTAINABLE AND ROBUST RCRE IN THE CARIBBEAN

ORAL GUCY2C LIGAND BLOCKS COLORECTAL TUMOR PROGRESSION IN PATIENTS

DETERMINE THE IMPACT OF NOVEL BRCA1 TRANSLATIONAL START SITES ON THERAPY RESISTANCE IN OVARIAN CANCER

NETRIN G1 LIGAND: A NEW IMMUNOMODULATORY TARGET AND EARLY BIOMARKER IN PANCREATIC CANCER

PRELIMINARY EVALUATION OF FDG-PET WITH ANTI-IGF-1R TARGETED THERAPY IN GISTS

CA140228: PANCREATIC CANCER'S DESMOPLASIA: THE POSSIBLE BRIDGE IMPENDING NERVE INFILTRATION AND NEOPLASTIC ESCAPE

FORMATION OF HETEROCHROMATIN AND CELLULAR SENESCENCE DRIVEN BY HIRA AND ASF 1A

NEUROTRANSMITTER SIGNALING CONTROLS STEM CELL FATE - PROJECT SUMMARY/ABSTRACT THE EQUILIBRIUM BETWEEN STEM CELL SELF-RENEWAL AND DIFFERENTIATION IS A CORNERSTONE OF TISSUE HEALTH. STEM CELLS MUST MAINTAIN HEALTHY, HETEROGENEOUS STEM CELL POOLS THROUGHOUT THE LIFETIME OF THE ANIMAL, WHILE ALSO PRODUCING THE DIFFERENTIATED DAUGHTER CELLS NECESSARY FOR OPTIMAL TISSUE FUNCTION. CONTROLLED SHIFTS MEDIATED BY CHANGES IN THE SPECIFIC SIGNALS THAT PROMOTE SELF-RENEWAL VERSUS DIFFERENTIATION MAY BE LEVERAGED FOR TISSUE REPAIR AFTER INJURY OR PREVENTION OF AGING SYMPTOMS. IN CONTRAST, CONTINUOUS IMBALANCE CAN LEAD TO ABERRANT STATES SUCH AS TUMOR FORMATION WHEN SELF-RENEWAL IS FAVORED, OR STEM CELL LOSS WHEN DIFFERENTIATION IS THE PRIMARY OUTCOME. DEFINING THE MOLECULAR MECHANISMS THAT DETERMINE STEM CELL FATE IS THEREFORE A PRESSING NEED. HERE, WE INVESTIGATE THE POSSIBILITY THAT EPITHELIAL FOLLICLE STEM CELLS (FSCS) IN THE FLY OVARY UTILIZE CLASSICAL NEUROTRANSMITTER SIGNALING TO DICTATE SELF-RENEWAL VERSUS DIFFERENTIATION FATE DECISIONS. IN RECENT WORK, WE DEMONSTRATED THAT AXON-LIKE PROJECTIONS EXTEND FROM FSCS IN RESPONSE TO FEEDING, FORMING INTERACTIVE WEBS THAT SPAN THE NICHE. DISRUPTION OF PROJECTION GROWTH AND INTERACTIONS VIA MUTATION OF THE AXON REGULATORS STILL LIFE (SIF, TIAM-1), AND SICKIE (NAV2) LEADS TO DEVELOPMENTAL DEFECTS AND, IMPORTANTLY, DISRUPTS THE BALANCE OF CELL FATE MARKERS THAT INSTRUCT SELF-RENEWAL OR DIFFERENTIATION. PROJECTION GROWTH DEPENDS ON HEDGEHOG (HH) SIGNALING, WITH THE TRANSCRIPTIONAL ACTIVATOR CUBUITUS INTERRUPTUS (CI) NECESSARY FOR EXTENSION. REASONING THAT CI TRANSCRIPTIONAL TARGETS MIGHT THUS BE CRITICAL FOR MEDIATING COMMUNICATION BETWEEN FSC PROJECTIONS AND THEIR TARGETS (OTHER FSCS OR GERM CELLS), WE DEFINED THE GENE EXPRESSION CHANGES THAT OCCUR IN FSCS AT 3 HOURS TIMEPOINTS AFTER FEEDING. THE PROPOSED WORK FOCUSED ON A HIGHLY ENRICHED SET OF GENES WITH KNOWN FUNCTIONS AT NEUROMUSCULAR JUNCTION SYNAPSES, AND THE MODEL THAT FSC FATE IS DETERMINED BY THE BALANCE OF GABA VERSUS GLUTAMATE SIGNALING. THE IDEA THAT NON-NEURONAL STEM CELLS COMMUNICATE VIA NEUROTRANSMITTER SIGNALING MAY BE APPLICABLE TO OTHER STEM CELL SYSTEMS, EMPHASIZING THAT OUR PRECISE MOLECULAR DISSECTION OF THE SPATIO-TEMPORAL FUNCTION OF CANDIDATE REGULATORS MAY UNCOVER A NEW FUNDAMENTAL MECHANISM FOR REGULATION OF STEM CELL FATE.

CHARACTERIZATION OF NEW ALLOSTERIC INHIBITORS THAT DISRUPT HIV-1 INTEGRASE DIMERIZATION - PROJECT SUMMARY HIV INFECTION REMAINS A MAJOR WORLD HEALTH ISSUE REQUIRING NEW METHODS TO TREAT AIDS. INTEGRASE (IN) IS A VIRUS- ENCODED ENZYME THAT IS ESSENTIAL FOR RETROVIRAL REPLICATION AND IS AN ESTABLISHED TARGET FOR THE DEVELOPMENT OF DRUGS TO TREAT HIV/AIDS. FIVE FDA-APPROVED DRUGS THAT TARGET THE ACTIVE SITE ARE IN CLINICAL USE TO TREAT AIDS PATIENTS, BUT CROSS-RESISTANT VIRUS VARIANTS HAVE BEEN WELL DOCUMENTED. TO COMBAT RESISTANCE TO EXISTING IN ACTIVE SITE INHIBITORS, WE NEED DRUGS THAT UTILIZE A MECHANISM OF ACTION TARGETING OTHER REQUIRED VIRAL PROTEIN FUNCTIONS, SUCH AS MULTIMERIZATION OR INTERACTION WITH VIRAL AND CELLULAR CO-FACTORS. A PROMISING NEW APPROACH IS CENTERED ON DEVELOPING INHIBITORS TARGETING NON-ACTIVE SITE (OR “ALLOSTERIC”) LOCATIONS, BUT NONE OF THESE HAVE BEEN APPROVED FOR CLINICAL USE. FOR PROPER FUNCTION, INTEGRASE MUST FORM MULTIMERS COMPETENT TO PERFORM THE COORDINATED INSERTION OF TWO VIRAL DNA ENDS INTO THE HOST TARGET DNA, CALLED CONCERTED INTEGRATION. WE WILL TEST THE POTENTIAL FOR INHIBITING PROPER IN MULTIMERIZATION AS AN EFFECTIVE ANTIVIRAL STRATEGY. IN ADDITION TO THE WELL-CHARACTERIZED CATALYTIC CORE DIMER INTERFACE, OUR STUDIES HAVE REVEALED A DIMER INTERFACE MEDIATED BY INTERACTIONS BETWEEN THE N-TERMINAL AND CATALYTIC CORE DOMAINS, WHICH IS ALSO OBSERVED IN THE RECENT CRYO-EM STRUCTURE OF HIV INTASOMES. THE PROPOSED RESEARCH TARGETS THIS NOVEL PROTEIN-PROTEIN INTERACTION AND PROPOSES TO CHARACTERIZE COMPOUNDS THAT DISRUPT THIS INTERFACE REQUIRED FOR IN ACTIVITY. AS A UNIQUE APPROACH TO IDENTIFY ALLOSTERIC INHIBITORS THAT TARGET THE PROTEIN-PROTEIN INTERACTIONS REQUIRED FOR FUNCTIONAL INTEGRASE MULTIMERIZATION, WE DESIGNED A FRET-BASED ASSAY THAT SPECIFICALLY DETECTS FORMATION OF THE N-TERMINAL DOMAIN-CATALYTIC CORE DOMAIN DIMER. IN THE FIRST VERSION OF THIS ASSAY, WE IDENTIFIED SEVERAL COMPOUNDS THAT ALSO INHIBITED IN CATALYTIC ACTIVITIES, AND IMPORTANTLY TWO OF THESE COMPOUNDS INHIBITED HIV INFECTION OF CELLS IN CULTURE. HOWEVER, TOXICITY CONCERNS LIMITED THE USEFULNESS OF THESE EARLY HITS. WE HAVE DEVELOPED AN IMPROVED, SECOND-GENERATION SCREEN AND HAVE IDENTIFIED 25 NEW HIT COMPOUNDS FROM SPECIALIZED CHEMICAL LIBRARIES DESIGNED TO TARGET PROTEIN-PROTEIN INTERACTIONS. EIGHT OF THESE NEW CANDIDATE COMPOUNDS WERE DEEMED ACCEPTABLE BY STRICT STANDARDS OF DRUG-LIKE QUALITIES AND POSSESS STRONG MEDICINAL CHEMISTRY POTENTIAL FOR ADVANCEMENT. THE PURPOSE OF THE PROPOSED WORK IS TO: AIM 1 - VALIDATE THESE HIT COMPOUNDS INCLUDING A DETAILED BIOCHEMICAL CHARACTERIZATION; AND AIM 2 - TEST COMPOUNDS FOR CELL TOXICITY AND THE ABILITY TO BLOCK VIRUS INFECTION. THE INFORMATION GAINED FROM THE EXPERIMENTS IN THIS APPLICATION WILL HAVE THE POTENTIAL FOR MAJOR IMPACT IN DEVELOPMENT OF ANTI-AIDS DRUGS THAT FUNCTION AS EFFECTIVE ALLOSTERIC INHIBITORS OF HIV IN, FOR USE IN COMBINATION WITH EXISTING DRUGS TO PREVENT THE EMERGENCE OF RESISTANT VIRUS STRAINS.

NECROPTOSIS IN SARS-COV-2 PATHOGENESIS, EVOLUTION, AND THERAPY - PROJECT SUMMARY/ABSTRACT OUR LABORATORY HAS RECENTLY IMPLICATED NECROPTOSIS AS A PATHOGENIC AND TARGETABLE HOST PATHWAY DURING PULMONARY INFLUENZA A VIRUS (IAV) INFECTIONS. IN THIS PROPOSAL, WE SEEK TO EXTEND THESE FINDINGS TO SARS-COV-2 BECAUSE WE HAVE STRONG REASON TO BELIEVE THAT SARS-COV-2, LIKE IAV, ACTIVATES NECROPTOSIS. WE HAVE IDENTIFIED A MECHANISM BY WHICH SARS-COV-2 MAY TRIGGER NECROPTOSIS, AND PROPOSE THAT SUCH NECROPTOSIS UNDERLIES THE ALVEOLAR CELL DEATH AND INFLAMMATORY ‘CYTOKINE STORM’ OBSERVED IN SEVERE COVID-19 DISEASE. IMPORTANTLY, NECROPTOSIS CAN BE TARGETED BY DEDICATED RIPK3 KINASE INHIBITORS, OPENING UP A NEW AND UNANTICIPATED THERAPEUTIC ENTRY-POINT FOR COVID-19. SPECIFICALLY, WE HAVE DISCOVERED THAT A SARS-COV-2 NONSTRUCTURAL PROTEIN CONTAINS A FUNCTIONAL RHIM MOTIF THAT IS ESSENTIAL FOR PROPAGATING NECROPTOSIS SIGNALING. IN ALL KNOWN CELL TYPES, NECROPTOSIS IS INITIATED WHEN THE KINASE RIPK3 ENGAGES IN RHIM-RHIM INTERACTIONS WITH OTHER RHIM-CONTAINING PROTEINS. FOR EXAMPLE, DURING IAV INFECTION, THE RHIM IN RIPK3 INTERACTS WITH THE RHIM IN THE IAV SENSOR PROTEIN ZBP1 TO TRIGGER NECROPTOSIS. WE THUS HYPOTHESIZED THAT THE RHIM IN THE COV-2 PROTEIN ALLOWS IT TO INTERACT WITH RIPK3 TO ACTIVATE NECROPTOSIS. INDEED, WE FOUND THAT THE SARS-COV-2 PROTEIN ENGAGES RIPK3 AND ACTIVATES NECROPTOSIS IN HUMAN CELLS. THE PRECISE MECHANISM RESPONSIBLE REMAINS UNKNOWN. WE HAVE ALSO FOUND THAT ALL THREE PATHOGENIC COVS (SARS-COV, MERS-COV, AND SARS-COV-2) HAVE A RHIM IN THIS PROTEIN, WHEREAS NONE OF THE HUMAN-ADAPTED STRAINS (HKU-1, CO43, NL63, AND 229E) POSSESS ONE. FINALLY, WE HAVE FOUND THAT BATS, THE LIKELY NATURAL HOSTS OF SARS-COV-2 AND OTHER PATHOGENIC COVS, ENCODE A VARIANT OF RIPK3 WHICH CONTAINS A SINGLE AMINO ACID CHANGE FROM NON-BAT RIPK3. THIS CHANGE SIGNIFICANTLY DAMPENS NECROPTOSIS SIGNALING, SUGGESTING THAT THE NECROPTOSIS MACHINERY IS DEFECTIVE OR NON-FUNCTIONAL IN BATS. BASED ON THESE AND OTHER OBSERVATIONS, WE HYPOTHESIZE THAT SARS-COV-2 AND ALLIED PATHOGENIC COVS ACTIVATE NECROPTOSIS IN HUMAN PULMONARY EPITHELIA, VIA A RHIM-RHIM INTERACTION INVOLVING THE COV-2 RHIM-CONTAINING PROTEIN AND RIPK3, AND THAT SUCH NECROPTOSIS INITIATES AND AMPLIFIES THE LUNG INJURY AND INFLAMMATION SEEN IN SEVERE CASES OF COVID- 19. WE FURTHER PROPOSE THAT DAMPENED NECROPTOSIS SIGNALING IN BATS ALLOWS THEM TO HARBOR PATHOGENIC (TO HUMANS) COVS WITHOUT APPARENT HYPER-INFLAMMATORY CONSEQUENCES. IN THIS PROPOSAL, WE WILL EXAMINE HOW SARS-COV ACTIVATES NECROPTOSIS IN HUMAN CELLS, AND IF SUCH NECROPTOSIS IS A NEW THERAPEUTIC OPPORTUNITY IN VIVO BY EVALUATING FDA-APPROVED AND NEW, HIGH POTENCY RIPK3 INHIBITORS IN A MOUSE MODEL OF SARS-COV-2 INFECTION. WE HAVE ALSO DEVELOPED A KNOCK-IN MOUSE HARBORING THE BAT RIPK3 POLYMORPHISM, AND WILL TEST IF SARS-COV-2-INITIATED LUNG PATHOLOGY IS DAMPENED IN THIS MOUSE, COMPARED TO CONTROLS. THE SUCCESSFUL COMPLETION OF THESE STUDIES WILL PROVIDE PIONEERING INSIGHT INTO THE MECHANISM AND EVOLUTIONARY BIOLOGY OF NECROPTOSIS SIGNALING IN SARS-COV-2 PATHOGENESIS AND STAND TO HAVE IMPORTANT RAMIFICATIONS FOR THE TREATMENT OF SEVERE COVID-19.

ANTIBODY-MEDIATED BRCC36 SILENCING: A NOVEL APPROACH FOR TARGETED BREAST CANCER THERAPY

VALIDATION OF BLOOD-BASED PREDICTIVE BIOMARKERS OF THERAPEUTIC RESPONSE TO NEOADJUVANT CHEMORADIATION THERAPY IN PATIENTS WITH LOCALLY ADVANCED RECTAL CANCER - PROJECT SUMMARY/ABSTRACT NEOADJUVANT CHEMORADIATION THERAPY (NCRT) FOLLOWED BY SURGERY IS THE STANDARD OF CARE FOR PATIENTS WITH LOCALLY ADVANCED RECTAL CANCER (LARC), WHICH ACCOUNTS FOR ~60% OF NEWLY DIAGNOSED RECTAL CANCER CASES. ALTHOUGH NCRT BENEFITS MANY PATIENTS, IT IS CURRENTLY NOT KNOWN WHO WILL OR WILL NOT RESPOND FAVORABLY. ABOUT 20% PATIENTS THAT RECEIVE NCRT WILL EXPERIENCE A PATHOLOGIC COMPLETE RESPONSE (PCR), WHILE ~25% PATIENTS WILL EXHIBIT NO RESPONSE. RECENTLY, SEVERAL CLINICAL TRIALS HAVE ASSESSED NEW TREATMENT PARADIGMS, AND THEIR RESULTS PRESENT NEW TREATMENT STRATEGIES WHICH WERE PREVIOUSLY NOT AVAILABLE FOR LARC PATIENTS. WITH THE AVAILABILITY OF THESE NEW STRATEGIES, IT IS CRUCIAL TO BE ABLE TO A PRIORI IDENTIFY LARC PATIENTS, VIA A PREDICTIVE BIOMARKER, WHO HAVE A HIGHER LIKELIHOOD OF RESPONDING OR NOT RESPONDING TO NCRT. OUR GOAL IS TO OPTIMIZE AND VALIDATE AN EFFICIENT ASSAY THAT IS ACCURATE, PRECISE, AND MINIMALLY INVASIVE TO ASSESS BIOMARKER(S) THAT WILL PREDICT RESPONSE TO NCRT IN THE SETTING OF LARC. THE ASSAY THAT WILL BE VALIDATED IN THIS PROPOSAL IS A LUMINEX MULTIPLEXED ASSAY THAT USES THE XMAP TECHNOLOGY. WE HAVE DEFINED SIX CANDIDATE BIOMARKERS THAT WILL BE VALIDATED IN THIS STUDY. HERE, USING THE OPTIMIZED AND VALIDATED ASSAY WE WILL THEN ACHIEVE THE CLINICAL VALIDATION OF THE CANDIDATE BIOMARKER(S) IN A REAL-WORLD CLINICAL LABORATORY SETTING USING LARC PATIENT SPECIMENS. AT THE END OF THIS STUDY, WE WILL ACHIEVE A MINIMALLY INVASIVE, BLOOD-BASED ASSAY FOR PATIENT TREATMENT STRATIFICATION WHICH WILL BE OF TREMENDOUS BENEFIT TO LARC PATIENT(S) AND THE HEALTHCARE SYSTEM. USING THE XMAP ASSAY, WE ARE DETECTING CANDIDATE BIOMARKERS OF DNA DAMAGE RESPONSE (DDR) SIGNALING IN CELL LYSATES FROM CRYOPRESERVED PERIPHERAL BLOOD MONOCYTES (PBMCS) OF LARC PATIENTS. IN OUR PRELIMINARY WORK, THE CHANGE IN THE EXPRESSION OF THESE BIOMARKERS SIGNIFICANTLY ASSOCIATED WITH RESPONSE TO NCRT IN LARC PATIENTS. THESE CANDIDATE BIOMARKERS WERE IDENTIFIED THROUGH OUR RECENT HYPOTHESIS-DRIVEN TRANSLATIONAL STUDY FUNDED BY THE DOD. THIS PROPOSAL WAS DEVELOPED THROUGH A COLLABORATION BETWEEN THE TWO PRIMARY INVESTIGATORS BRINGING TOGETHER COMPLEMENTARY EXPERTISE. THE ASSEMBLED MULTI-DISCIPLINARY TEAM BRINGS TOGETHER EXPERTISE IN CLINICAL AND BASIC SCIENCE, ASSAY DEVELOPMENT/VALIDATION, AND THEIR CLINICAL DEPLOYMENT. HERE, WE WILL ANALYTICALLY VALIDATE OUR ASSAY (UH2 PHASE) AND THEN ESTABLISH THE CLINICAL VALIDITY BY USING BIOSPECIMENS FROM LARC PATIENTS (UH3 PHASE). THE BIOSPECIMENS USED ARE FROM LARC PATIENTS AND HEALTHY CONTROLS FROM THE FOX CHASE BIOSAMPLE REPOSITORY FACILITY, AND FROM LARC CLINICAL STUDIES/TRIALS EVALUATING THERAPEUTIC RESPONSE. IN THE UH2 PHASE WE WILL PERFORM PRE-ANALYTICAL (BIOSPECIMEN VARIABILITY) AND ANALYTICAL (E.G., PRECISION, ACCURACY) VALIDATION. IN THE UH3 PHASE, WE WILL ESTABLISH CLINICAL VALIDITY BY EVALUATING CLINICAL UTILITY PARAMETERS (E.G., SENSITIVITY/SPECIFICITY, OPTIMAL CUT-OFFS) AND COMPARE WITH NCRT RESPONSE STATUS. SUCCESSFUL COMPLETION WILL YIELD VALIDATED BIOMARKERS/ASSAYS FOR USE AS INVESTIGATIONAL ASSAYS IN CLINICAL TRIALS/STUDIES. OVER THE LONG-TERM, THIS WORK MAY IMPROVE PATIENT STRATIFICATION FOR TREATMENT IN LARC PATIENTS.

CHARACTERIZATION OF TYPE-2 CYTOKINE-PRODUCING NK CELLS

A NEW IFN-? ACTIVATED CELL DEATH PATHWAY IN SALMONELLA-INFECTED NON-PHAGOCYTIC CELLS

UNDERSTANDING NUCLEAR SHAPE DEFECTS AND HETEROCHROMATIN DISORGANIZATION IN AGED CELLS

MECHANISMS AND VULNERABILITIES OF ERG-DRIVEN LUMINAL FATE IN PROSTATE CANCER - PROJECT SUMMARY AND ABSTRACT: PROSTATE CANCER (PCA) IS THE MOST FREQUENT CANCER IN AMERICAN MEN. LUMINAL HISTOLOGY IS A HALLMARK OF PCA. HORMONE THERAPY EFFECTIVELY TARGETS LUMINAL CELLS, BUT RESISTANCE INEVITABLY OCCURS. THE ERG ONCOPROTEIN IS OVEREXPRESSED IN HALF OF PCA CASES. PROSTATIC ERG EXPRESSION IN MICE RECAPITULATES INVASION WITH A LUMINAL PROGRAM SEEN IN HUMAN PCA, THUS PRESENTING A CLINICALLY RELEVANT MODEL TO STUDY PCA. HOWEVER, THE MOLECULAR MECHANISMS BY WHICH ERG DRIVES A LUMINAL FATE AND INVASIVE PCA REMAIN UNCLEAR, INSIGHTS FROM WHICH MAY REVEAL NEW TREATMENT PARADIGMS. PROJECT OBJECTIVE: TO ELUCIDATE THE MECHANISMS AND VULNERABILITIES OF ERG-DRIVEN LUMINAL FATE AND PCA INVASION. PRELIMINARY DATA: 1) PSEUDO-BASAL CELLS (THOSE WITH A MIXTURE BASAL/LUMINAL MARKER PROFILE) RATHER THAN LUMINAL CELLS ARE THE MOST PROLIFERATIVE, AND INVASION-ASSOCIATED POPULATION IN PCA; 2) A GENOME-WIDE CRISPR SCREEN REVEALS THAT ERG STIMULATES LUMINAL FATE BY ALLEVIATING ARYL-HYDROCARBON RECEPTOR (AHR) SIGNALING, WHICH PROVIDES A DRUGGABLE VULNERABILITY. CENTRAL HYPOTHESIS: ERG STIMULATES A PROGENITOR STATE, CHARACTERIZED AS PSEUDO-BASAL CELLS, THAT SUSTAINS INVASION AND LUMINAL OUTPUT OF PCA. THE PROPOSED PROJECT LEVERAGES INNOVATIVE MOUSE AND ORGANOID MODELS, GENOME-WIDE SCREEN DATA, AND PATIENT SAMPLES TO TEST THIS HYPOTHESIS. SPECIFIC AIMS: 1) DETERMINE THE LUMINAL PROGENITOR AND ONCOGENIC POTENTIAL OF PSEUDO-BASAL CELLS IN ERG-DRIVEN PCA; 2) DEFINE HOW AHR AND OTHER SCREEN CANDIDATES MODULATE LINEAGE OUTPUT AS A MECHANISM AND VULNERABILITY OF ERG FUNCTION; 3) CHARACTERIZE THE PSEUDO-BASAL STATE IN HUMAN PCA. IMPACT: SUCCESS OF THIS WORK WILL 1) ADVANCE MECHANISTIC UNDERSTANDING, 2) IDENTIFY NOVEL VULNERABILITIES OF ERG-DRIVEN PCA, THE MOST FREQUENT PCA SUBTYPE, AND 3) PROVIDE TOOLS AND APPROACHES WITH WIDE APPLICABILITY TO STUDYING LINEAGE FATE CHOICES IN CANCER. THIS WORK WILL BE PERFORMED UNDER THE COLLABORATIVE AND RESOURCEFUL RESEARCH ENVIRONMENT AT MSKCC. I HAVE RECENTLY DEVELOPED CRISPR EDITING TOOLS FOR RAPID PCA MODELING (PROC NATL ACAD SCI), WHICH WILL BE CRITICAL TO ADVANCE THE PROPOSED WORK. MY LONG-TERM CAREER GOAL IS TO ESTABLISH AN INDEPENDENT RESEARCH TEAM THAT FOCUSES ON MECHANISTIC UNDERSTANDING OF PCA TO DEVELOP NOVEL THERAPEUTIC STRATEGIES. I HAVE DEVELOPED A DETAILED CAREER PLAN TO OBTAIN SKILLS IN LEADERSHIP, MANAGEMENT, MENTORING, GRANT WRITING, AND SCIENTIFIC COMMUNICATIONS. I WILL WORK UNDER THE MENTORSHIP OF DR. CHARLES SAWYERS, A LEADER IN PCA RESEARCH WITH A STELLAR TRACK RECORD OF TRAINEES THAT WENT ON TO FACULTY POSITIONS. IN ADDITION, I HAVE ASSEMBLED AN ADVISORY COMMITTEE THAT WILL COLLABORATE WITH ME AND OFFER TRAINING ON SCIENCE AND CAREER DEVELOPMENT, INCLUDING DRS. MICHAEL SHEN (PROSTATE LINEAGE SPECIFICATION), YU CHEN (ERG BIOLOGY), GARY PERDEW (AHR BIOLOGY), ANURADHA GOPALAN (PATIENT SAMPLE ASSESSMENT), AND CHRISTINA LESLIE (COMPUTATIONAL BIOLOGY). MY RESEARCH AND CAREER DEVELOPMENT PLAN, TOGETHER WITH MY MENTOR, ADVISORS AND THE EXCEPTIONAL ACADEMIC ENVIRONMENT AT MSKCC WILL PROVIDE A SOLID FOUNDATION FOR MY INDEPENDENCE IN TRANSLATIONAL PROSTATE CANCER RESEARCH.

RNA VIRUS PERSISTENCE AND REACTIVATION IN THE BRAIN

MECHANISMS FOR CCCDNA FORMATION AND PERSISTENCE

ENHANCING THE PROPERTIES OF HIV-1 INTEGRASE AND DETERMINATION OF ITS STRUCTURE IN COMPLEX WITH DNA SUBSTRATES

GENERATION AND CHARACTERIZATION OF HUMAN B1 B CELLS INDUCED BY LIN28B REPROGRAMMING OF ADULT HEMATOPOIETIC PROGENITORS

CONTROL OF INTERFERON-ACTIVATED NECROSIS BY A VIRUS-TRIGGERED FADD CHECKPOINT

PICORNAVIRUS-INITIATED INFLAMATION: NOVEL PARALLELS FROM DROSOPHILA

DESIGNER NUCLEASES TO CURE CHRONIC HEPATITIS B

ROLE OF RPL22 IN ER STRESS AND COLITIS

KINETOCHORE STRUCTURE AND FUNCTION

ASSESSMENT OF EFFICACY AND TOXICITY OF T3 FOR MEDULLOBLASTOMA TREATMENT - PROJECT SUMMARY/ABSTRACT MEDULLOBLASTOMA (MB) IS THE MOST COMMON MALIGNANT BRAIN TUMOR IN CHILDREN. DESPITE CONVENTIONAL TREATMENT INCLUDING SURGERY, CHEMOTHERAPY AND RADIATION, A SIGNIFICANT PROPORTION OF MB PATIENTS STILL SUCCUMBS TO THIS DISEASE. MOREOVER, ALMOST ALL PATIENTS SUFFER LONG-TERM SIDE EFFECTS OF THE AGGRESSIVE TREATMENT, SUCH AS HEARING LOSS AND COGNITIVE DEFICIT. IMPROVED STRATEGIES TO TREAT MB ARE URGENTLY NEEDED. OUR RECENT STUDIES HAVE UNVEILED THAT T3, THE ACTIVE FORM OF THYROID HORMONE, INHIBITS MB TUMOR GROWTH BY INDUCING TERMINAL DIFFERENTIATION OF TUMOR CELLS IN MICE, WITHOUT CAUSING NOTICEABLE WEIGHT LOSS. THESE FINDINGS SUGGEST THAT T3, AN FDA-APPROVED DRUG FOR HYPOTHYROIDISM, HOLDS PROMISE AS A POTENTIAL APPROACH FOR MB TREATMENT. TO TRANSLATE OUR DISCOVERIES INTO CLINICAL TRIALS, WE PROPOSE TO DELVE DEEPER INTO THE TOXICITY AND THERAPEUTIC EFFICACY OF T3 IN MICE. SPECIFICALLY, OUR RESEARCH WILL FOCUS ON TWO SPECIFIC AIMS: 1. AIM 1: EVALUATE THE TOXICITY, PHARMACOKINETIC, AND PHARMACODYNAMIC PROPERTIES OF T3 IN TUMOR-BEARING MICE. 2. AIM 2: EXAMINE THE THERAPEUTIC EFFICACY OF T3 IN COMBINATION WITH CYTOTOXIC DRUGS OR IRRADIATION. OUR STUDIES AIM TO FURNISH THE PRECLINICAL DATA NECESSARY FOR DESIGNING CLINICAL TRIALS TO ASSESS T3 AS A POTENTIAL TREATMENT FOR MB IN PATIENTS, PAVING THE WAY TO APPLY T3 AS A NOVEL THERAPEUTIC MODALITY FOR MB.