Fred Hutchinson Cancer Center

LEADERSHIP GROUP FOR A GLOBAL HIV VACCINE CLINICAL TRIALS NETWORK

HVTN LABORATORY PROGRAM

LEADERSHIP FOR HIV/AIDS CLINICAL TRIALS NETWORKS; HIV VACCINE TRIALS NETWORK

CANCER CENTER SUPPORT GRANT (COMPREHENSIVE)

LEADERSHIP FOR HIV/AIDS CLINICAL TRIALS NETWORKS; HIV PREVENTION TRIALS NETWORK

SWOG STATISTICS AND DATA MANAGEMENT CENTER

ADULT LEUKEMIA RESEARCH CENTER

EARLY DETECTION RESEARCH NETWORK: DATA MANAGEMENT AND COORDINATING CENTER

THE PACIFIC NORTHWEST PROSTATE CANCER SPORE

MIXED HEMATOPOIETIC CHIMERISM AFTER STEM CELL ALLOGRAFTS

SEATTLE VACCINE TRIALS UNIT

CELL AND GENE THERAPY FOR HIV CURE

COLORECTAL CANCER GENOME-WIDE ASSOCIATION STUDIES CONSORTIUM

PARTNERSHIP FOR THE ADVANCEMENT OF CANCER RESEARCH: NMSU-FHCRC (2 OF 2)

CANCER IMMUNOTHERAPY TRIALS NETWORK CENTRAL OPERATIONS AND STATISTICAL CENTER

HAWAIIAN, ASIAN AMERICAN, AND PACIFIC ISLANDER (HAAPI) COORDINATING CENTER - SUMMARY/ABSTRACT PEOPLE OF ASIAN, HAWAIIAN, OR PACIFIC ISLANDER (ASA-NHPI) ANCESTRY, WHILE REPRESENTING 7.7% OF THE US POPULATION, HAVE BEEN LARGELY UNDERREPRESENTED FROM NIH-FUNDED PROSPECTIVE EPIDEMIOLOGIC STUDIES. AS A RESULT, THERE ARE LARGE GAPS IN OUR KNOWLEDGE OF THE BURDEN AND CAUSES OF CARDIOVASCULAR, METABOLIC, AND MENTAL HEALTH DISORDERS IN THESE POPULATIONS. INDIVIDUALS OF THESE BACKGROUNDS HAVE EXPERIENCED, TO VARYING DEGREES, THE BARRIERS, STRESSES, AND STEREOTYPING EXPERIENCED BY OTHER MINORITIES WHILE ALSO HAVING CHALLENGES THAT ARE UNIQUE TO THEM. UNDERSTANDING THE HETEROGENEITY OF THEIR LIFESTYLES AND SOCIETAL AND ENVIRONMENTAL CIRCUMSTANCES, AS WELL AS THEIR ANCESTRY, IS A CRITICAL FIRST STEP IN DETERMINING THEIR HEALTH NEEDS AND HOW TO ADDRESS THEM. THE HETEROGENEITY IN THESE POPULATIONS, FOLLOWED LONGITUDINALLY AND CONTRASTED WITH OTHER POPULATIONS, MAY ADD UNIQUE INSIGHTS INTO THE ETIOLOGY OF BOTH PHYSICAL AND MENTAL HEALTH CONDITIONS. IN THIS APPLICATION FOR THE HAWAIIAN, ASIAN AMERICAN, AND PACIFIC ISLANDER COORDINATING CENTER (HAAPI-CC), WE PROPOSE TO: (1) BRING EXCEPTIONAL SCIENTIFIC, STATISTICAL, AND CULTURAL EXPERTISE TO THE EFFORT OF ASSESSING THE PHYSICAL AND MENTAL HEALTH AND THEIR DETERMINANTS IN PEOPLE OF HAWAIIAN, ASIAN, AND PACIFIC ISLANDER ANCESTRY; (2) PROVIDE THE OPERATIONAL, DATA SCIENCE, AND BIOREPOSITORY INFRASTRUCTURE AND LEADERSHIP TO SUPPORT THE SCIENTIFIC PRIORITIES OF THE COHORT AND STIMULATE AND ENHANCE ANCILLARY STUDY OPPORTUNITIES BROADLY; (3) COORDINATE AND SUPPORT CLINICAL OR COMMUNITY FIELD CENTER (CCFC) ACTIVITIES TO ENHANCE RECRUITMENT AND RETENTION AND BROADER COMMUNITY ENGAGEMENT; AND (4) ENHANCE CAREER DEVELOPMENT OF EARLY STAGE INVESTIGATORS, PARTICULARLY THOSE FROM UNDER-REPRESENTED BACKGROUNDS. THROUGH THIS EFFORT, WE CAN ESTIMATE THE PREVALENCE OF CARDIOVASCULAR DISEASES AND RISK FACTORS AND MENTAL HEALTH CONDITIONS, STUDY THEIR INTERPLAY AND TRAJECTORIES OVER TIME, AND EXAMINE ASSOCIATIONS WITH NOVEL EXPOSURES DERIVED FROM DATA LINKAGES AND BIOSPECIMENS. WE ANTICIPATE LEADING A NUMBER OF ANCILLARY STUDIES TO OBTAIN ADDITIONAL RICH DATA FROM NOVEL SOURCES (WEARABLES, MHEALTH, GENOMICS, PROTEOMICS, METABOLOMICS, MICROBIOME, CARDIAC AND BRAIN IMAGING). THROUGH THESE EFFORTS, WE AND OUR CCFC COLLEAGUES, WILL ADVANCE THE KNOWLEDGE OF THE HEALTH CONDITIONS OF ASIAN, HAWAIIAN, AND PACIFIC ISLANDERS AND PROVIDE THE INFRASTRUCTURE FOR DEEPER UNDERSTANDING OF THEIR BIOLOGICAL, ENVIRONMENTAL, AND SOCIOLOGICAL UNDERPINNINGS. ,

HEMATOPOPIETIC STEM CELL TRANSPLANTATION

FRED HUTCHINSON CANCER RESEARCH CENTER LUNG SPORE

BREAST AND OVARY CANCER CLINICAL VALIDATION CENTER

CELL AND GENE THERAPY FOR NONMALIGNANT BLOOD DISORDERS

NUTRITION AND PHYSICAL ACTIVITY ASSESSMENT STUDY (NPAAS)

PREVENTION OF LETHAL METASTATIC BREAST CANCER BY IDENTIFYING AND ERADICATING CLINICALLY RELEVANT DISSEMINATED TUMOR CELLS

PREVENTION OF LETHAL METASTATIC BREAST CANCER BY IDENTIFYING AND ERADICATING CLINICALLY RELEVANT DISSEMINATED TUMOR CELLS

COLABORACION EVITA: HPV-RELATED CANCER PREVENTION PARTNERSHIP CENTER

POLYGENIC RISK SCORES FOR DIVERSE POPULATIONS - BRIDGING RESEARCH AND CLINICAL CARE

CAREER DEVELOPMENT IN PEDIATRIC AND MEDICAL ONCOLOGY

1/2 GANCICLOVIR TO PREVENT REACTIVATION OF CYTOMEGALOVIRUS IN PATIENTS WITH ACUTE RESPIRATORY FAILURE AND SEPSIS - PROJECT SUMMARY SEPSIS-ASSOCIATED ACUTE RESPIRATORY FAILURE IS A LEADING CAUSE OF MORBIDITY, MORTALITY AND HEALTH CARE EXPENDITURE WORLD-WIDE, AND IS INCREASING IN INCIDENCE. DESPITE INTENSIVE INVESTIGATION, THERE ARE FEW PHARMACOLOGIC INTERVENTIONS, AND CARE IS LARGELY SUPPORTIVE. CYTOMEGALOVIRUS (CMV) IS A HUMAN HERPESVIRUS THAT INFECTS 50- 80% OF HEALTHY ADULTS AND ESTABLISHES LIFELONG LATENCY IN THE LUNG, GENERALLY CAUSING OVERT DISEASE ONLY IN SEVERELY IMMUNOSUPPRESSED PATIENTS. CMV REACTIVATION (VIRAL REPLICATION) FROM LATENCY OCCURS IN ~40% OF CMV SEROPOSITIVE, OTHERWISE IMMUNOCOMPETENT PERSONS DURING CRITICAL ILLNESS AND IS ASSOCIATED WITH WORSE CLINICAL OUTCOMES INCLUDING INCREASED MORTALITY, PROLONGED MECHANICAL VENTILATION, AND INCREASED ICU LENGTH OF STAY. COMPELLING EVIDENCE IMPLICATING CMV REACTIVATION AS A CAUSAL CONTRIBUTOR TO MORBIDITY AND MORTALITY IN SEPSIS- ASSOCIATED RESPIRATORY FAILURE COMES FROM ANIMAL MODELS AND OUR RECENTLY COMPLETED NHLBI-FUNDED PHASE 2 RANDOMIZED PLACEBO-CONTROLLED TRIAL (RCT) OF GANCICLOVIR PROPHYLAXIS. IN THIS TRIAL, AMONG CMV SEROPOSITIVE ADULTS WITH SEPSIS-ASSOCIATED RESPIRATORY FAILURE, GANCICLOVIR EFFECTIVELY SUPPRESSED CMV REPLICATION, HAD AN ACCEPTABLE SAFETY PROFILE, AND WAS ASSOCIATED WITH IMPROVED CLINICAL OUTCOMES, INCLUDING INCREASED VENTILATOR-FREE DAYS (VFD), SHORTER DURATION OF MECHANICAL VENTILATION AMONG SURVIVORS, SHORTER ICU LENGTH OF STAY, AND IMPROVED PAO2/FIO2 RATIO IN DAY-7 SURVIVORS. WE HYPOTHESIZE THAT IV GANCICLOVIR ADMINISTERED EARLY IN CRITICAL ILLNESS WILL EFFECTIVELY SUPPRESS CMV REACTIVATION IN CMV SEROPOSITIVE ADULTS WITH SEPSIS-ASSOCIATED ACUTE RESPIRATORY FAILURE, THEREBY REDUCING LUNG DAMAGE, ACCELERATING RECOVERY, AND LEADING TO IMPROVED CLINICAL OUTCOMES. WE PROPOSE TO CONDUCT A PHASE 3 RCT TO DETERMINE WHETHER THE ANTIVIRAL DRUG GANCICLOVIR GIVEN AS PROPHYLAXIS IMPROVES VFDS AND OTHER CLINICALLY RELEVANT OUTCOMES WHEN ADMINISTERED WITHIN 5 DAYS OF ICU ADMISSION TO CMV SEROPOSITIVE IMMUNOCOMPETENT ADULTS WITH SEPSIS-ASSOCIATED ACUTE RESPIRATORY FAILURE. WE WILL MEASURE THE EFFECT OF THE STUDY INTERVENTION ON THE PRIMARY TRIAL OUTCOME (VFDS) AND SECONDARY OUTCOMES (MORTALITY AT 28 DAYS, DURATION OF MECHANICAL VENTILATION IN SURVIVORS, OXYGENATION, STATIC RESPIRATORY SYSTEM COMPLIANCE, CMV PLASMA AND LUNG REACTIVATION, AND A CORE SET OF LONGER-TERM OUTCOMES AT 6 MONTHS). IN EXPLORATORY ANALYSES, WE WILL ASSESS BASELINE FACTORS AS PREDICTORS FOR CMV REACTIVATION, AND CHARACTERIZE THE RELATIONSHIP OF CMV VIRAL LOAD KINETICS WITH VFDS AND OTHER CLINICAL OUTCOMES. OUR INTERDISCIPLINARY TEAM HAS UNIQUE EXPERIENCE IN SUCCESSFULLY COORDINATING MULTI-SITE MULTI-PI ICU-BASED RCTS. WE HAVE ESTABLISHED A NETWORK OF 19 CLINICAL SITES IN THE US, ALL OF WHICH HAVE ROBUST INFRASTRUCTURE FOR ICU CLINICAL TRIALS AND PROVEN ABILITY TO RECRUIT PATIENTS INTO RCTS. IF IT IS EFFECTIVE, THIS INEXPENSIVE AND FEASIBLE INTERVENTION HAS THE POTENTIAL TO SIGNIFICANTLY IMPROVE CARE OF PATIENTS WITH SEPSIS-ASSOCIATED RESPIRATORY FAILURE, SUBSTANTIALLY CHANGE CLINICAL PRACTICE, AND OFFER NEW INSIGHTS INTO THE SEPSIS-CMV REACTIVATION RELATIONSHIP.

USING FUNCTIONAL GENOMICS TO INFORM GENE ENVIRONMENT INTERACTIONS FOR COLORECTAL CANCER

MOLECULAR ANALYSIS OF GENETIC RECOMBINATION AND DNA BREAK REPAIR

EXPANSION AND TARGETED MATURATION OF GERMLINE HIV-1 BNAB-ASSOCIATED BCRS

IMPROVING OUTCOMES ASSESSMENT IN CHRONIC GVHD

THE ROLE OF ANTIBODIES IN MOTHER TO CHILD HIV TRANSMISSION

NCI CANCER SCREENING RESEARCH NETWORK: COORDINATING AND COMMUNICATION CENTER - SUMMARY/ABSTRACT THIS APPLICATION IS BEING SUBMITTED IN RESPONSE TO THE NOSI IDENTIFIED AS NOT-CA-24-111. THE NCI-INITIATED CANCER SCREENING RESEARCH NETWORK (CSRN) IS A COOPERATIVE GROUP DEVELOPED TO ADVANCE EARLY DETECTION RESEARCH INTO POPULATION-LEVEL TRIALS AND RELATED STUDIES TO EVALUATE NOVEL APPROACHES TO CANCER SCREENING. THE VANGUARD TRIAL IS THE FIRST CSRN STUDY AND ITS PRIMARY OBJECTIVES ARE 1) TO DETERMINE THE FEASIBILITY OF A RANDOMIZED CONTROLLED TRIAL OF TWO NOVEL MULTICANCER DETECTION (MCD) ASSAYS AND 2) TO ENSURE EQUITABLE PARTICIPATION THROUGH RECRUITING AND RETAINING DIVERSE POPULATIONS. FRED HUTCHINSON CANCER CENTER SERVES AS THE COORDINATING AND COMMUNICATIONS CENTER (CCC) FOR THE VANGUARD STUDY AND CSRN, PROVIDING SCIENTIFIC LEADERSHIP, TRAINING, IMPLEMENTATION SUPPORT AND MONITORING FOR NINE ACCRUAL AND ENROLLMENT SITES (“ACCESS HUBS”) LOCATED ACROSS THE UNITED STATES IN DIVERSE GEOGRAPHICAL, SOCIOECONOMIC, AND CULTURAL COMMUNITIES. IN YEAR 1, THE CCC HAS DEVELOPED AND SUPPORTED THE CSRN COMMITTEE STRUCTURE, LED PROTOCOL DEVELOPMENT, INITIATED STAFF TRAINING AND SERVED AS THE PRIMARY POINT OF CONTACT FOR ACCESS HUBS. THROUGH THESE INTERACTIONS, THE CCC HAS BECOME AWARE OF THE LARGER NUMBER AND GREATER DIVERSITY AND COMPLEXITY OF THE ACCESS HUBS AND THEIR RECRUITMENT PLANS TO REACH UNDER-REPRESENTED AND UNDERSERVED POPULATIONS. EACH ACCESS HUB WILL COORDINATE MULTIPLE RECRUITMENT SITES, SOME CONCENTRATED IN WELL-CIRCUMSCRIBED URBAN AREAS AND OTHERS DISPERSED REGIONALLY OR EVEN NATIONALLY. SOME WILL RECRUIT FROM A SINGLE, CLOSED HEALTH SYSTEM WHILE OTHERS WILL USE A COMBINATION OF ACADEMIC MEDICAL CENTERS, PRIVATE CLINICS AND FEDERALLY QUALIFIED HEALTH CENTERS. AN ADDITIONAL COMPLEXITY OF THE VANGUARD TRIAL IS IN SUPPORTING DIAGNOSTIC WORKFLOWS FOR MCD TESTS, SINCE NEITHER THE SCREENING PROGRAM SENSITIVITY NOR THE ACCURACY OF TISSUE OF ORIGIN PREDICTIONS ARE KNOWN AND THE FACILITIES AVAILABLE AND ASSOCIATED COSTS CONCERNS VARY CONSIDERABLY ACROSS SITES. TO MEET THE UNANTICIPATED DEMANDS OF THIS FIRST RCT OF MCD ASSAYS IN THE US, WE PROPOSE TO: 1) EXPAND COMMUNITY ADVISORY BOARD (CAB) PARTICIPATION; 2) PROVIDE ADDITIONAL LANGUAGE TRANSLATIONS OF PARTICIPANT MATERIALS; 3) PROVIDE ADDITIONAL RECRUITMENT AND RETENTION MATERIALS; 4) INCREASE TRAINING AND MONITORING RESOURCES; 5) INCREASE INVESTIGATOR TIME FOR COMMITTEE WORK, ENGAGEMENT WITH HUBS, AND IMPLEMENTATION OF A DIAGNOSTIC REVIEW BOARD.

PROTEOGENOMIC STUDIES AIMED AT UNDERSTANDING OVARIAN TUMOR RESPONSES TO AGENTS TARGETING THE DNA DAMAGE RESPONSE AND TRANSLATING THIS KNOWLEDGE INTO CLINICAL BENEFIT

CORE CENTER FOR STEM CELL AND TRANSPLANTATION BIOLOGY

SELF-AMPLIFYING MRNA-BASED VACCINES TO ELICIT VRC01-CLASS BNABS - ABSTRACT OVERALL THE MAIN GOAL OF OUR IPCAVD PROGRAM GRANT IS TO EVALUATE IN HUMANS SELF-AMPLIFYING MRNA (SARNA) VACCINES THAT EXPRESS TWO HIV-1 ENV-DERIVED PROTEIN IMMUNOGENS THAT ACTIVATE AND INITIATE THE MATURATION OF VRC01-CLASS B CELL RECEPTORS (BCRS). THE FIRST IMMUNOGEN, 426C.MOD.CORE, WAS SPECIFICALLY DESIGNED TO BIND WITH HIGH AFFINITY TO THE UNMUTATED (GERMLINE, GL) FORMS OF THOSE BCRS AS THEY ARE EXPRESSED ON THE SURFACE OF NAÏVE B CELLS. THE SECOND IMMUNOGEN, HXB2.WT.CORE, ALTHOUGH UNABLE TO BIND GERMLINE VRC01-CLASS BCRS, BINDS THE VRC01-CLASS BCRS THAT BECAME ACTIVATED BY 426C.MOD.CORE AND HAVE ACCUMULATED SOME SOMATIC MUTATIONS. AS A RESULT, THE BOOST IMMUNIZATION WITH HXB2.WT.CORE FURTHERS THE MATURATION OF THE VRC01-CLASS ANTIBODIES ELICITED BY THE 426C.MOD.CORE. THESE OBSERVATIONS WERE MADE WITH THE ADJUVANTED RECOMBINANT (REC) FORMS OF THESE TWO IMMUNOGENS. AS MRNA- BASED VACCINES ARE LESS COSTLY AND MORE EASILY GMP-MANUFACTURED THAT REC PROTEINS, WE BELIEVE THAT THEY WILL ACCELERATE THE PRECLINICAL AND CLINICAL EVALUATION OF HIV-1 ENV-DERIVED IMMUNOGENS. HERE, WE PROPOSE TO FIRST COMPARE PRECLINICALLY THE VRC01 B CELL AND ANTIBODY RESPONSES ELICITED BY THESE TWO ENV IMMUNOGENS WHEN DELIVERED BY SARNA VACCINES TO THOSE ELICITED BY THE CORRESPONDING ADJUVANTED REC PROTEINS. AND THEN, IF THE RESULTS ARE PROMISING, THE SARNA VACCINES EXPRESSING THE TWO IMMUNOGENS WILL BE GMP-MANUFACTURED FOR CLINICAL EVALUATION. AS THE 426C.MOD.CORE ADJUVANTED REC PROTEIN WILL BE EVALUATED CLINICALLY (PHASE I) IN THE SPRING OF 2022 (HVTN301) AND THE HXB2.WT.CORE REC PROTEIN IS CURRENTLY BEING GMP MANUFACTURED FOR A FOLLOW-UP PHASE I CLINICAL EVALUATION IN 2023, WE WILL BE IN A UNIQUE POSITION TO COMPARE THE VRC01 B CELL AND ANTIBODY RESPONSES ELICITED BY HUMANS IMMUNIZED WITH THESE TWO HIV-1 ENV-DERIVED IMMUNOGENS WHEN DELIVERED AS ADJUVANTED REC PROTEINS AND AS EXPRESSED BY SARNA VACCINES. TO ACCOMPLISH OUR GOALS IN THIS IPCAVD GRANT WE WILL TAKE ADVANTAGE OF OUR EXPERTISE IN IMMUNOGEN-DESIGN AND TESTING, EXPERTISE IN THE ANALYSIS OF B CELL AND ANTIBODY RESPONSES ELICITED BY VACCINATION AND DURING INFECTION, OUR ABILITY TO RAPIDLY SEQUENCE BCR GENES USING HIGH THROUGH PUT TECHNOLOGIES, THE AVAILABILITY OF APPROPRIATE ANIMAL MODELS, OUR EXPERTISE IN SARNA VACCINE TECHNOLOGY, OUR UNIQUE EXPERTISE IN CONDUCTING CLINICAL TESTING OF HIV-1 VACCINES, THE EXISTING COLLABORATION AMONG THE PARTICIPATING GROUPS AND THE DOCUMENTED EXPERTISE OF THE PARTICIPANTS TO SUCCESSFULLY MANAGE COMPLEX PROGRAMS.

MODULATING THE IMPACT OF CRITICAL EVENTS IN EARLY HIV INFECTION: EFFECT OF EARLY ART INITIATION AND ALCOHOL USE

GENETIC AND MOLECULAR BASIS FOR SRSF2 MUTATIONS IN MYELODYSPLASIA

UPGRADING INSTITUTIONAL CAPACITY WITH A BSL-3 FACILITY FOR MULTIDISCIPLINARY BIOMEDICAL RESEARCH - PROJECT SUMMARY/ABSTRACT: THE FRED HUTCHINSON CANCER CENTER (FRED HUTCH) PROPOSES THE CONSTRUCTION OF AN ENHANCED BIOSAFETY LEVEL 3 (BSL-3)/ANIMAL BSL-3 FACILITY TO ADDRESS CRITICAL GAPS IN REGIONAL CAPACITY FOR HIGH-CONTAINMENT RESEARCH ON PATHOGENS OF SIGNIFICANT PUBLIC HEALTH CONCERN, PARTICULARLY HIGHLY PATHOGENIC AVIAN INFLUENZA (HPAI) AND OTHER EMERGING INFECTIOUS AGENTS. DESPITE FRED HUTCH’S LEADERSHIP IN INFECTIOUS DISEASE RESEARCH, THE ABSENCE OF AN ON-SITE BSL-3 FACILITY LIMITS THE INSTITUTION’S ABILITY TO FULLY SUPPORT MULTIDISCIPLINARY BIOMEDICAL RESEARCH AND RESPOND RAPIDLY TO OUTBREAKS. NOTABLY, SEATTLE CHILDREN’S RESEARCH INSTITUTE LACKS SHOWER-OUT AND EFFLUENT DECONTAMINATION SYSTEMS, AND THE UNIVERSITY OF WASHINGTON’S BSL-3 FACILITY ALSO LACKS AN EFFLUENT DECONTAMINATION SYSTEM. THE PROPOSED 5,145-SQUARE-FOOT FACILITY, LOCATED ON THE FRED HUTCH CAMPUS IN SEATTLE, WASHINGTON, WILL INCORPORATE NEXT-GENERATION BIOSAFETY FEATURES, INCLUDING A SHOWER-OUT SYSTEM, AN EFFLUENT DECONTAMINATION SYSTEM (EDS), AND DEDICATED CONTAINMENT ZONES. THE DESIGN INCLUDES FLEXIBLE LABORATORY SPACES, SPECIALIZED AREAS FOR PATHOGEN-SPECIFIC RESEARCH, AND ADVANCED FACILITIES FOR AUTOMATION, FLOW CYTOMETRY AND WASTE PROCESSING. THESE FEATURES ENSURE COMPLIANCE WITH NIH, CDC AND USDA BIOSAFETY STANDARDS, FURTHER ENABLING CUTTING-EDGE RESEARCH. THIS NEXT-GENERATION BSL-3 FACILITY WILL SERVE AS A REGIONAL HUB FOR COLLABORATION, LEVERAGING EXPERTISE FROM SEATTLE CHILDREN’S RESEARCH INSTITUTE, THE UNIVERSITY OF WASHINGTON, AND OTHER STAKEHOLDERS. BY APPLYING LESSONS FROM THE COVID-19 PANDEMIC AND EXPANDING RESEARCH CAPACITY FOR HIGH-PRIORITY PATHOGENS, THE FACILITY WILL STRENGTHEN PUBLIC HEALTH PREPAREDNESS, SUPPORT SUSTAINABLE INFRASTRUCTURE, AND BOLSTER THE SEATTLE AREA’S LEADERSHIP IN INFECTIOUS DISEASE RESEARCH. THE PROJECT DIRECTLY ALIGNS WITH FRED HUTCH’S MISSION TO ADVANCE GLOBAL HEALTH AND BIOMEDICAL INNOVATION BY PROVIDING CRITICAL INFRASTRUCTURE TO ADDRESS PATHOGENS WHICH CAUSE SEVERE DISEASE IN OUR IMMUNOCOMPROMISED TRANSPLANT PATIENTS AS WELL AS EMERGING INFECTIOUS DISEASE CHALLENGES. ITS CONSTRUCTION WILL POSITION FRED HUTCH AND ITS PARTNERS AS LEADERS IN COLLABORATIVE AND HIGH-IMPACT RESEARCH, DRIVING LONG-TERM SCIENTIFIC AND PUBLIC HEALTH ADVANCEMENTS.

UNDERSTANDING ADENOMA PROGRESSION: INTERPLAY AMONG TISSUE MICROENVIRONMENT, CLONAL ARCHITECTURE, AND GUT MICROBIOME - SUMMARY COLORECTAL CANCER (CRC) AFFECTS ~145,000 PEOPLE/YEAR IN THE US AND IS THE 3RD MOST COMMON CAUSE OF CANCER RELATED DEATHS. CRC ARISES FROM EARLY LESIONS THAT ARE PRE-CANCEROUS; THESE EARLY LESIONS ARE COLON ADENOMAS AND SERRATED SESSILE LESIONS (SSL). COLON ADENOMAS ACCOUNT FOR 80-85% OF THE CRC PRECANCEROUS LESIONS AND PROGRESS TO CRC VIA AN EARLY ADENOMAAADVANCED ADENOMAACRC SEQUENCE. IN LIGHT OF THE WELL CHARACTERIZED CLINICAL NATURAL HISTORY OF ADENOMAS, WE PLAN TO STUDY THEM AS EARLY LESIONS AND TO DETERMINE THE MECHANISMS INVOLVED IN THE FORMATION AND PROGRESSION OF EARLY PRECANCEROUS LESIONS. NOTABLY, ONLY A FEW EARLY ADENOMAS WILL PROGRESS TO ADVANCED ADENOMAS (AA) AND EVEN FEWER WILL PROGRESS TO CRC. OUR GROUP AND OTHERS HAVE SHOWN THAT MUTATIONS ALONE ARE NOT SUFFICIENT TO CAUSE ADENOMA INITIATION AND/OR PROGRESSION IN THE MAJORITY OF CASES. THERE ARE LIKELY MULTIPLE ADENOMA NONAUTONOMOUS MECHANISMS THAT COOPERATE WITH THE DNA ALTERATIONS IN THE ADENOMAS TO CAUSE PROGRESSION, AND THESE MECHANISMS ARE LIKELY OPERATIVE IN DISCRETE SUBSETS OF AFFECTED INDIVIDUALS. WE AND OTHERS HAVE OBSERVED ALTERATIONS, SUCH AS TISSUE SENESCENCE, HIGH CANCER DRIVER GENE MUTATION LOADS, ABERRANT DNA METHYLATION PATTERNS, AND DYSBIOTIC GUT MICROBIOMES, IN THE NORMAL COLON OF PEOPLE WITH ADVANCED ADENOMAS AND CRC PATIENTS. WE HAVE TERMED NORMAL COLONS WITH THESE FEATURES “PRIMED COLONS” AND PROPOSE THAT THESE FEATURES ARE PLAUSIBLE MECHANISMS THAT AFFECT ADENOMA INITIATION AND PROGRESSION. BASED ON THESE OBSERVATIONS AND OUR PRIOR STUDIES, WE HYPOTHESIZE THAT EARLY LESION PROGRESSION REQUIRES A SUITE OF HALLMARK BEHAVIORS AND THAT THESE BEHAVIORS ARE INDUCED BY ADENOMA AUTONOMOUS FACTORS (E.G. CANCER DRIVER GENE MUTATIONS) AND ADENOMA NONAUTONOMOUS FACTORS FROM THE “PRIMED COLON” OR ADENOMA MICROENVIRONMENT. OUR PROPOSED STUDIES WILL INTEGRATE BASIC AND TRANSLATIONAL CANCER RESEARCH PROJECTS TO ITERATIVELY EXAMINE THE DIRECT CAUSAL RELATIONSHIPS AND INTERACTIONS OF ADENOMAS, THE COLON “PRIMED” MICROENVIRONMENT, AND HOST- SYSTEMIC FACTORS AS “CO-ORGANIZERS” OF ADENOMA INITIATION AND/OR PROGRESSION. THE SPECIFIC AIMS ARE: AIM 1) TO DETERMINE THE ADENOMA CELL AUTONOMOUS MOLECULAR FACTORS THAT DISTINGUISH NONADVANCED ADENOMAS FROM ADVANCED ADENOMAS AND THAT REGULATE NONADVANCED ADENOMA PROGRESSION. (PROJECTS 1 AND 2) AIM 2) TO DETERMINE THE ADENOMA NONAUTONOMOUS FACTORS FROM THE “PRIMED” COLON AND FROM THE ADENOMA MICROENVIRONMENT THAT ASSOCIATE WITH ADVANCED HUMAN COLON ADENOMAS AND REGULATE ADENOMA PROGRESSION. THESE FACTORS WILL INCLUDE THE FOLLOWING “PRIMED” COLON STATES: 1. SENESCENCE STATE; 2. CANCER DRIVER GENE MUTATION BURDEN; 3. GUT MICROBIOME STATE; 4. COLON METHYLOME, AND 5. COLON IMMUNE ACTIVITY STATE. (PROJECTS 1-3) AIM 3)TO DETERMINE HOW ADENOMA AUTONOMOUS AND NONAUTONOMOUS FACTORS FROM THE ADENOMA MICROENVIRONMENT AND THE “PRIMED” COLON COOPERATE TO DRIVE ADENOMA FORMATION AND PROGRESSION.(PROJCTS 1-3)

PHYSICAL ACTIVITY TO IMPROVE CV HEALTH IN OLDER WOMEN: A PRAGMATIC TRIAL - THIS IS A COMPETITIVE RENEWAL APPLICATION FOR THE WOMEN’S HEALTH INITIATIVE (WHI) STRONG & HEALTHY (WHISH) TRIAL. AMERICA’S 65-AND-OLDER POPULATION IS PROJECTED TO DOUBLE IN SIZE FROM 49 MILLION TODAY TO 95 MILLION BY 2060, WITH WOMEN FAR OUTNUMBERING MEN, PARTICULARLY AMONG ADULTS AGED 85-AND-OLDER. COMPELLING EVIDENCE SUPPORTS THE HYPOTHESIS THAT PHYSICAL ACTIVITY (PA) REDUCES CARDIOVASCULAR (CV) DISEASE (CVD), PRESERVES PHYSICAL FUNCTION (PF) AND PROMOTES OTHER ASPECTS OF CV HEALTH IN OLDER ADULTS. WHISH IS A LANDMARK, PRAGMATIC RANDOMIZED CONTROLLED TRIAL TESTING WHETHER A CENTRALIZED, PUBLIC HEALTH INTERVENTION DESIGNED TO INCREASE AND/OR MAINTAIN PA LEVELS AND REDUCE SEDENTARY BEHAVIOR WILL REDUCE MAJOR CVD (MI, STROKE, CV DEATH) IN OLDER WOMEN. USING A RANDOMIZED CONSENT DESIGN TO SIMULATE REAL-WORLD PROGRAMMATIC IMPLEMENTATION, WHISH RANDOMIZED 49,333 ELIGIBLE PARTICIPANTS IN THE WHI EXTENSION STUDY TO A BEHAVIORAL INTERVENTION VERSUS USUAL FOLLOW-UP IN MAY 2015. A PASSIVE CONSENT PROCESS IN THE INTERVENTION GROUP (N=24,663) RESULTED IN <4% OF WOMEN “OPTING OUT” OF RECEIVING INTERVENTION MATERIALS. WHISH DELIVERS A TARGETED, ADAPTIVE, INSTRUCTIONAL INTERVENTION, BASED ON 2008 AND 2018 DHHS PA GUIDELINES AND DESIGNED TO COMPLEMENT THE NATIONAL INSTITUTE ON AGING’S (NIA) GO4LIFE® CAMPAIGN, USING SEASONAL NEWSLETTERS, MANUALS, PEDOMETERS, RESISTANCE BANDS, TELEPHONE AND E-MAIL MOTIVATIONAL MESSAGES, AND A WEBSITE DESIGNED FOR OLDER WOMEN. THE INTERVENTION ADAPTS TO PARTICIPANT FEEDBACK FROM ANNUAL SURVEYS AND OTHER INPUT REGARDING ACTIVITY PREFERENCES AND IS CUSTOMIZED AND TARGETED TO THEIR CURRENT PF AND PA LEVELS. PRIMARY EFFECTIVENESS AND SAFETY OUTCOMES (CVD, FRACTURE) ARE EVALUATED USING INTENTION-TO-TREAT IN THE ENTIRE RANDOMIZED COHORT. BY THE END OF THE CURRENT GRANT PERIOD (FEB. 2020), 4 YEARS OF FOLLOW-UP WILL BE AVAILABLE. BASED ON WHISH OBSERVED CVD EVENT RATES, INTERVENTION EFFECTS ON PA AND SEDENTARY BEHAVIOR, AND NEW WHI DATA RELATING PA BEHAVIORS TO CVD ENDPOINTS, REVISED POWER CALCULATIONS SUGGEST WE WILL HAVE ONLY 65% POWER TO EVALUATE THE IMPACT OF THE WHISH INTERVENTION ON CVD EVENTS. WE ESTIMATE THAT 4 ADDITIONAL YEARS OF FOLLOW-UP (8 YEARS OVERALL) WILL YIELD 85-89% POWER TO PROVIDE A DEFINITIVE TEST OF THE PRIMARY WHISH HYPOTHESIS. THIS APPLICATION PROPOSES TO EXTEND THE WHISH INTERVENTION AND FOLLOW-UP OF OUTCOMES FOR 4 ADDITIONAL YEARS SO THAT THE TRIAL CAN REACH A DEFINITIVE CONCLUSION ON THE BENEFITS AND RISKS OF THE PA INTERVENTION. WE ALSO PROPOSE TO LEVERAGE DATA AND BIOSPECIMEN COLLECTIONS IN A PLANNED WHI EXTENSION STUDY HOME VISIT TO ENABLE EVALUATION OF KEY MARKERS OF HEALTHY CVD AGING INCLUDING PHYSICAL PERFORMANCE, SLEEP DURATION AND INSOMNIA SYMPTOMS, AND DEPRESSIVE SYMPTOMS. PILOT STUDIES WILL BE EXECUTED TO EXPLORE LONG-TERM EFFECTS OF THE WHISH INTERVENTION ON CHANGES IN ESTABLISHED AND NOVEL BIOMARKERS KNOWN OR POSTULATED TO BE INFLUENCED BY PA LEVELS AND INDICATIVE OF VARIOUS UNDERLYING MECHANISMS RELATED TO CVD AGING. THE OUTCOMES OF WHISH, WHETHER POSITIVE, NULL, OR ADVERSE, COULD HAVE IMMENSE TRANSLATIONAL IMPACT ON THE FUTURE OF PA DISSEMINATION PROGRAMS FOR HEALTHY CV AGING.

LIFE AND LONGEVITY AFTER CANCER (LILAC): THE WOMEN'S HEALTH INITIATIVE CANCER SURVIVOR COHORT

GENETIC REQUIREMENTS OF HELICOBACTER PYLORI INFECTION

CLINICAL SIGNIFICANCE OF MHC HAPLOTYPES IN HCT

STRATEGIES TO ENHANCE ADOPTIVE TRANSFER T CELL CLONES

MYOTONIC DYSTROPHY LOCUS CONTROL

MOLECULAR PATHOEPIDEMIOLOGY OF CONTRALATERAL BREAST CANCER

DECODING THE INTERACTIONS BETWEEN T CELL RECEPTORS AND PEPTIDE-MHC

NOVEL GENE EDITING APPROACHES FOR HEMOGLOBINOPATHIES

EARLY AND REINFECTION IN HIGH RISK WOMEN

TARGETING NRF2 FOR CANCER CHEMOPREVENTION

PROSTATE CANCER ACTIVE SURVEILLANCE STUDY (PASS) COHORT: INFRASTRUCTURE SUPPORT FOR CANCER RESEARCH

MECHANISMS OF TRANSCRIPTIONAL REGULATION AND TRANSCRIPTION FACTOR SPECIFICITY - SUMMARY PRECISE REGULATION OF TRANSCRIPTION IS REQUIRED FOR MANY CELLULAR PROCESSES AND MISREGULATION OF GENE EXPRESSION IS LINKED TO MANY HUMAN DISEASES. IN PRIOR WORK, GREAT PROGRESS HAS BEEN MADE IN IDENTIFYING IMPORTANT MECHANISMS AND PRINCIPLES OF TRANSCRIPTIONAL REGULATION. WITH THIS BACKGROUND, AND USING NEW TECHNOLOGIES AND APPROACHES, THIS IS AN EXCELLENT TIME TO TACKLE THE NEXT SET OF FUNDAMENTAL PROBLEMS IN GENE REGULATION THAT HAVE BEEN DIFFICULT TO ADDRESS IN PRIOR WORK. TWO RELATED AND IMPORTANT QUESTIONS IN THE TRANSCRIPTION FIELD ARE: WHAT ARE THE PRIMARY MECHANISMS OF GENE REGULATION BY SEQUENCE-SPECIFIC TRANSCRIPTION FACTORS? AND, HOW DO THESE FACTORS COOPERATE TO ORCHESTRATE TRANSCRIPTION OF CELLULAR GENES? TO ADDRESS THESE QUESTIONS, WE WILL FOCUS ON THREE AREAS INVOLVING TRANSCRIPTION FACTOR AND COACTIVATOR SPECIFICITY AND THE ACTIVATION MECHANISMS USED AT MANY GENES: (I) MECHANISMS LEADING TO THE GENOME-WIDE SPECIFICITIES OF THE COACTIVATORS TFIID AND SAGA. DIFFERENTIAL USE OF THESE COACTIVATORS DEFINES TWO FUNDAMENTAL GENE CLASSES THAT DICTATE THE MECHANISMS OF PREINITIATION COMPLEX (PIC) ASSEMBLY AND THE RESPONSE TO TRANSCRIPTION FACTORS AND CHROMATIN. (II) THE GENE-SPECIFIC FUNCTIONS OF THE COACTIVATOR MEDIATOR IN TRANSCRIPTIONAL REGULATION. AT LEAST TWO DISTINCT PATHWAYS ARE USED BY TRANSCRIPTION FACTORS TO MODULATE MEDIATOR FUNCTION THAT ARE TRANSCRIPTION FACTOR AND PROMOTER-SPECIFIC, BUT THE MOLECULAR BASIS OF THESE MECHANISMS IS NOT WELL UNDERSTOOD. (III) MECHANISMS OF TRANSCRIPTION ACTIVATOR SPECIFICITY AND FUNCTION. WE WILL BROADEN OUR CURRENT STUDIES ON THE FUNCTION OF ACIDIC ACTIVATION DOMAINS TO EXAMINE MECHANISMS USED BY OTHER WIDELY USED ACTIVATOR TYPES AND TO EXAMINE HOW TRANSCRIPTION FACTORS BOUND AT NATIVE UAS/ENHANCER ELEMENTS COOPERATE. TO ADDRESS THESE FUNDAMENTAL PROBLEMS, AS IN PAST WORK, WE WILL USE A COMBINATION OF METHODS AND TECHNOLOGIES THAT INCLUDE MOLECULAR, BIOCHEMICAL, GENOMIC, COMPUTATIONAL, AND STRUCTURAL APPROACHES. IN COMBINATION WITH OUR STRONG PRELIMINARY RESULTS, THESE NEW APPROACHES AND DIRECTIONS WILL REVEAL IMPORTANT CONSERVED MECHANISMS AND PRINCIPLES THAT ILLUSTRATE HOW TRANSCRIPTION FACTORS, COACTIVATORS, CHROMATIN, AND THE BASAL TRANSCRIPTION MACHINERY WORK TOGETHER TO MODULATE GENOME-WIDE TRANSCRIPTION.

HUMAN PAPILLOMAVIRUS AND POLYOMAVIRUS ASSOCIATED MALIGNANCIES.

PREVENTING GVHD BY INHIBITION OF ALLOANTIGEN PRESENTATION IN THE GUT

MODELING PRECISION INTERVENTIONS FOR PROSTATE CANCER CONTROL

THE MYC TRANSCRIPTION FACTOR NETWORK AND THE PATH TO CANCER

STATISTICAL METHODS IN HIV VACCINE EFFICACY TRIALS

BIOLOGY AND THERAPY OF C11ORF95-RELA FUSION-DRIVEN EPENDYMOMA

CLONAL HEMATOPOIESIS IN THE WOMENS HEALTH INITIATIVE MEMORY STUDY

DEFINING BCR EVOLUTION DURING IMMUNIZATION

COORDINATING CENTER FOR POPULATION-BASED RESEARCH TO OPTIMIZE CANCER SCREENING (PROSPR) (U24)

PROTEOGENOMIC STUDIES TO UNDERSTAND MECHANISMS AND DRIVERS OF RESISTANCE TO IMMUNOTHERAPIES - PROJECT SUMMARY/ABSTRACT MELANOMA IS THE DEADLIEST FORM OF SKIN CANCER. ITS INCIDENCE IS ON THE RISE WITH 106,000 NEW CASES EXPECTED IN THE U.S. IN 2021. IMMUNE CHECKPOINT INHIBITORS (ICIS) HAVE REVOLUTIONIZED THE TREATMENT OF EARLY AND ADVANCED MELANOMA, WITH CONCURRENT ANTI-CTLA-4 AND ANTI-PD-1 MONOCLONAL ANTIBODIES DEMONSTRATING A RESPONSE IN ~50% OF PATIENTS, INCLUDING HIGHLY DURABLE RESPONSES. UNFORTUNATELY, THERE ARE NO ADEQUATE BIOMARKERS TO PREDICT RESPONSE TO SINGLE AGENT OR COMBINATION ICI, AND DUAL CHECKPOINT BLOCKADE IS ASSOCIATED WITH SIGNIFICANT GRADE 3/4 IMMUNE-RELATED ADVERSE EVENTS (IRAES) IN ~55% OF PATIENTS. THE GOALS OF OUR PTRC ARE DESIGNED TO ADDRESS TWO UNMET CLINICAL NEEDS: (I) IMPROVE OUR UNDERSTANDING OF MECHANISMS OF RESISTANCE TO ICIS TO DESIGN MORE EFFECTIVE IMMUNOTHERAPIES AND COMBINATIONS, AND (II) IDENTIFY POTENTIAL BIOMARKERS TO SELECT PATIENTS APPROPRIATELY FOR SINGLE AGENT VS COMBINATION IMMUNOTHERAPIES AND TO PREDICT AND MONITOR IRAES. IN OUR PRECLINICAL ARM, WE WILL PERFORM INTEGRATED PROTEOGENOMIC ANALYSIS OF CLINICALLY ANNOTATED, PRE-TREATMENT BIOPSIES FROM MELANOMA PATIENTS WHO RECEIVED ICI. THE DATA WILL BE ANALYZED IN THE CONTEXT OF CLINICAL ANNOTATIONS TO REFINE AN EXISTING SIGNATURE OF MELANOMA ICI RESPONSE IDENTIFIED BY OUR TEAM AND TO FURTHER ELUCIDATE MECHANISMS OF ICI RESPONSE/RESISTANCE AND SIGNATURES ASSOCIATED WITH IRAES. IN OUR CLINICAL ARM, WE WILL ANALYZE CLINICAL TRIAL BIOSPECIMENS USING MRM-BASED ASSAYS TO CONFIRM & EXTEND FINDINGS GENERATED IN THE PRECLINICAL ARM.

THE ROLE AND MECHANISM OF ALTERNATIVE RNA SPLICE VARIANTS AND GENE FUSIONS AS DRIVERS OF CANCER - ABSTRACT MY LAB HAS BEEN THE LEADER IN THE FIELD OF MOUSE MODELING FOR BRAIN TUMORS OVER THE PAST 15 YEARS. WE HAVE DEVELOPED A SUITE OF GENETICALLY ENGINEERED MOUSE MODELS THAT ARE DEMONSTRABLY REPRESENTATIVE OF HUMAN GLIOMAS AND OTHER TUMOR TYPES. THESE MODELS HAVE BEEN USED TO INFORM TREATMENT OPTIONS FOR CLINICAL AGENTS, AND THIS NOW ENABLES US TO PROPOSE THESE MODELS ARE SUITABLE TESTBEDS FOR TESTING POTENTIAL MAJOR IMPROVEMENTS TO HOW THESE DISEASES ARE TREATED. WE HAVE THREE PROJECTS. 1) WE ARE UNDERSTANDING THE CENTRAL ROLE OF SPECIFIC SPLICE VARIANTS OF TRKB IN EMBRYONIC DEVELOPMENT AND ONCOGENESIS THROUGHOUT THE BODY. THE RCAS MODELING SYSTEM HAS BEEN USED HERE TO SHOW THAT FORCED EXPRESSION OF THE EMBRYONIC SPLICE VARIANT IN ADULT TISSUES LEADS TO CANCER FORMATION BROADLY. IN THIS PROJECT WE WILL INVESTIGATE THE MECHANISMS OF ONCOGENESIS FOR THIS SPLICE VARIANT AND DETERMINE IF IT COULD BE A GOOD DIAGNOSTIC OR THERAPEUTIC TARGET. 2) WE ARE NOW USING THE MODELING SYSTEM DEVELOPED FOR GLIOMA TO ADDRESS THE BIOLOGY OF RARE TUMORS DRIVEN BY GENE FUSIONS. IN THIS GRANT WE PROPOSE TO UNDERSTAND THE MECHANISMS OF ONCOGENESIS FOR YAP1 GENE FUSIONS IN THE RARE TUMORS EPENDYMOMA, POROCARCINOMA AND AGGRESSIVE MENINGIOMA (ALL FOR WHICH WE HAVE YAP1 GENE FUSION DRIVEN MODELS CURRENTLY). 3) AND, WE WILL USE THESE MOUSE MODELS TO STUDY THERAPEUTIC RESPONSE AND IDENTIFY THERAPEUTIC STRATEGIES FOR THESE FUSION DRIVEN TUMORS INCLUDING IDENTIFICATION OF FDA APPROVED DRUGS THAT WOULD INTERVENE DOWNSTREAM OF THE ACTION OF THE GENE FUSION.

REGULATION OF CHROMOSOME SEGREGATION

PCPT AND SELECT COHORTS: CORE INFRASTRUCTURE SUPPORT FOR CANCER RESEARCH

PEDIARIC ONCOLOGY RESEARCH TRAINING PROGRAM

CLINICAL TRANSLATION OF A NEXGEN PLATFORM FOR QUANTIFYING PROTEIN NETWORKS IN HUMAN BIOSPECIMENS

DEFINING HUMAN CORRELATES OF SUPER-EVASIVE DISSEMINATED TUMOR CELLS, THEIR PATHOLOGICAL RELEVANCE AND HOW TO ERADICATE THEM

FECAL MICROBIOTA TRANSPLANTATION AND FIBER FOR THE TREATMENT OF GRAFT-VERSUS-HOST DISEASE AFTER HEMATOPOIETIC CELL TRANSPLANTATION - PROJECT SUMMARY ALLOGENEIC HEMATOPOIETIC CELL TRANSPLANTATION (HCT) IS A LIFE-SAVING TREATMENT FOR HEMATOLOGIC MALIGNANCIES THAT REMAINS THE TREATMENT OF CHOICE FOR CONDITIONS SUCH AS HIGH RISK LEUKEMIAS. GRAFT-VERSUS-HOST DISEASE (GVHD) IS A COMMON COMPLICATION OF ALLOGENEIC HCT, AFFECTING >50% OF PATIENTS. DESPITE DECADES OF PROGRESS IN TRANSPLANTATION BIOLOGY, WE HAVE LIMITED TREATMENT OPTIONS FOR THIS COMMON CONDITION ASSOCIATED WITH SUBSTANTIAL MORBIDITY AND MORTALITY. GVHD HAS BEEN LINKED TO LOSS OF GUT BACTERIAL DIVERSITY AND CHANGES IN BACTERIAL COMMUNITY COMPOSITION AFTER HCT. THERE IS COMPELLING EVIDENCE FROM ANTIBIOTIC INTERVENTION STUDIES IN ANIMALS AND HUMANS THAT MANIPULATION OF THE GUT MICROBIOTA INFLUENCES SUBSEQUENT RISK OF GVHD. OBSERVATIONAL STUDIES OF FECAL MICROBIOTA TRANSPLANTATION (FMT) HAVE GENERATED INTRIGUING DATA SUGGESTING THAT FMT IS A PROMISING INTERVENTION FOR SAFELY REPOPULATING THE GUT MICROBIOTA IN HCT RECIPIENTS WITH GVHD. HOWEVER, THE EFFECT OF FMT DELIVERY ROUTE ON MICROBIAL RECONSTITUTION HAS NOT BEEN INVESTIGATED IN A CONTROLLED MANNER, THE ROLE OF DIETARY SUPPLEMENTATION ON MAINTAINING A BENEFICIAL GUT MICROBIOTA AFTER FMT REMAINS UNEXPLORED IN THIS POPULATION, AND THERE IS LIMITED INSIGHT INTO MECHANISMS FOR HOW THE MICROBIOTA MAY IMPACT CLINICAL OUTCOMES AFTER FMT. FOR EXAMPLE, ADMINISTERING FMT VIA ORAL CAPSULES MAY SEED A LARGER AREA OF THE INTESTINAL TRACT YIELDING MORE DURABLE CHANGES IN GUT MICROBIAL COLONIZATION, BUT CONVERSELY COULD LEAD TO LOSS OF FUNCTIONALLY IMPORTANT BACTERIAL SPECIES THROUGH KILLING BY GASTRIC ACID AND BILE SALTS IN THE UPPER TRACT. SIMILARLY, COLONIZATION EFFICIENCY MAY BE ENHANCED BY PROVIDING BACTERIA WITH KEY NUTRIENTS SUCH AS DIETARY FIBER. IN ADDITION, DIETARY FIBER IS A SUBSTRATE FOR BACTERIAL PRODUCTION OF SHORT CHAIN FATTY ACIDS SUCH AS BUTYRATE LINKED TO IMMUNE MODULATION AND INTESTINAL HEALTH. IT IS UNKNOWN IF DIETARY FIBER SUPPLEMENTATION ENHANCES MICROBIOLOGICAL ENGRAFTMENT AFTER FMT IN THESE PATIENTS OR FOSTERS A METABOLIC ENVIRONMENT THAT PROMOTES HEALING AFTER HCT RELATED GUT INJURY. THERE ARE NO PUBLISHED RANDOMIZED CONTROLLED TRIALS OF FMT FOR TREATMENT OF GVHD. OUR PROPOSED F2 STUDY (FMT X FIBER) IN PATIENTS WITH GUT GVHD WILL INVESTIGATE HOW ROUTE OF FMT (ORAL CAPSULE, UPPER VS. COLONIC INSTILLATION, LOWER) AND DIETARY FIBER SUPPLEMENTATION INFLUENCE RECONSTITUTION OF A BENEFICIAL MICROBIOTA. THIS STUDY WILL FEATURE FREQUENT STOOL SAMPLING, ROBUST ANALYSIS OF BACTERIAL COMMUNITY COMPOSITION AND METAGENOMIC CONTENT IN STOOL, EVALUATION OF THE IMPACT OF THE INTERVENTIONS ON RECOVERY OF T-CELL SUBSETS IN BLOOD WITH KNOWN ASSOCIATIONS WITH GVHD, ASSESSMENT OF METABOLITES SUCH AS SHORT CHAIN FATTY ACIDS PRODUCED BY THE GUT MICROBIOTA THAT MAY AMELIORATE GVHD, AND FOLLOW-UP TO ASSESS RESOLUTION OF GVHD SYMPTOMS, STAGE, AND GRADE. THESE IN-DEPTH LONGITUDINAL MICROBIAL, METABOLIC, NUTRITIONAL, IMMUNOLOGICAL, AND CLINICAL DATA WILL ALLOW A MUCH-NEEDED, MECHANISTIC INVESTIGATION OF HOW A BENEFICIAL GUT MICROBIOME CAN BE OPTIMALLY RESTORED AND MAINTAINED THROUGH FMT FOR TREATMENT OF GVHD.

GENETIC CONFLICT SHAPES CENTROMERES AND HETEROCHROMATIN

CHROMOSOME METABOLISM AND CANCER TRAINING GRANT

INFLAMMATION-DRIVEN T CELL RESPONSES AND THEIR DICHOTOMOUS EFFECT ON HOST IMMUNITY

TRANSLATIONAL RESEARCH PROGRAM IN COLORECTAL CANCER DISPARITIES - PROJECT SUMMARY/ABSTRACT – OVERALL RACIAL AND ETHNIC DISPARITIES IN COLORECTAL CANCER (CRC) ARE PARTICULARLY PRONOUNCED IN AFRICAN AMERICAN AND ALASKA NATIVE PEOPLE. THESE DIFFERENCES CANNOT BE EXPLAINED BY ACCESS TO SCREENING AND HEALTH CARE ALONE, SUGGESTING UNDERLYING YET UNDERSTUDIED CONTRIBUTORS TO DISEASE ETIOLOGY, PROGRESSION, AND RESPONSE TO TREATMENT. ONGOING INNOVATIONS IN BIOTECHNOLOGY THAT ENABLE DETAILED EVALUATIONS OF THE UNDERPINNINGS OF TUMOR AND HOST MOLECULAR GENETICS AND GENOMIC BIOLOGY HAVE BEEN INADEQUATELY LEVERAGED TO ADDRESS THESE DISPARITIES. COLLECTIVELY, OUR OUTSTANDING TRANSDISCIPLINARY TEAM HAS THE EXPERTISE TO USE CUTTING-EDGE TECHNOLOGIES TO DRIVE INNOVATIVE TRANSLATIONAL CANCER DISPARITIES RESEARCH DIRECTLY FOCUSED ON DEVELOPING NOVEL PREVENTION, EARLY DETECTION, DIAGNOSIS, AND TREATMENT APPROACHES. TO ACHIEVE OUR OVERARCHING GOAL OF REDUCING PERSISTENT CRC DISPARITIES, PARTICULARLY THOSE PRESENT AMONG ALASKA NATIVE AND AFRICAN AMERICAN PEOPLE, WE PROPOSE THE FOLLOWING SPECIFIC AIMS: AIM 1: IMPROVE RISK STRATIFIED SCREENING AND EARLY DETECTION OF CRC ACROSS RACIAL AND ETHNIC POPULATIONS BY DEVELOPING RISK PREDICTION MODELS THAT PERFORM EQUALLY WELL ACROSS RACIAL AND ETHNIC GROUPS. AIM 2: REDUCE RACIAL AND ETHNIC DISPARITIES IN CRC-SPECIFIC MORTALITY BY DISCOVERING AND VALIDATING NOVEL MOLECULAR AND BIOLOGICAL CHANGES RELATED TO RISK OF LETHAL CRC AND RESPONSE TO TREATMENT IN RACIALLY AND ETHNICALLY DIVERSE PATIENTS THAT CAN GUIDE SURVEILLANCE AND TREATMENT SELECTION FOR CRC SURVIVORS. AIM 3: DISCOVER NOVEL THERAPEUTIC TARGETS FOR CRC ACROSS RACIALLY AND ETHNICALLY DIVERSE POPULATIONS AND TEST POTENTIAL CLINICAL INTERVENTIONS AIMED AT REDUCING CRC DISPARITIES BY ADVANCING OUR UNDERSTANDING OF DIFFERENCES AND SIMILARITIES IN THE GENETIC, MOLECULAR, AND MICROBIAL CHARACTERISTICS OF CRC IN DIVERSE POPULATIONS AND TESTING THE EFFECTIVENESS OF NOVEL INTERVENTIONS IN CLINICAL TRIALS THAT ENROLL DIVERSE CRC PATIENTS. OUR WORLD- CLASS INVESTIGATOR TEAM HAS EXPERTISE IN BASIC SCIENCE, CLINICAL AND TRANSLATIONAL RESEARCH, MINORITY HEALTH, AND CANCER DISPARITIES. DURING THE P20 SPORE PLANNING PHASE WE HAVE BROUGHT TOGETHER A LARGE BIOREPOSITORY OF VARIOUS BIOSPECIMEN TYPES AND DETAILED CLINICAL DATA FROM A LARGE, RACIALLY AND ETHNICALLY DIVERSE CRC PATIENT POPULATION WITH EQUAL NUMBERS OF AFRICAN AMERICAN, ALASKA NATIVE, HISPANIC AND NON-HISPANIC WHITE PATIENTS, AND THROUGH OUR LONG-TERM LEADERSHIP IN GENETIC EPIDEMIOLOGY WE HAVE ACCESS TO THE WORLD'S LARGEST AND MOST RACIALLY AND ETHNICALLY DIVERSE CRC GERMLINE GENETIC DATA SET. UTILIZING THESE UNIQUE RESOURCES, OUR PROGRAM WILL CONDUCT FOUR TRANSLATIONAL PROJECTS SUPPORTED BY THREE ESSENTIAL CORES THAT WILL PROVIDE CENTRALIZED EXPERTISE IN: A) LEADERSHIP AND ADMINISTRATION, B) BIOSPECIMENS, PATHOLOGY AND MOLECULAR TECHNOLOGIES, AND C) BIOSTATISTICS AND BIOINFORMATICS. OUR CAREER ENHANCEMENT AND DEVELOPMENTAL RESEARCH PROGRAMS WILL ENSURE THAT WE RECRUIT TALENTED AND DIVERSE INVESTIGATORS AND DEVELOP A PIPELINE OF NOVEL TRANSLATIONAL CANCER DISPARITIES RESEARCH PROJECTS. THROUGH THIS INTEGRATED EFFORT WE ENVISION REALIZING OUR GOAL OF A SUSTAINED TRANSLATIONAL RESEARCH PROGRAM FOCUSED ON ELIMINATING CRC DISPARITIES AND MORE BROADLY REDUCING CRC-RELATED MORBIDITY AND MORTALITY.

CANOE PARTNERSHIP: CANCER AWARENESS, NAVIGATION, OUTREACH, AND EQUITABLE INDIGENOUS HEALTH OUTCOMES - PROJECT SUMMARY/ABSTRACT THE CANOE PARTNERSHIP: CANCER AWARENESS, NAVIGATION, OUTREACH, AND EQUITABLE INDIGENOUS HEALTH OUTCOMES U19 COOPERATIVE AGREEMENT IS PROPOSED IN RESPONSE TO THE NEED TO IMPROVE CANCER OUTCOMES FOR AMERICAN INDIAN AND ALASKA NATIVE (AI/AN) COMMUNITIES NATIONALLY, WITH AN EMPHASIS ON THE WASHINGTON STATE (WA) CATCHMENT AREA OF THE FRED HUTCH/UNIVERSITY OF WASHINGTON/SEATTLE CHILDREN’S CANCER CONSORTIUM, A NATIONAL CANCER INSTITUTE (NCI) DESIGNATED COMPREHENSIVE CANCER CENTER. THE PROPOSED WORK BUILDS ON THE CONSORTIUM’S SUBSTANTIAL COMMUNITY ENGAGEMENT WITH TRIBES AND TRIBAL ORGANIZATIONS OVER THE PAST 22 YEARS, BEGINNING WITH THE SPIRIT OF EAGLES SPECIAL POPULATION NETWORK IN 2002, UP TO AND INCLUDING AN ONGOING R01 “ DIGITAL SMOKING CESSATION INTERVENTION FOR NATIONALLY-RECRUITED AMERICAN INDIANS AND ALASKA NATIVES: A FULL-SCALE RANDOMIZED CONTROLLED TRIAL ” (R01CA284687; PI: BRICKER) DISPARITIES IN CANCER OUTCOMES FOR THE AI/AN POPULATION ARE DUE TO MULTIPLE SOCIAL DETERMINANTS. THREE MAJOR SOURCES OF THESE DISPARITIES, AMENABLE TO INTERVENTION, ARE: 1) BEHAVIORS TO REDUCE CANCER RISK (E.G., SMOKING CESSATION), 2) ACCESS TO APPROPRIATE SCREENING BY WAY OF IMAGING TECHNOLOGIES (E.G., APPROPRIATE APPLICATION OF CHEST COMPUTED TOMOGRAPHY AND MAMMOGRAPHY) AND COLORECTAL CANCER (CRC) SCREENING PROCEDURES SUCH AS FECAL IMMUNOCHEMICAL TEST (FIT), AND COLONOSCOPY; AND 3) PRIMARY PREVENTION. WE PROPOSE A MULTIDIMENSIONAL APPROACH TO ADDRESSING THESE SOURCES OF DISPARATE CANCER OUTCOMES IN PARTNERSHIP WITH OUR TRIBAL AND COMMUNITY COLLABORATORS AT THE SOUTH PUGET INTERTRIBAL PLANNING AGENCY (REPRESENTING THE CHEHALIS, NISQUALLY, SKOKOMISH, SHOALWATER BAY, AND SQUAXIN ISLAND TRIBES) AND THE BLACK HILLS CENTER FOR AMERICAN INDIAN HEALTH (RAPID CITY, SD). TOGETHER, WE WILL USE COMMUNITY BASED PARTICIPATORY RESEARCH (CBPR) APPROACHES AND THE INDIGENOUS CANCER HEALTH EQUITY INITIATIVE MODEL TO EMPOWER AND ENGAGE TRIBES AND TRIBAL ORGANIZATIONS THROUGH OUR THREE RESEARCH PROJECTS. OUR OVERALL SPECIFIC AIMS ARE: 1) IMPROVE RATES OF CESSATION OF COMMERCIAL TOBACCO SMOKING AMONG A NATIONALLY RECRUITED SAMPLE OF AI/AN ADULTS (RESEARCH PROJECT 1); 2) IMPROVE RATES OF LUNG, COLORECTAL, AND BREAST CANCER SCREENINGS AMONG OUR TRIBAL PARTNER POPULATIONS IN THE CONSORTIUM’S CATCHMENT AREA (RESEARCH PROJECTS 2 & 3); 3)PREPARE THE NEXT GENERATION OF RESEARCHERS IN INDIGENOUS CANCER EQUITY AND PROVIDE THEM WITH RESOURCES TO OBTAIN PRELIMINARY DATA TO INFORM FUTURE CANCER EQUITY RESEARCH IN INDIAN COUNTRY (PILOT GRANT PROGRAM); AND 4) DEVELOP INFRASTRUCTURE TO SUPPORT EQUITABLE ENGAGEMENT OF TRIBAL PARTNERS AND INDIGENOUS FRAMEWORKS IN CANCER RESEARCH. (ADMINISTRATIVE AND COMMUNITY ENGAGEMENT CORES). THE OVERALL PUBLIC HEALTH IMPACT OF THE PROPOSED WORK WILL BE HIGH, GIVEN THE FOCUS ON SMOKING CESSATION, CANCER SCREENINGS AND VACCINATIONS THAT ALTOGETHER WILL PREVENT AND CONTROL CANCERS THAT ARE HIGHLY PREVALENT AND ARE RESPONSIBLE FOR A LARGE SHARE OF DISPARATE MORTALITY RATES AMONG INDIGENOUS POPULATIONS. THE PUBLIC HEALTH IMPACT OF THIS WORK WILL BE HIGH, GIVEN ITS FOCUS ON MODIFIABLE BEHAVIORS AND ON FUTURE GENERATIONS OF INDIGENOUS CANCER HEALTH EQUITY RESEARCHERS.

CHARACTERIZING THE BROAD ANTIBODY RESPONSE TO HIV SUPERINFECTION

CONSORTIUM ON TRANSLATIONAL RESEARCH IN EARLY DETECTION OF LIVER CANCER: DATA MANAGEMENT AND COORDINATING CENTER (DMCC)

STATISTICS AND DATA MANAGEMENT CENTER (SDMC) FOR THE NCI CANCER SCREENING RESEARCH NETWORK (CSRN) - MULTI-CANCER DETECTION ASSAYS OFFER NEW OPPORTUNITIES TO SCREEN FOR MANY DIFFERENT CANCERS THAT CURRENTLY HAVE LIMITED OPTIONS FOR EARLY DETECTION. THE CANCER SCREENING RESEARCH NETWORK (CSRN) WILL CONDUCT DEFINITIVE CLINICAL TRIALS AND STUDIES TO EVALUATE THESE ASSAYS. DESIGN AND IMPLEMENTATION OF SCREENING TRIALS INVOLVE MANY CHALLENGES. CANCER INCIDENCE AND DEATH ARE RARE EVENTS IN AN AVERAGE RISK POPULATION.TRIAL DESIGNS MUST BALANCE SCREENING FREQUENCY, TRIAL DURATION, AND SAMPLE SIZE TO ACHIEVE TRIAL OBJECTIVES IN A COST-EFFICIENT MANNER. IMPLEMENTATION MUST ANTICIPATE ISSUES SUCH AS NON-ADHERENCE, NON-COMPLIANCE, AND CONTAMINATION. ANALYSIS MUST ACCOMMODATE THE DESIGN WHILE ADAPTING TO THE CIRCUMSTANCES OF IMPLEMENTATION. THE STATISTICS AND DATA MANAGEMENT CENTER (SDMC) OF THE CSRN WILL OFFER A RIGOROUS SYSTEM FOR CSRN TRIAL DESIGN, MANAGEMENT AND ANALYSIS SO THAT THE INFORMATION GENERATED BY CSRN TRIALS FORMS A SOUND BASIS FOR NATIONAL CANCER SCREENING POLICY. OUR TEAM BRINGS TOGETHER STATISTICAL LEADERS AND CLINICAL TRIAL MANAGEMENT EXPERTS WITH EXPERIENCE IN MAJOR CLINICAL TRIALS NETWORKS, INCLUDING THE WOMEN’S HEALTH INITIATIVE CLINICAL COORDINATING CENTER, THE SWOG STATISTICS AND DATA MANAGEMENT CENTER AND THE EARLY DETECTION RESEARCH NETWORK DATA MANAGEMENT AND COORDINATING CENTER. WE HAVE EXPERTLY DESIGNED, IMPLEMENTED, ANALYZED AND REPORTED CANCER SCREENING, PREVENTION, AND TREATMENT TRIALS. THIS WORK HAS REQUIRED DEVELOPING PROCEDURES AND PROCESSES FOR EXPERT EXECUTION OF TRIALS AND PRODUCTION OF RELIABLE RESULTS. IT HAS NECESSITATED CREATING CLOSE COLLABORATIONS WITH CLINICIANS, SCIENTISTS, PATIENT ADVOCATES, AND SUBJECT MATTER EXPERTS. AND, PARTICULARLY IN THE CASE OF SCREENING TRIALS, IT HAS INSPIRED DEVELOPMENT OF NOVEL STATISTICAL METHODS THAT HAVE BECOME ESTABLISHED IN THE FIELD. OUR GOAL IS TO PROMOTE EXCELLENCE IN ALL ASPECTS OF STATISTICAL AND DATA MANAGEMENT FOR THE CSRN. TO ADDRESS THE CRITICAL QUESTIONS REGARDING POTENTIAL BENEFITS AND RISKS OF NEW CANCER SCREENING METHODOLOGIES, THE CSRN CLINICAL TRIALS MUST BE DESIGNED AND IMPLEMENTED WITH GREAT INTEGRITY AND EFFICIENCY TO PRODUCE THE MOST KNOWLEDGE POSSIBLE WITHIN REALISTIC CONSTRAINTS OF TIME AND RESOURCES. TO ATTAIN THESE GOALS, THE SDMC FOR THE CSRN HAS FOUR SPECIFIC AIMS: (1) INTEGRATE THE SDMC WITH THE OTHER CSRN COMPONENTS. (2) PROVIDE RIGOROUS AND HIGH-QUALITY DESIGNS AND ANALYSIS FOR CSRN STUDIES. (3) BUILD A STATE-OF-THE-ART DATA SYSTEM TO ENSURE DATA QUALITY AND INTEGRITY FOR CSRN TRIALS. (4) DEVELOP STATISTICAL AND DATA MANAGEMENT APPROACHES TO A LARGE CSRN SCREENING CLINICAL TRIAL THAT WOULD BUILD UPON THE VANGUARD STUDY. MCD TESTING REPRESENTS A POTENTIAL PARADIGM SHIFT FOR CANCER EARLY DETECTION. SUCCESSFUL EXECUTION OF THESE AIMS WILL ENSURE THAT THE CSRN PRODUCES VALID AND RELIABLE QUANTITATIVE RESULTS CONCERNING THE EFFICACY AND BENEFIT-HARM TRADEOFFS OF CANDIDATE PRODUCTS TO SUPPORT EVIDENCE-BASED POLICIES CONCERNING THEIR USE.

SEATTLE DIETARY BIOMARKER DEVELOPMENT CENTER

IMMUNO AND EPIGENETICS OF HEMATOPOIETIC CELL TRANSPLANTATION

IMMUNOPROTECTIVE PROPERTIES OF TISSUE-RESIDENT MEMORY T CELLS IN MICE AND HUMANS WITHIN MUCOSAL SITES

THE SYNGENICDNA AND ?POET PLATFORM: OVERCOMING INNATE BARRIERS TO GENETIC ENGINEERING IN BACTERIA.

MOLECULAR AND CELLULAR MECHANISMS OF WOUND REPAIR

DEFINING THE PROTECTIVE EFFICACY OF ANTIBODIES AGAINST THE EBV GH/GL GLYCOPROTEIN COMPLEX

DETERMINANTS OF RESPONSE TO CANCER IMMUNOTHERAPY - PROJECT SUMMARY/ABSTRACT WHILE IMMUNOTHERAPY IS TRANSFORMING CANCER TREATMENT, THE MAJORITY OF PATIENTS DO NOT ACHIEVE DURABLE RESPONSES. WE HAVE BEEN STUDYING RESPONSE AND RESISTANCE TO DIFFERENT IMMUNE CHECKPOINT INHIBITORS AND ARE NOW POISED TO PROPOSE MECHANISTIC STUDIES AIMED AT PROVIDING AN UNDERSTANDING OF THE IMMUNE STATES AND PATHWAYS THAT MEDIATE OR INHIBIT RESPONSE TO IMMUNE CHECKPOINT BLOCKADE. USING HIGH-DIMENSIONAL UNBIASED SINGLE-CELL RNA-SEQ (SCRNASEQ), WE CAN IDENTIFY BOTH CANONICAL AND NON-CANONICAL IMMUNE EFFECTORS THAT CAN MEDIATE ANTI-TUMOR RESPONSES. WE BELIEVE THAT NON-CANONICAL EFFECTORS SUCH AS CYTOTOXIC CD4 T CELLS, WHICH WE HAVE RECENTLY DESCRIBED, ARE NOT EFFECTIVELY TRIGGERED BY OUR CURRENT TREATMENTS. USING THE SAME SINGLE-CELL APPROACHES, WE CAN IDENTIFY BOTH KNOWN AND NOVEL CELL TYPES IN CANCER PATIENTS THAT CAN MEDIATE IMMUNE SUPPRESSION. IN OUR FIRST OBJECTIVE, WE WILL DETERMINE WHETHER COMBINATION IMMUNOTHERAPIES THAT INCLUDE DRUG(S) TARGETING SPECIFIC IMMUNOSUPPRESSIVE CELLS CAN ENHANCE THE FUNCTION OF THESE CYTOTOXIC CD4+ T CELLS. BY LEVERAGING NEOADJUVANT CLINICAL TRIALS WHERE PATIENTS RECEIVE IMMUNOTHERAPY PRIOR TO SURGERY, WE WILL USE SINGLE CELL GENOMICS AND PROTEOMICS TO DEFINE WHETHER THESE COMBINATIONS CAN 1) TARGET THE DESIRED IMMUNOSUPPRESSIVE MECHANISMS, AND 2) ENHANCE CANONICAL AND/OR NON-CANONICAL EFFECTORS WITHIN THE RESECTED TUMORS. WE WILL ALSO USE THIS APPROACH TO DETERMINE WHETHER WE CAN MAP THESE SPECIFIC CELL STATES INTO THE CIRCULATING COMPARTMENT. THE SECOND OBJECTIVE IS BASED ON A LONGSTANDING INTEREST IN OUR GROUP TO DEFINE THE DYNAMICS OF ANTIGEN-SPECIFIC RESPONSES. USING SINGLE-CELL T CELL RECEPTOR SEQUENCING, WE CAN IDENTIFY EXPANDED T CELL CLONES AS WELL AS FOLLOW THEIR LOCALIZATION. IN ADDITION TO UNDERSTANDING HOW IMMUNOTHERAPY COMBINATIONS INDUCE AND MODULATE SPECIFIC T CELL CLONOTYPES WITHIN THE TUMOR, WE CAN DETERMINE HOW IMMUNOTHERAPIES CAN INDUCE FUNCTIONAL PLASTICITY TO DESIRED OR UNDESIRED STATES. THE THIRD OBJECTIVE BUILDS ON OUR 20 YEAR EXPERIENCE USING MOUSE MODELS TO DISSECT MECHANISMS UNDERLYING RESPONSE OR RESISTANCE TO IMMUNOTHERAPY. WE WILL DETERMINE THE FUNCTIONAL SIGNIFICANCE OF NON-CANONICAL IMMUNE EFFECTORS USING DEPLETION AND KNOCK-OUT STRATEGIES. WE WILL ALSO DETERMINE HOW COMBINATION IMMUNOTHERAPIES CAN ELICIT BOTH EFFECTIVE OR INEFFECTIVE ANTI- TUMOR IMMUNE RESPONSES, THEREBY GUIDING THE DESIGN OF FUTURE CLINICAL TRIALS. IN CONCLUSION, OUR PROPOSAL IS BASED ON HYPOTHESIS-DRIVEN BENCH-TO-BEDSIDE AND BEDSIDE-TO-BENCH MECHANISTIC STUDIES WITH THE GOAL OF ADVANCING CANCER IMMUNOTHERAPY. WITH OUR DEEP EXPERTISE IN THIS FIELD, EXPERIENCE LEADING MULTI-DISCIPLINARY TEAMS FOCUSED ON TRANSLATIONAL RESEARCH, AND A RICH NETWORK OF BASIC SCIENCE AND CLINICAL COLLABORATORS; WE ARE UNIQUELY POSITIONED TO SUCCEED IN THE RESEARCH PLAN OUTLINED IN THIS PROPOSAL.

COMBINING TARGETED RIT AND SYNERGISTIC NOVEL AGENTS TO ERADICATE AML

DEVELOPMENT OF INNOVATIVE RESOURCES TO ADVANCE MDS RESEARCH - (PLEASE KEEP IN WORD, DO NOT PDF) ENTER THE TEXT HERE THAT IS THE NEW ABSTRACT INFORMATION FOR YOUR APPLICATION. THIS SECTION MUST BE NO LONGER THAN 30 LINES OF TEXT. MYELODYSPLASTIC SYNDROME (MDS) IS A HETEROGENEOUS GROUP OF CLONAL HEMATOPOIETIC STEM CELL DISEASES, RESULTING PREDOMINANTLY FROM ACQUISITION OF SOMATIC MUTATIONS IN HEMATOPOIETIC STEM/PROGENITOR CELLS (HSPC), WHICH CAUSE INEFFECTIVE HEMATOPOIESIS, CYTOPENIAS, AND POSSIBLE PROGRESSION TO LEUKEMIA. THE ACQUIRED AND GERMLINE GENOMIC ALTERATIONS IMPACT GENES IN DIVERSE BIOLOGICAL PATHWAYS, GLOBALLY MODIFYING GENE EXPRESSION OR GENOMIC INTEGRITY, INCLUDING EPIGENETIC REGULATION, RNA SPLICING, DNA REPAIR, AND TRANSCRIPTION. AT PRESENT A COMPREHENSIVE UNDERSTANDING OF BIOLOGY PROMOTING THE DEVELOPMENT, PROGRESSION AND MDS RESISTANCE TO THERAPY IS LACKING. ONE MAJOR OBSTACLE FOR ADVANCING OUR UNDERSTANDING OF MDS BIOLOGY HAS BEEN THE PAUCITY OF INFORMATIVE DISEASE MODELS. IN THIS PROPOSAL WE WILL DEVELOP CRITICAL RESOURCES FOR INVESTIGATORS PURSUING MDS RESEARCH INCLUDING A) KEY INFORMATION, A ‘ROADMAP’, OF THE MUTATIONAL ARCHITECTURE OF MDS; B) A REPOSITORY OF INDUCED PLURIPOTENT STEM CELL (IPSC)-DERIVED MDS HSPC CELL LINES; C) A COMPREHENSIVE RESOURCE CONTAINING MOLECULARLY-DEFINED DRUG SENSITIVITIES FOR MDS LINKED TO KEY CLINICAL DATA; D) A CATALOGUE OF NOVEL ANTIGENIC TARGETS AND MODELS TO ADVANCE ADOPTIVE T CELL IMMUNOTHERAPY FOR MDS PATIENTS. THIS RESEARCH WILL ENABLE A MORE RATIONAL APPROACH TO DEVELOPING SPECIFIC TREATMENT STRATEGIES AND PREDICTING PATIENT OUTCOMES. THE PROPOSED STUDIES WILL USE A UNIQUE, LARGE COHORT OF MDS MARROW SAMPLES FROM A DIVERSE POPULATION OF PATIENTS WITH COMPREHENSIVE CLINICAL AND GENOMIC ANNOTATIONS. IN AIM 1, WE WILL REPROGRAM MDS CELLS INTO IPSC, GENERATING A PANEL OF CELL LINES BASED ON PATIENT GENOTYPES, AND EMPLOY IPSCS AND MOLECULAR DATA TO RECONSTRUCT CLONAL HISTORIES AND ASSESS THE FUNCTIONAL CONSEQUENCE OF MUTATION ORDER. AIM 2 WILL FOCUS ON THE FUNCTIONAL CONSEQUENCES OF MDS MUTATIONS, USING A PLATFORM THAT INTEGRATES MUTATIONS, GENE EXPRESSION, AND HIGH-THROUGHPUT SENSITIVITY SCREENS EMPLOYING A LARGE CUSTOM PANEL OF DRUGS, TARGETED INHIBITORS, AND COMBINATIONS RATIONALLY DESIGNED FOR THIS DISEASE. IN AIM 3, WE WILL USE MDS PRIMARY SAMPLES AND IPSC LINES TO PERFORM PROTEOMIC ANALYSIS, LINKING MUTATIONAL AND PROTEOMIC DATA TO DISCOVER POTENTIAL NEW TARGET ANTIGENS FOR T CELL IMMUNOTHERAPIES, PERMISSIVE FOR NORMAL HEMATOPOIESIS WHILE ERADICATING MDS PROGENITORS. OUR PROPOSED COLLABORATIVE AND SYNERGISTIC STUDIES WILL ADVANCE OUR UNDERSTANDING OF THE PATH FROM MUTATIONAL PERTURBATION TO FUNCTIONAL CONSEQUENCES IN MDS AND CREATE A LIBRARY OF RESOURCES THAT CAN BE SHARED WITH THE GREATER MDS SCIENTIFIC COMMUNITY TO ENABLE FURTHER PROGRESS TOWARD IMPROVED TREATMENT STRATEGIES.

MOLECULAR MECHANISMS AND FUNCTIONS OF GLOBAL CHROMATIN CONTROL - PROJECT SUMMARY/ABSTRACT THE LONG TERM GOAL OF THE PROPOSED STUDY IS TO DETERMINE, AT THE MOLECULAR LEVEL, MECHANISMS AND FUNCTIONS OF CHROMATIN REGULATION AT A GLOBAL LEVEL. CHROMATIN REGULATION PROFOUNDLY AFFECTS A WIDE VARIETY OF DNA-DEPENDENT PROCESSES, INCLUDING TRANSCRIPTION, DNA REPLICATION, RECOMBINATION, DNA REPAIR, AND DNA DAMAGE RESPONSE. THEREFORE, ELUCIDATING THE MECHANISMS OF CHROMATIN REGULATION IS A NECESSARY PREREQUISITE FOR UNDERSTANDING HOW THESE ESSENTIAL PROCESSES ARE CONTROLLED. ONE OF THE MAJOR CHALLENGES THE CHROMATIN FIELD IS TO ELUCIDATE HOW CHROMATIN IS GLOBALLY REPROGRAMMED DURING PROCESSES LIKE CELL FATE DETERMINATION, DEVELOPMENT AND CELL-CYCLE CONTROL. THIS IS A PARTICULARLY IMPORTANT CHALLENGE, BECAUSE IT WAS RECENTLY DETERMINED THAT MUTATIONS IN CHROMATIN REGULATORS REPRESENT ONE MAJOR CLASS OF SO CALLED CANCER DRIVER MUTATIONS, YET HOW THESE MUTATIONS DRIVE CANCER REMAINS UNKNOWN. THEREFORE, ELUCIDATING THE MECHANISMS OF CHROMATIN REGULATION IMPACTS NOT ONLY THE RESEARCHERS WHO STUDY FUNDAMENTAL PRINCIPLES OF DNA-DEPENDENT PROCESSES, BUT ALSO CANCER BIOLOGISTS. WE HAVE PREVIOUSLY ELUCIDATED HOW CHROMATIN REGULATION AFFECTS TRANSCRIPTION, DNA REPLICATION, S PHASE CHECKPOINT AND RECOMBINATION USING BUDDING YEAST AS A MODEL ORGANISM. LIKE MOST STUDIES IN THE FIELD, WE DID OUR WORK DURING THE MITOTIC CELL-CYCLE. HOWEVER, YEAST CELLS IN THE WILD, LIKE OTHER EUKARYOTIC CELLS, SPEND MOST OF THEIR TIME IN QUIESCENCE. QUIESCENCE IS ASSOCIATED WITH MASSIVE CHROMATIN REPROGRAMMING FOR GLOBAL CONDENSATION. BECAUSE THE VAST MAJORITY OF WORK ON CHROMATIN REGULATION HAS BEEN DONE DURING MITOTIC CELL-CYCLE, WE HAVE LITTLE IDEA OF HOW CHROMATIN IS REGULATED DURING THE TIME CELLS SPEND MOST OF THEIR TIME. IN ORDER TO UNDERSTAND THE WHOLE PICTURE OF CHROMATIN REGULATION IN VIVO, IT IS ESSENTIAL TO UNDERSTAND MECHANISMS AND FUNCTIONS OF CHROMATIN REGULATION DURING QUIESCENCE. IN THE NEXT FUNDING PERIOD, WE WILL ASK THE FOLLOWING QUESTIONS IN QUIESCENT STATE: 1) HOW IS CHROMATIN GLOBALLY REPROGRAMMED BY ATP-DEPENDENT CHROMATIN REMODELING FACTORS? 2) HOW ARE CHROMATIN DOMAINS AND NUCLEOSOME ARRAY FOLDING REGULATED? 3) HOW IS GENE EXPRESSION REGULATED POST-TRANSCRIPTIONALLY AT A GLOBAL SCALE? WE WILL USE THE COMBINATION OF GENOMICS, MOLECULAR GENETICS, EM, MODELING AND BIOCHEMISTRY TO IDENTIFY NOVEL MECHANISMS BY WHICH HIGHLY CONSERVED CHROMATIN REGULATORS FUNCTION TO MASSIVELY REPROGRAM CHROMATIN IN A GENOME-WIDE SCALE. IN THE LONG RUN, THESE STUDIES WILL ALLOW US TO COMPARE AND INTEGRATE THE PRINCIPLES OF CHROMATIN REGULATION THROUGHOUT THE MITOTIC CELL-CYCLE AND QUIESCENCE, SUCH THAT WE CAN OBTAIN THE FULL PICTURE OF CHROMATIN REGULATION.

THERAPEUTIC USE OF HPV L1 VACCINE IN ANOGENITAL NEOPLASIA: VIVA TRIAL

TARGETING A NOVEL HEMATOPOIETIC STEM CELL POPULATION IN NON-HUMAN PRIMATES FOR EFFECTIVE AND SUSTAINED GENE THERAPY

SMCHD1 PATHWAYS AS CANDIDATE TARGETS FOR FSHD

STATISTICAL METHODS FOR ANALYZING OBJECTIVELY MEASURED PHYSICAL ACTIVITY DATA

NOVEL APPROACHES TO CD33-DIRECTED RADIOIMMUNOTHERAPY

HIV-CRISPR: A NOVEL APPROACH TO THE COMPREHENSIVE DISCOVERY OF HIV LATENCY FACTORS

IDENTIFYING PLASMA PROTEOMIC PROFILES OF CHRONIC PAIN DEVELOPMENT IN ENDOMETRIOSIS FROM ADOLESCENCE TO ADULTHOOD - ABSTRACT ENDOMETRIOSIS IS A DEBILITATING GYNECOLOGIC DISEASE PRESENTING WITH SEVERE PELVIC PAIN AND IS CHARACTERIZED BY THE GROWTH OF ENDOMETRIAL-LIKE TISSUE OUTSIDE OF THE UTERUS IMPACTING 10% OF REPRODUCTIVE AGED WOMEN OR AN ESTIMATED 200 MILLION WOMEN AND ADOLESCENTS WORLDWIDE. COMPARED TO WOMEN WITHOUT ENDOMETRIOSIS, WOMEN WITH ENDOMETRIOSIS, ESPECIALLY ADOLESCENTS AND YOUNG ADULTS WITH ENDOMETRIOSIS, ARE AT AN INCREASED RISK OF CHRONIC OPIOID USE, DEPENDENCE, AND OVERDOSE. THEREFORE, OPTIMAL PAIN MANAGEMENT IN ENDOMETRIOSIS PATIENTS, ESPECIALLY STARTING IN ADOLESCENCE, IS CRITICAL AND WILL HAVE SIGNIFICANT POSITIVE IMPACT ON RESOLVING THE OPIOID HEALTH CRISIS. CURRENTLY, PRIMARY TREATMENT OPTIONS FOR ENDOMETRIOSIS FOCUS ON HORMONAL SUPPRESSION AND/OR EXCISION OF THE ENDOMETRIOTIC LESIONS, ALTHOUGH RESPONSE TO THESE CONVENTIONAL TREATMENTS IS VARIABLE AND AS A RESULT, MANY OF THOSE WITH ENDOMETRIOSIS ARE PLAGUED WITH PERSISTENT PELVIC PAIN. EMERGING EVIDENCE SUGGESTS THAT ENDOMETRIOSIS PATIENTS WHO DEVELOP PERSISTENT PELVIC PAIN HAVE DEVELOPED CENTRALIZED PAIN, AND THEREFORE SURGICAL REMOVAL OF ENDOMETRIOTIC TISSUE DOES NOT FULLY IMPROVE THEIR PAIN. SINCE MANY WOMEN WITH DIAGNOSED ENDOMETRIOSIS REPORT THEIR SYMPTOMS STARTED DURING ADOLESCENCE, THIS TRANSITION FROM ACUTE TO CHRONIC PAIN IS LIKELY HAPPENING DURING ADOLESCENCE AND YOUNG ADULTHOOD. THUS, STUDYING ADOLESCENTS AND YOUNG ADULTS WITH ENDOMETRIOSIS, WHO ARE IN THE EARLY STAGES OF THEIR DISEASE TRAJECTORY, IS CRITICAL TO FULLY UNDERSTANDING WHO IS AT HIGHER RISK OF DEVELOPING CHRONIC PAIN. HOWEVER, DATA ON LONGITUDINAL CHANGES IN BIOMARKERS AND ENDOMETRIOSIS- ASSOCIATED PAIN IN ADOLESCENTS IS LACKING, RESULTING IN LOST OPPORTUNITY FOR EARLY INTERVENTIONS. THE OVERARCHING GOAL OF THIS INNOVATIVE APPLICATION IS TO IMPROVE AND OPTIMIZE PAIN MANAGEMENT FOR ENDOMETRIOSIS THROUGH IDENTIFYING PLASMA PROTEIN BIOMARKERS OF CHRONIC PAIN DEVELOPMENT IN ADOLESCENTS AND YOUNG ADULTS WITH ENDOMETRIOSIS. SPECIFICALLY, WE PROPOSE TO CONDUCT A LONGITUDINAL ANALYSIS OF ENDOMETRIOSIS CASES DIAGNOSED IN ADOLESCENCE WITH FOLLOW-UP DATA AND PAIRED BLOOD SAMPLES COLLECTED 10 YEARS APART FROM ADOLESCENCE TO ADULTHOOD AND APPLY A STATE OF THE ART 7000-PLEX PROTEOMICS ASSAY TO IDENTIFY PLASMA PROTEIN BIOMARKERS OF CENTRALIZED, CHRONIC PAIN DEVELOPMENT. IN ADDITION, WE WILL EXAMINE CHANGE IN PLASMA PROTEOMIC BIOMARKERS IN PAIRED BLOOD SAMPLES DRAWN 10 YEARS APART (I.E. AT ADOLESCENCE AND ADULTHOOD), AND TOGETHER THESE UNIQUE RESOURCES WILL ALLOW PROSPECTIVE INVESTIGATION OF PREDICTORS AND BIOLOGICAL FACTORS RELATED TO TRANSITIONING FROM ACUTE TO CHRONIC PAIN OR CHRONIFICATION OF PAIN. RESULTS FROM THIS STUDY WILL GENERATE IMPORTANT NOVEL DATA IDENTIFYING ADOLESCENTS AND YOUNG WOMEN WITH ENDOMETRIOSIS WHO ARE AT GREATER RISK OF DEVELOPING CHRONIC PAIN DESPITE RECEIVING CURRENT STANDARD OF CARE, LEADING TO DEVELOPMENT OF NOVEL PAIN INTERVENTIONS TARGETED TO A YOUNGER POPULATION TO PREVENT CHRONIFICATION OF PAIN, WHICH WILL BE A CRITICAL STEP FORWARD TO RESOLVING THE ONGOING OPIOID CRISIS.

PERSONALIZED CANCER MODELS TO DISCOVER AND DEVELOP NEW THERAPEUTIC TARGETS.

ORIGIN FIRING AT REPETITIVE SEQUENCES AND GENOME REPLICATION

HUTCHINSON CENTER AS LEAD ACADEMIC PARTICIPATING SITE (UG1)

OPTIMIZING MYELOMA-SPECIFIC IMMUNITY AFTER AUTOLOGOUS STEM CELL TRANSPLANTATION

METHODS FOR INTEGRATING FUNCTIONAL DATA INTO COMPLEX DISEASE GENETIC ANALYSES

COMPREHENSIVE CHARACTERIZATION OF THE T-CELL RESPONSE TO KSHV TO ENABLE SPECIFIC IMMUNE THERAPY - PROJECT SUMMARY KAPOSI SARCOMA HERPESVIRUS (KSHV) IS THE ETIOLOGIC AGENT OF KAPOSI SARCOMA (KS), PRIMARY EFFUSION LYMPHOMA, AND MULTICENTRIC CASTLEMAN’S DISEASE. KS CAUSES SIGNIFICANT MORBIDITY AND MORTALITY WORLDWIDE, PARTICULARLY IN PEOPLE LIVING WITH HIV (PLWH) AND IN SUB-SAHARAN AFRICA (SSA) WHERE KSHV SEROPREVALENCE IS HIGH. IT IS ESTIMATED THAT 80% OF THE KS BURDEN IN SSA, WHERE THE IMPACT OF KS IS HEAVIEST, IS ATTRIBUTABLE TO HIV INFECTION. KS MOST OFTEN DEVELOPS IN THE SETTING OF T-CELL DEFICIENCY OR DYSFUNCTION, SUCH AS IN KSHV-SEROPOSITIVE INDIVIDUALS WITH HIV INFECTION OR KSHV-SEROPOSITIVE RECIPIENTS OF SOLID ORGAN OR ALLOGENEIC HEMATOPOIETIC CELL TRANSPLANTS. IN THESE SETTINGS KS CAN REMIT FOLLOWING INITIATION OF ANTIRETROVIRAL THERAPY (ART) OR WITHDRAWAL OF IMMUNE SUPPRESSION. IN SSA, PRIMARY INFECTION WITH KSHV IS THOUGHT TO OCCUR IN CHILDHOOD, BUT MOST CASES OF KS AND OTHER KSHV-ASSOCIATED DISEASE IN BOTH PLWH AND PEOPLE WITHOUT HIV INFECTION DEVELOP MANY YEARS, OFTEN SEVERAL DECADES, LATER. THESE OBSERVATIONS SUGGEST THAT LOSS OR IMPAIRMENT OF A T-CELL COMPONENT OF PRE- EXISTING KSHV-SPECIFIC IMMUNITY UNDERLIE THE DEVELOPMENT OF THESE DISEASES. STRATEGIES THAT PRESERVE OR RESTORE THE T-CELL COMPONENT OF KSHV-SPECIFIC IMMUNITY IN PLWH AND OTHERS AT RISK SHOULD, THEREFORE, HAVE POTENTIAL FOR THE PREVENTION OR TREATMENT OF KSHV-ASSOCIATED DISEASE. OUR STUDIES OF TUMOR BIOPSIES AND BLOOD SAMPLES FROM PEOPLE IN UGANDA LIVING WITH HIV AND KS (EPIDEMIC KS) AS WELL AS ADULTS WITH KS BUT NO CONCURRENT HIV INFECTION (ENDEMIC KS) HAVE IDENTIFIED A LARGE REPERTOIRE OF T- CELLS THAT ARE LIKELY TO BE SPECIFIC FOR KSHV. WE HAVE BEGUN TO IDENTIFY THE ANTIGENIC TARGETS OF THESE PUTATIVE KSHV-SPECIFIC T-CELLS AND FIND THAT THEY DEMONSTRATE HIGH AVIDITY FOR KSHV-ENCODED PEPTIDES, RECOGNIZE KSHV- INFECTED CELLS, ARE DETECTABLE IN KS TUMORS, CIRCULATE IN BLOOD, AND PERSIST ACROSS TIME. ADDITIONAL PRELIMINARY DATA FROM WHOLE EXOME SEQUENCING AND TRANSCRIPTIONAL PROFILING OF KS TUMORS REVEAL A SPARSE MUTATIONAL LANDSCAPE BUT CONSISTENT EXPRESSION OF LATENT AND LYTIC CYCLE KSHV GENES, SUPPORTING THE CONCEPT THAT IMMUNE INTERVENTIONS THAT PRESERVE, ENHANCE, OR RESTORE THE T-CELL RESPONSE TO KSHV COULD PROVE EFFECTIVE FOR THE PREVENTION OR TREATMENT OF KS, PARTICULARLY IN PLWH WHO ARE AT GREATEST RISK. COMPREHENSIVE DEFINITION OF THE TARGETS OF THE KSHV-SPECIFIC T-CELL RESPONSE IN KSHV-SEROPOSITIVE INDIVIDUALS AND OF HOW THAT T-CELL RESPONSE IS IMPAIRED OR DISABLED IN INDIVIDUALS WHO DEVELOP KS WILL PROVIDE THE BLUEPRINT FOR SUCH IMMUNE INTERVENTIONS. THE STUDIES IN THIS APPLICATION WILL LAY THE FOUNDATION FOR SPECIFIC IMMUNE THERAPY FOR KS BY IDENTIFYING THE MAJOR TARGETS OF THE T-CELL RESPONSE TO KSHV, IDENTIFYING THOSE THAT ARE NATURALLY PRESENTED BY KSHV-INFECTED CELLS, AND DEFINING MECHANISMS BY WHICH KSHV ATTEMPTS TO EVADE THAT RESPONSE.

STATISTICAL METHODS FOR RNA-SEQ DATA ANALYSIS

MEMBRANE CURVATURE SENSING MECHANISMS FOR SYNAPTIC VESICLE ENDOCYTOSIS

DIFFERENTIATION BALANCES ONCOGENE-DRIVEN PROLIFERATION TO MAINTAIN EPIDERMAL HOMEOSTASIS

TARGETING COLLECTIVITY TO ERADICATE BREAST CANCER METASTASIS

IDENTIFYING VULNERABILITIES IN THE LONG-LIVED HIV RESERVOIR TO ACCELERATE ITS DECAY - PROJECT SUMMARY LATENTLY INFECTED CD4+ T CELLS HARBORING INTEGRATED AND REPLICATION-COMPETENT HIV GENOMES PERSIST DURING ART AND ARE THE MAIN OBSTACLE TO HIV ERADICATION. IN MOST PEOPLE WITH HIV (PWH), THE RESERVOIR IS EXTREMELY STABLE WITH A HALF-LIFE OF OVER 3 YEARS. ALL PRIOR ATTEMPTS TO SIGNIFICANTLY REDUCE ITS SIZE OR ACCELERATE ITS DECAY HAVE FAILED. USING SAMPLES FROM PARTICIPANTS IN THE MERLIN CLADE B PRIMARY HIV INFECTION COHORT (LIMA, PERU), WE OBSERVED 5 TO 10-TIMES FASTER DECAY OF THE HIV RESERVOIR IN INDIVIDUALS INITIATING ART DURING THE FIRST 3 MONTHS OF INFECTION COMPARED TO THOSE RANDOMIZED TO START ART LATER, SUGGESTING THAT HIV-INFECTED CELLS IN PEOPLE TREATED EARLY ARE MORE SUSCEPTIBLE TO ELIMINATION. DIFFERENCES IN THE HALF-LIFE OF THE RESERVOIR, WHICH ARE MAINTAINED DURING AT LEAST THE FIRST 4 YEARS OF ART, OFFER A UNIQUE OPPORTUNITY TO IDENTIFY MECHANISMS THAT COULD BE HARNESSED TO REDUCE THE RESERVOIR IN ALL PWH ON ART. IN THIS PROJECT, WE PROPOSE TO UNRAVEL THE CELLULAR AND VIRAL FEATURES RESPONSIBLE FOR THE RAPID CLEARANCE OR LONG-TERM PERSISTENCE OF INDIVIDUAL HIV RESERVOIR CELLS. WE WILL TEST THE HYPOTHESIS THAT THE CAPACITY OF RESERVOIR CELLS TO PERSIST FOR PROLONGED PERIODS IS DRIVEN BY A COMBINATION OF CELLULAR AND VIRAL FEATURES, WHICH DIFFER BETWEEN EARLY AND LATE TREATED INDIVIDUALS AND RESULT IN DIFFERENTIAL RESERVOIR DECAY. WE WILL TAKE ADVANTAGE OF THE UNIQUE MERLIN COHORT TO STUDY HIV RESERVOIR CELLS IN 12 PARTICIPANTS WHO INITIATED ART LESS THAN 3 MONTHS AFTER HIV ACQUISITION (EARLY ART: RAPID DECAY) AND 12 PARTICIPANTS WHO DEFERRED TREATMENT FOR 6 MONTHS (LATE ART: SLOW DECAY). WE WILL STUDY THE EARLY, INTERMEDIATE AND LATE RESERVOIRS, USING CRYOPRESERVED LEUKAPHERESES (COLLECTED AT 1 & 2-3 YEARS OF ART) AND NEWLY COLLECTED LEUKAPHERESIS FROM THE SAME CONTINUALLY- SUPPRESSED PARTICIPANTS AT >7 YEARS OF ART. IN AIM 1, WE WILL TEST THE HYPOTHESIS THAT INTRINSIC CELLULAR FEATURES OF HIV RESERVOIR CELLS UNDERLIE DIFFERENCES IN RESERVOIR DECAY. WE WILL EMPLOY A SINGLE CELL APPROACH TO IDENTIFY PRO-SURVIVAL FACTORS ASSOCIATED WITH RESERVOIR STABILITY (BCL-2, TCF-1, FOXO3A ETC.) OR THAT MAY PROTECT INFECTED CELLS FROM IMMUNE CLEARANCE (LIGANDS OF IMMUNE CHECKPOINT MOLECULES, SERPIN B9, TGF-SS). WE WILL ALSO EVALUATE THE CLONALITY OF THE RESERVOIR WITH THE HYPOTHESIS THAT CLONAL EXPANSIONS OF INTACT GENOMES WILL BE MORE COMMON IN LATE TREATED PARTICIPANTS. IN AIM 2, WE WILL TEST THE HYPOTHESIS THAT SPECIFIC VIRAL CHARACTERISTICS ALSO CONTRIBUTE TO THE PERSISTENCE OF HIV-INFECTED CELLS AND WILL BE GRADUALLY ENRICHED OVER TIME ON ART. TO DETERMINE IF SPECIFIC VIRUSES ARE SELECTED AGAINST DURING THERAPY, WE WILL USE AN ASSAY THAT COUPLES INTEGRATION SITE SEQUENCING WITH HIV TRANSCRIPTION ASSESSMENT, TO DETERMINE THE PROPORTION OF RESERVOIR CELLS THAT ARE TRANSCRIPTIONALLY ACTIVE. WE WILL USE A NOVEL APPROACH TO RECONSTRUCT MOLECULAR VIRAL CLONES FROM THE LATENT RESERVOIR, AND WILL MEASURE THE FITNESS OF THESE VIRUSES AND FUNCTIONALLY ASSESS THEIR HIV PROTEOMES. IN THIS WAY, WE WILL DETERMINE IF THE RESERVOIR IS GRADUALLY ENRICHED IN PROVIRUSES ENCODING FUNCTIONAL NEF AND VPU, WHICH CAUSE ESCAPE OF ANTIGEN PRESENTATION AND IMPEDE CTL-MEDIATED KILLING AS WELL AS NEUTRALIZATION AND ADCC BY AUTOLOGOUS ANTIBODIES. RESULTS FROM THIS STUDY WILL IDENTIFY CELLULAR AND VIRAL MECHANISMS THAT CAN BE TARGETED TO ACCELERATE DECAY OF THE HIV RESERVOIR.

MECHANISMS AND CONSEQUENCE OF HELICAL SHAPE GENERATION IN HELICOBACTER PYLORI

REAL-TIME TRACKING OF VIRUS EVOLUTION FOR VACCINE STRAIN SELECTION AND EPIDEMIOLOGICAL INVESTIGATION

REGULATION OF PROTEIN SYNTHESIS BY SYNONYMOUS CODON USAGE

NOVEL INTERVENTION APPROACHES TO ALLEVIATE ALLOGENEIC TRANSPLANT-RELATED MORBIDITY AND MORTALITY

INVESTIGATING HOW CELLULAR MECHANISMS INTERFACE TO MAINTAIN ENERGY BALANCE

PATHWAYS TO CANCER RESEARCH

NONGENOTOXIC CONDITIONING FOR GENE THERAPY AND ALLOGENEIC TRANSPLANTATION IN FANCONI ANEMIA

MECHANISMS OF EPITHELIAL REMODELING DURING ORGAN DEVELOPMENT IN C. ELEGANS

THE GUT MICROBIOTA AND GRAFT VERSUS HOST DISEASE (GVHD)

TRAINING PROGRAM IN INFECTIOUS DISEASES IN THE IMMUNOCOMPROMISED HOST

IDENTIFICATION OF NOVEL MUCOSAL IMMUNE MECHANISMS INVOLVED IN PROTECTION FROM HIV-1

MATERNAL-INFANT VIROME TRANSMISSION: THE ROLE OF HIV AND ANTIRETROVIRAL THERAPY

BIOLOGIC CORRELATIVES OF CHRONIC GVHD ONSET

THE GENETICS OF POST-TRANSPLANT RELAPSE IN MYELOID MALIGNANCY

MODELING AND ANALYTICS FOR CANCER DIAGNOSTICS: TRAVERSING THE DATA-EVIDENCE DIVIDE - THE FIELD OF CANCER DIAGNOSTICS IS IN A RAPIDLY EXPANDING GROWTH PHASE THAT GOES HAND IN GLOVE WITH THE PRECISION MEDICINE REVOLUTION. HOWEVER, THE RAPID PACE AT WHICH NEW TECHNOLOGIES ARE ENTERING THE MARKETPLACE MAKES RIGOROUS EVALUATION VIA CONTROLLED STUDIES INFEASIBLE FOR ALL BUT A RELATIVE FEW. THIS MEANS THAT WHILE WE TYPICALLY HAVE SOME DATA ABOUT DIAGNOSTIC TEST PERFORMANCE, WE FREQUENTLY LACK EVIDENCE REGARDING THE OUTCOMES THAT DRIVE CLINICAL AND POLICY DECISIONS. THE RESEARCH PROGRAM OUTLINED IN THIS APPLICATION WILL TACKLE THIS DATA- EVIDENCE DIVIDE USING THE TOOLS OF MODELING AND ANALYTICS. MODELING IS AN INCREASINGLY ACCEPTED DISCIPLINE FOR INTEGRATING KNOWLEDGE ABOUT THE PROCESS BY WHICH DIAGNOSTIC PERFORMANCE DRIVES OUTCOMES. ANALYTICS IS THE USE OF STATISTICAL LEARNING TECHNIQUES TO FILL IN THE KNOWLEDGE GAPS AND TO PROPAGATE UNCERTAINTY FROM MODEL INPUTS TO OUTCOMES. THE PRINCIPAL INVESTIGATOR HAS BUILT A LEADING RESEARCH PROGRAM IN MODELING AND ANALYTICS FOR EVIDENCE GENERATION IN CANCER POLICY. AMONG MANY METHODOLOGIC AND SUBSTANTIVE CONTRIBUTIONS, HER WORK HAS INFORMED PROSTATE CANCER SCREENING GUIDELINES FROM NATIONAL POLICY PANELS, ESTABLISHED BEST PRACTICES FOR ESTIMATION OF OVERDIAGNOSIS, AND PRODUCED SPECIFIC DIRECTIONS FOR SCREENING HIGH-RISK POPULATIONS INCLUDING BLACK MEN. THE RESEARCH PROGRAM OUTLINED IN THIS APPLICATION WILL HARNESS THE MODELING AND ANALYTICS SKILLSET DEVELOPED BY THE PRINCIPAL INVESTIGATOR OVER NEARLY THREE DECADES TO BUILD A FRAMEWORK AND TOOLS FOR EVIDENCE GENERATION AROUND CANCER DIAGNOSTICS. THE APPLICATION DETAILS A SEQUENCE OF PROJECTS FOR TWO TECHNOLOGIES THAT ARE GENERATING INTENSE CURRENT INTEREST WITH WIDE-RANGING PRACTICE IMPLICATIONS AND SERIOUS EVIDENCE GAPS: MULTI-CANCER EARLY DETECTION TESTING, AND PSMA-PET/CT FOR NEWLY DIAGNOSED AND RECURRENT PROSTATE CANCER. THE MCED WORK WILL DEEPEN OUR UNDERSTANDING OF PERFORMANCE CHARACTERISTICS, PROVIDE GUIDANCE REGARDING A DEFENSIBLE TEST CONFIRMATION STRATEGY, PROJECT BENEFITS AND HARMS OF DIFFERENT MCED STRATEGIES AND OFFER NEW IDEAS FOR SHORTCUTTING THE TYPICALLY LENGTHY PROCESS OF CANCER SCREENING TRIALS. THE PSMA-PET/CT WORK WILL DEVELOP AN APPROACH FOR UPDATING TREATMENT BENEFIT ESTIMATED DERIVED FROM TRIALS THAT INCLUDED A MIXTURE OF PATIENTS WITH UNKNOWN PSMA STATUS AND WILL PROJECT LIVES SAVED OF TREATMENT REALLOCATION ON THE BASIS OF PSMA-PET.CT RESULT. THE TOOLS AND PROCESSES DEVELOPED FOR MODELING THESE TECHNOLOGIES WILL BE APPLICABLE TO OTHER NEW DIAGNOSTICS THAT EMERGE DURING THE LIFETIME OF THE RESEARCH PROGRAM. THE MODELING WORK WILL BE ACCOMPANIED BY A SEQUENCE OF REAL-WORLD ANALYTICS PROJECTS TO ASSESS DISSEMINATION OF AND DISPARITIES IN UPTAKE OF NOVEL DIAGNOSTICS AND THEIR CONSEQUENCES FOR HEALTHCARE UTILIZATION AND COSTS. THIS WORK WILL ESTABLISH COLLABORATIONS WITH NEW REAL-WORLD DATA PARTNERS AND MATERIALLY EXPAND THE PRINCIPAL INVESTIGATOR’S SKILLSET TO ENCOMPASS A GREATER COMPETENCY IN MEDICAL INFORMATICS. THE SUCCESSFUL EXECUTION OF THE RESEARCH PROGRAM WILL IMPROVE OUR UNDERSTANDING OF HOW NOVEL CANCER DIAGNOSTICS IMPACT CLINICAL AND POLICY RELEVANT OUTCOMES SO THAT THESE TECHNOLOGIES CAN BE USED WISELY AND EQUITABLY TO IMPROVE CARE FOR ALL CANCER PATIENTS.

STATISTICAL METHODS FOR EVALUATING MARKERS FOR TREATMENT SELECTION

LONGITUDINAL IMPACT OF RESPIRATORY VIRUSES ON BRONCHIOLITIS OBLITERANS SYNDROME IN ALLOGENEIC HEMATOPOIETIC CELL TRANSPLANT RECIPIENTS - PROJECT SUMMARY/ABSTRACT BRONCHIOLITIS OBLITERANS SYNDROME (BOS) IS THE MOST SEVERE MANIFESTATION OF CHRONIC GRAFT-VERSUS-HOST DISEASE (CGVHD) IN SURVIVORS OF ALLOGENEIC HEMATOPOIETIC CELL TRANSPLANT (ALLOHCT), LEADING TO IRREVERSIBLE PULMONARY IMPAIRMENT, POOR QUALITY OF LIFE, AND 5-YEAR SURVIVAL OF 40%. FUNDAMENTAL GAPS IN KNOWLEDGE OF THE PATHOGENIC EVENTS THAT CONTRIBUTE TO PROGRESSIVE LUNG DYSFUNCTION IN BOS HAVE NOT BEEN WELL CHARACTERIZED, HAMPERING OUR ABILITY TO INTERVENE EFFECTIVELY. OUR PRELIMINARY DATA SUGGEST THAT RESPIRATORY VIRUSES, INCLUDING RESPIRATORY SYNCYTIAL VIRUS (RSV), PARAINFLUENZA (PIV), HUMAN METAPNEUMOVIRUS (HMPV), AND INFLUENZA (FLU), ARE INDEPENDENT RISK FACTORS FOR THE DEVELOPMENT OF BOS. ADDITIONALLY, WE SHOW THAT ASYMPTOMATIC RESPIRATORY VIRAL INFECTIONS (RVI) ARE COMMON POSTTRANSPLANT. WE HAVE SHOWN THAT MOBILE WIRELESS HOME SPIROMETRY IS FEASIBLE IN PATIENTS WITH CGVHD AND CAN ENABLE EARLY DIAGNOSIS AND A GRANULAR UNDERSTANDING OF THE TRAJECTORY OF LUNG FUNCTION DECLINE. OUR OVERARCHING HYPOTHESIS IS THAT CUMULATIVE RESPIRATORY VIRAL EXPOSURE LEADS TO THE DEVELOPMENT OF BOS AND POOR OUTCOMES IN THE CONTEXT OF ALLOIMMUNITY. THE OVERALL AIM OF THIS PROPOSAL IS TO ESTABLISH THE TEMPORAL RELATIONSHIP BETWEEN RVI ALONG THE CONTINUUM OF DISEASE PRESENTATIONS, FROM ASYMPTOMATIC TO SYMPTOMATIC UPPER RESPIRATORY TRACT TO LOWER TRACT DISEASE, AND THE LUNG FUNCTION TRAJECTORY OF BOS. WE PROPOSE TO CONDUCT A MULTICENTER PROSPECTIVE LONGITUDINAL STUDY OF THE NATURAL HISTORY OF RVI AND LUNG FUNCTION WITH AN INNOVATIVE HOME MONITORING APPROACH THAT OVERCOMES THE BARRIERS TO UNDERSTANDING CLINICAL EVENTS THAT LEAD TO BOS AND SEVERE BOS PHENOTYPES. AIM 1 INVESTIGATES THE ROLE OF RVI AS TRIGGERS BOS. WE WILL ENROLL ALLOHCT RECIPIENTS AT RISK FOR BOS (COHORT 1, N=200), INCLUDING THOSE WITH A DIAGNOSIS OF CGVHD OR A HISTORY OF HIGH-RISK RVI (RSV/PIV/HMPV/FLU/SARS-COV2). PATIENT WILL PERFORM WEEKLY HOME SPIROMETRY AND PROTOCOLIZED SURVEILLANCE AND SYMPTOM-PROMPTED SELF-COLLECTED NASAL SWAB VIRAL PCR. IN ADDITION, SERUM WILL BE COLLECTED QUARTERLY VIA A NEEDLE-LESS HOME BLOOD COLLECTION KIT AND ASSAYED WITH VIRSCAN, A NOVEL COMPREHENSIVE SEROSURVEY THAT DETECTS EPITOPES OF >1000 VIRUS STRAINS, IN ORDER TO ASSESS THE IMPACT OF CUMULATIVE RESPIRATORY VIRAL BURDEN ON BOS OUTCOMES. AIM 2 EXAMINES THE ROLE OF RVI ON PULMONARY EXACERBATIONS IN BOS, AS WELL AS THE ASSOCIATION OF CUMULATIVE RVI EXPOSURE (AS DETERMINED BY VIRSCAN) ON ACCELERATED FEV1 DECLINE IN PATIENTS WITH A SEVERE BOS PHENOTYPE. PATIENTS WITH A CLINICAL DIAGNOSIS OF BOS (COHORT 2, N=80), WILL PERFORM THE SAME PROCEDURES AS COHORT 1. FOR BOTH AIMS, VIRAL PCR AND VIRSSCAN RESULTS WILL BE COMPARED AND ANALYZED AS PREDICTORS FOR BOS DEVELOPMENT OR ACCELERATED FEV1 DECLINE. THE CRITICAL DATA GENERATED BY THIS STUDY WILL IMPROVE RECOGNITION OF EARLY BOS IN THE CONTEXT OF RVI, RISK STRATIFY PATIENTS AT HIGHEST RISK FOR INTENSIVE MONITORING, AND IDENTIFY TANGIBLE ENDPOINTS AND BIOLOGIC RATIONALE FOR TESTING EARLY INTERVENTIONS AND NOVEL THERAPIES. IMPORTANTLY, THIS PROPOSAL WILL ALSO ESTABLISH A UNIQUE ADULT AND PEDIATRIC MULTICENTER CONSORTIUM WITH THE SPECIFIC GOAL OF ADDRESSING LUNG DISEASE IN HCT RECIPIENTS, AN AREA OF SIGNIFICANT AND URGENT UNMET NEED.

FAST AND FLEXIBLE BAYESIAN PHYLOGENETICS VIA MODERN MACHINE LEARNING - PROJECT ABSTRACT/SUMMARY THE SARS-COV-2 PANDEMIC UNDERLINES BOTH OUR SUSCEPTIBILITY TO AND THE TOLL OF A GLOBAL PATHOGEN OUTBREAK. PHYLOGENETIC ANALYSIS OF VIRAL GENOMES PROVIDES KEY INSIGHT INTO DISEASE PATHOPHYSIOLOGY, SPREAD AND PO- TENTIAL CONTROL. HOWEVER, IF THESE METHODS ARE TO BE USED IN A VIRAL CONTROL STRATEGY THEY MUST RELIABLY ACCOUNT FOR UNCERTAINTY AND BE ABLE TO PERFORM INFERENCE ON 1,000S OF GENOMES IN ACTIONABLE TIME. SCALING BAYESIAN PHYLOGENET- ICS TO MEET THIS NEED IS A GRAND CHALLENGE THAT IS UNLIKELY TO BE MET BY OPTIMIZING EXISTING ALGORITHMS. WE WILL MEET THIS CHALLENGE WITH A RADICALLY NEW APPROACH: BAYESIAN VARIATIONAL INFERENCE FOR PHYLOGENET- ICS (VIP) USING EXIBLE DISTRIBUTIONS ON PHYLOGENETIC TREES THAT ARE T USING GRADIENT-BASED METHODS ANALOGOUS TO HOW ONE EFCIENTLY TRAINS MASSIVE NEURAL NETWORKS. BY TAKING A VARIATIONAL APPROACH WE WILL ALSO BE ABLE TO INTEGRATE PHYLOGENETIC ANALYSIS INTO VERY POWERFUL OPEN-SOURCE MODELING FRAMEWORKS SUCH AS TENSORFLOW AND PYTORCH. THIS WILL OPEN UP NEW CLASSES OF MODELS, SUCH AS NEURAL NETWORK MODELS, TO INTEGRATE DATA SUCH AS SAMPLING LOCATION AND MIGRATION PATTERNS WITH PHYLOGENETIC INFERENCE. THESE EXIBLE MODELS WILL INFORM STRATEGIES FOR VIRAL CONTROL. IN AIM 1 WE WILL DEVELOP THE THEORY NECESSARY FOR SCALABLE AND RELIABLE VIP, INCLUDING SUBTREE MARGINAL- IZATION, LOCAL GRADIENT UPDATES NEEDED FOR ONLINE ALGORITHMS, CONVERGENCE DIAGNOSTICS, AND PARAMETER SUPPORT ESTIMATES. WE WILL IMPLEMENT THESE ALGORITHMS IN OUR C++ FOUNDATION LIBRARY FOR VIP. IN AIM 2 WE WILL DEVELOP A EXIBLE TENSORFLOW-BASED MODELING PLATFORM FOR PHYLOGENETICS, ENABLING A WHOLE NEW REALM OF PHYLOGENETIC MODELS BASED ON NEURAL NETWORKS TO LEARN PHYLODYNAMIC HETEROGENEITY WITH MINIMAL PROGRAM- MING EFFORT. WE WILL PROVIDE EFCIENT GRADIENTS TO THIS IMPLEMENTATION VIA OUR C++ LIBRARY. IN AIM 3 WE WILL USE THE FACT THAT VIP POSTERIORS ARE DURABLE AND EXTENSIBLE DESCRIPTIONS OF THE FULL DATA POSTERIOR TO ENABLE DYNAMIC ONLINE COMPUTATION OF VARIATIONAL POSTERIORS, INCLUDING DIVIDE-AND-CONQUER BAYESIAN PHYLOGENETICS. THIS WORK WILL ENABLE A CLOUD-BASED VIRAL PHYLOGENETICS SOLUTION TO RAPIDLY UPDATE OUR CURRENT ESTIMATE OF THE POSTERIOR DISTRIBUTION WHEN NEW DATA ARRIVE OR THE MODEL IS MODIED. 1

SALSA - STUDY OF ACTIVE LIFESTYLE ACTIVATION - PROJECT SUMMARY / ABSTRACT CHILDREN AND ADOLESCENTS DIAGNOSED WITH CANCER NOW HAVE, ON AVERAGE, NEARLY 85% 5-YEAR SURVIVAL. HOWEVER, PREMATURE CARDIOVASCULAR (CV) DISEASE HAS BECOME THE LEADING NON-CANCER CAUSE OF LATE MORTALITY AMONG CHILDHOOD CANCER SURVIVORS. THERE IS A ROBUST BODY OF EVIDENCE FROM THE GENERAL POPULATION, AND INCREASINGLY, AMONG CANCER SURVIVORS (EVEN THOSE EXPOSED TO CARDIOTOXIC CANCER THERAPIES), THAT GREATER PHYSICAL ACTIVITY (PA) AND IMPROVED DIET QUALITY CAN REDUCE FUTURE CV-RELATED MORBIDITY. HOWEVER, WHILE MANY GENERAL POPULATION AND CANCER-SPECIFIC INTERVENTION STUDIES HAVE FOCUSED ON A SINGLE LIFESTYLE FACTOR (E.G., PA OR DIET ALONE), GIVEN THE INTERPLAY BETWEEN PA AND DIETARY FACTORS IN INFLUENCING CV HEALTH, A MULTI-FACETED APPROACH MAY RESULT IN OVERALL BETTER LONG-TERM CV HEALTH PROFILES. RESEARCH ON LIFESTYLE INTERVENTIONS IN CANCER SURVIVORS ALSO HAS BEEN PREDOMINANTLY CONDUCTED IN WOMEN WITH BREAST CANCER, AND THE EVIDENCE FOR SURVIVORS OF CHILDHOOD CANCER IS LIMITED. TO ACCOMPLISH OUR AIMS, WE WILL USE THE LARGEST PROSPECTIVELY FOLLOWED CHILDHOOD CANCER SURVIVOR COHORT IN THE WORLD, THE CHILDHOOD CANCER SURVIVOR STUDY (CCSS; N>24,000), TO RECRUIT ADULT-AGED PARTICIPANTS AT INCREASED RISK OF EARLY CV DISEASE (N=403) FOR A REMOTELY CONDUCTED 12-MONTH RANDOMIZED CONTROLLED TRIAL TESTING A MULTI-FACETED APPROACH AT IMPROVING PA AND DIET QUALITY. SPECIFICALLY, THE STUDY WILL USE A SEQUENTIAL MULTIPLE ASSIGNMENT RANDOMIZED TRIAL (SMART) DESIGN, WHERE PARTICIPANTS WITH LOW PA OR POOR DIET WILL FIRST BE RANDOMIZED BETWEEN INTERVENTION AND CONTROL CONDITIONS. INTERVENTION PARTICIPANTS WILL BE FURTHER RANDOMIZED TO RECEIVE EITHER CLINICIAN-LED TELEHEALTH SESSIONS FOCUSED ON RISK FACTOR SELF-MANAGEMENT, OR WEEKLY MOBILE HEALTH (MHEALTH) SUPPORTED INDIVIDUALIZED PA AND DIETARY GOAL-SETTING WITH SOCIAL MEDIA PEER SUPPORT. THE ADAPTIVE SMART DESIGN WILL ALLOW FURTHER TAILORING OF THE INTERVENTION EXPERIENCE BASED ON INITIAL RESPONSE, WHICH MAY INCREASE OVERALL INTERVENTION EFFICACY. PARTICIPANTS NOT INITIALLY RESPONSIVE TO THEIR ASSIGNED INTERVENTION WILL BE FURTHER RANDOMIZED TO RECEIVE AN ALTERNATE INTERVENTION. THE STUDY WILL USE CONSUMER-GRADE MHEALTH APPLICATIONS THAT TRACK PA AND DIET, THEREBY INCREASING FUTURE DISSEMINATION CAPACITY. THE STUDY’S PRIMARY ANALYSES WILL DETERMINE THE OVERALL INTERVENTION EFFICACY AND WHETHER SPECIFIC INTERVENTION STRATEGIES AND SEQUENCE OF STRATEGIES ARE ASSOCIATED WITH OPTIMAL OUTCOMES. SECONDARY ANALYSES WILL EXAMINE POTENTIAL PREDICTORS, MEDIATORS, AND MODERATING FACTORS ASSOCIATED WITH PA AND DIETARY CHANGES OVER TIME, AS WELL AS CHANGES IN PARTICIPANTS’ CARDIOMETABOLIC PROFILES. IN SUMMARY, LIFESTYLE CHANGE REPRESENTS ONE OF THE FEW AVAILABLE STRATEGIES TO MITIGATE CV RISK IN CHILDHOOD CANCER SURVIVORS. SIGNIFICANT BARRIERS (E.G., TIME, TRAINING, RESOURCES) LIMIT THE ABILITY OF HEALTHCARE SYSTEMS TO FACILITATE SUCH CHANGE. TO FILL THIS VOID, REMOTE-BASED, PERSONALIZED, AND EASILY DISSEMINATED MULTI-FACETED MHEALTH-SUPPORTED INTERVENTIONS MAY PLAY A TRANSFORMATIVE ROLE.

IMMUNOGENETICS OF OUTCOMES DISPARITIES AFTER ALLOGENEIC HCT

TELEPHONE DELIVERED ACCEPTANCE & COMMITMENT THERAPY FOR WEIGHT LOSS

IN VIVO GENE EDITING OF B CELLS WITH NICE-AAV VECTORS - ABSTRACT HIV-SPECIFIC GENE THERAPIES ARE A POWERFUL AND PROMISING MEANS TO ACHIEVE HIV CURE/STABLE REMISSION IN THE ABSENCE OF ANTIRETROVIRAL THERAPY (ART). BROADLY NEUTRALIZING ANTIBODIES (BNABS) AND ANALOGOUS MOLECULES SUCH AS ECD4-IG OFFER ONE OF THE CLEAREST PATHS TO A CURE, BUT ARE HINDERED BY THREE KEY OBSTACLES. FIRST, PASSIVE ADMINISTRATION OF BNAB/ECD4-IG PROTEINS IS BY DEFINITION A TRANSIENT THERAPY; WHEN CIRCULATING LEVELS OF THESE POTENT ANTI-HIV FACTORS DECLINE, VIRUS REPLICATION IS ABLE TO RESUME. SECOND, GENE THERAPY VECTOR-BASED APPROACHES INCLUDING ADENO-ASSOCIATED VIRUS (AAV) SUPPORT PROLONGED EXPRESSION OF BNABS AND OTHER ANTIVIRAL TRANSGENES, BUT ARE FREQUENTLY LIMITED BY HOST IMMUNE RESPONSES. THIRD, POTENT ART REGIMENS SUPPRESS VIRAL REPLICATION TO EXTREMELY LOW LEVELS, RENDERING ENGINEERED HIV-SPECIFIC LYMPHOCYTES UNABLE TO RECOGNIZE AND CLEAR PERSISTENTLY INFECTED CELLS. WE HAVE GENERATED AN EXCITING SET OF TOOLS AND PRELIMINARY DATA THAT DIRECTLY ADDRESSES EACH OF THESE BARRIERS. TO OVERCOME THE TRANSIENT NATURE OF BNABS AND ASSOCIATED IMMUNOGENICITY OF VECTORED DELIVERY APPROACHES, WE HAVE PERFORMED AN IN VIVO SCREEN IN NONHUMAN PRIMATES (NHP) AND IDENTIFIED ENGINEERED AAV VARIANTS THAT PERSIST LONG TERM (CONSISTENT WITH A LACK OF RECOGNITION BY THE HOST IMMUNE SYSTEM), AND SPECIFICALLY TARGET B CELLS. B CELL TROPIC VECTORS WILL BE PACKAGED WITH CRISPR-CAS9 GENE EDITING MACHINERY, APPLYING HIGHLY INNOVATIVE COVALENT LINKAGE METHODOLOGY TO DOUBLE OUR VECTORS’ PACKAGING CAPACITY. WE REFER TO OUR NOVEL IN VIVO DELIVERY APPROACH AS NON-IMMUNOGENIC, CARGO-ENHANCED (NICE) AAV: IN A SINGLE DOSE, NICE- AAV VECTORS WILL SPECIFICALLY REPROGRAM B CELLS WITH BNAB OR ECD4-IG SEQUENCES TARGETED TO THE NATIVE IGG LOCUS. FINALLY, WE WILL OVERCOME THE SIGNIFICANT PROBLEM OF INSUFFICIENT VIRAL ANTIGEN BY SUPPLYING CELL-ASSOCIATED HIV-1 ENV IN TRANS. OUR RECENT PUBLICATION IN THE NHP MODEL DEMONSTRATES THE IMMENSE SUCCESS OF THIS STRATEGY TO STIMULATE HIV-1-SPECIFIC CHIMERIC ANTIGEN RECEPTOR (CAR) T CELLS AND SHOULD SIMILARLY BOOST AND TRIGGER EXPANSION OF OUR GENE-EDITED B CELLS. THE CENTRAL GOALS OF OUR PROPOSAL ARE TO VALIDATE THE EFFICIENCY AND SPECIFICITY OF B CELL-TARGETED NICE-AAV (AIM 1), TO DEMONSTRATE THAT THIS IN VIVO DELIVERY APPROACH ENABLES PERSISTENT BNAB/ECD4-IG EXPRESSION IN HIV ANATOMICAL COMPARTMENTS AND RESERVOIR SITES (AIM 2), AND MOST IMPORTANTLY, TO ACHIEVE A THERAPEUTIC IMPACT IN HUMANIZED MOUSE AND NHP MODELS OF HIV PERSISTENCE (AIM 3). WE WILL MERGE ONE OF THE MOST PROMISING THERAPEUTIC MODALITIES FOR HIV CURE (BNABS/ECD4-IG) WITH OUR EXTREMELY UNIQUE IN VIVO DELIVERY PLATFORM (NICE-AAV). IMPORTANTLY, THIS APPROACH WILL BE APPLICABLE NOT ONLY FOR HIV-1, BUT FOR THE BROAD RANGE OF PATHOLOGIES WHERE MONOCLONAL ANTIBODY THERAPIES OFFER CLINICAL BENEFIT.

SERRATED COLORECTAL CANCER: AN EMERGING DISEASE SUBTYPE

IMPROVING TREATMENT OF CARDIOVASCULAR RISK FACTORS IN CHILDHOOD CANCER SURVIVORS

HUMORAL IMMUNITY AFTER CAR-T CELL THERAPY FOR B CELL MALIGNANCIES: THE HICAR STUDY

BIOMARKERS FOR OPTIMIZING RISK PREDICTION AND EARLY DETECTION OF CANCERS OF THE COLON AND ESOPHAGUS - PROJECT SUMMARY GASTROINTESTINAL (GI) CANCERS ARE A MAJOR CAUSE OF MORTALITY AND MORBIDITY IN THE U.S. AND THEIR TREATMENT USES A SUBSTANTIAL PROPORTION OF HEALTHCARE RESOURCES. OF THE GI CANCERS, COLORECTAL CANCER (CRC) AND ESOPHAGEAL CANCER (EAC) ACCOUNT FOR A MAJORITY OF THE CANCER RELATED DEATHS, AND BOTH ARE PREVENTABLE BY SCREENING AND SURVEILLANCE. THE CURRENT SCREENING TESTS ARE SUBOPTIMAL AND HAVE VARIABLE SUCCESS. A MAJOR GOAL OF CRC SCREENING TESTS IS TO IDENTIFY ADVANCED TUBULAR AND SERRATED ADENOMAS, WHICH ARE HIGH-RISK FOR BECOMING CRC, AS WELL AS EARLY STAGE CRC. THE RISK FOR CRC IS VARIABLE WITH SOME PEOPLE BEING AT HIGH RISK BECAUSE OF FAMILY HISTORIES OF CRC, HEREDITARY CANCER SYNDROMES, OR A PERSONAL HISTORY OF ADENOMAS. HIGH RISK PEOPLE ARE PLACED ON AGGRESSIVE COLONOSCOPY BASED SURVEILLANCE PROGRAMS AND LOW-RISK PEOPLE ARE PLACED ON MINIMAL SURVEILLANCE PROGRAMS. UNFORTUNATELY, OUR CURRENT SYSTEM FOR IDENTIFYING HIGH AND LOW CRC RISK IS SUBOPTIMAL RESULTING IN UNDER AND OVER SURVEILLANCE AND PREVENTABLE INTERVAL CRCS. BETTER RISK MARKERS FOR CRC TO ARE NEEDED TO PREVENT INTERVAL CRCS AND IMPROVE THE OVERALL EFFECTIVENESS OF CRC SCREENING. ANALOGOUS TO CRC, EAC ARISES FROM A PRECANCEROUS CONDITION OF THE ESOPHAGUS CALLED BARRETTS ESOPHAGUS (BE), WHICH IS A SPECIALIZED INTESTINAL METAPLASIA OF THE ESOPHAGUS AND THE HIGHEST RISK FACTOR FOR EAC. IT IS PRESENT IN 5% OF THE US POPULATION. BE PROGRESSES TO EAC THROUGH SUCCESSIVE HISTOLOGIC STEPS OF LOW GRADE DYSPLASIA (LGD), HIGH GRADE DYSPLASIA (HGD) AND THEN EAC. SCREENING AND SURVEILLANCE FOR BE IS RECOMMENDED USING SERIAL UPPER ENDOSCOPY, WHICH IS CONTROVERSIAL IN ITS EFFECTIVENESS FOR PREVENTING DEATHS FROM EAC. THIS IS IN PART BECAUSE, AS WITH CRC, BE PATIENTS HAVE VARIABLE RISK OF EAC AND ARE PLACED ON HIGH- RISK AND LOW-RISK SCREENING PROGRAMS. HOWEVER, THE CURRENT SYSTEM FOR ASSIGNING RISK IS NOT ACCURATE AND THE CURRENT SCREENING TEST IS EXPENSIVE. MORE COST EFFECTIVE AND ACCURATE EAC AND HGD SCREENING/SURVEILLANCE ASSAYS AND ACCURATE BE RISK BIOMARKERS ARE NEEDED. WE PROPOSE TO DEVELOP AN EDRN BCC THAT IS INTEGRATED INTO THE EDRN CONSORTIUM AND, THROUGH COLLABORATIONS WITHIN AND OUTSIDE THE EDRN, WILL DEVELOP EFFECTIVE GI CANCER SCREENING BIOMARKERS. WE PROPOSE TO IDENTIFY, VALIDATE, AND DEVELOP ACCURATE CLIA COMPLIANT RISK BIOMARKERS FOR CRC AND FOR EAC IN ORDER TO PREVENT EAC AND CRC MISSED UNDER CURRENT SCREENING PROTOCOLS. MOREOVER, THE ACCURATE RISK STRATIFICATION OF PATIENTS FOR CRC AND EAC WILL REDUCE THE FINANCIAL IMPACT OF CURRENT CRC AND EAC PREVENTION PROGRAMS. WE ALSO PROPOSE TO IDENTIFY AND VALIDATE ACCURATE CLIA COMPLIANT EARLY DETECTION MARKERS FOR HGD AND EARLY STAGE EAC THAT CAN BE USED IN AN INEXPENSIVE, NON-ENDOSCOPIC SURVEILLANCE TEST.

SCALABLE MULTI-MODE EDUCATION TO INCREASE USE OF ITCR TOOLS BY DIVERSE ANALYSTS

INTEGRATING HEALTH INFORMATICS IN A SCALABLE STEPPED CARE SELF-MANAGEMENT PROGRAM FOR SURVIVORS AFTER HEMATOPOIETIC CELL TRANSPLANTATION

INTERDISCIPLINARY EPIDEMIOLOGIC CONSORTIUM TO INVESTIGATE T-CELL RESPONSE IN COLORECTAL CANCER

GENETICS, EPIGENETICS, AND RISK PREDICTION FOR ESOPHAGEAL ADENOCARCINOMA - PROJECT SUMMARY/ABSTRACT ESOPHAGEAL ADENOCARCINOMA (EAC) IS ONE OF THE MOST LETHAL CANCERS, WITH A 5-YEAR SURVIVAL RATE LESS THAN 20%. INCIDENCE OF EAC HAS RISEN SHARPLY IN THE U.S. AND OTHER WESTERN COUNTRIES OVER THE PAST FOUR DECADES, LARGELY DUE TO RISING PREVALENCE OF TWO RISK FACTORS – GASTROESOPHAGEAL REFLUX DISEASE AND OBESITY. EAC DEVELOPS FROM BARRETT’S ESOPHAGUS (BE), A CANCER PRECURSOR DEFINED BY A SPECIALIZED COLUMNAR METAPLASIA OF THE DISTAL ESOPHAGUS. ALTHOUGH BE FOLLOWS AN INDOLENT COURSE IN MOST PATIENTS, 5-10% EVENTUALLY PROGRESS TO CANCER, AND A SIZABLE FRACTION OF BE REMAIN UNDETECTED IN THE POPULATION. A CRITICAL UNMET NEED IS TO IDENTIFY INDIVIDUALS WITH HIGH-RISK BE WHO ARE MOST LIKELY TO DEVELOP EAC AND THUS BENEFIT FROM SCREENING AND ENDOSCOPIC SURVEILLANCE. CONVERSELY, IDENTIFYING THE MAJORITY WHO ARE UNLIKELY TO PROGRESS WILL REDUCE RISKS AND COSTS ASSOCIATED WITH UNNECESSARILY FREQUENT SURVEILLANCE. BIOMARKER-ASSISTED RISK STRATIFICATION, HOWEVER, CONTINUES TO BE HINDERED BY OUR LIMITED UNDERSTANDING OF THE MOLECULAR PATHWAYS UNDERLYING EARLY STEPS IN THE DEVELOPMENT OF EAC. IN RECENT YEARS, GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE IDENTIFIED ~20 NOVEL GENETIC SUSCEPTIBILITY LOCI, YET MOST HERITABILITY REMAINS UNEXPLAINED, AND ONLY ONE SNP IS LINKED SPECIFICALLY TO BEEAC PROGRESSION. THE EPIGENOME, AN IMPORTANT INTERFACE BETWEEN THE ENVIRONMENT AND THE GENOME, HAS NOT BEEN STUDIED FOR ITS POTENTIAL MEDIATING ROLES IN RELATION TO GENOTYPES, STRONG ENVIRONMENTAL RISK FACTORS AND PROGRESSION TO EAC. TO ADDRESS THESE GAPS, OVERCOME SAMPLE SIZE LIMITATIONS FOR A RARE CANCER, AND INVIGORATE EXISTING RESEARCH EFFORTS, NEWER MOLECULAR AND STATISTICAL APPROACHES ARE NEEDED TO SYSTEMATICALLY INTEGRATE MULTI-OMICS DATA WITH ESTABLISHED DISEASE EXPOSURES. IN THIS PROJECT WE WILL CONDUCT THE MOST COMPREHENSIVE MULTI-OMICS STUDY OF BE, THE KEY CANCER PRECURSOR, PROFILING THE TRANSCRIPTOME AND METHYLOME OF 500 BIOPSIES FROM THE NCI-FUNDED BARRETT’S AND ESOPHAGEAL ADENOCARCINOMA CONSORTIUM AND ROSWELL PARK COMPREHENSIVE CANCER CENTER, AND PERFORM INTEGRATIVE ANALYSES LEVERAGING GENOTYPES AND ENVIRONMENTAL RISK FACTORS ALREADY AVAILABLE THROUGH THE LARGEST GWAS META-ANALYSIS FOR BE/EAC (N˜27,000). THE GOAL IS TO IDENTIFY NEW GENETIC RISK LOCI THROUGH EQTL MAPPING AND TRANSCRIPTOME-WIDE ASSOCIATION STUDY (AIM 1), NEW EPIGENETIC LOCI MEDIATING AND PREDICTING THE RISK OF BE PROGRESSION TO EAC (AIM 2), AND DEVELOP RISK PREDICTION MODELS INTEGRATING GENOME-WIDE POLYGENIC RISK SCORE AND ENVIRONMENTAL EXPOSURES (AIM 3). THE UNIFYING THEME OF THE THREE AIMS IS DEVELOPMENT AND IMPLEMENTATION OF INNOVATIVE ANALYTICAL STRATEGIES, LEVERAGING TRANSCRIPTOME AND METHYLOME DATA. ULTIMATELY, GENETICS, EPIGENETICS, AND ENVIRONMENTAL EXPOSURES WILL BE INCORPORATED TO IDENTIFY HIGH-RISK POPULATIONS FOR TAILORED SCREENING AND SURVEILLANCE, AND PREVENT CANCER DEVELOPMENT.

FULL SCALE RANDOMIZED TRIAL OF AN INNOVATIVE CONVERSATIONAL AGENT FOR SMOKING CESSATION

AN INTERACTIVE SURVIVORSHIP PROGRAM TO IMPROVE HEALTHCARE RESOURCES [INSPIRE] FOR ADOLESCENT AND YOUNG ADULT (AYA) CANCER SURVIVORS

PROMOTING T CELL RECONSTITUTION AFTER HEMATOPOIETIC CELL TRANSPLANTATION - PROJECT SUMMARY THE THYMUS, WHICH IS THE PRIMARY SITE OF T CELL GENERATION, IS EXTREMELY SENSITIVE TO INJURY; BUT ALSO HAS A REMARKABLE CAPACITY FOR ENDOGENOUS REPAIR. HOWEVER, EVEN THOUGH THERE IS CONTINUAL THYMIC INVOLUTION AND REGENERATION IN RESPONSE TO EVERYDAY INSULTS LIKE STRESS AND INFECTION, PROFOUND THYMIC DAMAGE CAUSED BY COMMON CANCER THERAPIES AND THE CONDITIONING REGIMES FOR HEMATOPOIETIC CELL TRANSPLANTATION (HSCT) LEAD TO PROLONGED T CELL LYMPHOPENIA. FURTHERMORE, IN THE CONTEXT OF ALLOGENEIC HCT, THE THYMUS IS AN EXTREMELY SENSITIVE TARGET TO ALLOREACTIVE T CELLS DURING GRAFT VERSUS HOST DISEASE (GVHD). CONSEQUENTLY, IDENTIFICATION OF THERAPIES THAT CAN BOOST T CELL RECONSTITUTION IN RECIPIENTS OF HSCT IS A CLINICAL PRIORITY. WE HAVE PREVIOUSLY IDENTIFIED TWO DISTINCT PATHWAYS OF ENDOGENOUS THYMIC REGENERATION, CENTERED ON THE PRODUCTION OF THE REGENERATION FACTORS IL-22 BY INNATE LYMPHOID CELLS (ILCS), AND BMP4 BY ENDOTHELIAL CELLS (ECS); BOTH OF WHICH MEDIATE THEIR REGENERATIVE EFFECTS BY TARGETING THYMIC EPITHELIAL CELLS (TECS). MORE RECENTLY WE HAVE FOUND THAT THE TRIGGER FOR THESE DISTINCT REGENERATIVE PATHWAYS HINGE ON THE BALANCE BETWEEN FORMS OF CELL DEATH, WITH IMMUNOLOGICALLY SILENT APOPTOSIS (WHICH IS ABUNDANT IN THYMOCYTES DURING STEADY-STATE) SUPPRESSIVE TO THE REGENERATIVE PROGRAM. ON THE OTHER HAND, AFTER THYMIC DAMAGE CAUSED BY RADIATION INJURY, WE FOUND A SWITCH TOWARD IMMUNOGENIC CELL DEATH, WITH THE RESULTING RELEASE OF DAMAGE-ASSOCIATED MOLECULAR PATTERNS (DAMPS) SUFFICIENT TO PROMOTE REGENERATION. SPECIFICALLY, WE IDENTIFIED THAT INTRACELLULAR ZN WAS RELEASED AFTER RADIATION INJURY, WHERE IT COULD SIGNAL THROUGH THE G-PROTEIN COUPLED RECEPTOR 39 (GPR39) TO STIMULATE PRODUCTION OF BMP4 AND IL-23, A KEY UPSTREAM REGULATOR OF IL-22 PRODUCTION. SEPARATELY, WE ALSO FOUND THAT THE RELEASE OF THE PROTOTYPICAL DAMP, ATP, WAS ABLE TO SIGNAL DIRECTLY ON THYMIC EPITHELIAL CELLS THROUGH PURINERGIC (P2) RECEPTORS AND PROMOTE THEIR EXPRESSION OF FOXN1, KEY MICROENVIRONMENTAL DRIVERS OF T CELL DEVELOPMENT. IMPORTANTLY, OUR PRELIMINARY DATA ALSO SUGGESTS THAT EACH OF THESE PATHWAYS CAN BE THERAPEUTICALLY TARGETED TO IMPROVE THYMIC RECOVERY IN MOUSE MODELS OF HCT. OUR PRELIMINARY DATA HAS ALSO IDENTIFIED PUTATIVE TEC PRECURSORS THAT ARE IMPORTANT FOR REGENERATING THE EPITHELIAL COMPARTMENT AND THUS PROMOTING REGENERATION, AS WELL AS THE EMERGENCE WITH AGE OF ABERRANT EPITHELIAL CELLS THAT LIMIT THYMIC FUNCTION, INCLUDING IN ITS REPARATIVE CAPACITY AFTER ACUTE DAMAGE. OUR RESEARCH PROGRAM IS THUS EXPLORING SEVERAL KEY QUESTIONS: WHAT ARE THE TRIGGERS AND UPSTREAM REGULATORS OF ENDOGENOUS TISSUE REGENERATION IN THE THYMUS? WHICH CELLS MEDIATE TISSUE REGENERATION IN THE THYMUS AFTER ACUTE INJURY? ARE THERE LIMITATIONS TO ENDOGENOUS REGENERATION AFTER HCT ACROSS SEX AND LIFESPAN? CAN WE EXPLOIT THESE MECHANISMS OF ENDOGENOUS REGENERATION TO DEVELOP THERAPEUTIC STRATEGIES TO BOOST T CELL RECONSTITUTION IN HCT RECIPIENTS? THE STUDIES OUTLINED IN THIS PROPOSAL NOT ONLY HAVE THE POTENTIAL TO DEFINE IMPORTANT PATHWAYS UNDERLYING TISSUE REGENERATION BUT COULD ALSO RESULT IN INNOVATIVE CLINICAL APPROACHES TO ENHANCE THYMIC FUNCTION.

UNDERSTANDING EFFICACY AND FE(II)-PROMOTED ACTIVATION OF 1,2,4-TRIOXOLANES IN CANCER - PROJECT SUMMARY/ABSTRACT SUMMARY: PRECISION CANCER MEDICINE’S FOUNDATION LIES IN DISCOVERING AND EXPLOITING PATHWAYS THAT ARE ESSENTIAL FOR CANCER CELLS, BUT DISPENSABLE FOR CANCER CELLS. WHILE SUCH PATHWAYS EXIST, THEY ARE RELATIVELY UNCOMMON. MUCH MORE OFTEN THE ONCOGENIC PATHWAYS ACTIVATED IN CANCER CELLS ARE ESSENTIAL FOR MANY HEALTHY CELLS AS WELL, AT LEAST IN SOME ADULT TISSUE. THIS UNFORTUNATE FACT IS REFERRED TO AS A LOW THERAPEUTIC INDEX (TI), AND FRUSTRATES MANY PROMISING CANCER TREATMENTS. THIS PROJECT SEEKS TO IMPROVE THE TI OF INHIBITORS OF CRITICAL EFFECTORS OF THE RAS MEK ERK PATHWAY IN THE DEADLIEST HUMAN CANCERS USING FE(II) ACTIVATION OF DRUGS AND DEVELOPING NEW, FE(II) ACTIVATABLE THERAPIES. BACKGROUND: AS CANCER CELLS TRANSFORM FROM NORMAL TO MALIGNANT, THEY INCUR METABOLIC AND POTENTIALLY PHARMACOLOGIC LIABILITIES. THEIR HANDLING OF IRON IN ITS MOST DANGEROUS FORM, THE FE(II) STATE, IS PARTICULARLY DYSREGULATED, LEADING TO AN INCREASED LABILE IRON POOL (LIP). WE INVENTED A NEW WAY TO PREFERENTIALLY TARGET TUMOR CELLS BASED ON INCREASED AVIDITY FOR, AND ELEVATED CONCENTRATIONS OF LABILE FE2+ WITH AN IRON-ACTIVATED DRUG CONJUGATE (FEADC) AP PRO ACH INSPIRED BY A CLINICALLY VALIDATED 1,2,4-TRIOXOLANE (TRX) MOIETY WITH FE2+- DEPENDENT PHARMACOLOGY. THE CANCER CELL THEN ACTIVATES THE FEADC AND IS EXPOSED TO THE PAYLOAD. WE ARE FOCUSING ON MEK INHIBITORS BECAUSE 1) THEIR THERAPEUTIC INDEX IS LOW, 2) THEY HOLD PROMISE IN KRAS-DRIVEN SOLID TUMORS AND 3) THE KRAS ONCOGENE DRIVES INCREASES IN THE LIP TO A LEVEL WE THINK EXPLOITABLE. METHODS: FIRST WE WILL VALIDATE THE EFFICACY OF OUR MODIFIED MEK INHIBITOR AND A MODIFIED CHEMOTHERAPEUTIC IN AN AUTOCHTHONOUS, IMMUNOCOMPETENT MODEL OF MOUSE LUNG CANCER DRIVEN BY KRASG12D. WE WILL THEN USE CUTTING EDGE FUNCTIONAL SCREENING TO IDENTIFY THE CELLULAR ENZYMES NEEDED TO ACTIVATE (UNCAGE) THE FEADC INTO ACTIVE PAYLOADS IN THE CANCER CELL. WE WILL THEN FURTHER DEVELOP THE FE(II)-PROMOTED ACTIVATION OF 1,2,4-TRIOXOLANES TO INDUCE A SPECIALIZED FORM OF CELLULAR DEATH KNOWN AS FERROPTOSIS IN CANCER CELLS. IMPACT: THIS PROJECT FOCUSES ON A IMPROVING THE THERAPEUTIC INDEX OF TARGETED INHIBITORS, ESPECIALLY IN THE MOST UNDERSERVED TUMORS; THOSE WITH KRAS MUTATIONS. WE HAVE THE POTENTIAL TO IMMEDIATELY IMPACT A LARGE SWATH OF ANTICANCER THERAPEUTICS VIA OUR FLEXIBLE AND POWERFUL PRODRUG APPROACH. THROUGH BETTER UNDERSTANDING OF THE MECHANISMS OF CELLULAR FE(II)-PROMOTED ACTIVATION OF 1,2,4-TRIOXOLANES, WE MAY ALSO DEVELOP NEW CLASSES OF ANTICANCER COMPOUNDS CALLED FEADCS AND LEVERAGING FERROPTOSIS AS A THERAPEUTIC ENDPOINT IN OUR DEVELOPMENTAL STUDIES.

ASSESSING THE EFFECTS OF ORAL PRE-EXPOSURE PROPHYLAXIS ON PHARMACOKINETICS OF MONOCLONAL AND VACCINE-INDUCED ANTIBODIES AMONG WOMEN VULNERABLE TO HIV-1 - ABSTRACT IN THIS PROPOSAL, WE WILL DETERMINE THE INFLUENCE OF ORAL PRE-EXPOSURE PROPHYLAXIS (PREP) ON THE PHARMACOKINETICS (PK) OF PASSIVELY ADMINISTERED MONOCLONAL ANTIBODIES (MABS) AND VACCINE-INDUCED POLYCLONAL ANTIBODIES (ABS) IN FEMALES VULNERABLE TO HIV-1, USING DATA AND SPECIMENS FROM PAST HIV-1 PREVENTION TRIALS. THIS RESEARCH WILL HAVE A SIGNIFICANT IMPACT ON GLOBAL HEALTH BECAUSE ORAL PREP IS CURRENTLY THE MOST ACCESSIBLE PHARMACEUTICAL HIV-1 PREVENTION OPTION, AND ABS ARE CRITICAL FOR IMMUNE PROTECTION AND THERAPEUTIC EFFICACY. AIM 1 FOCUSES ON DETERMINING WHETHER ORAL PREP AFFECTS THE PK OF VRC01, A BROADLY NEUTRALIZING HIV-1 MAB, IN FEMALE PARTICIPANTS FROM THE RECENTLY COMPLETED ANTIBODY MEDIATED PREVENTION (AMP) STUDY. WE WILL IDENTIFY BIOMARKERS OF PREP USE THAT CORRELATE WITH INCREASED MAB CLEARANCE, WITH A SPECIFIC EMPHASIS ON ASSESSING PREP’S EFFECTS ON TWO INTESTINAL AB CLEARANCE MECHANISMS: DISRUPTION OF THE EPITHELIAL BARRIER AND INCREASED FC RECEPTOR (FCR) MEDIATED AB DEGRADATION. AIM 2 EXTENDS THIS INVESTIGATION BY EXAMINING THE IMPACT OF ORAL PREP ON THE MAGNITUDE AND DURABILITY OF HIV-1 VACCINE-INDUCED ANTIBODIES (ABS) IN FEMALE PARTICIPANTS FROM TWO COMPLETED HIV-1 VACCINE EFFICACY TRIALS. TO EXTEND BEYOND HIV-1, WE WILL ALSO ASSESS DURABILITY OF HEPATITIS B (HB) VACCINE-INDUCED ABS IN FEMALE AND MALE PARTICIPANTS FROM AMP AND THE VACCINE TRIALS. CONSISTENT WITH WHAT WAS OBSERVED FOR VRC01 PK IN MALES FROM THE AMP TRIAL, OUR PRELIMINARY DATA IN TWO PRE-EFFICACY VACCINE TRIALS SUGGEST AN ASSOCIATION BETWEEN PREP USE AND FASTER DECAY OF HIV-1 VACCINE-INDUCED ABS. WE PLAN TO IDENTIFY PREP BIOMARKERS ASSOCIATED WITH VACCINE AB KINETICS. IN BIOPSY DONORS, WE WILL ALSO DETERMINE THE ASSOCIATION BETWEEN HB VACCINE AB KINETICS AND IDENTIFIED BIOMARKERS WITH THE TWO POTENTIAL INTESTINAL MECHANISMS OF AB CLEARANCE. CHARACTERIZING ANY PREP EFFECTS ON ABS IS CRUCIAL FOR PEOPLE WHO TAKE ORAL PREP AND RELY ON MAB IMMUNOTHERAPIES AND/OR AB-INDUCING VACCINES FOR PROTECTION AGAINST PATHOGENS. AIM 3 FOCUSES ON DEVELOPING A PHARMACOKINETIC AND STATISTICAL MODELING FRAMEWORK TO RANK AND SELECT MAB REGIMENS FOR EFFICACY TESTING. THIS FRAMEWORK WILL ACCOUNT FOR PREP USE AND MAB PK BIOMARKERS IDENTIFIED IN AIM 1. IT WILL ALSO INCORPORATE MAB LEVELS IN SERUM AND RECTAL TISSUE FROM BOTH MALES AND FEMALES, RECOGNIZING THE IMPORTANCE OF TISSUE LEVELS IN PREDICTING PROTECTION AGAINST HIV-1 AND INTESTINAL PREP EFFECTS ON MAB PK. BY BUILDING AND VALIDATING ADVANCED PK MODELS AND STATISTICAL METHODS FOR BRIDGING DIFFERENCES IN STUDY POPULATIONS, WE SEEK TO ENHANCE THE ACCURACY OF SELECTING THE MOST PROMISING MAB REGIMENS FOR FUTURE CLINICAL TRIALS, ULTIMATELY CONTRIBUTING TO MORE EFFECTIVE HIV-1 PREVENTION STRATEGIES.

BASE-EDITED HEMATOPOIETIC STEM AND PROGENITOR CELLS TO ENABLE SAFE USE OF HIGHLY POTENT CD33-TARGETED RADIOIMMUNOTHERAPY - ABSTRACT ANTIGEN-SPECIFIC THERAPIES HAVE LONG BEEN PURSUED TO IMPROVE OUTCOMES IN ACUTE MYELOID LEUKEMIA (AML). SO FAR MOST EXPLOITED ARE MONOCLONAL ANTIBODIES (MABS) TARGETING CD33, A GLYCOPROTEIN DISPLAYED ON THE CELL SURFACE OF LEUKEMIC BLASTS IN ALMOST ALL CASES AND POSSIBLY LEUKEMIA STEM CELLS IN SOME. LONGER SURVIVAL OF SOME PATIENTS TREATED WITH THE CD33 ANTIBODY-DRUG CONJUGATE GEMTUZUMAB OZOGAMICIN (GO) VALIDATES THIS APPROACH, BUT GO IS OFTEN INEFFECTIVE, PROMPTING EFFORTS TO DEVELOP IMPROVED, MORE POTENT CD33-DIRECTED THERAPEUTICS. BECAUSE AML CELLS ARE EXQUISITELY SENSITIVE TO RADIATION IN A DOSE-DEPENDENT FASHION, RADIONUCLIDES ARE IDEAL TO ARM ANTI- CD33 MABS. INDEED, EARLY PHASE CLINICAL TRIALS DEMONSTRATED SUBSTANTIAL ANTI-AML EFFICACY OF THE ANTI-CD33 MAB LINTUZUMAB (HUM195, SGN-33) WHEN COUPLED WITH THE A-EMITTER ACTINIUM-225 (225AC). A-EMITTERS DELIVER A VERY HIGH AMOUNT OF RADIATION OVER JUST A FEW CELL DIAMETERS, THEREBY ENABLING PRECISE AND EFFICIENT TARGET CELL KILL, RENDERING THEM PARTICULARLY INTERESTING FOR SPECIFIC TARGETING OF AML WITH RADIOIMMUNOCONJUGATES (“RIT”). HOWEVER, EVEN WITH 225AC-LINTUZUMAB, AN IMPORTANT SHORTCOMING IS CD33 EXPRESSION ON NORMAL MYELOID CELLS, WHICH LEADS TO “ON-TARGET, OFF-TUMOR CELL” TOXICITIES THAT MANIFEST AS SEVERE AND PROLONGED MYELOSUPPRESSION WITH LIFE-THREATENING SEQUELAE (E.G. INFECTION). THUS, CLINICAL USE OF CD33-DIRECTED RIT WITHOUT IMMEDIATE STEM CELL RESCUE IS CURRENTLY LIMITED TO SUBOPTIMAL DRUG DOSES. WE HAVE RECENTLY DEMONSTRATED IN MICE AND NONHUMAN PRIMATES THAT CRISPR/CAS9 NUCLEASE-BASED EDITING OF CD33 RESULTS IN FUNCTIONALLY NORMAL HEMATOPOIESIS THAT EXPRESSES REDUCED LEVELS OF CD33 AND IS PROTECTED FROM GO AND CD33-DIRECTED T CELL-ENGAGING THERAPEUTICS. WE HYPOTHESIZE CD33-EDITED NORMAL HEMATOPOIETIC STEM AND PROGENITOR CELLS (HSPCS) WILL RESIST CD33-DIRECTED RIT WITH A-PARTICLE-EMITTING RADIONUCLIDES AND ENABLE THEIR SAFE USE AT MAXIMALLY EFFECTIVE DRUG DOSES. HOWEVER, THE CRISPR/CAS9-BASED CD33 GENE EDITING STRATEGY SUFFERS FROM SIGNIFICANT OFF-TARGET ACTIVITY, AND DNA DOUBLE STRAND BREAKS (DSBS) CAN GENERATE LARGER DELETIONS AND COMPLEX CHROMOSOMAL REARRANGEMENTS AND CAUSE TP53-DEPENDENT DNA DAMAGE RESPONSE AND CELL CYCLE ARREST. TO ADDRESS THIS LIMITATION, WE WILL OPTIMIZE AND CHARACTERIZE A NOVEL GENE-EDITING STRATEGY TO PROTECT NORMAL HEMATOPOIESIS FROM HIGHLY POTENT CD33-DIRECTED RIT BY UTILIZING THE RECENTLY DESCRIBED BASE EDITOR (BE) TECHNOLOGY. BES INDUCE PRECISE NUCLEOTIDE MODIFICATIONS WITHOUT INTENTIONAL INTRODUCTION OF DSBS, MAKING THEM AN ATTRACTIVE STRATEGY TO GENERATE CD33NULL “NORMAL” HEMATOPOIETIC CELLS. WE HAVE ASSEMBLED A MULTIDISCIPLINARY TEAM OF INVESTIGATORS WITH COMPLEMENTARY EXPERTISE IN CD33-DIRECTED THERAPIES, PRECLINICAL OPTIMIZATION OF RIT, AND RADIOPHARMACEUTICS TO CONDUCT WELL-CONTROLLED PRECLINICAL IND-ENABLING STUDIES TO DEVELOP BE-BASED CD33 ENGINEERING OF NORMAL HUMAN HSPCS FOR CLINICAL USE WITH A-EMITTER CD33-DIRECTED RIT FOR PATIENTS WITH AML AND OTHER CD33-EXPRESSING DISORDERS.

USTEKINUMAB FOR GRAFT VERSUS HOST DISEASE PREVENTION (IND 144540)

DIGITAL SMOKING CESSATION INTERVENTION FOR NATIONALLY-RECRUITED AMERICAN INDIANS AND ALASKA NATIVES: A FULL-SCALE RANDOMIZED CONTROLLED TRIAL - PROJECT SUMMARY/ABSTRACT (DESCRIPTION) SINCE THE EARLY 1980S, AMERICAN INDIANS AND ALASKA NATIVES (AIANS) HAVE MAINTAINED THE HIGHEST RATES OF COMMERCIAL CIGARETTE SMOKING OF ANY RACIAL/ETHNIC GROUP IN THE US. CURRENTLY, 27% OF AIANS SMOKE CIGARETTES. COMPARED TO OTHER RACIAL/ETHNIC GROUPS, THEY HAVE 6 TIMES HIGHER RATES OF DEVELOPING SMOKING-RELATED CANCERS. AIANS ARE ONLY HALF AS LIKELY TO QUIT SMOKING COMPARED TO OTHER RACES/ETHNICITIES. THE RESULT IS THAT COMMERCIAL CIGARETTE SMOKING ACCOUNTS FOR HALF OF ALL DEATHS AMONG AIANS NATIONWIDE. A MAJOR CAUSE OF THESE LONGSTANDING INEQUITIES IS THE LACK OF ACCESS TO EFFICACIOUS SMOKING CESSATION INTERVENTIONS AMONG AIANS. COMPOUNDING THE BARRIER OF LACK OF ACCESS TO SMOKING CESSATION INTERVENTIONS IS THE BARRIER OF LACK OF RESEARCH ON THE EFFICACY OF SMOKING CESSATION INTERVENTIONS FOR AIANS. DESPITE HAVING THE HIGHEST SMOKING PREVALENCE OF ANY RACIAL/ETHNIC GROUP IN THE US FOR OVER 40 YEARS, A MERE 0.3% OF ALL FULL-SCALE SMOKING CESSATION RANDOMIZED CONTROLLED TRIALS (RCTS) HAVE FOCUSED ON AIANS. REGARDING ACCESSIBILITY, A SMARTPHONE APPLICATION (“APP”) HAS THE POTENTIAL TO DELIVER A LOW-COST SMOKING CESSATION INTERVENTION WITH WIDE GEOGRAPHIC REACH TO AIANS AND IN REGIONS OF THE US WITH SMOKING RATES AS HIGH AS 57% IN THIS GROUP (I.E., NORTHERN PLAINS). REGARDING EFFICACY, OUR PRELIMINARY DATA PROVIDES PROMISING EVIDENCE FOR OUR ACCEPTANCE AND COMMITMENT THERAPY (ACT)-BASED SMARTPHONE APP, CALLED ICANQUIT, TO HELP AIANS QUIT SMOKING. WE COMPARED THE ICANQUIT APP WITH THE NCI’S QUITGUIDE APP AMONG THE AIAN SUBSAMPLE (N = 165 RECRUITED FROM 32 US STATES) ENROLLED IN OUR FULL-SCALE RCT. THIS SECONDARY ANALYSIS OF AIANS SHOWED DESCRIPTIVELY HIGHER RATES OF SMOKING CESSATION AT THE 12-MONTH FOLLOW-UP (30% FOR ICANQUIT VS. 18% FOR QUITGUIDE; OR = 1.96; 95% CI = 0.90, 4.26, P = .089). WHILE ENCOURAGING, ANALYSES WERE EXPLORATORY, NON-SIGNIFICANT, AND NOT A SUBSTITUTE FOR A FULL-SCALE EFFICACY TEST. TO ADDRESS WEAKNESSES OF PRIOR RESEARCH, A FULLY-POWERED COMPARATIVE EFFICACY RCT OF ICANQUIT VS. QUITGUIDE FOCUSING NATIONWIDE ON AIANS WHO SMOKE IS NOW NEEDED. THUS, THE GOAL OF THIS PROJECT IS TO CONDUCT A NATIONALLY RECRUITED AND FULLY-POWERED TWO-ARM RCT COMPARING ICANQUIT (N = 388) TO QUITGUIDE (N = 388), IN ORDER TO DETERMINE: (1) THE EFFICACY OF ICANQUIT RELATIVE TO THE QUITGUIDE APP FOR BIOCHEMICALLY VERIFIED 30-DAY POINT PREVALENCE ABSTINENCE (PPA) AT 12 MONTHS POST-RANDOMIZATION AND (2) WHETHER ICANQUIT’S (BUT NOT QUITGUIDE’S) 12-MONTH SMOKING CESSATION OUTCOMES ARE SIGNIFICANTLY MEDIATED BY IMPROVEMENTS IN CORE ACT-BASED PROCESSES. THIS STUDY WILL BE THE FIRST FULL-SCALE RCT OF A DIGITAL INTERVENTION FOR HELPING AIANS NATIONWIDE STOP SMOKING. QUALITATIVE INTERVIEWS WITH (1) A SUBSAMPLE OF ICANQUIT PARTICIPANTS TO THEMATIZE TESTIMONIALS OF THEIR EXPERIENCE WITH ICANQUIT AND (2) AIAN MEMBERS FROM OUR STUDY COMMUNITY ADVISORY BOARD (CAB) WILL GUIDE OUR PLAN FOR BROADLY DISSEMINATING ICANQUIT TO AIAN ADULTS NATIONWIDE. POSITIVE RESULTS WOULD IMPROVE HEALTH EQUITY BY PROVIDING A HIGHLY ACCESSIBLE AND EFFICACIOUS INTERVENTION WITH POTENTIAL FOR SUSTAINABILITY AND BROAD DISSEMINATION FOR AIANS NATIONWIDE.

AN INTEGRATIVE OMICS APPROACH TO INVESTIGATE GENE-ENVIRONMENT INTERACTION IN COLORECTAL CANCER RISK - PROJECT SUMMARY/ABSTRACT COLORECTAL CANCER (CRC) REMAINS ONE OF THE LEADING CAUSES OF CANCER-RELATED DEATHS AROUND THE WORLD. MANY ENVIRONMENTAL RISK FACTORS AND OVER 200 GENETIC RISK VARIANTS HAVE BEEN IDENTIFIED FOR THIS COMPLEX, MULTIFACTORIAL DISEASE. HOWEVER, DESPITE THE STRONG BIOLOGICAL RATIONALE FOR THE IMPORTANCE AND ABUNDANCE OF GENE-ENVIRONMENT (GXE) INTERACTIONS, THE EXTENT TO WHICH ENVIRONMENTAL RISK FACTORS (BROADLY DEFINED HERE AS LIFESTYLE, DIET, OBESITY, DRUG USE AND INTERMEDIATE BIOMARKERS) MODULATE GENETIC RISK FACTORS IS POORLY UNDERSTOOD. TO ACHIEVE THE PROMISE OF PRECISION PREVENTION, WE URGENTLY NEED TO GAIN A DEEPER UNDERSTANDING OF GXE INTERACTIONS IN CRC RISK. UNDERSTANDING WHICH MODIFIABLE RISK FACTORS MODULATE GENETIC RISK, WHICH IS FIXED, PROVIDES BIOLOGICAL INSIGHTS AND ACTIONABLE TARGETS FOR NEW PREVENTION INTERVENTION STRATEGIES. TO ACCELERATE THE DISCOVERY OF GXE INTERACTIONS IN CRC RISK AND TO TAKE AN IMPORTANT NEXT STEP TOWARDS TRANSLATION, WE PROPOSE A COMPREHENSIVE INNOVATIVE APPROACH THAT COMBINES SINGLE-CELL MULTI-OMICS DATA, INDIVIDUAL-LEVEL HARMONIZED EPIDEMIOLOGICAL AND CLINICAL DATA, AND GENOME-WIDE DATA FROM LARGE, WELL-CHARACTERIZED, DIVERSE STUDY POPULATIONS, WITH NOVEL COMPUTATIONAL AND STATISTICAL APPROACHES. DRAMATIC IMPROVEMENTS IN SINGLE-CELL MULTIMODAL OMICS TECHNOLOGIES, COMBINED WITH NEW COMPUTATIONAL TOOLS BASED ON POWERFUL DEEP-LEARNING MODELING APPROACHES NOW ALLOW US TO PREDICT THE IMPACT OF GENETIC VARIANTS ON GENE REGULATION IN A CELL-TYPE- SPECIFIC HOLISTIC MANNER. BECAUSE SIMULTANEOUSLY MEASURED SINGLE-CELL GENE EXPRESSION (SCRNA-SEQ) AND CHROMATIN ACCESSIBILITY (SCATAC-SEQ) DATA FOR NORMAL COLORECTAL MUCOSA TISSUE IS LACKING FOR RACIALLY AND ETHNICALLY DIVERSE SAMPLES WITH DETAILED ASSESSMENT OF ENVIRONMENTAL RISK FACTORS, WE PROPOSE IN AIM 1 TO GENERATE SUCH DATA FOR 50 INDIVIDUALS. THIS RESOURCE, TOGETHER WITH OTHER SINGLE CELL MULTI-OMICS COMPENDIA FOR COLORECTAL TISSUE (LIKE HTAN), WILL BE LEVERAGED TO DEVELOP FUNCTIONAL PREDICTION SCORES FOR GENETIC VARIANTS ACROSS THE GENOME. IN AIM 2, WE WILL USE THESE FUNCTIONAL PREDICTION SCORES TO BOOST STATISTICAL POWER FOR DISCOVERY OF NOVEL GXE INTERACTIONS. WE WILL PERFORM GENOME-WIDE GXE SCANS IN OVER 230,000 RACIALLY AND ETHNICALLY DIVERSE CRC CASES AND CONTROLS ACROSS KEY ENVIRONMENTAL RISK FACTORS, INCLUDING OBESITY, DIABETES, SMOKING, ALCOHOL, DRUG USE, DIETARY FACTORS AND INTERMEDIATE BIOMARKERS LINKED TO METABOLIC DYSREGULATION AND CHRONIC INFLAMMATION. TO EXPAND THE NUMBER OF KEY RISK FACTORS WE CAN EVALUATE, WE WILL UTILIZE EXISTING GENETIC INSTRUMENTS. IN AIM 3, WE WILL COMPREHENSIVELY CHARACTERIZE AND TRANSLATE GXE INTERACTIONS. TO DO SO, WE WILL STRATIFY GXE FINDINGS BY CLINICAL FACTORS, INCLUDING AGE OF ONSET, RACIAL AND ETHNIC GROUP, SEX, AND TUMOR SUBTYPES. ADDITIONALLY, WE WILL INCORPORATE GXE INTERACTIONS AND GENETICALLY PREDICTED BIOMARKERS IN A COMPREHENSIVE TRANS-ANCESTRAL RISK PREDICTION MODEL TO IMPROVE PREDICTION AND PROVIDE ACTIONABLE INFORMATION TO REDUCE THE BURDEN OF CRC. OUR COMMUNITY ADVISORS HAVE STRESSED THE IMPORTANCE OF INCLUDING THE INTERPLAY BETWEEN GENETIC AND ENVIRONMENTAL RISK FACTORS IN RISK PREDICTION MODELING TO ENHANCE THE ACCEPTANCE OF RISK PREDICTION MODELS IN THE COMMUNITY.

A COMPASS FOR THOSE WITH RELAPSED LEUKEMIA AFTER TRANSPLANT - ABSTRACT RELAPSE OF LEUKEMIA OCCURS IN NEARLY HALF OF PATIENTS AFTER HEMATOPOIETIC CELL TRANSPLANTATION (HCT). WHILE THERE ARE A GROWING NUMBER OF THERAPEUTIC OPTIONS FOR LEUKEMIC RELAPSE AFTER HCT, WE LACK A CLINICAL ASSAY CAPABLE OF SIMULTANEOUSLY DETECTING DISEASE AND TRIAGING PATIENTS TO TREATMENT WHICH WILL MOST LIKELY BENEFIT THEM. IN THIS APPLICATION, WE PROPOSE TO RIGOROUSLY EVALUATE AND EMPLOY NOVEL SINGLE-CELL GENOMIC METHODS AND THEIR ACCOMPANYING COMPUTATIONAL APPROACHES TO DETECT DISEASE AT LOW LEVELS, INFORM MECHANISMS OF RELAPSE, AND DIRECT FUTURE THERAPY. IN AIM 1, WE WILL OPTIMIZE COMPUTATIONAL METHODS FOR DETECTING NATURAL GENETIC VARIATION BETWEEN DONOR AND RECIPIENT, A DIAGNOSTIC MANEUVER WE BELIEVE WILL IMPROVE THE SENSITIVITY OF DETECTING MALIGNANT CELLS AFTER HCT. WE WILL THEN VALIDATE THESE METHODS USING SAMPLES FROM PATIENTS IN A RETROSPECTIVE FASHION. TO PROVIDE INSIGHT INTO MECHANISMS OF RELAPSE, WE HAVE DEVELOPED A NOVEL MOLECULAR APPROACH FOR IDENTIFYING PERTURBATIONS IN HLA AND RELATED GENES, A COMMON MEANS BY WHICH LEUKEMIA EVADES THE IMMUNE SYSTEM AFTER HCT. IN AIM 2, WE WILL VALIDATE THIS METHOD IN A MANNER THAT EXPLORES THE LOWER LIMIT OF DETECTION FOR HLA- PERTURBED CELLS. FINALLY, IN AIM 3, WE WILL BUILD ON DECADES OF WORK USING FLOW CYTOMETRY TO ASSESS THE HETEROGENEITY OF MYELOID NEOPLASMS BY INTEGRATING OUR SINGLE-CELL MOLECULAR MEASURES WITH CELL-SURFACE IMMUNOPHENOTYPE. USING THIS APPROACH, WE SEEK TO DEFINE COMMON MOLECULAR SIGNATURES IN LEUKEMIA-INITIATING CELLS (LICS), A SUBSET OF CELLS IN MYELOID NEOPLASMS THOUGHT TO BE A CHEMO-RESISTANT RESERVOIR OF LEUKEMIA. THE PROPOSED STUDIES WILL ESTABLISH A NEW METHOD FOR SURVEILLANCE OF RESIDUAL DISEASE AFTER HCT, WHICH WE BELIEVE WILL PROVIDE A DEEPER LEVEL OF CONFIDENCE AND INSIGHT INTO LEUKEMIC RELAPSE POST-TRANSPLANT. WE EXPECT THESE STUDIES TO FORM THE FOUNDATIONAL PRECLINICAL DATA FOR A SINGLE-CELL GENOMICS CLINICAL ASSAY CAPABLE OF RISK-STRATIFYING PATIENTS WITH EARLY EVIDENCE OF LEUKEMIC RELAPSE AFTER HCT.

DEVELOPMENT OF 211ASTATINE-CONJUGATED ANTI-CD45 ANTIBODY-BASED CONDITIONING FOR HEMATOPOIETIC STEM CELL GENE THERAPY AND EDITING

EPIGENOMIC PROFILING OF COMPLEX TISSUES WITH SINGLE-CELL CUT&RUN

ADVANCING EQUITY IN COLORECTAL CANCER GENETIC RISK PREDICTION THROUGH EXPANSION OF RACIAL/ETHNIC MINORITY REPRESENTATION

QUIT2HEAL: RIGOROUS RANDOMIZED TRIAL OF A SMARTPHONE APPLICATION TO HELP CANCER PATIENTS STOP SMOKING

DEVELOPING THE FRAMEWORK FOR FIRST-IN-CLASS IMMUNOTHERAPIES THAT TARGET DISSEMINATED TUMOR CELLS AND PREVENT BREAST CANCER METASTASIS

MECHANISMS UNDERLYING OLFACTORY EFFECTS ON APPETITE

BLENDING DEEP LEARNING WITH PROBABILISTIC MECHANISTIC MODELS TO PREDICT AND UNDERSTAND THE EVOLUTION AND FUNCTION OF ADAPTIVE IMMUNE RECEPTORS

TRANSLATIONAL RESEARCH PROGRAM IN COLORECTAL CANCER DISPARITIES

DEVELOPING DURABLE, ENV-BOOSTED CAR T CELLS FOR HIV CURE - PROJECT SUMMARY/ABSTRACT MODIFICATION OF AUTOLOGOUS T CELLS WITH CHIMERIC ANTIGEN RECEPTOR (CAR) MOLECULES WAS FIRST PROPOSED NEARLY 30 YEARS AGO AS A THERAPY FOR PEOPLE LIVING WITH HIV. SINCE THEN, CAR-T CELLS HAVE EMERGED AS A POTENT AND HIGHLY SUCCESSFUL THERAPY FOR LIQUID TUMORS, WHILE HIV-SPECIFIC CAR-T CELLS HAVE ONLY BEGUN TO SHOW EFFICACY IN LARGE ANIMAL MODELS AND CLINICAL TRIALS. BASED ON OUR LONGSTANDING INTEREST IN CAR-T CELL THERAPIES FOR HIV, WE POSIT THREE PRIMARY BARRIERS THAT LIMIT THE CURATIVE POTENTIAL OF THIS APPROACH. FIRST, LOW LEVELS OF HIV-1 ANTIGEN AT THE CELL SURFACE (NAMELY ENV PROTEIN), ESPECIALLY DURING ANTIRETROVIRAL THERAPY (ART), RENDER LATENTLY INFECTED CELLS NEARLY INVISIBLE TO CAR-T CELLS AND OTHER VIRUS-SPECIFIC IMMUNE EFFECTORS. SECOND, THE WEALTH OF KNOWLEDGE REGARDING CELLULAR TRAFFICKING OF THE VIRAL ENV PROTEIN HAS YET TO BE THOROUGHLY APPLIED IN THE CONTEXT OF ENV- DEPENDENT HIV CURE STRATEGIES. THIRD, CAR-T CELL PERSISTENCE AND FUNCTION WANE OVER TIME, PRIOR TO COMPLETE CLEARANCE OF THE LATENT HIV RESERVOIR. OUR GROUNDBREAKING PRELIMINARY DATA OUTLINES A PATH TO OVERCOME THESE LIMITATIONS. WE RECENTLY REPORTED FINDINGS IN FOUR RHESUS MACAQUES THAT WERE INFECTED WITH AN HIV-LIKE VIRUS, SUPPRESSED BY ART AND THEN INFUSED WITH VIRUS-SPECIFIC CAR-T CELLS CONTAINING THE CD4 EXTRACELLULAR DOMAIN (CD4CAR). TO EXPAND THESE POTENT ANTIVIRAL EFFECTORS IN VIVO, ANIMALS WERE NEXT BOOSTED WITH AN IRRADIATED CELL LINE STABLY EXPRESSING HIV-1 ENV. FOLLOWING ART TREATMENT INTERRUPTION (ATI), VIRAL CONTROL WAS OBSERVED IN 2 OF 4 ANIMALS, CONSISTENT WITH ROBUST AND ENV-DEPENDENT EXPANSION OF CD4CAR-T CELLS. THE CENTRAL GOAL OF THIS PROPOSAL IS TO INCREASE THE POTENCY AND FEASIBILITY OF THIS APPROACH. IN AIM 1, WE WILL TRANSITION OUR ENV BOOSTING STRATEGY FROM AN IMMORTALIZED CELL LINE TO AN FDA-APPROVED MRNA LIPID NANOPARTICLE (MRNA-LNP) PLATFORM, ANALOGOUS TO THE MODERNA AND PFIZER/BIONTECH VACCINES FOR SARS-COV-2. ENV IMMUNOGENS WILL BE OPTIMIZED FOR CD4CAR T CELL INTERACTIONS AND DEVELOPED AS ENV MRNA-LNP VACCINES. IN AIM 2, WE WILL USE CRISPR- CAS9 GENE EDITING TO EXTEND THE DURABILITY AND FUNCTION OF CD4CAR-T CELLS. WE WILL COMPARE A SERIES OF CAR PRODUCTS THAT CARRY INACTIVATED IMMUNE CHECKPOINT ALLELES, WHICH WE HYPOTHESIZE WILL SUPPORT MORE DURABLE FUNCTION AND EFFICIENTLY CLEAR PERSISTENT VIRAL RESERVOIRS. IN AIM 3, WE WILL BENCHMARK ENV MRNA-LNP AND IMMUNE CHECKPOINT GENE EDITING STRATEGIES IN OUR VETTED NONHUMAN PRIMATE (NHP) MODEL OF HIV GENE THERAPY. THESE EXPERIMENTS WILL FEATURE A POWERFUL COMPETITIVE REPOPULATION STUDY DESIGN, PROVIDING CRITICAL INFORMATION ON BASIC CAR BIOLOGY THAT CANNOT BE GATHERED IN CLINICAL STUDIES. TOGETHER, THESE AIMS BUILD ON WHAT WE BELIEVE TO BE THE MOST PROMISING ANTI-HIV CELL AND GENE THERAPY APPROACH REPORTED TO DATE. OUR UNIQUE AND HIGHLY INFORMATIVE NHP MODEL OF HIV PERSISTENCE AND CAR-T CELL THERAPY WILL FILL IN CRITICAL GAPS IN KNOWLEDGE REGARDING CAR-T CELL SAFETY AND FUNCTION IN LIMITED ANTIGEN ENVIRONMENTS, AND FACILITATE CLINICAL TRANSLATION BOTH IN DEVELOPED AND DEVELOPING NATIONS. THE LESSONS WE LEARN FROM THESE STUDIES WILL BE APPLICABLE NOT ONLY AS A CURATIVE THERAPY FOR HIV-1, BUT FOR A RANGE OF DISEASES SUCH AS SOLID TUMORS WHERE CAR-T CELL THERAPIES MUST BE SIMILARLY AUGMENTED.

HARNESSING TISSUE RESIDENT MEMORY T CELLS FOR IMMUNOTHERAPY OF HERPES VIRUS INFECTIONS

INVESTIGATING CHROMATIN MECHANISMS USING VIRAL SYSTEMS

DISRUPTING THE IMMUNE AND DRUG-PRIVILEGED MICROENVIRONMENT IN PANCREAS CANCER

DISSECTING THE KAPOSI SARCOMA TUMOR MICROENVIRONMENT AT THE SINGLE CELL LEVEL

A UNIQUE APPROACH COMBINING AVATAR MICE AND TARGETED MASS SPECTROMETRY TO IDENTIFY BLOOD BIOMARKERS FOR EARLY DETECTION OF BREAST CANCER

NICHE SIGNALS IN HSC GENESIS

ODOR BLOCKING OF STRESS

(PQ6) RADIOGENOMICS OF COLORECTAL POLYPS TO ASSESS BENIGN PROLIFERATIVE VS. PREMALIGNANT STATES.

TARGETED GENETIC ENGINEERING OF B CELLS TO INDUCE PROTECTIVE ANTIBODY RESPONSES TO VIRAL PATHOGENS - PROJECT SUMMARY / ABSTRACT IN THE UNITED STATES ALONE, RESPIRATORY VIRAL PATHOGENIC INFECTIONS SUCH AS INFLUENZA CAUSE MILLIONS OF PROVIDER VISITS AND TENS OF THOUSANDS OF WORK DAYS LOST, HUNDREDS OF THOUSANDS OF HOSPITALIZATIONS AND DEATHS. ACCORDING TO THE WORLD HEALTH ORGANIZATION, THE NUMBER OF VIRAL PATHOGENIC INFECTIONS CONTINUES TO RISE WITH HIGHER MORTALITIES IN RESOURCE LIMITED COUNTRIES. WHILE A SUCCESSFUL VACCINE STRATEGY IS HIGHLY DESIRABLE, THIS APPROACH RELIES ON THE INDUCTION OF B CELLS TO PRODUCE PROTECTIVE ANTIBODIES THAT EITHER PREVENT VIRUSES FROM ENTERING CELLS OR TARGET INFECTED CELLS FOR DESTRUCTION. UNFORTUNATELY, SUCCESSFUL VACCINES FOR MANY VIRUSES ARE NOT YET AVAILABLE AFTER DECADES OF RESEARCH SUCH A RESPIRATORY SYNCYTIAL VIRUS (RSV). IN THIS PROPOSAL, WE LEVERAGE A NOVEL APPROACH DEVELOPED BY DR. JUSTIN TAYLOR’S LABORATORY TO GENETICALLY ENGINEER B CELLS TO EXPRESS ANTIBODIES PROTECTIVE AGAINST RESPIRATORY VIRUSES INCLUDING RSV AND INFLUENZA. THIS STRATEGY HAS ALREADY BEEN SHOWN TO RESULT IN THE PRODUCTION OF PROTECTIVE ANTIBODIES AGAINST INFLUENZA, RSV, AND HUMAN IMMUNODEFICIENCY VIRUS INFECTION [MOFFETT ET AL., SCIENCE IMMUNOLOGY, 2019]. WHILE THIS APPROACH CAN ENSURE PROTECTIVE ANTIBODY PRODUCTION, THE GENETIC ENGINEERING PROCESS REQUIRED 10 DAYS OF COMPLICATED EX VIVO MANUFACTURING AND IS NOT BROADLY DISTRIBUTABLE. TO OVERCOME THESE BARRIERS, WE WILL CO-OPT A NOVEL, SYNTHETIC NANOPARTICLE THAT WAS DEVELOPED IN DR. JENNIFER ADAIR’S LABORATORY TO DELIVER GENETIC ENGINEERING IN A SINGLE, PASSIVE STEP [SHAHBAZI ET AL., NATURE MATERIALS, 2019]. WE SHOW THAT THIS NANOPARTICLE CAN BE ASSEMBLED TO GENETICALLY ENGINEER PRIMARY HUMAN BLOOD CELLS IN LESS THAN 2 DAYS, AND CAN BE MODIFIED TO SPECIFICALLY INTERACT WITH TARGET BLOOD CELL TYPES IN VIVO. HERE WE WILL DEVELOP THIS SCALABLE NANOFORMULATION AS A VACCINE-LIKE IN VIVO DELIVERY SYSTEM TO DIRECT IMMUNE RESPONSES AGAINST RESPIRATORY VIRUSES SUCH AS RSV. WE WILL USE THESE NANOPARTICLES TO DIRECTLY GENETICALLY ENGINEER THE MOST PROTECTIVE PRIMARY B CELL SUBTYPES, AND HEMATOPOIETIC STEM AND PROGENITOR CELLS, WHICH CAN PROVIDE LIFELONG REPLENISHMENT OF PROTECTIVE B CELLS AND ANTIBODIES. THIS RESEARCH WILL NOT ONLY DEVELOP A UNIQUE TOOL SET AGAINST VIRAL PATHOGENS, BUT WILL PROVIDE TRANSFORMATIVE ADVANCES IN EQUITABLE DISTRIBUTION OF GENE EDITING THERAPIES.

MOLECULAR BASIS AND PROTECTIVE EFFICACY OF CROSS-NEUTRALIZING ANTIBODIES AGAINST FOUR MAJOR RESPIRATORY VIRUSES - PROJECT SUMMARY/ABSTRACT TENS OF THOUSANDS OF OTHERWISE DEADLY CANCERS ARE CURED WORLDWIDE EACH YEAR BY HEMATOPOIETIC STEM CELL TRANSPLANTATION (HCT), BUT UNFORTUNATELY OVER ONE IN TEN PATIENTS WILL DEVELOP A VIRAL LOWER RESPIRATORY TRACT INFECTION, WITH ALMOST HALF OF THESE PATIENTS SUCCUMBING TO THE INFECTION. WITHOUT AN INTACT IMMUNE SYSTEM IN THE FIRST FEW MONTHS AFTER TRANSPLANT, THESE LIFE-THREATENING INFECTIONS OFFSET THE BENEFIT DERIVED FROM POTENTIALLY LIFE- SAVING TRANSPLANT. OVER HALF OF THESE INFECTIONS ARE CAUSED BY FOUR VIRUSES: RSV, HMPV, HPIV3, AND HPIV1, NONE OF WHICH CURRENTLY HAVE ANY PHARMACOLOGIC INTERVENTIONS FOR TREATMENT OR PREVENTION AFTER HCT. ALTHOUGH ADULTS ARE UNIVERSALLY INFECTED WITH THESE VIRUSES IN CHILDHOOD, HCT RECIPIENTS LOSE THEIR IMMUNITY, MAKING THEM VULNERABLE TO SEVERE COMPLICATIONS. PASSIVE IMMUNIZATION WITH MONOCLONAL ANTIBODIES (MABS) REPRESENTS A STRATEGY TO REDUCE THE RISK OF THESE INFECTIONS. WHILE SEVERAL ANTI-RSV MAB CANDIDATES HAVE PROGRESSED THROUGH CLINICAL TRIALS, THEIR USE IS LIMITED TO INFANTS IN WHOM RSV IS RESPONSIBLE FOR VIRTUALLY ALL CASES OF LUNG INFECTION. HOWEVER, THE CLINICAL EFFICACY OF THESE MABS IS EXPECTED TO BE SUBSTANTIALLY LOWER IN HCT PATIENTS BECAUSE OTHER IMPORTANT VIRUSES LIKE HMPV, HPIV3, AND HPIV1 CONTRIBUTE SIGNIFICANTLY TO DISEASE. TO FILL THIS CLINICAL GAP FOR HCT PATIENTS, WE HAVE DISCOVERED TWO CROSS-NEUTRALIZING MABS: ONE THAT TARGETS BOTH RSV AND HMPV AND ANOTHER THAT TARGETS BOTH HPIV3 AND HPIV1. TOGETHER, THESE MABS COULD BE COMBINED TO SIMULTANEOUSLY PROTECT AGAINST THE FOUR VIRUSES THAT CAUSE MOST LUNG INFECTIONS AFTER HCT. TO TEST EFFICACY, WE WILL ADMINISTER THESE MABS PROPHYLACTICALLY AND THERAPEUTICALLY TO IMMUNOCOMPETENT AND IMMUNOCOMPROMISED ANIMALS. WE WILL ALSO TEST THE PHARMACOKINETICS OF THESE MABS WITH MODIFICATIONS DESIGNED FOR INCREASED HALF-LIFE AND LUNG BIOAVAILABILITY, SUCH THAT A SINGLE DOSE COULD BRIDGE THE ENTIRE PERIOD OF VULNERABILITY AFTER TRANSPLANT. ANOTHER OFTEN NEGLECTED PITFALL IN BRINGING NOVEL ANTIBODY THERAPIES TO THE BEDSIDE IS THE POTENTIAL FOR RESISTANCE. RECENT FAILED CLINICAL TRIALS OF ANTI-RSV MABS HAVE SHOWN THAT THE EMERGENCE OF ESCAPE VARIANTS CAN CRIPPLE CLINICAL DEVELOPMENT. HOW TO PREDICT SUCCESS OR FAILURE DURING THE PRECLINICAL PHASE BEFORE CANDIDATES PROGRESS INTO CLINICAL TRIALS IS AN IMPORTANT QUESTION, AND THE ANSWERS COULD SAVE MASSIVE AMOUNTS OF RESOURCES, EFFORT, AND TIME. TO FILL THIS KNOWLEDGE GAP, WE HAVE DEVELOPED AN INNOVATIVE APPROACH CALLED DEEP MUTATIONAL SCANNING THAT PROVIDES A COMPREHENSIVE PICTURE OF THE VIRAL MUTATIONAL LANDSCAPE, ALLOWING AN UNPRECEDENTED PRECLINICAL EVALUATION OF RESISTANCE. SINCE THE TWO CROSS-NEUTRALIZING MABS DESCRIBED IN THIS PROPOSAL BIND TO CONSERVED EPITOPES, THESE AND SIMILAR MABS MAY HAVE A HIGH BARRIER OF RESISTANCE. TO PREPARE FOR AND COUNTER RESISTANCE BY FUTURE VIRAL VARIANTS, WE WILL LEVERAGE PREDICTIONS FROM OUR COMPLETE MUTATIONAL MAPS TO IDENTIFY NEXT- GENERATION MABS, ALLOWING US TO STAY A FEW STEPS AHEAD OF VIRAL EVOLUTION. THESE NOVEL CROSS-NEUTRALIZING MABS AND THE INNOVATIVE AND RIGOROUS APPROACHES WE HAVE DEVELOPED TO VET THEM COULD PROVIDE A NEW STANDARD OF CARE FOR HCT PATIENTS AND INFORM THE DESIGN AND TESTING OF OTHER CANDIDATES WITH THE GREATEST CHANCE FOR SUCCESS.

DEEPLY ANALYZING MHC CLASS I-RESTRICTED PEPTIDE PRESENTATION MECHANISTICS ACROSS ALLELES, PATHWAYS, AND DISEASE COUPLED WITH TCR DISCOVERY/CHARACTERIZATION - PROJECT ABSTRACT/SUMMARY - OUR FRAMING HYPOTHESIS IS THAT THE COMBINED CONSTRAINTS OF PEPTIDE PROCESSING, HLA ALLELIC SPECIFICITY, AND PEPTIDE EDITING GENERATE A SIGNIFICANT “FUNNEL EFFECT”, WHERE THE PEPTIDOME CONSTITUTES ONLY A TINY PERCENTAGE OF ALL POSSIBLE PEPTIDES OBTAINABLE FROM A CELL’S PROTEOME AND THE LIGANDOME CONSTITUTES ONLY A SMALL PERCENTAGE OF ALL PEPTIDES FROM A CELL’S PEPTIDOME. OUR RESEARCH FOCUS IS UNDERSTANDING HOW THE INTERPLAY OF DIFFERENTIAL SEQUENCE RECOGNITION AT EACH STEP ULTIMATELY INFORMS FUNCTIONAL PRESENTATION OF A HIGHLY RESTRICTED SUBSET OF ALL POSSIBLE PROTEOME-DERIVED PEPTIDES – AND HOW TO IDENTIFY THE MOST “TRANSLATABLE” PHLA TARGETS FROM LIGANDOMES. - WE WILL RIGOROUSLY TEST THIS HYPOTHESIS USING OUR ALLELE-SPECIFIC MASS-SPEC PLATFORM FOR PEPTIDE DISCOVERY, ARTEMIS, TO IDENTIFY RELEVANT, HLA-RESTRICTED PEPTIDES FROM MESOTHELIN AND HIGH-RISK HPV E6/E7 ONCOPROTEINS. IDENTIFIED PEPTIDES WILL BE VALIDATED AND CHARACTERIZED BIOCHEMICALLY. CELL-SURFACE DISPLAYED PEPTIDE ARRAYS FROM E6/E7 AND MESOTHELIN WILL BE USED TO DETERMINE THE MAGNITUDE OF THE “FUNNEL EFFECT” OF PEPTIDE PROCESSING ON PEPTIDOME COMPOSITION. PATIENT T CELL RESPONSES TO IDENTIFIED MESOTHELIN PEPTIDES WILL BE MAPPED USING STATE- OF-THE-ART METHODOLOGIES. UNUSUAL PEPTIDES AND ALTERNATE BINDING CONFORMATIONS WILL BE CHARACTERIZED CRYSTALLO- GRAPHICALLY. WE WILL ASSESS VIRAL IMMUNOEVASION MECHANISMS, HLA-G PRESENTATION AND RECEPTOR INTERACTIONS, AND THE PRESENTATION OF GLYCOSYLATED PEPTIDES. DELIVERABLES INCLUDE MAPPING THE FULL MESOTHELIN AND E6/E7 PRESENTOMES ACROSS MULTIPLE ALLELES AND PRESENTATION MODALITIES, RANKED FOR FUTURE CLINICAL EXPLOITATION AS IMMU- NOTHERAPY TARGETS. - SIGNIFICANCE: FROM A BASIC SCIENCE PERSPECTIVE, ASSAYING CELLULAR PEPTIDOMES AND LIGANDOMES IS FUNDAMENTAL FOR UNDERSTANDING HOW THE IMMUNE SYSTEM RESPONDS TO INFECTIONS AND CANCER, IMMUNOEVASION MECHANISMS, THE RECOGNITION RULES OF MHC PROTEINS, THE MECHANISTICS OF ANTIGEN PROCESSING/EDITING, AND HOW SELF IS DEFINED. FROM A TRANSLATIONAL PERSPECTIVE, VALIDATED HLA-RESTRICTED PEPTIDES REPRESENT TARGETS FOR DIAGNOSIS AND THERAPY, THROUGH THERAPEUTIC VACCINATION, ENGINEERED T CELL-BASED ADOPTIVE IMMUNOTHERAPIES, AND ANTIBODY-BASED RECOG- NITION OF SPECIFIC, DISEASE-ASSOCIATED PEPTIDE/HLA COMPLEXES OUR PROPOSED STUDIES ADVANCE BOTH OBJECTIVES BY ELUCIDATING THE UNDERLYING MOLECULAR PRINCIPLES GOVERNING PEPTIDE PROCESSING AND PRESENTATION THROUGH INTE- GRATED STUDIES OF AN EXTENDED SET OF CLASSICAL AND NON-CLASSICAL HUMAN HLA CLASS I PROTEINS AND, IN THE PROCESS, IDENTIFY SPECIFIC PHLAS USEFUL FOR FUTURE CLINICAL APPLICATIONS.

A PATIENT-CENTRIC APPROACH TO ADVANCE FUNCTIONAL PRECISION ONCOLOGY - PROJECT SUMMARY/ABSTRACT THE DEVELOPMENT OF DRUG RESISTANCE IS A MAJOR CAUSE OF CANCER TREATMENT FAILURE AND MORTALITY. ALTHOUGH MUCH IS KNOWN ABOUT THE MECHANISMS BY WHICH TUMOR CELLS CAN BECOME RESISTANT TO A GIVEN DRUG, TRANSLATING THIS INTO EFFECTIVE THERAPEUTIC SOLUTIONS REMAINS AN UNMET CLINICAL NEED. HERE WE PROPOSE TO PIONEER THE USE OF PATIENT DERIVED TUMOR ORGANOIDS (PDTOS) AS A PLATFORM TO IDENTIFY AND VALIDATE NOVEL TARGETS AND EFFECTIVE DRUGS TO OVERCOME DRUG RESISTANCE IN OVARIAN CANCER, PANCREATIC CANCER, AND OTHER TUMOR TYPES. IN OUR PRELIMINARY STUDIES, WE SHOW THAT PDTOS GENETICALLY AND PHENOTYPICALLY MATCH THE TUMOR FROM WHICH THEY WERE DERIVED AND CAN BE USED TO STUDY THE PHENOTYPIC CONSEQUENCES OF TUMOR HETEROGENEITY, TUMOR EVOLUTION, AND DRUG RESISTANCE. USING A CLINICAL LABORATORY IMPROVEMENT AMENDMENTS (CLIA) APPROVED HIGH COMPLEXITY ASSAY, WE SHOW THAT PDTO DRUG SENSITIVITIES ARE HIGHLY CONCORDANT WITH KNOWN GENETIC BIOMARKERS, RETROSPECTIVE TREATMENT HISTORY AND PROSPECTIVE PATIENT RESPONSES. TUMOR ORGANOIDS DERIVED FROM PATIENTS WHO DEVELOPED IN SITU DRUG RESISTANCE DEMONSTRATE EX VIVO RESISTANCE TO THOSE SAME DRUGS BUT ALSO DEMONSTRATE SENSITIVITY TO OTHER ALTERNATIVE ONCOLOGY DRUGS. ADDITIONAL PRELIMINARY STUDIES SHOW STABLE DISEASE OR TUMOR REGRESSION IN PATIENTS TREATED WITH DRUGS IDENTIFIED FROM ORGANOID DRUG SCREENS. HERE, WE PROPOSE TO COMBINE DRUG SCREENING AND MOLECULAR PROFILING OF PDTOS DERIVED FROM A GIVEN PATIENT FROM DIFFERENT ANATOMIC TUMOR SITES AND BEFORE AND AFTER THERAPY TO ELUCIDATE THE MECHANISTIC BASIS FOR DRUG SENSITIVITY OR RESISTANCE AND TO IDENTIFY NOVEL TARGETS AND EFFECTIVE DRUGS TO TREAT METASTATIC, DRUG RESISTANT CANCERS. ACCOMPANYING COMPUTATIONAL PREDICTION MODELS THAT INTEGRATE LARGE PUBLIC DATASETS AS WELL AS INNOVATIVE METHODS OF MECHANISTIC TARGET VALIDATION INCLUDING CRISPR, TARGETED PROTEIN DEGRADATION TECHNOLOGIES, AND EPIGENETIC PROFILING, WILL BE USED TO PRIORITIZE AND ADVANCE TARGETS AND ASSOCIATED BIOMARKERS WITH GREATEST CLINICAL POTENTIAL. THE RATIONALE BEHIND OUR APPROACH IS THAT IDENTIFYING TARGETS AND EFFECTIVE DRUGS DIRECTLY IN PATIENT DERIVED SAMPLES WITH KNOWN CLINICAL HISTORY AND OUTCOMES WILL SIGNIFICANTLY ENHANCE TRANSLATION OF OUR FINDINGS. THIS PROPOSAL IS SIGNIFICANT BECAUSE IT WILL DEMONSTRATE THE UTILITY OF PDTOS AS BOTH A RESEARCH TOOL FOR TARGET DISCOVERY AND VALIDATION BUT ALSO AS A CLINICALLY USEFUL PLATFORM TO GUIDE FUNCTIONAL PRECISION MEDICINE. THE FINDINGS AND METHODS DEVELOPED CAN BE READILY APPLIED TO OTHER CANCER TYPES AND CLINICAL CHALLENGES, WILL ACCELERATE PRECLINICAL DRUG AND DRUG TARGET DEVELOPMENT, AND WILL TRANSLATE TO CLINICAL STUDIES. THE MODELS, APPROACHES, AND EXPECTED OUTCOMES OF THIS PROPOSAL ARE HIGHLY RESPONSIVE TO THE REQUIREMENTS OF PAR-21-274.

ALPHA RADIOIMMUNOTHERAPY FOR LYMPHOMA TREATMENT

HORMONE SIGNALING AND TRANSLATION CONTROL IN ADVANCED PROSTATE CANCER

TISSUE REGULATORY T CELLS IN MUCOSAL INFECTION

UNDERSTANDING AND EXPLOITING NOVEL THERAPEUTIC VULNERABILITIES OF RIT1-DRIVEN LUNG CANCER - PROJECT SUMMARY/ABSTRACT RECENT ADVANCES IN TARGETED THERAPIES HAVE REVOLUTIONIZED LUNG CANCER CLINICAL PRACTICE. LUNG ADENOCARCINOMAS HARBOR FREQUENT MUTATIONS/AMPLIFICATIONS/FUSIONS IN RECEPTOR TYROSINE KINASE (RTK) AND RAS PATHWAY ONCOGENES, MANY OF WHICH CAN BE TARGETED BY FDA-APPROVED THERAPIES. HOWEVER, THE MAJORITY OF PATIENTS DO NOT HAVE TARGETED TREATMENT OPTIONS. OUR PREVIOUS WORK IDENTIFIED SOMATIC RIT1 MUTATIONS IN LUNG ADENOCARCINOMAS AND DISCOVERED THAT RIT1 VARIANTS ACT AS GAIN-OF-FUNCTION MUTATIONS TO PROMOTE CELLULAR TRANSFORMATION AND DRUG RESISTANCE. RIT1 AMPLIFICATION AND OVEREXPRESSION MAY PLAY A SIMILAR PATHOGENIC ROLE. RIT1 MUTATIONS ALSO ARE FOUND IN MYELOID LEUKEMIAS AND IN THE GERMLINE OF INDIVIDUALS WITH NOONAN SYNDROME. IN ALL DISEASES, MUTATIONS IN RIT1 ARE MUTUALLY EXCLUSIVE WITH OTHER RAS-PATHWAY MUTATIONS, IMPLICATING RIT1 AS A RAS-PATHWAY DRIVER GENE. HOWEVER, OUR RECENT PRELIMINARY DATA SHOW THAT RIT1 AND KRAS SUBSTANTIALLY DIFFER IN THE DOWNSTREAM EFFECTORS NEEDED TO PROMOTE TUMORIGENESIS. FURTHER UNDERSTANDING THE CELLULAR CONSEQUENCES OF RIT1 MUTATIONS WILL OPEN UP NEW STRATEGIES FOR TREATMENT OF RIT1-MUTANT CANCERS. IN THIS PROPOSAL, WE DEFINE THE MECHANISM OF ACTION OF RIT1 MUTATIONS IN LUNG CANCER AND TEST THE EFFICACY OF TWO NEW TREATMENT STRATEGIES. BUILDING ON OUR PRELIMINARY STUDIES THAT CONSTITUTE THE FIRST GLOBAL PROFILING OF RIT1 FUNCTION, WE NOW WILL: (1) IDENTIFY THE MECHANISM OF RIT1-YAP1 SYNERGY IN LUNG CANCER, (2) DETERMINE HOW A USP9X-RIT1 AXIS REGULATES THE SPINDLE ASSEMBLY CHECKPOINT AND SENSITIVITY TO ANTI-MITOTIC THERAPIES, AND (3) DEFINE THE THERAPEUTIC POTENTIAL OF ANTI-YAP1/TEAD AND ANTI-MITOTIC THERAPIES IN RIT1-MUTANT LUNG CANCER. ULTIMATELY, THIS WORK WILL ADVANCE OUR UNDERSTANDING OF THE ROLE AND MECHANISM OF RIT1 MUTATIONS IN CANCER AND CONTRIBUTE THE RATIONALE AND PRE-CLINICAL DATA NEEDED TO TRANSLATE THESE FINDINGS INTO NEW CLINICAL TRIALS. OUR ACCESS TO NOVEL PATIENT-DERIVED AND GENETICALLY-ENGINEERED MOUSE MODELS, COUPLED WITH OUR EXPERTISE IN BOTH FUNCTIONAL GENOMICS AND PRE-CLINICAL STUDIES, MAKE OUR LABORATORY UNIQUELY WELL-SUITED TO DISCOVER NEW THERAPEUTIC OPTIONS AND IMPROVE OUTCOMES FOR PATIENTS WITH RIT1-MUTANT CANCERS.

USING A SMART DESIGN TO EVALUATE REMOTELY DELIVERED, CULTURALLY TAILORED WEIGHT LOSS INTERVENTIONS AMONG LATINA BREAST CANCER SURVIVORS - PROJECT SUMMARY / ABSTRACT BREAST CANCER (BC) IS THE LEADING CAUSE OF CANCER DEATH AMONG US LATINAS. LATINAS ARE AT HIGH RISK OF OBESITY AND OBESITY-RELATED DISEASES, WHICH ARE ASSOCIATED WITH POORER CANCER OUTCOMES. THERE IS A SIGNIFICANT LACK OF AN EFFECTIVE INTERVENTION TO ADDRESS THE DIVERSE NEEDS OF LATINA BC SURVIVORS TO ACHIEVE A HEALTHY WEIGHT. WE HAVE DEVELOPED AND TESTED MULTI-COMPONENT WEIGHT LOSS, DIETARY CHANGE, AND PHYSICAL ACTIVITY (PA) INTERVENTIONS AMONG BC SURVIVORS, WITH A FOCUS ON EXPERIENTIAL LEARNING (EL) AMONG LATINAS. AS THE NEXT STEP, WE PROPOSE A SEQUENTIAL MULTIPLE ASSIGNMENT RANDOMIZED TRIAL (SMART) TESTING 12 MONTH ADAPTIVE CULTURALLY- TAILORED WEIGHT LOSS INTERVENTIONS IN A GEOGRAPHICALLY DIVERSE GROUP OF LATINA BC SURVIVORS. THE ADAPTIVE INTERVENTIONS WILL USE THE CDC’S DIABETES PREVENTION PROGRAM (DPP), AN EVIDENCE-BASED WEIGHT LOSS PROGRAM, AS THE CENTRAL EDUCATIONAL COMPONENT. BASED ON OUR PRIOR WORK, WE WILL ADAPT THE DPP TO BE REMOTELY DELIVERED, INCLUDE INFORMATION SPECIFIC TO BC SURVIVORS, AND BE CULTURALLY-TAILORED TO LATINAS. WOMEN WILL BE RECRUITED VIA 3 WEST COAST SEER REGISTRIES. INCLUSION CRITERIA: DIAGNOSIS OF STAGE I-III BC WITHIN 5 YEARS, NO EVIDENCE OF RECURRENT DISEASE, >60 DAYS POST-TREATMENT, AND BODY MASS INDEX (BMI) 30 KG/M2. BASELINE, 1, 3, 6, AND 12 MONTH ASSESSMENTS WILL INCLUDE QUESTIONNAIRES ON MEDICAL HISTORY, DIET, AND PATIENT-REPORTED PSYCHOSOCIAL/QUALITY OF LIFE OUTCOMES; OBJECTIVELY MEASURED WEIGHT; ACCELEROMETER MEASURED PA; AND DRIED BLOOD SPOTS TO MEASURE INFLAMMATORY/CARDIOMETABOLIC BIOMARKERS. QUALITATIVE INTERVIEWS WITH A SUBSET OF PARTICIPANTS WILL TAKE PLACE AT 1 AND 12 MONTHS. THE GOAL OF THE 12 MONTH ¡VIDA! (LIFE!) PROGRAM IS TO ACHIEVE 7% WEIGHT LOSS. FOLLOWING BASELINE ASSESSMENTS, PARTICIPANTS (N=410) WILL BE RANDOMIZED TO ¡VIDA! OR ¡VIDA! + EL. AT 1 MONTH, RESPONDERS (2% WEIGHT LOSS) WILL CONTINUE WITH THEIR INTERVENTION AND NON-RESPONDERS (<2% WEIGHT LOSS) WILL BE RE-RANDOMIZED TO RECEIVE AUGMENTED BEHAVIORAL SUPPORT (I.E., COMBINATIONS OF EL, INDIVIDUALIZED HEALTH COACHING, AND DELIVERED GROCERIES). AIM 1) TO COMPARE THE EFFECTIVENESS OF FOUR ADAPTIVE INTERVENTIONS FOR WEIGHT LOSS IN LATINA BC SURVIVORS, BEGINNING WITH ¡VIDA! OR ¡VIDA! + EL (STAGE 1) FOLLOWED BY AUGMENTED BEHAVIORAL SUPPORT FOR 11 MONTHS FOR NON-RESPONDERS (STAGE 2). AIM 2) TO USE A NOVEL DATA-DRIVEN APPROACH TO DETERMINE WHETHER KEY INDIVIDUAL BASELINE CHARACTERISTICS MODERATE THE EFFECT OF THE ADAPTIVE INTERVENTIONS ON WEIGHT LOSS, AND THUS LAY THE GROUNDWORK FOR MORE PERSONALIZED ADAPTIVE WEIGHT LOSS STRATEGIES. EXPLORATORY AIMS WILL I) ASSESS WHETHER INTERVENTION ENGAGEMENT MODERATES THE EFFECT OF THE ADAPTIVE INTERVENTIONS ON WEIGHT LOSS; II) COMPARE THE EFFECTS OF ADAPTIVE INTERVENTIONS ON CHANGES IN INFLAMMATORY AND CARDIOMETABOLIC BIOMARKERS, DIET QUALITY, AND PA; III) QUANTITATIVELY ASSESS BIOPSYCHOSOCIAL PREDICTORS/MEDIATORS OF BEHAVIOR CHANGE; AND IV) QUALITATIVELY ASSESS THE PARTICIPANT EXPERIENCE TO UNDERSTAND FACTORS THAT CONTRIBUTE TO STUDY OUTCOMES. THE TRIAL WILL GENERATE EVIDENCE ON THE BEST STRATEGIES FOR AN EFFECTIVE, SCALABLE WEIGHT LOSS PROGRAM TO PROMOTE HEALTHY CANCER SURVIVORSHIP AMONG LATINA BC SURVIVORS.

OPTIMIZING PANCREATIC CANCER MANAGEMENT WITH NEXT GENERATION IMAGING AND LIQUID BIOPSY - PROJECT SUMMARY: PANCREATIC DUCTAL ADENOCARCINOMA (PDA) WILL BECOME THE 2ND LEADING CAUSE OF CANCER DEATHS IN THE UNITED STATES BY 2030. MOST PATIENTS WITH PDA PRESENT WITH NONRESECTABLE/METASTATIC DISEASE, AND SYSTEMIC CHEMOTHERAPY IS THE ANCHORING TREATMENT IN THESE PATIENTS. SURGERY IS AN OPTION IN THE MINORITY OF PATIENTS (~30%) WHO PRESENT WITH LOCALIZED DISEASE, THOUGH MOST DEVELOP EARLY RECURRENCE AFTER A HIGHLY MORBID SURGERY DUE TO OCCULT METASTASES. THEREFORE, NEOADJUVANT THERAPY (NAT) IS AN EMERGING STANDARD APPROACH, BUT IS ONLY BENEFICIAL IF THE SELECTED SYSTEMIC THERAPY IS EFFECTIVE. INDEED, FOR ALL PATIENTS WITH PDA, METASTATIC OR OTHERWISE, THE DURATION OF EFFECTIVE SYSTEMIC THERAPY IS THE MOST IMPORTANT FACTOR IN THEIR SURVIVAL. THERE IS A CRITICAL UNMET NEED FOR ACCURATE AND TIMELY ASSESSMENT OF TREATMENT RESPONSE IN ORDER TO 1) GET PATIENTS ON EFFECTIVE SYSTEMIC THERAPY AS SOON AS POSSIBLE AND KEEP THEM ON IT AS LONG AS POSSIBLE, 2) EXPEDITIOUSLY DISCONTINUE TOXIC, COSTLY AND INEFFECTIVE THERAPIES, AND 3) FACILITATE EVIDENCE-BASED PERSONALIZED CLINICAL DECISIONS REGARDING CURATIVE- INTENT SURGERY. CURRENT MANAGEMENT OF PDA RELIES PRINCIPALLY ON COMPUTED TOMOGRAPHY (CT) AND TUMOR MARKERS (CA19-9). HOWEVER, THESE TOOLS ARE NOT SENSITIVE ENOUGH AND ARE TOO SLOW FOR ADJUDICATING BENEFIT IN PATIENTS WITH RAPIDLY LETHAL METASTATIC DISEASE, AND FOR IDENTIFYING SUITABLE CANDIDATES MOST LIKELY TO BENEFIT FROM SURGERY AFTER NAT. WE NOW HAVE CUTTING-EDGE TOOLS FOR MORE PRECISE QUANTIFICATION OF DISEASE BURDEN AT THE MOLECULAR AND METABOLIC LEVELS. WE HAVE PREVIOUSLY SHOWN THAT MUTANT KRAS CIRCULATING TUMOR (CT)DNA CAN BE DETECTED WITH HIGH SENSITIVITY IN PDA, TENDS TO DROP RAPIDLY WITH EFFECTIVE THERAPY, AND MAY BE A MORE DYNAMIC PREDICTOR OF THERAPY RESPONSE THAN CA19-9. WE HAVE ALSO SHOWN THAT METABOLIC IMAGING WITH HYBRID INTEGRATED 18-FLUORO- DEOXYGLUCOSE (FDG) POSITRON EMISSION TOMOGRAPHY/MAGNETIC RESONANCE IMAGING (PET/MRI) IMPROVES THE DETECTION OF SUBTLE METASTASES THAT ARE OCCULT ON CT, EARLY RESPONSE ASSESSMENT IN PATIENTS WITH NONRESECTABLE/METASTATIC PDA, AND PREDICTION OF PATHOLOGICAL RESPONSE TO NAT IN PATIENTS WHO UNDERGO RESECTION. BUILDING ON THESE PROMISING RESULTS, WE HYPOTHESIZE THAT THE APPROPRIATE COMBINATION OF KRAS CTDNA AND PET/MRI BIOMARKERS WILL ENABLE TIMELY ASSESSMENT OF THE CLINICAL UTILITY OF THERAPY IN PDA PATIENTS. IN AIM 1, WE WILL DEFINE THRESHOLDS FOR EARLY CHEMOTHERAPY SWITCH IN UNRESECTABLE/METASTATIC PDA USING DYNAMIC AND QUANTITATIVE CHANGES IN KRAS CTDNA AND FDG PET/MRI BIOMARKERS FOR USE IN FUTURE PROSPECTIVE TRIALS. IN AIM 2, WE WILL CONSTRUCT, TEST AND VALIDATE A MODEL OF SURGICAL BENEFIT OR FUTILITY FOR PATIENTS WITH POTENTIALLY RESECTABLE PDA USING DYNAMIC KRAS CTDNA AND FDG PET/MRI RESPONSE DATA. OUR OVERARCHING GOAL IS TO INTEGRATE RELIABLE BIOMARKERS THAT CAN ACCURATELY GUIDE THERAPY AND ENABLE PRECISION MEDICINE TO IMPROVE OUTCOMES OF PATIENTS WITH THIS DEADLY DISEASE.

THE ROLES OF EBV-SPECIFIC T CELLS IN RESPONSE TO CHECKPOINT BLOCKADE IMMUNOTHERAPY OF EBV-DRIVEN NASOPHARYNGEAL CARCINOMA - PROJECT SUMMARY/ABSTRACT NASOPHARYNGEAL CARCINOMA (NPC) IS AN EPSTEIN-BARR VIRUS (EBV)-DRIVEN MALIGNANCY THAT IS ENDEMIC TO EAST AND SOUTHEAST ASIA. THE OVERALL 5-YEAR SURVIVAL RATE FOR ENDEMIC NPC IS ONLY 51%, WHICH REPRESENTS AN UNMET CLINICAL NEED. WHILE NPC TUMORS ARE KNOWN TO BE INFECTED WITH EBV AND EXPRESS PD-L1, LITTLE IS KNOWN ABOUT THE ROLE OF EBV-SPECIFIC T CELLS IN THE CONTROL OF NPC AND ANTI-PD-1 THERAPY HAS SHOWN A LOW RATE OF EFFICACY (ORR ~20%). THE GOAL OF THIS STUDY IS TO BETTER UNDERSTAND THE ROLE OF EBV-SPECIFIC T CELL RESPONSES IN NPC IMMUNOPATHOLOGY AND IMMUNOTHERAPEUTIC RESPONSE. WE WILL TEST THE SPECIFIC HYPOTHESES THAT: 1. EBV-SPECIFIC T CELLS CONTRIBUTE TO TUMOR CONTROL ELICITED BY COMBINATION ANTI-PD-1 AND ANTI-CTLA-4 CHECKPOINT BLOCKADE IMMUNOTHERAPY, AND 2. THAT THE PHENOTYPIC AND CLONAL CHARACTERISTICS/DYNAMICS OF PERIPHERAL EBV-SPECIFIC T CELLS CAN BE USEFUL AS INDICATORS OF CLINICAL OUTCOMES FOR NPC PATIENTS. TO TEST THESE HYPOTHESES, WE WILL LEVERAGE OUR ACCESS TO TWO SINGAPOREAN NPC PATIENT COHORTS: COHORT 1. A 51-PATIENT COHORT OF NEW-DIAGNOSIS NPC FOR WHICH VIABLY FROZEN PBMCS AND ARCHIVAL FFPE TISSUES ARE AVAILABLE AND COHORT 2. A 50-PATIENT COHORT PARTICIPATING IN A PHASE II TRIAL (NCT03097939 - NATIONAL CANCER CENTRE SINGAPORE) TESTING THE COMBINATION OF IPILUMIMAB AND NIVOLUMIMAB (IPI.+NIVO.) IMMUNOTHERAPY WITH LONGITUDINALLY COLLECTED PBMCS AND TISSUE BIOPSIES. RECENTLY PUBLISHED PRELIMINARY ANALYSIS (AACR 2020) FROM THIS CLINICAL TRIAL SHOWS THAT COMBINED IPI.+NIVO. THERAPY IS SAFE AND ACHIEVED DURABLE RESPONSES IN RECURRENT AND METASTATIC NPC PATIENTS AND IDENTIFIED A NEGATIVE ASSOCIATION BETWEEN CIRCULATING EBV-DNA LEVELS AND RESPONSE. IN ADDITION, PRELIMINARY ANALYSIS OF NEW-DIAGNOSIS NPC PATIENT PERIPHERAL BLOOD SAMPLES FROM COHORT 1 SHOW ASSOCIATIONS BETWEEN CERTAIN PHENOTYPIC PROFILES OF CD8+ T CELLS AND CLINICAL PARAMETERS SUCH AS EBV-DNA LEVELS. THEREFORE, IN AIM 1. WE WILL INVESTIGATE THE CLINICAL RELEVANCE OF THESE PRELIMINARILY IDENTIFIED NPC-ASSOCIATED CD8+ T CELL PHENOTYPES. IN ADDITION TO IN-DEPTH SINGLE CELL TRANSCRIPTIONAL, FUNCTIONAL TCR SEQUENCE PROFILING OF THESE CELLS, CELLULAR IMAGING, TRANSCRIPTIONAL PROFILING AND BULK TCR SEQUENCING OF PATIENT-MATCHED TUMOR WILL ALLOW DISCOVERY OF NOVEL ASSOCIATIONS BETWEEN PERIPHERAL T CELLS AND THE TUMOR MICROENVIRONMENT. IN AIM 2., WE WILL CHARACTERIZE EBV-SPECIFIC T CELL RESPONSES IN THE NPC PERIPHERY AND TUMOR MICROENVIRONMENT DURING COMBINATION IPI.+NIVO. IMMUNOTHERAPY TREATMENT TO IDENTIFY NOVEL ASSOCIATIONS BETWEEN THE PHENOTYPIC PROFILES OF EBV-SPECIFIC T CELLS AND IMMUNOTHERAPEUTIC RESPONSE. IN AIM 3., WE WILL INVESTIGATE T CELL CLONAL DYNAMICS ASSOCIATED WITH TREATMENT INDUCED CHANGES TO THE NPC-SPECIFIC IMMUNE RESPONSE BY COMPARING THE TCR CLONAL DIVERSITY IN PERIPHERAL BLOOD AND TUMOR BIOPSY SAMPLES FROM DIFFERENT STAGES OF TREATMENT. OVERALL, CHARACTERIZATION OF EBV-SPECIFIC T CELLS PHENOTYPES IN THE NPC PERIPHERY AND THE TUMOR USING MULTIPLE CUTTING-EDGE APPROACHES WILL NOT ONLY IMPROVE OUR UNDERSTANDING OF THE NPC IMMUNE LANDSCAPE, BUT ALSO POTENTIALLY IDENTIFY CLINICALLY RELEVANT EBV-SPECIFIC T CELL PHENOTYPES THAT COULD BE TESTED IN FUTURE NPC IMMUNOTHERAPY TRIALS.

REGULATION OF CELL MIGRATION AND SIGNALING BY PHOSPHOTYROSINE AND UBIQUITIN

PAR-4 REGULATION OF ACTOMYOSIN CONTRACTILITY AS A TUMOR SUPPRESSIVE MECHANISM IN BREAST CANCER - PROJECT SUMMARY/ABSTRACT TUMOR PROGRESSION – INCLUDING RESISTANCE TO THERAPY, METASTASIS, AND RECURRENCE – IS RESPONSIBLE FOR THE MAJORITY OF CANCER DEATHS. UNDERSTANDING HOW CANCER CELLS SURVIVE TREATMENT, SPREAD TO DISTANT SITES, PERSIST AS DORMANT RESIDUAL CELLS, AND EVENTUALLY RECUR IS ESSENTIAL TO IMPROVING THE TREATMENT OF THIS DISEASE. THE LONG-TERM GOAL OF MY RESEARCH GROUP IS TO IDENTIFY THE PATHWAYS THAT REGULATE THESE PROCESSES IN ORDER TO PREVENT OR TREAT TUMOR RECURRENCE. TO ACHIEVE, THIS WE ARE USING CONDITIONAL GENETICALLY ENGINEERED MOUSE (GEM) MODELS OF BREAST CANCER THAT ALLOW FOR THE MECHANISTIC DISSECTION OF THE PROCESSES OF DORMANCY AND RECURRENCE. USING THESE MODELS, WE HAVE IDENTIFIED A FUNCTIONAL ROLE FOR THE TUMOR SUPPRESSOR PAR-4 IN REGULATING SURVIVAL AND RECURRENCE OF BREAST CANCER CELLS AFTER THERAPY. PAR-4 IS DOWNREGULATED IN RECURRENT TUMORS FROM THREE GEM MODELS, AND THIS DOWNREGULATION IS BOTH NECESSARY AND SUFFICIENT FOR TUMOR RECURRENCE. SIMILARLY, IN WOMEN WITH BREAST CANCER, LOW PAR-4 EXPRESSION IS ASSOCIATED WITH A POOR RESPONSE TO NEOADJUVANT THERAPY AND AN INCREASED RISK OF RECURRENCE. WE HAVE CHARACTERIZED THE UPSTREAM PATHWAYS THAT REGULATE PAR-4 EXPRESSION AND FUNCTION DURING DORMANCY AND RECURRENCE, AS WELL AS THE DOWNSTREAM PATHWAYS THAT PAR-4 REGULATES TO INHIBIT DORMANT CELL SURVIVAL AND RECURRENCE. THIS PROPOSAL WILL BUILD ON THIS WORK TO FURTHER EXPLORE THE MECHANISM BY WHICH PAR-4 ACTS AS A TUMOR SUPPRESSOR. THE OVERARCHING HYPOTHESIS OF THE PROPOSAL IS THAT PAR-4 PROMOTES CELL DEATH IN PART THROUGH INDUCING ACTOMYOSIN CONTRACTILITY, AND THIS CONTRIBUTES TO ITS TUMOR SUPPRESSIVE FUNCTIONS. WE WILL EXPLORE THIS HYPOTHESIS IN THE CONTEXT OF PAR-4’S ROLE IN RESIDUAL CELL SURVIVAL AND THE SURVIVAL OF INVASIVE LOBULAR CANCER CELLS. OUR WORK WILL REVEAL NEW INFORMATION ON HOW PAR-4 FUNCTIONS TO REGULATE DORMANT RESIDUAL CELL SURVIVAL AND MAY UNCOVER NOVEL OPPORTUNITIES FOR THERAPEUTIC INTERVENTION IN ELIMINATING RESIDUAL CELLS AND PREVENTING RECURRENCE.

ADDRESSING CANCER-RELATED FINANCIAL HARDSHIP THROUGH DELIVERY OF A PROACTIVE FINANCIAL NAVIGATION INTERVENTION

MODULATION OF SIGNALING FROM DAMAGE-ASSOCIATED MOLECULAR PATTERNS TO IMPROVE RADIATION-INDUCED THYMIC DYSFUNCTION - PROJECT SUMMARY THE THYMUS, WHICH IS THE PRIMARY SITE OF T CELL GENERATION, IS EXTREMELY SENSITIVE TO INSULT, BUT ALSO HAS A REMARKABLE CAPACITY FOR ENDOGENOUS REPAIR. EVEN THOUGH THERE IS LIKELY CONTINUAL THYMIC INVOLUTION AND REGENERATION IN RESPONSE TO EVERYDAY INSULTS LIKE STRESS AND INFECTION, PROFOUND THYMIC DAMAGE CAUSED BY RADIATION INJURY LEADS TO PROLONGED T CELL LYMPHOPENIA. CONSEQUENTLY, IDENTIFICATION OF THERAPIES THAT CAN BOOST T CELL RECONSTITUTION IN RECIPIENTS AFTER A DOSE OF RADIATION IS A CLEAR PRIORITY. WE HAVE PREVIOUSLY IDENTIFIED TWO DISTINCT PATHWAYS OF ENDOGENOUS THYMIC REGENERATION, CENTERED ON THE PRODUCTION OF THE REGENERATION FACTORS IL-22 BY INNATE LYMPHOID CELLS (ILCS), AND BMP4 BY ENDOTHELIAL CELLS (ECS); BOTH OF WHICH MEDIATE THEIR REGENERATIVE EFFECTS BY TARGETING THYMIC EPITHELIAL CELLS. MORE RECENTLY WE HAVE FOUND THAT THE TRIGGER FOR THESE DISTINCT REGENERATIVE PATHWAYS HINGE ON THE BALANCE BETWEEN FORMS OF CELL DEATH, WITH IMMUNOLOGICALLY SILENT APOPTOSIS (WHICH IS ABUNDANT IN THYMOCYTES DURING STEADY-STATE) SUPPRESSIVE TO THE REGENERATIVE PROGRAM. ON THE OTHER HAND, AFTER THYMIC DAMAGE CAUSED BY RADIATION INJURY, WE FOUND A SWITCH TOWARD IMMUNOGENIC CELL DEATH, WITH THE RESULTING RELEASE OF DAMAGE-ASSOCIATED MOLECULAR PATTERNS (DAMPS) SUFFICIENT TO PROMOTE REGENERATION. SPECIFICALLY, WE IDENTIFIED THAT INTRACELLULAR ZN WAS RELEASED AFTER RADIATION INJURY, WHERE IT COULD SIGNAL THROUGH THE G-PROTEIN COUPLED RECEPTOR 39 (GPR39) TO STIMULATE PRODUCTION OF BMP4 AND IL-23, A KEY UPSTREAM REGULATOR OF IL-22 PRODUCTION. SEPARATELY, WE ALSO FOUND THAT THE RELEASE OF THE PROTOTYPICAL DAMP, ATP, WAS ABLE TO SIGNAL DIRECTLY ON THYMIC EPITHELIAL CELLS THROUGH PURINERGIC (P2) RECEPTORS AND PROMOTE THEIR EXPRESSION OF FOXN1, KEY MICROENVIRONMENTAL DRIVERS OF T CELL DEVELOPMENT. IMPORTANTLY, OUR PRELIMINARY DATA ALSO SUGGESTS THAT EACH OF THESE PATHWAYS CAN BE THERAPEUTICALLY TARGETED TO IMPROVE THYMIC RECOVERY FOLLOWING RADIATION DAMAGE IN YOUNG MICE. BASED ON OUR PRELIMINARY DATA, WE HYPOTHESIZE THAT MODULATION OF PATHWAYS ASSOCIATED WITH THESE DAMPS CAN BE USED AS A COUNTERMEASURE TO IMPROVE IMMUNE FUNCTION AFTER RADIATION INJURY BY STIMULATING THE GENERATION OF NEW T CELLS IN THE THYMUS. SPECIFICALLY, OUR PROPOSAL HAS THE FOLLOWING AIMS: (1) TO VALIDATE AND OPTIMIZE THE TARGETING OF GPR39 OR P2 RECEPTORS TO IMPROVE THE PRODUCTION OF NEW T CELLS AND IMMUNE FUNCTION AFTER RADIATION INJURY; (2) TO EXAMINE THE ABILITY OF THE THYMUS TO RESPOND TO REGENERATIVE SIGNALS ACROSS MOUSE LIFESPAN AND SEX; AND (3) TO COMPREHENSIVELY EVALUATE THE POTENTIAL FOR TARGETING GPR39 OR P2 RECEPTORS TO IMPROVE THYMIC FUNCTION AFTER RADIATION DAMAGE ACROSS MOUSE LIFESPAN AND SEX. THE STUDIES OUTLINED IN THIS PROPOSAL NOT ONLY HAVE THE POTENTIAL TO DEFINE IMPORTANT PATHWAYS UNDERLYING TISSUE REGENERATION ACROSS LIFESPAN BUT COULD ALSO RESULT IN INNOVATIVE APPROACHES TO ENHANCE T CELL RECOVERY AFTER RADIATION DAMAGE.

AN ACADEMIC-INDUSTRY PARTNERSHIP TO ADVANCE FUNCTIONAL GENOMICS FOR PERSONALIZED ONCOLOGY.

DEFINING PROTECTIVE CMV IMMUNITY AFTER TRANSPLANTATION - PROJECT SUMMARY/ABSTRACT CYTOMEGALOVIRUS (CMV) INFECTION IS A FREQUENT AND LIFE-THREATENING COMPLICATION THAT SIGNIFICANTLY LIMITS THE SUCCESSFUL OUTCOME OF ALLOGENEIC HEMATOPOIETIC STEM CELL OR BONE MARROW TRANSPLANTATION (REFERRED TO HEREAFTER AT BMT). WE HAVE RECENTLY DEVELOPED LONG-DESIRED PRECLINICAL (MURINE) MODELS OF CMV REACTIVATION AFTER BMT AND SHOW FOR THE FIRST TIME, THAT HUMORAL IMMUNITY IS CRITICAL TO PREVENT VIRAL RECRUDESCENCE. WE NOW DEMONSTRATE THAT EITHER THE TRANSFER OF IMMUNE T CELLS OR STRAIN-SPECIFIC SERA (CONTAINING IGG ANTIBODY) PREVENTS VIRAL REACTIVATION, VIREMIA, END-ORGAN VIRAL REPLICATION AND CMV DISEASE DURING GRAFT-VERSUS-HOST DISEASE (GVHD). WE PLAN TO UTILIZE OUR UNIQUE, BUT WELL-ESTABLISHED PRECLINICAL MODELS TO DEFINE THE IMPACT OF PROTECTIVE ANTIBODY ON THE TEMPORAL AND SPATIAL CHARACTERISTICS OF CMV REACTIVATION, DISSEMINATION AND ANTIGEN PRESENTATION. SUBSEQUENTLY WE WILL DEFINE THE INTERPLAY OF T CELL AND HUMORAL RESPONSES THAT ARE REQUIRED FOR THE DURABLE CONTROL OF CMV REACTIVATION AFTER BMT. FINALLY, WE WILL DEVELOP CLINICALLY TRACTABLE PATHWAYS TO ENHANCE CMV IMMUNITY WHILST PREVENTING GVHD AND ASSOCIATED INFLAMMATION, TARGETING IL-6 INHIBITION. OUR PROPOSED STUDIES WILL PROVIDE CRITICAL INSIGHTS INTO THE IMMUNE REQUIREMENTS FOR EFFECTIVE AND LONG-TERM CONTROL OF CMV IN RECIPIENTS WITH GVHD AND/OR CLINICALLY RELEVANT IMMUNE SUPPRESSION AND INFLAMMATION THAT WILL ALLOW US TO OPTIMIZE CMV IMMUNITY IN CLINICAL BMT TO IMPROVE PATIENT OUTCOMES.

EXPANDING INDEPENDENT RESEARCH CAPACITY IN HIV-ASSOCIATED MALIGNANCIES IN UGANDA

FORECASTING INFLUENZA EVOLUTION ON A HETEROGENEOUS IMMUNE LANDSCAPE - PROJECT SUMMARY INFLUENZA VIRUS EVOLVES RAPIDLY TO ESCAPE IMMUNITY ELICITED BY PRIOR INFECTIONS AND VACCINATIONS. TO COMBAT THIS EVOLUTION, THE STRAINS IN THE INFLUENZA VACCINE ARE UPDATED EVERY SEASON TO KEEP PACE WITH VIRAL EVOLUTION. HOWEVER, IT IS CURRENTLY DIFFICULT TO ACCURATELY FORECAST WHICH VIRAL STRAIN WILL DOMINATE THE COMING SEASON, AND VACCINES ARE LESS EFFECTIVE WHEN THE WRONG STRAIN IS CHOSEN FOR THE VACCINE. HERE WE PROPOSE A COMBINED EXPERIMENTAL / COMPUTATIONAL APPROACH THAT WILL OVERCOME SOME OF THE FACTORS THAT CURRENTLY MAKE VACCINE STRAIN SELECTION SO DIFFICULT. FIRST, WE WILL USE A NEW DEEP MUTATIONAL SCANNING APPROACH TO DIRECTLY MAP THE GENOTYPES OF THE VIRAL SURFACE PROTEINS TO THEIR ANTIGENIC PHENOTYPE WITH RESPECT TO HUMAN ANTIBODY IMMUNITY. SECOND, WE WILL USE THIS NEW EXPERIMENTAL APPROACH TO RECONSTRUCT THE HETEROGENEOUS HUMAN IMMUNE LANDSCAPE OVER WHICH INFLUENZA VIRUS EVOLVES. FINALLY, WE WILL BUILD COMPUTATIONAL MODELS THAT FORECAST HOW INFLUENZA EVOLVES YEAR-TO- YEAR IN RESPONSE TO HUMAN IMMUNITY. ALL OF OUR DATA AND FORECASTS WILL BE INTEGRATED INTO EASY-TO-USE INTERACTIVE VISUALIZATIONS. OVERALL, THIS WORK WILL IMPROVE THE CAPACITY TO ACCURATELY IDENTIFY WHICH VIRAL STRAINS SHOULD BE SELECTED FOR THE SEASONAL INFLUENZA VACCINE.

PREDICTING PREP UPTAKE AND ADHERENCE AMONG ADOLESCENT GIRLS AND YOUNG WOMEN IN SUB-SAHARAN AFRICA: LEVERAGING PROGRAMMATIC AND CLINICAL TRIALS DATA

NRF2 SUPPRESSION OF INFLAMMATORY SIGNALING AND ITS ROLE IN TUMOR PROGRESSION - PROJECT SUMMARY/ABSTRACT TUMOR METASTASIS IS RESPONSIBLE FOR THE VAST MAJORITY OF DEATHS FROM EPITHELIAL CANCERS, INCLUDING BREAST CANCER. UNDERSTANDING HOW CANCER CELLS SPREAD TO DISTANT SITES, PERSIST AS DORMANT DISSEMINATED TUMOR CELLS (DTCS), AND EVENTUALLY RECUR IS ESSENTIAL TO IMPROVING THE TREATMENT OF THIS DISEASE. THE LONG-TERM GOAL OF MY RESEARCH GROUP IS TO IDENTIFY PATHWAYS THAT REGULATE THESE PROCESSES TO ENABLE THE DEVELOPMENT OF THERAPIES THAT CAN PREVENT OR TREAT METASTATIC RECURRENCES. WE RECENTLY IDENTIFIED A ROLE FOR THE ANTIOXIDANT STRESS RESPONSE TRANSCRIPTION FACTOR NRF2 IN PROMOTING THE SURVIVAL AND LOCAL RECURRENCE OF MAMMARY TUMORS FOLLOWING TARGETED THERAPY. WE FOUND THAT NRF2 IS ACTIVATED FOLLOWING DIVERSE TARGETED THERAPIES AS A CONSEQUENCE OF METABOLIC AND OXIDATIVE STRESS. NRF2 REMAINS CONSTITUTIVELY ACTIVATED IN RECURRENT TUMORS, WHERE IT FUNCTIONS TO PROMOTE RECURRENCE THROUGH REGULATING REDOX HOMEOSTASIS AND NUCLEOTIDE METABOLISM. WHILE THESE RESULTS IDENTIFY A FUNCTION FOR NRF2 IN LOCAL RECURRENCE, A ROLE FOR NRF2 IN PROMOTING METASTATIC DISSEMINATION REMAINS RELATIVELY UNEXPLORED. EMERGING EVIDENCE SUGGESTS THAT METASTATIC DISSEMINATION IS ASSOCIATED WITH METABOLIC AND OXIDATIVE STRESS. CONSISTENT WITH THIS, WE RECENTLY FOUND THAT THE NRF2 TRANSCRIPTIONAL PROGRAM IS ELEVATED IN METASTATIC TUMORS FROM PATIENTS WITH BREAST CANCER. HOWEVER, A THOROUGH UNDERSTANDING OF NRF2 REGULATION DURING METASTATIC DISSEMINATION, AND HOW NRF2 ACTIVATION FUNCTIONALLY AFFECTS METASTASIS, REMAINS UNKNOWN. THIS PROPOSAL WILL BUILD ON THIS WORK TO DEFINE THE REGULATION AND FUNCTION OF NRF2 DURING METASTASIS IN BREAST CANCER. IN NEW PRELIMINARY DATA, WE FOUND THAT NRF2 SUPPRESSES PRO-INFLAMMATORY SIGNALING IN BREAST CANCER. CONSISTENT WITH THIS, NRF2 KNOCKDOWN LEADS TO INFILTRATION OF IMMUNE CELLS INTO THE TUMOR MICROENVIRONMENT. BASED UPON THESE FINDINGS, THE CENTRAL HYPOTHESIS FOR THIS PROPOSAL IS THAT NRF2 PROMOTES BREAST CANCER PROGRESSION BY INHIBITING PRO-INFLAMMATORY SIGNALING BETWEEN CANCER CELLS AND THE TUMOR IMMUNE MICROENVIRONMENT. WE WILL TEST THIS HYPOTHESIS THROUGH THREE SPECIFIC AIMS. IN AIM 1, WE WILL DEFINE THE MECHANISM AND FUNCTION OF NRF2 REGULATION OF THE TUMOR IMMUNE MICROENVIRONMENT. IN AIM 2, WE WILL DETERMINE THE ROLE OF NRF2 SUPPRESSION OF INFLAMMATORY SIGNALING IN PROMOTING THE OUTGROWTH OF DISSEMINATED TUMOR CELLS. IN AIM 3 WE WILL TEST WHETHER TARGETING METABOLIC PATHWAYS CAN PREVENT THE GROWTH OF NRF2-HIGH TUMORS. OUR WORK WILL REVEAL NEW INFORMATION ON HOW NRF2 FUNCTIONS TO REGULATE TUMOR PROGRESSION AND MAY UNCOVER NOVEL THERAPEUTIC OPPORTUNITIES TO PREVENT METASTATIC RECURRENCE.

INFRASTRUCTURE SUPPORT AND PILOT TISSUE COLLECTION FOR THE CARET BIOREPOSITORY

MECHANISMS OF TREATMENT FAILURE IN CHIMERIC ANTIGEN RECEPTOR T CELL THERAPY

BREAST-CANCER FOCUSED BIOMARKER CHARACTERIZATION CENTER EMPLOYING TARGETED MASS SPEC ASSAYS IN A CLIA ENVIRONMENT - PROJECT SUMMARY/ABSTRACT (OVERALL COMPONENT, RFA-CA-22-040) WE PROPOSE TO DEVELOP A BLOOD-BASED TEST WHOSE INDICATED USE IS TO COMPLEMENT MAMMOGRAPHY IN THE EARLY DETECTION OF BREAST CANCERS. ALTHOUGH MAMMOGRAPHY SAVES LIVES THROUGH EARLY DETECTION, IT IS IMPERFECT. APPROXIMATELY ONE IN SEVEN BREAST CANCERS GOES UNDETECTED DESPITE SCREENING MAMMOGRAPHY, AND INTERVAL CANCERS THAT MANIFEST WITHIN A YEAR OF A NORMAL MAMMOGRAM REMAIN A VEXING PROBLEM, ESPECIALLY (ALTHOUGH NOT EXCLUSIVELY) FOR THE >27 MILLION WOMEN IN THE UNITED STATES WITH HETEROGENEOUSLY OR EXTREMELY DENSE BREASTS AT HIGH RISK FOR INTERVAL CANCERS. WE PROPOSE TO DEVELOP A BLOOD TEST THAT COULD BE USED AS AN ADJUNCT TO MAMMOGRAPHY TO IMPROVE EARLY DETECTION BY IMPROVING SENSITIVITY AND/OR SPECIFICITY OF MAMMOGRAPHY. USING A NOVEL BIOMARKER DISCOVERY APPROACH LEVERAGING HUMAN-IN-MOUSE BREAST CANCER PATIENT-DERIVED XENOGRAFT MODELS AND STATE-OF-THE-ART MASS SPECTROMETRY METHODS, WE PRIORITIZED 162 CANDIDATE BREAST CANCER PROTEIN BIOMARKERS FOR VALIDATION STUDIES. OUR BCC WILL PERFORM EDRN PHASE 2 BIOMARKER VALIDATION STUDIES OF OUR PRIORITIZED 162 CANDIDATE PLASMA PROTEIN BIOMARKERS OF BREAST CANCER. WE HAVE AN EXPERIENCED MULTIDISCIPLINARY TEAM (INCLUDING TWO JUNIOR INVESTIGATORS) WITH A STRONG TRACK RECORD OF PRODUCTIVE COLLABORATION AND REPRESENTING EXPERTISE IN CLINICAL ONCOLOGY, CANCER BIOMARKERS, PATHOLOGY, CLIA/CAP/GLP ASSAYS, EPIDEMIOLOGY, RADIOLOGY/BREAST IMAGING, CANCER SCREENING, ‘OMICS DATA GENERATION, AND BIOSTATISTICS. OUR TEAM INCLUDES 2 INDUSTRY PARTNERS, ENCOMPASSES 3 CLIA LABORATORIES, AND CAN PROVIDE EXPERTISE AND ACCESS TO MULTIPLE QUANTITATIVE PLATFORMS IN A CLIA/CAP/GLP ENVIRONMENT TO SUPPORT EDRN NETWORK COLLABORATIONS FOR BIOMARKER VALIDATION STUDIES WITH OTHER BCCS. THE BIOMARKER DEVELOPMENT LABORATORY WILL CONTRIBUTE TO THE BIOMARKER VALIDATION STUDIES BY: (I) DEVELOPING QUALIFIED REAGENTS & METHODS FOR QUANTIFYING 162 CANDIDATE PROTEIN BIOMARKERS, (II) PROCURING PLASMA BIOSPECIMENS (COMPLIANT WITH EDRN PROBE STUDY DESIGN) FOR PHASE 2 BIOMARKER VALIDATION STUDIES, (III) DELIVERING PLASMA ALIQUOTS TO OUR BRL CLIA LABS IN A BLINDED FASHION, AND (IV) ANALYZING EDRN PHASE 2 VALIDATION DATA GENERATED BY THE BRL, PROVIDING STATISTICAL, EPIDEMIOLOGICAL, AND BREAST IMAGING EXPERTISE TO SET AND EVALUATE PERFORMANCE METRICS TO ENSURE BIOMARKERS ARE ADEQUATE TO PROVIDE CLINICAL UTILITY FOR EARLY DETECTION. THE BIOMARKER REFERENCE LABORATORY WILL CONTRIBUTE TO THE PROPOSED VALIDATION STUDIES BY: (I) VALIDATING A CLIA- COMPLIANT STANDARD OPERATING PROCEDURE FOR AN IMMUNO-MRM ASSAY TO QUANTIFY UP TO 162 CANDIDATE PROTEIN BIOMARKERS OF EARLY-STAGE BREAST CANCER THAT WILL SERVE AS THE BASIS FOR OUR BIOMARKER VALIDATION STUDIES, (II) PERFORMING PHASE 2 BIOMARKER VALIDATION STUDIES, AND (III) PROVIDING REFERENCE LABORATORY SUPPORT FOR THE EDRN NETWORK (E.G., MASS SPECTROMETRIC ANALYSES, FLOW CYTOMETRY, NEXTGEN SEQUENCING AND ELISA ASSAYS. THE ADMINISTRATIVE CORE WILL SUPPORT ALL ASPECTS OF THE BCC, INCLUDING MANAGING ALL ADMINISTRATIVE AND PROJECT MANAGEMENT ASPECTS OF THE BCC AS WELL AS MANAGING ALL CENTER LOGISTICS AND COMMUNICATION.

DEVELOPING BIOINFORMATIC AND MICROFLUIDIC SINGLE CELL METHODS FOR STUDYING INTRATUMORAL HETEROGENEITY IN ACUTE MYELOID LEUKEMIA

TOPOGRAPHIC MAPPING BY CRANIAL MOTOR NEURONS

CHARACTERIZING DETERMINANTS OF PRIMARY KSHV INFECTION AMONG CHILDREN AND ADOLESCENTS IN UGANDA

SIRT2 INHIBITORS FOR THE TREATMENT OF B-CELL LYMPHOMA

HARNESSING ENDOGENOUS MECHANISMS OF THYMIC REGENERATION TOBOOST IMMUNE FUNCTION IN RECIPIENTS OF HEMATOPOIETIC CELL TRANSPLANT

TRANSLATING THE TUMOR REGULOME FROM CELL-FREE DNA FOR PRECISION ONCOLOGY - PROJECT SUMMARY/ABSTRACT AN ACCURATE TUMOR CLASSIFICATION IS PIVOTAL TO CLINICAL CANCER CARE AND PRECISION ONCOLOGY. TREATMENT OPTIONS ARE OFTEN INFORMED BY THE PATHOLOGY OR DIAGNOSTIC FROM THE TUMOR TISSUE. A MAJOR CHALLENGE FOR PATIENTS WITH METASTATIC CANCER IS THE LIMITED ACCESS TO TUMOR TISSUE BECAUSE SURGICAL BIOPSIES ARE NOT ROUTINELY NOR REPEATEDLY COLLECTED THROUGHOUT THE COURSE OF THERAPY. HOWEVER, TUMORS CAN UNDERGO DRASTIC MOLECULAR CHANGES DURING METASTATIC PROGRESSION AND RESISTANCE TO THERAPIES. CIRCULATING TUMOR DNA (CTDNA) RELEASED FROM TUMOR CELLS INTO THE BLOOD IS A NON-INVASIVE SOLUTION FOR ADDRESSING CHALLENGES IN TISSUE ACCESSIBILITY. CURRENT RESEARCH AND CLINICAL EFFORTS HAVE FOCUSED ON DETECTING GENOME ALTERATIONS IN CTDNA, BUT THEY DO NOT ALWAYS EXPLAIN TREATMENT FAILURE. TREATMENT-RESISTANT PHENOTYPES ARE DEFINED BY DISTINCT CHANGES IN THE GENETIC AND EPIGENETIC REGULATORY LANDSCAPE, WHICH COLLECTIVELY FORM THE TUMOR REGULOME. CURRENTLY, IT IS NOT POSSIBLE TO COMPREHENSIVELY PORTRAY THE TUMOR REGULOME IN PATIENTS DURING THE COURSE OF THERAPY. WE PROPOSE TO OVERCOME THESE LIMITATIONS BY DEVELOPING INNOVATIVE COMPUTATIONAL METHODS AND EPIGENETIC ASSAYS THAT WILL BE EMPLOYED TO PROFILE THE TUMOR REGULOME AND SURVEY THE REGULATION OF RESISTANT PHENOTYPES DIRECTLY FROM CTDNA. OUR METHODS WILL INTEGRATE THE ANALYSIS OF GENOME ALTERATIONS, CHROMATIN ACCESSIBILITY, TRANSCRIPTIONAL REGULATION, AND DNA METHYLATION FROM THE SAME CTDNA SAMPLE. THIS COST-EFFECTIVE STRATEGY PROVIDES A TEMPORAL WINDOW INTO THE PATIENT’S DISEASE BY MONITORING THE TUMOR EPIGENETIC REGULATION AND ITS CLINICAL PHENOTYPE. THE INNOVATIVE ASPECTS OF THIS PROJECT INCLUDE THE DEVELOPMENT OF DEEP NEURAL NETWORKS AND MACHINE LEARNING METHODS TO INTEGRATE THE MULTI-OMIC DATA EXTRACTED FROM A SINGLE CTDNA ASSAY. WE WILL EMPLOY UNIQUE SYSTEMS AND RESOURCES TO DEVELOP OUR METHODS AND ADVANCE OUR UNDERSTANDING OF TUMOR MOLECULAR HETEROGENEITY AND TREATMENT RESPONSE. (1) FROM RAPID AUTOPSY STUDIES, WE WILL ASSESS THE CONTRIBUTION OF DNA FROM MULTIPLE METASTATIC LESIONS TO DETERMINE THE KEY SOURCE OF CTDNA. (2) FROM PATIENT-DERIVED XENOGRAFT (PDX) MOUSE MODELS, WE WILL ESTABLISH A REPOSITORY OF HUMAN CTDNA FROM MOUSE PLASMA TO SUPPORT DEVELOPMENT ACTIVITIES AND STUDIES UNDER PDX TREATMENT CONDITIONS USING NOVEL THERAPIES. THIS FRAMEWORK IS GENERALIZABLE TO ADDRESS RESEARCH QUESTIONS RELATED TO TUMOR BIOLOGY AND TREATMENT RESPONSE, INCLUDING MONITORING CANCER-ASSOCIATED PATHWAYS AND THE EFFECTIVENESS OF TARGETED THERAPIES. SUCCESSFUL INNOVATIONS MADE IN THIS PROJECT WILL ESTABLISH A PARADIGM SHIFT IN CANCER RESEARCH AND ACCELERATE TRANSLATION OF NEW CLINICAL APPLICATIONS TO ADVANCE PRECISION ONCOLOGY.

(PQ5) EFFECT OF HIV INFECTION ON VIRAL AND HOST GENE EXPRESSION AND ANTITUMOR IMMUNITY IN KAPOSI SARCOMA IN AFRICA

EXPLORING THE EPIGENETIC CONTROL OF PANCREATIC CANCER SUBTYPES

ROLE OF TUMOR CELL CLUSTER-INDUCED SIGNALING IN BREAST CANCER METASTASIS

DEEP MOLECULAR AND CELLULAR PROFILING OF COLORECTAL CANCER TUMOR AND IMMUNE MICROENVIRONMENT IN ALASKA NATIVE PEOPLE - PROJECT SUMMARY ALASKA NATIVE PEOPLE HAVE THE HIGHEST INCIDENCE AND MORTALITY RATES OF COLORECTAL CANCER (CRC) GLOBALLY, WITH RATES THAT ARE MORE THAN DOUBLE THOSE OBSERVED IN THE GENERAL U.S. POPULATION (INCIDENCE: 89.0 VS. 38.6/100,000; MORTALITY: 39.6/100,000 VS. 13.8/100,000). THESE HIGH RATES CANNOT BE EXPLAINED BY ACCESS TO SCREENING, AS DEDICATED EFFORTS TO INCREASE CRC SCREENING HAVE RESULTED IN SCREENING RATES IN ALASKA NATIVE PEOPLE THAT ARE COMPARABLE TO THE US AVERAGE. THESE DISPARITIES HAVE PERSISTED FOR OVER 40 YEARS AND ARE OF NOTED CONCERN TO COMMUNITY MEMBERS AND TRIBAL HEALTH LEADERS ALIKE, MAKING THIS A PRIORITY RESEARCH AREA FOR ALASKA NATIVE PEOPLE. A KEY KNOWLEDGE GAP IS THE LACK OF SIZABLE AND COMPREHENSIVE STUDIES CHARACTERIZING THE MOLECULAR FEATURES OF COLORECTAL TUMORS IN ALASKA NATIVE PATIENTS. ACCORDINGLY, WE PROPOSE AN INTEGRATIVE APPROACH TO BETTER UNDERSTAND CRC TUMORIGENESIS AND MOLECULAR SUBTYPES IN THIS HIGH-RISK POPULATION, AND TO EVALUATE WHETHER VARIOUS TUMOR AND TUMOR MICROENVIRONMENT FEATURES CONTRIBUTE TO DISEASE PROGRESSION. SPECIFICALLY, WE AIM TO DEEPLY CHARACTERIZE THE MUTATIONAL, TRANSCRIPTIONAL, AND CELLULAR LANDSCAPES OF CRC TUMORS AND THEIR IMMUNE MICROENVIRONMENTS IN 500 ALASKA NATIVE PATIENTS AND LINK THESE CHARACTERISTICS TO CRC-SPECIFIC MORTALITY. WE WILL BUILD ON OUR EXISTING COLLABORATION BETWEEN THE ALASKA NATIVE TRIBAL HEALTH CONSORTIUM (ANTHC) AND THE FRED HUTCHINSON CANCER CENTER. WE WILL CAPITALIZE ON ANTHC’S UNIQUE BIOREPOSITORY (LINKABLE TO COMPREHENSIVE MEDICAL RECORDS) THAT CONTAINS TUMOR TISSUE SAMPLES OF THE MAJORITY OF ALASKA NATIVE CRC PATIENTS DIAGNOSED IN ALASKA. PILOT DATA GENERATED USING BIOSPECIMENS FROM THIS RESOURCE AND UTILIZING THE SAME PLATFORMS AS PROPOSED HERE DEMONSTRATE HIGH-QUALITY DATA AND ENSURE THAT IRB AND TRIBAL APPROVALS ARE IN PLACE TO ENABLE RAPID EXECUTION OF THE PROPOSED WORK. TO IDENTIFY CLINICALLY MEANINGFUL POPULATION DIFFERENCES, WE WILL COMPARE MOLECULAR PROFILES WITH THOSE FROM NON-HISPANIC WHITE CRC PATIENTS USING AVAILABLE DATA. IN AIM 1, WE WILL PERFORM WHOLE-EXOME SEQUENCING OF CRC TUMORS AND PAIRED NORMAL SAMPLES TO IDENTIFY DRIVER GENES AND CLINICALLY ACTIONABLE MUTATIONS PARTICULARLY RELEVANT TO THE ALASKA NATIVE POPULATION. TO GAIN ETIOLOGICAL INSIGHT, WE WILL ANALYZE MUTATIONAL SIGNATURES THAT MAY BE LINKED TO ENVIRONMENTAL EXPOSURES AND IDENTIFY GERMLINE MUTATIONS IN HIGH-PENETRANCE CRC RISK GENES TO INVESTIGATE THEIR ROLE IN THE INCREASED CRC RISK IN ALASKA NATIVE PEOPLE. IN AIM 2, WE WILL APPLY TWO COMPLEMENTARY CUTTING-EDGE SPATIAL PROFILING TECHNOLOGIES TO FULLY CHARACTERIZE THE TUMORAL IMMUNE RESPONSE AND DISCOVER MECHANISMS OF IMMUNE EVASION. WE WILL PERFORM SPATIAL WHOLE TRANSCRIPTOME PROFILING OF CRC TUMORS USING NANOSTRING’S GEOMX DIGITAL SPATIAL PROFILING TECHNOLOGY. WE WILL USE AKOYA BIOSCIENCES’ PHENOCYCLER PLATFORM FOR SPATIALLY RESOLVED SINGLE IMMUNE CELL PHENOTYPING. WE EXPECT THAT INSIGHTS GAINED THROUGH THIS WORK CAN INFORM THE DEVELOPMENT OF HIGH-VALUE, NOVEL THERAPEUTIC STRATEGIES. IN AIM 3, WE WILL LEVERAGE THESE MOLECULAR DATA TO DEVELOP NOVEL PREDICTORS OF CRC-SPECIFIC MORTALITY THAT COULD HELP GUIDE CLINICAL DECISION MAKING, IMPROVE OUTCOMES, AND REDUCE LONG-STANDING DISPARITIES.

IMMUNOGLOBULIN REPLACEMENT THERAPY AND INFECTIOUS COMPLICATIONS AFTER CD19-TARGETED CAR-T-CELL THERAPY - PROJECT SUMMARY/ABSTRACT CHIMERIC ANTIGEN RECEPTOR T CELL THERAPY (CARTX) HAS TRANSFORMED TREATMENT FOR B CELL MALIGNANCIES. HOWEVER, THE EFFECTS OF CARTX ON HUMORAL IMMUNITY AND INFECTION RISK ARE INCOMPLETELY UNDERSTOOD. THE HIGH PREVALENCE OF HYPOGAMMAGLOBULINEMIA IN CARTX RECIPIENTS HAS DRIVEN FREQUENT USE OF PROPHYLACTIC IMMUNOGLOBULIN G (IGG) REPLACEMENT THERAPY (IGRT) TO PREVENT INFECTIONS IN THIS PATIENT POPULATION. HOWEVER, LIMITED DATA EXIST TO SUPPORT THIS PRACTICE, AND SHORTAGES, SIDE EFFECTS, AND COST NECESSITATE CAREFUL STEWARDSHIP OF IGRT. EMERGING DATA INDICATE THAT PATHOGEN-SPECIFIC ANTIBODIES OFTEN PERSIST AFTER CD19-CARTX, POTENTIALLY CONTESTING THE NEED FOR IGRT. WELL CONTROLLED STUDIES ARE NEEDED TO ASCERTAIN THE CLINICAL UTILITY OF IGRT IN CARTX RECIPIENTS. WITHIN THIS CLINICAL CONTEXT, OTHER IMPORTANT AND CONNECTED QUESTIONS REMAIN ABOUT HOW IGRT AFFECTS CAR-T CELL FUNCTION, IN ADDITION TO THE POSSIBLE COSTS VERSUS BENEFITS OF THE EFFECT OF IGRT ON HEALTHCARE RESOURCE UTILIZATION. THIS TIMELY AND UNIQUE PROPOSAL WILL BE THE FIRST RANDOMIZED, CONTROLLED TRIAL OF IGRT USE IN CARTX RECIPIENTS AND PROVIDE CRITICAL INSIGHTS INTO THE POTENTIAL RISKS AND BENEFITS OF IGRT IN THIS PATIENT POPULATION. THE KEY OBJECTIVES OF THIS STUDY ARE TO EVALUATE WHETHER IGRT IN CARTX RECIPIENTS REDUCES INFECTION RATES COMPARED TO PLACEBO, AND TO UNDERSTAND THE IMPACT OF IGRT ON PREVIOUSLY UNEXPLORED OUTCOMES SUCH AS CAR-T CELL EXPANSION, CAR- T CELL PERSISTENCE, CAR-T CELL FUNCTION, AND HEALTHCARE RESOURCE UTILIZATION. FOR THE PROPOSED STUDY, WE HAVE ASSEMBLED AN INTERDISCIPLINARY GROUP OF PHYSICIANS AND SCIENTISTS FROM HIGH-VOLUME CARTX CENTERS WHO WILL LEVERAGE OUR EXPERTISE IN IMMUNO-ONCOLOGY, INFECTIOUS DISEASES, AND CANCER OUTCOMES RESEARCH. WE PROPOSE A RANDOMIZED TRIAL OF IGRT VERSUS PLACEBO IN 150 ADULTS WITH SERUM TOTAL IGG =400 MG/DL PRIOR TO CD19-CARTX. PARTICIPANTS WILL BE RANDOMIZED 1:1 TO RECEIVE IGRT OR PLACEBO WITHIN 14 DAYS PRIOR TO CARTX AND AT 28-DAY INTERVALS AFTER CARTX FOR 4 MONTHS. AIM 1 WILL COMPARE BETWEEN STUDY ARMS THE INCIDENCE RATE OF INFECTIONS THROUGH 6 MONTHS AFTER CD19-CARTX; WE WILL ALSO LONGITUDINALLY CHARACTERIZE AND COMPARE TOTAL AND PATHOGEN-SPECIFIC IGG LEVELS AND THEIR ASSOCIATION WITH INFECTIONS. AIM 2 WILL EXPLORE THE ASSOCIATION OF IGRT WITH HEALTHCARE RESOURCE UTILIZATION, CYTOKINE RELEASE SYNDROME, AND CARTX-ASSOCIATED NEUROTOXICITY. AIM 3 WILL CHARACTERIZE THE IMPACT OF IGRT ON CAR-T CELL EXPANSION, PERSISTENCE, AND FUNCTION. THIS WILL BE THE FIRST RANDOMIZED CONTROLLED STUDY OF IGRT AFTER CARTX AND WILL PROVIDE FOUNDATIONAL DATA TO ESTABLISH EVIDENCE-BASED ESTIMATES OF THE CLINICAL EFFICACY AND RISK-BENEFIT OF IGRT IN CD19-CARTX RECIPIENTS. IN PARALLEL, THIS STUDY WILL EXPLORE OTHER POTENTIAL EFFECTS OF IGRT ON CAR-T CELL DYNAMICS AND HEALTHCARE RESOURCE UTILIZATION. THE DATA GENERATED BY THIS PROPOSAL WILL PROVIDE THE GROUNDWORK FOR FUTURE STUDIES TO REFINE INFECTION PREVENTION STRATEGIES IN THE GROWING POPULATION OF CARTX RECIPIENTS.

INTEGRATIVE GENOMICS INTO GENETIC ASSOCIATION STUDIES OF BLOOD PRESSURE AND STROKE IN AFRICAN AMERICANS - PROJECT SUMMARY STROKE IS THE THIRD LEADING CAUSE OF DEATH AMONG AFRICAN AMERICANS (AAS): THEY ARE TWICE AS LIKELY TO DIE FROM STROKE AS EUROPEAN AMERICANS (EAS), AND THEIR INCIDENCE RATE IS ALMOST DOUBLE THAT OF EAS. RECENT GENOME- WIDE STUDIES (GWAS) SUGGEST THERE IS A SUBSTANTIAL GENETIC CONTRIBUTION TO STROKE RISK IN AFRICAN ANCESTRY POPULATIONS, WITH HERITABILITY ESTIMATES OF ABOUT 35%. HOWEVER, TO DATE, GENETIC STUDIES IN AAS ARE GREATLY LAGGING BEHIND THOSE IN EAS DESPITE THEIR INCREASED STROKE BURDEN. AMONG THE RISK FACTORS FOR STROKE, BLOOD PRESSURE IS A MAJOR CONTRIBUTOR: 4 IN 10 AAS SUFFER FROM HYPERTENSION, 50% MORE THAN EAS. THESE DISPARITIES HAVE BEEN CONSIDERED TO BE MEDIATED BY ENVIRONMENTAL AND SOCIAL DETERMINANTS, YET THEY REMAIN AFTER ADJUSTING FOR DEMOGRAPHICS, SOCIOECONOMIC STATUS, CLINICAL CHARACTERISTICS, AND MODIFIABLE HEALTH BEHAVIORS. HERITABILITY ANALYSIS SUGGESTS AFRICAN ANCESTRY IS ASSOCIATED WITH HYPERTENSION, WITH HERITABILITY ESTIMATES FROM 30–40% FOR SYSTOLIC AND DIASTOLIC BLOOD PRESSURE. HOWEVER, GENETIC SUSCEPTIBILITY TO HYPERTENSION AMONG AAS IS LESS WELL STUDIED COMPARED TO OTHER ETHNIC GROUPS. THEREFORE, THERE IS CONSIDERABLE MOTIVATION FOR IDENTIFYING THE GENETIC COMPONENTS OF STROKE AND HIGH BLOOD PRESSURE IN AAS. DISCOVERY OF GENETIC VARIANTS THAT PREDISPOSE TO BLOOD PRESSURE AND STROKE IS A CRUCIAL STEP TOWARD UNDERSTANDING GENETIC MECHANISMS THAT MAY LEAD TO NOVEL PREVENTION AND TREATMENT STRATEGIES. YET, GWAS HAVE THUS FAR IDENTIFIED GENETIC LOCI THAT TOGETHER ACCOUNT FOR ONLY A SMALL PROPORTION OF THE HERITABLE RISK. SUBSTANTIAL EFFORTS HAVE BEEN DEVOTED TO STUDYING THE ASSOCIATION OF GENETIC VARIATION WITH GENE EXPRESSION AND OTHER MOLECULAR CHARACTERISTICS THROUGH LARGE COLLABORATIVE INITIATIVES SUCH AS GENOTYPE-TISSUE EXPRESSION (GTEX) AND ENCYCLOPEDIA OF DNA ELEMENTS. THESE INITIATIVES HAVE PROVIDED A DEEPER UNDERSTANDING OF FUNCTIONAL ELEMENTS ACROSS THE GENOME, WHICH HAVE BEEN USED TO INFORM GENETIC ASSOCIATION AND IDENTIFIED MANY NOVEL LOCI. HOWEVER, MOST OF THE DATA IN THESE STUDIES HAVE FOCUSED ON EUROPEAN ANCESTRY AND LITTLE HAS BEEN DONE IN AAS. OUR RECENT WORK IN NATURE SHOWS THAT GENETIC DISCOVERIES IN ONE POPULATION DO NOT READILY TRANSFER TO OTHER POPULATIONS. THE OBJECTIVE OF THIS STUDY IS TO IDENTIFY VARIANTS PREDICTING VARIOUS GENOMIC FEATURES (GENE EXPRESSION, METHYLATION AND PROTEIN) IN AA SAMPLES THAT HAVE BEEN RECENTLY COLLECTED THROUGH TRANS-OMICS FOR PRECISION MEDICINE, THE COMMONMIND CONSORTIUM, AND GTEX, AND TO INTEGRATE THIS FUNCTIONAL INFORMATION INTO GENETIC ASSOCIATION ANALYSIS OF BLOOD PRESSURE AND STROKE IN AAS. INSIGHT INTO BOTH MOLECULAR ACTIVITY AND GENETIC VARIATION CAN INFORM ASSOCIATION ANALYSIS AND ENABLE NOVEL GENOME-WIDE DISCOVERIES. IN PARTICULAR, WE PROPOSE TO DEVELOP METHODS THAT LEVERAGE THE DATA FOR EAS TO IMPROVE POWER FOR IDENTIFYING GENETIC VARIANTS THAT REGULATE VARIOUS TYPES OF GENOMIC FEATURES IN AAS, AND FOR INTEGRATING THE GENOMIC REGULATION MODELS INTO GWAS WITH THE ULTIMATE GOAL TO IDENTIFY NOVEL LOCI FOR STROKE RISK AND BLOOD PRESSURE IN AAS. TO FACILITATE THESE AIMS WE HAVE ASSEMBLED THE LARGEST NUMBER OF AAS FOR GENOMIC STUDIES AND AA STROKE CASES AND BLOOD PRESSURE DATA FOR GWAS.

MEGATALS: HYPERSPECIFIC REAGENTS FOR TARGETED GENE MODIFICATION AND CORRECTION