Brigham And Women'S Hospital

NIH Research Projects · FY 2024 · 2021-09

PROJECT SUMMARY Hypertrophic cardiomyopathy (HCM) is a primary disorder of the myocardium that is characterized by unexplained left ventricular hypertrophy (LVH), myocyte disarray, and fibrosis. It is the most prevalent genetic heart disorder, affecting ~1 in 500 people. HCM has been the focus of intense clinical and basic science study for decades. These efforts have provided remarkable insights into the molecular basis and clinical course of disease-- defining sarcomere mutations as the most common genetic etiology and characterizing the phenotypic spectrum. Additionally, prior studies have underscored the great heterogeneity of HCM. Although many patients have serious outcomes, including arrhythmias, advanced heart failure, and sudden cardiac death, many others experience mild disease with low symptom burden and normal longevity. Moreover, there is striking diversity in cardiac morphology and function, even amongst patients with identical underlying sarcomere mutations. The factors that drive such marked heterogeneity are poorly understood, highlighting the critical need to better characterize determinants of disease expression and clinical outcomes. This proposal seeks to identify genotypic and phenotypic features that account for the highly diverse manifestations of HCM. These goals will be addressed by leveraging the recently established Sarcomeric Human Cardiomyopathy Registry (SHaRe), containing data on over 9000 HCM patients, and applying state-of- the-art genetic, imaging, and statistical analyses. Our aims are: (1) To identify common genetic variation that impacts disease expression in HCM patients both with and without a driving sarcomere mutation (sarcomeric and non-sarcomeric HCM). These analyses will interrogate background genetic variation to examine how an individual’s genetic make-up influences their susceptibility or resistance to disease. We will also develop polygenic risk scores to assess the cumulative effect of common genetic variants on disease expression. (2) To characterize phenotypic factors that influence disease expression by utilizing machine-learning techniques to identify novel, quantitative high-dimensional imaging features from routinely-performed cardiac magnetic resonance (CMR) studies. We will then incorporate these features into rigorous prediction models to improve clinical risk stratification. This approach will allow us to look more deeply into the structure and function of the heart by using the full array of digital data available from CMR imaging, thereby drawing new correlations between phenotype, disease manifestations, and clinical outcomes. Successful completion of these aims will advance our understanding of why disease experience can be so different from patient to patient, provide new insights into mechanism and therapeutic targets, and identify novel biomarkers of disease severity. These results will impact clinical management of patients with HCM by improving the precision and accuracy of diagnosis and risk stratification. Finally, insights gained will likely inform more common forms of heart disease, such as heart failure with preserved ejection fraction, with similarly highly heterogeneous manifestations.

NIH Research Projects · FY 2025 · 2021-09

Project Summary/Abstract More than 10% of the U.S. population seeks care for spine pain each year with rates of surgical procedures on the rise. One of the most challenging yet common sequelae of lumbar spine surgery is chronic post-surgical pain (CPSP). CPSP is associated with poor physical function and remains difficult to treat. Indeed, it is frequently treated with opioid medications, despite evidence that long term opioid use for the treatment of chronic pain may not be effective and may increase the risk of overdose-related death. Therefore, the need to prevent the transition from acute to chronic post-surgical pain is great, especially for patients undergoing lumbar spine surgery. Acceptance and Commitment Therapy (ACT) is a psychosocial intervention that has been effective in improving physical function and quality of life among patients with chronic pain as well treating opioid use disorders. Thus, it stands to reason that ACT may be a promising tool for the prevention of CPSP and long-term opioid use. It has also been modified into brief formats in order increase adherence and minimize treatment barriers such as cost and access. The present study aims to adapt and modify a brief presurgical ACT intervention aimed at preventing the transition to CPSP and reducing long-term opioid use. We will then assess the acceptability, feasibility, and preliminary efficacy of the finalized intervention to prevent the transition to CPSP and reduce post-surgical opioid use six months following lumbar spine surgery. Finally, we will identify psychosocial and psychophysical phenotypes associated with response to this intervention. Together, this study will afford me the opportunity to gain training in treatment development and implementation and development and execution of clinical trial while advancing my long-term goal of developing mechanistically-based nonpharmacologic interventions to prevent the development of CPSP and reduce the risk of long-term opioid use.

NIH Research Projects · FY 2025 · 2021-09

Summary/Abstract With our increasing ability to measure biological data at scale and the digitalization of health records, computational thinking is becoming ever more important in the biological science and healthcare. The research directions proposed in this grant look to build robust machine learning models and tool for computational biology by including principles and analysis from other engineering fields, like control, that have a proven record of incorporating robustness into the systems they have automated. This increased robustness will save resources during the development of these machine learning models. It will also lead to more reliable diagnostics, clinical tools, and machine learning based biological discoveries. We have proposed three future research directions at the intersection of machine learning, control, and computational biology (a) modeling dynamical systems, (b) robust optimization schemes (c) control principles for in vivo modeling of microbial communities. The first proposed research area involves the development of flexible models for performing inference on dynamical systems models with time-series data. Dynamical systems models are able to learn mathematically causal relationships between variables, compared to other models whose parameters may only have correlative relationships. Our flexible models will be differentiable allowing them to be trained using the same efficient algorithms and hardware that have propelled deep learning models into the spotlight. These differentiable methods will allow for us to more easily integrate the uncertainty associated with biological measurements into our models. The second research area looks to develop more robust gradient optimization algorithms, the work horse for training deep neural networks. Many of the popular algorithms used to train deep neural networks were not explicitly designed to be robust. By developing more robust optimization techniques machine learning models trained on disparate data sets at different hospital or labs will be more reproducible and will require less time for tuning parameters, ultimately saving resources as well. These robust optimization techniques will also aid in the certification of machine learning based tools that will ultimately be deployed in the clinic. The third research area we propose is an approach for the discovery and design of robust microbial communities. Communities of commensal, or engineered, bacteria have long been proposed as alternative therapies for the treatment of gut related illness (“bugs as drugs”). We propose a top down approach to identifying putative microbial consortia members from time-series experiments with germ free mice colonized by complex flora. By beginning the consortia design process in vivo we hope to overcome the challenge that many other attempts at consortia construction have encountered where in vitro designed communities do not reproduce their intended properties once transferred into living host organisms. The tools from this work will be built using open access software and all data will be made easily accessible and explorable to the public.

NIH Research Projects · FY 2025 · 2021-08

ABSTRACT Sleep apnea (SA) and insomnia are the two most common sleep disorders, and both contribute individually and jointly to the risk of cardiopulmonary, metabolic, and psychiatric diseases. Despite their high prevalence, treatments for SA and insomnia remain suboptimal. SA and insomnia are thought to be comprised of distinct subtypes, which remain poorly defined and may contribute to differing risks for health outcomes. Our goal is to use machine learning to apply precise phenotyping to biobanks to identify the genetic bases of SA and insomnia and discover SA and insomnia subtypes based on genetics and comorbidities in order to reduce phenotype heterogeneity, guide patient stratification and aid in the discovery of more personalized treatments. Our approach is to combine health care system biobank data with research polysomnography (PSG) to achieve statistical power to discover genetic variants for SA and insomnia-related phenotypes and characterize their associated clinical outcomes and endophenotypes (physiological mechanisms). We will use advanced natural language processing (NLP) methods to substantially improve the accuracy of SA and insomnia phenotyping. Our anticipated sample size will be >11-fold larger than prior genetic studies of SA, providing the necessary statistical power for genetic discovery. Polygenic risk scores derived from our results can be used to quantify sleep disorder risk, even among those without sleep phenotypes. Machine learning methods can identify predictors of diagnosis-clustered patient groups contained within the medical record. Precision deeply- phenotyped PSG data (eg hypoxic burden) can characterize endophenotypes at associated genetic loci using genetic localization. We will derive advanced SA and insomnia phenotypes robust to demographic differences across biobank sites, perform the largest genetic analysis of validated SA and insomnia phenotypes to date, characterize novel loci, and study associations with clinical diagnosis data to improve patient classification in three biobanks. We will explore sex-specific associations and validate lead genetic associations in two biobanks. Our specific aims are: 1) to construct advanced SA and insomnia phenotying algorithms across diverse demographic groups and sites; 2) to identify and characterize the genetic associations with SA and insomnia; and 3) to identify and characterize distinct SA and insomnia patient subgroups based on related comorbidity profiles. The proposed project has a goal of improving the treatment of heart, lung, blood, and sleep disorders by potentially resolving disease heterogeneity, discovering novel genetic associations with sleep disorders, and helping to clarify the overlap of SA and insomnia with cardiopulmonary, metabolic, and psychiatric disease.

NIH Research Projects · FY 2025 · 2021-08

PROJECT SUMMARY Shehzad Basaria, MD, an Associate Professor of Medicine and Endocrinology in the Division of Endocrinology, Diabetes, & Metabolism at Brigham and Women's Hospital, Harvard Medical School, submits this application for a K24 Mid-Career Development award to provide protected time to mentor trainees in Patient-Oriented Research (POR) in Endocrine aspects of Gero-Oncology. Dr. Basaria is one of the few endocrinologists worldwide specializing in endocrine and cardio-metabolic disorders in older men with cancer and androgen deficiency. He will pursue additional training to hone his mentoring skills in order to build on his established record of mentorship and foster the research careers of early investigators. Candidate: Dr. Basaria is a highly productive clinical researcher in the field of Endocrinology, Aging and Cancer. Since 2003, he has been continuously NIH-funded to investigate: i) endocrine and cardio-metabolic complications of androgen deprivation therapy (ADT) in men with prostate cancer (PCa), ii) benefits and risks of androgen replacement in older men, and iii) endocrinology of aging. He has conducted his investigations using NIH-supported infrastructure, including RO1s and R21 grants, data from the Baltimore Longitudinal Study of Aging (BLSA), the InChianti Study, and the Boston Pepper Center for Function-Promoting Therapies. With his uncommon skill set and strong POR program in Endocrinology and Gero-Oncology, he has been a sought-after collaborator and mentor at Brigham/Harvard and at national and international institutions. Mentoring Plan/Environment: This application will leverage the extensive training resources at Brigham/Harvard, including the Center for Clinical Investigation, the Brigham Research Institute for Clinical and Translational Research, and T32 training grants in a variety of specialties. It will also draw on the unparalleled resources of the Boston Pepper Center and other funded studies to serve as a platform for POR trainees at multiple levels. Research Plan: The novel research supported by this K24 award will make significant contributions to the 1A) The impact of ADT-induced profound hypogonadism and the resulting decline in muscle mass on physical function, 1B) The impact of ADT on fat infiltration of skeletal muscles and the association of this deterioration in muscle quality on physical function, and 2) The mechanisms by which testosterone replacement improves Cancer- Related Fatigue in older men with cancer. understanding of the impact of androgen deficiency in older men with cancer in three major areas: These novel aims will build on the ongoing work in Dr. Basaria's current R01s, explore new hypotheses, and expand opportunities for trainees.

NIH Research Projects · FY 2025 · 2021-08

PROJECT SUMMARY In an effort to provide pain relief to tens of millions of patients with chronic pain, opioids are one of the most commonly prescribed medications in the United States. Large segments of the population are thus exposed to the detrimental side effects of opioids, which can be life threatening and include addiction and respiratory failure. Compulsive opioid use despite these negative consequences defines opioid use disorder, a condition that is responsible for nearly 50,000 deaths and $80 billion in medical costs annually. Thus, there is an urgent need for the development of improved treatments for opioid use disorder. One of the greatest challenges in treating opioid use disorder is its chronic nature with patients often relapsing after long periods of drug abstinence. Persistent epigenomic changes in the nucleus accumbens of patients with opioid use disorder are thought to contribute to its chronic, relapsing course. It has remained challenging, however, to translate this knowledge into novel therapeutic approaches because it has not been possible to selectively target the epigenomically-modified neurons involved in drug-seeking behavior without also affecting nearby cells in unrelated circuits. Here we present an innovative approach to label cells that drive opioid-seeking behavior based on their unique epigenomic profile. To do this, we will first map at single-cell resolution, the regions of chromatin that are selectively accessible in mouse nucleus accumbens neurons after morphine self-administration, an established model of opioid use disorder. Some of these genomic regions will act as functional gene regulatory elements that activate gene expression (e.g. gene enhancers) after morphine self-administration. To identify these functional gene enhancers, we will generate an adeno-associated viral library in which each putative element promotes the expression of a unique barcode. We will then use single-nucleus RNA-sequencing to rapidly screen this viral library in vivo for the elements that selectively drive expression of their barcode in the nucleus accumbens neurons that have been epigenomically altered by morphine self-administration. The most selective viral candidate will be used to express inhibitory chemogenetic channels for controlling morphine-seeking behavior. Successful completion of this proposal will establish a fundamentally new approach to selectively label, purify, and control cells that drive opioid-seeking behavior. This approach offers a number of advantages over current state-of-the-art technologies including the ability to label cells involved in drug-seeking behavior without need for transgenic mice or precisely timed conditioned stimuli. By using evolutionarily-conserved gene regulatory elements to drive viral expression, this approach also has the potential to translate to patients with refractory opioid use disorder.

NIH Research Projects · FY 2025 · 2021-08

Abstract/Summary This application for continuing support focuses on the mechanisms by which the cysteinyl leukotrienes (cysLTs), a class of potent lipid inflammatory mediators, facilitate type 2 (eosinophilic) immunopathology (T2I) that underlies prevalent and burdensome respiratory diseases, including asthma and chronic rhinosinusitis with nasal polyps (CRSwNP). The proposal tests the hypothesis that leukotriene E4 (LTE4) initiates respiratory T2I through engagement of the type 3 cysLT receptor (CysLT3R) and nucleotide signaling to P2Y2 receptors on brush cells (BrCs). A second hypothesis is that LTE4-induced BrC activation elicits activation of group 2 innate lymphoid cells (ILC2s) and type 2 cytokine generation through synergistic actions of IL-25 and endogenously generated LTC4. A third hypothesis is that IL-25-driven eosinophil recruitment provides a pool of LTC4-driven platelet-derived IL-33 to incrementally activate ILC2s and MCs, further amplifying T2I and its consequences, including upstream BrC expansion. The proposal uses a combination of novel transgenic mice, ex vivo approaches, and unique models to dissect a complex pathway by which cysLTs act in series downstream of epithelial perturbation by leukotriene E4, the most stable cysLT, to activate MC, potently elicit ILC2 activation, and induce severe immunopathology. The studies seek to explain the selective hyperresponsiveness of asthmatic subjects to leukotriene E4, and to develop therapeutic strategies through the selective targeting of receptors other than CysLT1R.

NIH Research Projects · FY 2025 · 2021-08

Abstract Although circadian rhythms are established as a fundamental mechanism in various biologic processes, including metabolic and cardiovascular functioning, less is known regarding how disruption of circadian rhythms may contribute to development of cardiometabolic disease in broader human populations. Prior epidemiologic studies have predominantly focused on specific populations who experience extreme circadian disruption, such as rotating night shift workers. In this application, we will consider irregular sleep schedules as a ubiquitous marker of chronic circadian disruption and evaluate its role in cardiometabolic disease development. First, we will leverage the wealth of data from the UK Biobank (UKB), which has measured habitual sleep using accelerometer among 92,644 participants. We will characterize the dose-response relationships of irregular sleep schedules with risk of hypertension, diabetes and cardiovascular disease and identify potential threshold to define what level of sleep variability may be cardiometabolically unhealthy. We will also evaluate whether the observed associations differed by sociodemographic factors (e.g., age, sex, race/ethnicity) or other sleep traits (e.g., average sleep duration and insomnia symptoms). Further, given that sleep regularity represents a highly modifiable risk factor, we will evaluate whether regular sleep schedules may counteract genetic predisposition to cardiometabolic disease. Second, in the Nurses’ Health Study 3 (NHS3), we propose to measure habitual sleep using Fitbit and plasma metabolomics among 1,000 nurses, encompassing a wide range of variations in sleep schedules (including a random subset with night shift work). We hypothesize that irregular sleep schedules are associated with altered metabolites exhibiting circadian rhythms, such as omega-3 fatty acids, linoleate, arginine and tyrosine. We further hypothesize that this metabolic profile mediates the associations between irregular sleep and cardiometabolic traits including obesity, blood pressure and heart rate variability. In addition, we will collect new data on several emerging risk factors for irregular sleep that have not been examined in previous work, including mobile device use, late eating, breakfast skipping, pet ownership and childbearing/rearing in women. To increase rigor, reproducibility and generalizability, we will confirm our primary findings from UKB and NHS3 in the diverse Multi-Ethnic Study of Atherosclerosis (n=2,156), which have existing data on objectively measured habitual sleep, genomics, metabolomics and conventional epidemiologic risk factors. Overall, this project will provide larger-scale, more diverse and more in-depth evidence for the cardiometabolic impact of irregular sleep schedules in US and European populations, elucidate underlying biologic mechanisms, and ultimately foster development of potential public health recommendations and interventions to reduce irregular sleep and improve cardiometabolic health.

NIH Research Projects · FY 2025 · 2021-08

Project Summary . Over 1 million older (≥65 years) adults with serious illness have major surgery or severe trauma each year. After surgery or trauma, older seriously ill patients are at risk for increased healthcare use, functional and cognitive decline, and mortality. National quality guidelines highlight that palliative care focused on aligning treatments with health goals, improving quality of life, alleviating physical and psychological suffering, and addressing social needs, should be provided alongside surgical care at all stages of serious illness. Palliative care for hospitalized seriously ill patients is associated with reduced symptoms and less healthcare utilization after discharge. Although seriously ill surgical patients benefit from palliative care, they are less likely than other hospitalized patients to receive it; this is in part due to research gaps that have inhibited implementation of practical palliative care interventions for older seriously ill surgical patients. Gaps include a dearth of data on patient-oriented surgical outcomes such as pain, depression, and caregiving that can be targeted by palliative care, methodological barriers to measuring palliative care delivery in surgical practice, and little understanding of contextual factors that influence implementation of palliative care in surgery. The proposed study will address these gaps by providing an innovative and layered examination of the role of palliative care in surgery. The study has three specific aims. Aim 1 identifies a cohort of seriously ill older surgical patients (≥66y) using Health and Retirement Study data linked to Medicare claims, and determines the association between direct targets of palliative care (pain, depression, and caregiving needs) and less proximal benefits (reduced healthcare utilization) to demonstrate the important role of palliative care in surgery. Aim 2 identifies a retrospective cohort of older seriously ill surgical patients (≥66y) in a large regional health system and uses Natural Language Processing in electronic health data linked to Medicare Claims to identify palliative care processes (goals of care discussions, healthcare proxy documentation, pain and caregiver assessments) delivered during the surgical episode. The association between palliative care and healthcare utilization in the year after surgical discharge will be tested. Aim 3 uses qualitative interviews and direct observations to obtain an in-depth understanding of contextual factors influencing implementation of palliative care processes in the care of seriously ill older surgical patients (≥65 years). This proposal uses complementary data sources to assess patient-centered outcomes in older seriously ill surgical patients, uses novel methods to evaluate the impact of palliative care processes on outcomes, and deeply examines barriers to implementation of perioperative palliative care in clinical practice. These results will directly inform bedside clinical decisions and the implementation of targeted palliative care interventions to improve care for seriously ill older surgical patients.

NIH Research Projects · FY 2024 · 2021-08

Recent advances in the multi-parametric MRI of the prostate have led to a surge in new research methods for the detection and diagnosis of prostate cancer - with the goal of accurate risk- stratification of prostate cancer. Specifically, a traditional Transrectal Ultrasound (TRUS)-guided biopsy tends to fail, as samples are randomly collected from the prostate without aiming at suspicious lesions often visible in MRI. Currently, several new MRI biopsy approaches have come to the forefront. They are being evaluated and adopted in clinical practice, including in-bore MRI- guided biopsy and TRUS-guided MRI-fusion biopsy, collectively called ‘MRI-targeted biopsy.’ While recent literature shows that MRI-targeted biopsies can detect more clinically significant cancer than a conventional TRUS-guided biopsy, there is still a substantial issue with the precision placement of the needle in these procedures particularly in transperineal approach, resulting in clinicians being overly conservative with the amount of tissue removal (Zhang et al., 2019). Need to address needle placement accuracy in transperineal biopsy is further heightened lately as the fluoroquinolone- resistant Escherichia coli is becoming a significant concern in public health, and clinicians are shifting to use transperineal biopsies to avoid post-biopsy infections and overuse of antibiotics. Literature, as well as our preliminary studies, found that needle deflection is a substantial obstacle for precision aiming in transperineal biopsies. Abundant literature on needle deflection analysis, needle steering, and image-guided robots are available in pre-clinical engineering studies. Yet, clinically viable or proven solutions to address the needle deflection is yet to be seen. Therefore, the objective of this application is to develop and test a cooperative robotic intervention with closed-loop error compensation in MRI targeted biopsies and focal therapies, resulting in more precisely targeted instrument placement. Accurately, we will aim to address needle deflection by the synergic use of advanced imaging and robotics. Guided by robust preliminary data, this objective is achieved by pursuing three specific aims: 1) We will develop novel tracking techniques and clinically deploy a cooperatively controlled, hands-on robotic needle placement manipulator to enable fine instrument control at the periphery of the MRI bore. 2) We will test the usefulness of a cooperatively controlled robot to increase the accuracy of needle placement in animal studies mimicking MRI-guided biopsies of the prostate. Our approach is innovative in its application of novel cooperative robotic control, in which the clinician maintains ultimate control with the direction of motion being autonomous to ensure the desired path is followed to the intended target. The proposed study is also clinically significant since the completion of this current engineering study will enable machine- assisted semi-autonomous percutaneous therapy, much discussed in the recent editorial article in Science Robotics (Yang et al., 2018). The impact of the study reaches beyond MRI-targeted prostate intervention; the technology developed can be translated into other forms of MRI-guided or ultrasound-guided intervention.

NIH Research Projects · FY 2024 · 2021-08

Summary The primary aim of this 90-day randomized trial in older adults with Alzheimer's Disease and mild dementia will determine whether nicotinamide mononucleotide (NMN), a NAD+ precursor, crosses the blood-brain barrier, and engages the hypothesized target mechanism. We hypothesize that βNMN administration will cross the blood-brain barrier and increase brain NAD+ concentrations. This application for administrative supplement requests funds to support the addition of a second clinical trial site to expedite participant recruitment and enable the completion of the trial and accomplishment of the proposed aims of the project. This request for supplemental funds was necessitated by the delay in trial's completion due to multiple unanticipated factors that included: 1) longer than expected time for securing Food and Drug Administration's approval of the IND; 2) longer than expected time for IRB review of the study protocol; 3) unanticipated mechanical problems with the head coil required for the 7T magnetic resonance spectroscopy which delayed trial's initiation; 4) reluctance of the many participants to undergo lumbar puncture for the collection of the cerebrospinal fluid; 5) participants excluded because of ineligibility for lumbar puncture or 7T MRS; 6) a large number of competing AD trials in the Boston metropolitan area; and 7) in the wake of the COVID pandemic, many older adults, especially those with AD, have been reluctant to come into a healthcare facility for research studies. To overcome these barriers and expedite enrollment, we have made several changes in the study protocol with the approval of the DSMB, IRB, and program staff; added a recruiter at BWH; and plan to add a second trial site at Beth Israel Deaconess Medical Center (BIDMC) under the leadership of Dr. Daniel Press, an NIH-funded investigator and cognitive neurologist with expertise in conducting AD clinical trials. We plan to continue to randomize an average of 1 participant each month at the BWH site and will have enrolled an additional 9 participants at the BWH site. The BIDMC site also will enroll one participant per month for a total of 8 subjects over the next 8 months. This should enable us to complete the enrollment by August 31, 2024, with the last participant completing the intervention by November 30, 2024. The data clean-up, data-lock, analyses and preparation of the primary manuscript will take an additional 4 months. We will request a no cost extension for one year. We are requesting supplemental funds to support the trial activities at BIDMC site and a nominal additional effort (7.5%) for the Project Manager for project coordination and additional administrative and reporting tasks. This planned addition of a second trial site has been discussed and approved by the trial's DSMB and the program staff. The cost saving associated with fewer laboratory tests, procedures, and subject payments due to fewer subjects having been enrolled will be carried forward to support the BWH site during the no-cost extension year and no additional funds have been requested for these activities.

NIH Research Projects · FY 2024 · 2021-08

Project Summary/Abstract Background: Cardiovascular disease (CVD) is the leading cause of mortality in both women and men. Preterm delivery (PTD) occurs in 10% of US pregnancies and is associated with twice the risk of long-term CVD morbidity and mortality in mothers. Only 13-17% of the association between PTD and CVD is explained by subsequent development of established cardiovascular risk factors such as hypertension, diabetes, hyperlipidemia and obesity. Our poor understanding of the physiologic pathways from PTD to CVD limits our ability to use PTD as an `early warning system' to better prevent and treat CVD in women. The goal of this project is to expand our understanding of PTD and CVD through discovery and validation of metabolomic signatures and scores among women with a history of PTD, confirming their association with CVD events and performing mediation analysis. We will also examine the association of PTD clinical phenotypes with CVD. Setting: We have assembled an exceptional team with deep expertise in CVD, pregnancy exposures, metabolomics, and biostatistics/ bioinformatics. Investigators on this project have decades of experience studying CVD, pregnancy complications, and metabolomic epidemiological studies. This application will leverage U01-funded infrastructure and biosamples of the Nurses' Health Study (NHS) 2 and 3 cohorts, as well as CVD outcomes and previously measured metabolomic profiles in NHS1 and the Women's Health Initiative. Research Plan: We will measure metabolomic profiles in 1500 women, including 400 women with a history of PTD, and 400 parous women with no preterm deliveries. Metabolomics will be performed at the Broad Institute. Using a robust methodology of discovery and validation, we will: 1) Discover and validate metabolomic profiles and PTD metabolite (M-PTD) scores for midlife women with a history of PTD (NHS2/3). PTD phenotypes to be examined: a) Total PTD; b) Clinical PTD: Preterm prelabor rupture of membranes, spontaneous preterm labor with intact membranes, medically-indicated PTD; c) Timing of PTD: <32 weeks, 32- <37 weeks; Exploratory: Agnostically derived metabolite endotypes of PTD; 2) Examine the association of clinical PTD phenotypes with CVD incidence (NHS2 full dataset); 3) Test the association of M-PTD scores with incident CVD (NHS1, NHS2, WHI) and determine mediation of the observed increased CVD risk from PTD metabolites (NHS2). Relevance to Public Health: CVD is an issue of major public health importance. The proposed analyses have the potential to identify precursors and pathways integral to CVD incidence after PTD, a female-specific cardiovascular risk factor, which may then be used to improve prevention strategies, enhance treatment options, and generate additional testable hypotheses that will guide future CVD research. Our approach leverages decades of prospective data collection in the NHS2 and NHS3 and our strong preliminary data support a high likelihood of success.

NIH Research Projects · FY 2024 · 2021-07

ABSTRACT Two-thirds of Americans report regularly obtaining an insufficient amount of sleep. Chronic sleep deficiency is associated with a multitude of negative health consequences, including obesity, cardiovascular disease, diabetes, and metabolic syndrome. Habitually sleeping less than the recommended seven hours per night has been linked to increased all-cause mortality and increased risk of mortality associated with metabolic syndrome, and prospective epidemiological studies have found an association between short sleep duration and increased risk of type 2 diabetes. Laboratory studies have shown that sleep restriction to 4-6 hours per night for durations varying from one to 14 days reduces glucose tolerance in otherwise healthy adults. It is now recognized that sleep restriction decreases insulin sensitivity. Multiple additional causative pathways have been explored, including reduced brain glucose utilization, increased sympathetic nervous activity, elevated evening cortisol levels, etc. However, sleep restriction in both free-ranging humans and prior experimental studies is accompanied by longer exposure to Artificial Light At Night (ALAN), an endocrine disruptor which can disrupt circadian rhythmicity. It has recently been recognized that circadian disruption itself can impair glucose metabolism. We hypothesize that endocrine and circadian disruption caused by extended duration ALAN may contribute to the adverse metabolic effects induced by chronic sleep restriction. To test this hypothesis, we will systematically evaluate glucose metabolism in healthy adults in controlled laboratory conditions (light, temperature, diet and activity patterns) using a crossover design consisting of a 7-day baseline, 7-day sleep restriction (to 5h per night) with (Light:Dark 19:5) or without (Light:Dark 14:10) ALAN, 9-day washout, and another 7-day sleep restriction with or without ALAN. Glucose metabolism (using an intravenous glucose tolerance test and a Standardized Mixed Meal Response) and circadian rhythms (using 24-h profiles of plasma melatonin and cortisol) will be assessed before and after each sleep restriction segment. Understanding whether extended duration ALAN is a primary upstream exposure that contributes to the sleep-restriction-induced impairment of glucose metabolism and consequent increase in diabetes risk is important given the widespread prevalence of sleep deficiency. By clarifying a potential modifiable mechanism by which sleep restriction adversely affects whole-body energy homeostasis, our findings will lay the groundwork for the development of novel treatments and countermeasures to mitigate the adverse metabolic effects of chronic sleep restriction.

NIH Research Projects · FY 2025 · 2021-07

Abstract Dr. Lichterfeld is an infectious disease physician-scientist with a strong record of mentoring research fellows in high-profile, patient-oriented research studies related to HIV-1 cure and eradication. He conducts a broad and diverse research program of patient-oriented studies that include molecular and cellular immunologic studies with patient-derived cells, translational human investigations and interventional clinical trials designed to explore novel therapeutic approaches to reduce HIV-1 reservoirs. These research activities provide attractive and exciting training opportunities for physicians and scientists interested and invested in developing strategies for a functional or sterilizing cure for HIV-1 infection; in the past, several of his mentees and co-mentees have progressed to receive R-level funding, and have been offered independent faculty positions at highly-selective universities around the world. In the proposed K24 application, Dr. Lichterfeld will extend and expand his successful mentoring activities in the context of three cutting-edge research areas: He will mentor trainees in the conceptualization, design, implementation and conduct of interventional clinical trials designed to explore novel therapeutic strategies for HIV-1 eradication (Specific Aim 1). These activities will initially focus on an already ongoing, NIAID-funded clinical trial in which Dr. Lichterfeld serves as the PI, but will be expanded in the future to translate novel ideas and concepts into exploratory, proof-of-concept clinical trials. These studies take advantage of advanced clinical trial research infrastructure and a highly motivated HIV-1 patient population at the Brigham and Women’s Hospital and the Massachusetts General Hospital, the two hospitals Dr. Lichterfeld is affiliated with. In addition, Dr. Lichterfeld will train his mentees in innovative next-generation sequencing and proteomics approaches involving single-genome, near full-length viral sequencing, combined with viral integration site analysis, chromatin accessibility assays and chromatin immunoprecipitation assays to profile residual viral reservoirs in patient-derived cell samples at an unprecedented breadth (Specific Aim 2). This work will be facilitated by unique technical resources and cross-disciplinary collaborations at the Ragon Institute and the Broad Institute of MIT and Harvard, where Dr. Lichterfeld holds Associate Member status. Finally, Dr. Lichterfeld will offer a distinct training experience in pediatric HIV-1 infection, focusing on the development of interventions that may enable a long-term, drug free remission of HIV-1 infection in neonates from Botswana (Specific Aim 3). These collaborative investigations will be performed in the context of ongoing, NIAID-funded clinical trials investigating effects of standard antiretroviral therapy and broadly-neutralizing antibodies on viral reservoirs and antiviral immune responses in HIV-1-infected infants started on therapy within the first days after birth. Together, these studies provide distinct but interrelated training opportunities for physicians and scientists to acquire the knowledge, skills, creativity and collaborations that are needed for an independent career in patient-oriented studies focused on finding a cure for HIV-1 infection.

NIH Research Projects · FY 2025 · 2021-07

Abstract Epstein-Barr virus (EBV) establishes lifelong infection in 95% of adults worldwide. EBV causes infectious mononucleosis, lymphomas, nasopharyngeal and gastric cancer, and oral hairy leukoplakia. EBV is transmitted between hosts through saliva, from which it translocates across the oral cavity and tonsillar epithelium to reach the B-cell compartment. Upon B-cell infection, the ~170 kilobase linear double-stranded DNA (dsDNA) EBV genome is delivered to the nucleus. EBV then uses a series of latency programs to navigate the B-cell compartment, and colonize the memory B-cell compartment. Ultimately, to spread between cells and to the tonsillar epithelium for transfer to a new host, EBV must undergo lytic replication, in which nearly 80 viral proteins are expressed and infectious virion are produced. Lytic replication is increasingly implicated in oncogenesis. Yet, much remains to be learned about how the viral lytic switch is controlled. We therefore used a human genome-wide CRISPR/Cas9 screen to identify host factors that control the viral lytic switch. Our analyses a network of host factors that repress lytic reactivation, centered on the transcription factor MYC, including cohesins, FACT, STAGA, and Mediator. Depletion of MYC or factors important for MYC expression, reactivated the lytic cycle, including in Burkitt xenografts. MYC bound the EBV genome origin of lytic replication and suppressed its looping to the lytic cycle initiator BZLF1 promoter. Our central hypothesis is that the MYC:MAX control the EBV lytic switch through regulation of viral genome loop extrusion. Our Aims are to (1) Define key MYC roles in regulation of oriLyt loop extrusion to control the EBV lytic switch; (2) Define MYC-gated cohesin roles in regulation of oriLyt loop extrusion in EBV lytic switch control (3) Define MYC-gated CTCF roles in regulation of oriLyt loop extrusion to control the EBV lytic switch. Collectively, these studies are expected to identify how EBV subverts host DNA loop extrusion pathways to control the viral lytic switch. Our studies may therefore support strategies to develop rational lytic induction therapeutic therapies for EBV-associated diseases.

NIH Research Projects · FY 2025 · 2021-07

Abstract In this 5-year R01 project entitled “Mapping the superficial white matter connectome of the human brain using ultra high resolution multi-contrast diffusion MRI,” we propose to create the first atlas of the human brain’s superficial white matter (SWM) using sub-millimeter ultra high resolution diffusion MRI (dMRI). The SWM is located between the deep white matter and the cortex. It plays an important role in neurodevelopment and aging, and it has been implicated in a large number of diseases including Alzheimer’s, Huntington’s, epilepsy, autism spectrum disorder, schizophrenia, and bipolar disorder. Despite its significance in health and disease, the SWM is vastly underrepresented in current descriptions of the human brain connectome. The SWM contains short, u- shaped association fiber bundles called u-fibers. Multiple challenges have thus far prevented comprehensive mapping of the human brain’s SWM. These challenges include the inadequate spatial resolution of dMRI data, which prevents u-fiber tracing using current tractography methods, as well as the small size, high curvature, and high inter-subject variability of the u-fibers. An additional challenge is the lack of ground truth information. Our understanding of human neuroanatomy relies heavily on the results of invasive tracer studies in monkeys, but the detailed neuroanatomy of the SWM in monkeys has not yet been systematically compiled or analyzed. We propose to address these challenges to create the most comprehensive description of the SWM to date. Our strategy includes using ultra high spatial resolution dMRI acquisitions (~700µm isotropic or better) at multiple echo times (TE), novel dMRI tractography methods designed for tracing u-fibers, anatomically informed machine learning to parcellate the u-fibers, and expert neuroanatomical generation of the SWM connectivity matrix from monkey tracer studies. Furthermore, we will develop a novel ontological framework to organize and name the SWM systems of the monkey and human brains. Overall, these steps will enable robust in-vivo tracing and capturing of inter-subject variability of the SWM of the human brain at an unprecedented spatial resolution. Our proposed deliverables will be the first comprehensive, anatomically curated atlases of the SWM in human and monkey, which will enable the study of the SWM in health and disease. We will publicly release all image data, tractography atlases, monkey connectivity matrices, extracted fascicles, and all software as open source.

NIH Research Projects · FY 2025 · 2021-07

ABSTRACT Androgen receptor (AR) is ligand-activated transcription factor and a driver of prostate cancer (PCa). Understanding the molecular mechanisms of AR-mediated transcription is a key for the development of novel therapeutic strategies for both castration-sensitive prostate cancer (CSPC) and castration-resistant prostate cancer (CRPC). It is well-known that AR transcriptional activity is prominently dictated by the transcription activator FOXA1, which acts as a ‘pioneer’ factor opening the condensed chromatin and facilitating the recruitment of AR. Genome sequencing studies have revealed that FOXA1 is one of the most frequently mutated genes in primary PCa and even more common in metastatic CRPC. Aberrant FOXA1 function is implicated in PCa development and progression likely through its impact on AR signaling. Therefore, inhibition of AR through targeting FOXA1 is a promising therapeutic approach for CRPC. However, to date FOXA1 has been deemed undruggable. We recently reported that critical to the function of FOXA1 is its modulation by poly-(ADP-ribose) polymerase 2 (PARP-2), conventionally known as a DNA repair protein. Our studies have demonstrated that PARP-2 is a critical component in AR signaling through interacting with FOXA1 and facilitating AR recruitment to prostate-specific enhancers. Expression of PARP-2 is significantly elevated in primary PCa tumors compared to benign prostate tissues, and even higher in CRPC tumors. Selective targeting of PARP-2 by genetic or pharmacological means blocks PARP-2/FOXA1 interaction, which in turn attenuates AR-mediated gene expression and PCa growth. These results lead us to the hypothesis that PARP- 2 plays a central role in AR-mediated transcription through interacting with FOXA1. Therefore, PARP-2 Inhibition attenuates AR signaling through disrupting FOXA1 function, which provides an alternative therapeutic strategy for AR inhibition without involving AR ligand binding. The overall objective of this project is to determine the molecular mechanisms by which selective targeting of PARP-2 inhibits CRPC growth through disruption of FOXA1 function and define PARP-2 as an alternative therapeutic target for CRPC. To attain the overall objective, we propose two specific aims: Aim 1: Determine the molecular mechanisms by which targeting the PARP-2/FOXA1 interaction inhibits AR signaling. Aim 2: Determine to what extent selective targeting of PARP-2 inhibits CRPC tumor growth in preclinical models. The successful implementation of this project will greatly advance our understanding of multifaceted biology of PARP proteins and their evolving impact on cancer therapeutics. More specifically, the results from the proposed research are expected to provide a strong basis for future development and clinical application of selective PARP-2 inhibitors benefiting patients with incurable metastatic CRPC.

NIH Research Projects · FY 2024 · 2021-07

ABSTRACT With the ability to silence individual genes and to drug the ‘undruggable’, RNA interference (RNAi) therapy has recently shown clinical success by delivering small interfering RNA (siRNA) to the liver for genetic diseases. However, new delivery strategies will be needed to expand the targeting possibilities of siRNA therapy beyond the liver for treatment of other diseases like atherosclerotic cardiovascular disease. We have therefore formed a team with complementary expertise in siRNA delivery and atherosclerosis, and developed a targeted siRNA delivery strategy to silence calcium/calmodulin-dependent kinase-IIγ (CaMKIIγ), a kinase that is activated in the macrophages of human and mouse advanced atherosclerotic lesions and promotes progression of clinically dangerous plaques. We showed that targeted siCamk2g treatment improved plaque stability by reducing necrotic core area and increasing fibrous cap thickness. Nevertheless, due to the transient nature of siRNA-mediated gene silencing, a critical challenge for siRNA therapy is the short duration of action. In this project, we propose to i) explore a novel siRNA delivery strategy that can dramatically extend the duration of CaMKIIγ silencing in atherosclerotic lesional macrophages; and ii) engineer the new siCamk2g platform for dual-cell targeting for integrated treatment of obesity-induced type 2 diabetes and atherosclerosis. Our new preliminary work has identified a distinct type of synthetic lipid-poly(ethylene glycol) (lipid-PEG) biomaterials that can markedly prolong siRNA silencing and its blood circulation. We thus hypothesize that the new lipid-PEG-mediated long-acting siCamk2g therapy could effectively target both atherosclerosis and insulin resistance with low dosing frequency. In Aim 1, we will synthesize a series of such distinct lipid-PEG biomaterials; systematically explore the lipid-PEG effects on the duration of action and pharmacokinetics of siRNA; and optimize the unique siRNA delivery platform in a mouse model with established atherosclerosis. The lead candidate with longest duration of macrophage CaMKIIγ silencing will be evaluated for efficacy in dampening atherosclerosis, with an emphasis on plaque necrosis, fibrous cap thickness, and efferocytosis and other inflammation resolution endpoints. In Aim 2, we will expand the long-acting siRNA therapy to dual-cell targeting for cardiometabolic disease, based upon the fact that CaMKIIγ is a common upstream target in both hepatocytes in obesity-induced insulin resistance and lesional macrophages in atherosclerosis. We will iteratively optimize the dual-targeting siCamk2g system in vitro and in vivo, including in a new mouse model with combined insulin resistance and atherosclerosis, in a manner to effectively improve type 2 diabetes and suppress atherosclerosis. We expect that successful completion of this project will lead to fundamental understanding of how the new lipid-PEG chemistry controls siRNA delivery and the development of a novel class of long-acting RNAi therapy for atherosclerosis and cardiometabolic disease.

NIH Research Projects · FY 2025 · 2021-07

Project Summary The broad goal of this project is to determine whether restricting meal timing to the biological day shows beneficial effects on metabolic markers of health, which holds great translational value for vulnerable populations such as night shift workers. Shift work increases the risk for diabetes, which cannot be fully explained by differences in life style and socioeconomic status. We have demonstrated that misalignment between the central circadian clock and the behavioral sleep/wake and fasting/feeding cycle, typical in night shift workers, leads to adverse metabolic changes, which may help explain the increased diabetes risk in night workers. Animal data show similar adverse metabolic effects of circadian misalignment and further show that normalizing the circadian food timing prevents these adverse effects. In humans, our preliminary data from a stringently-controlled circadian experiment suggest that restricting meal timing to the biological day can mitigate the glucoregulatory consequences of circadian misalignment. However, while our unpublished preliminary data show a proof-of- principle for restricting food intake to the biological day, this has limited translational value, because meal times were required to be given during the sleep episodes, which is clearly not advisable to chronic shift workers. Therefore, a key gap that will be addressed in the current application is testing whether restriction of meal timing to the biological day - without disrupting sleep - can mitigate the adverse metabolic effects of circadian misalignment, as compared to when the same individuals have their meals scheduled during their night work shift (Specific Aim 1). To achieve this goal, we will simulate realistic night shifts in laboratory with meals scheduled during the biological night (control protocol) or with meals restricted to the biological day (intervention protocol) using a highly-controlled, within-subject, randomized, crossover design. In addition, common genetic variants in the melatonin receptor gene, MTNR1B, confers diabetes risk, playing a key role in the circadian organization of melatonin and glucoregulation. Thus, we will also examine whether the common MTNR1B genetic variants modulate the effects of meal timing on glucoregulation (Specific Aim 2). Last, intestinal microbiota plays a key role in metabolic health, and its disruption has been observed under circadian misalignment. Therefore, we plan to test whether restricting meal timing to the biological day can mitigate its disruption (Specific Aim 3), which may alleviate the deleterious metabolic consequences of circadian misalignment. This study will help uncover potential mechanisms underlying the adverse metabolic effects of circadian misalignment and will aid in the development of novel interventions based on meal timing for night shift work and other circadian rhythm disturbances.

NIH Research Projects · FY 2024 · 2021-07

PROJECT SUMMARY Thalidomide and its analogs, lenalidomide and pomalidomide, have revolutionized the treatment of patients with multiple myeloma (MM) and other hematologic malignancies. However, therapeutic resistance still limits their efficacy and represents a critical unmet medical need. These drugs work through a unique mechanism leading to the targeted degradation of oncoproteins. Because only the protein levels of the drug targets are affected, they have been difficult to study using conventional technologies. We developed a novel targeted mass spectrometry assay to measure these proteins and now propose in Aim 1 to use this assay to study the relationship between the level of thalidomide analog targets and the development of lenalidomide resistance in patients. In an orthogonal study to identify mediators of thalidomide analog resistance downstream of substrate degradation I have performed multiple genetic screens in a MM cell line and have identified the retinoic acid receptor alpha and the nuclear corepressor as potential mediators of lenalidomide resistance. In Aim 2 I propose to further characterize these genes and their roll in mediating the response to thalidomide analogs in MM cells. Collectively, this work will further outline two major pathways of resistance to a clinically important class of drugs and shed new light on methods to overcome resistance. The applicant, Dr. Adam Sperling, is an oncologist at the Dana-Farber Cancer Institute (DFCI). He spends 80% of his time in translational research and 20% in clinical practice caring for patients with cancer. He has outlined a five-year career development plan to meet his goal of becoming an independent investigator in translational research. Dr. Sperling has assembled an Advisory Committee of internationally recognized experts to provide scientific and career mentorship. He has established collaborations with experts in cancer epigenetics, mass spectrometry, and applied biostatistics to provide experimental advice and specific training in the field. Dr. Sperling will conduct this research at the DFCI and leverage the exceptional research and teaching environment at the DFCI, Harvard, and the Broad Institute. The Dana-Farber Cancer Institute, which harbors an outstanding research community and has a long track record for successful mentorship of independent physician scientists, is an ideal environment for completion of these experiments and the realization of Dr. Sperling’s long-term career goal of being an independent physician- scientist.

NIH Research Projects · FY 2025 · 2021-07

Project Summary/Abstract This proposal presents a five year research career development program focused on the study of the role of the IL-23 receptor (IL-23R) on CD4+ T cells in cutaneous lupus erythematosus (CLE). The candidate is currently an Instructor in Dermatology at Harvard Medical School in the Department of Dermatology at the Brigham and Women's Hospital. The outlined proposal builds upon the candidate's previous research and clinical experience in molecular and cellular immunology and cutaneous biology by leveraging the use of emerging genomic technologies within Dr. Vijay Kuchroo's, his primary mentor's, laboratory. The proposed experiments and didactic work will position the candidate with a unique set of cross disciplinary skills that will enable him to transition to independence as a physician scientist in autoimmune cutaneous biology. Cutaneous involvement is a major feature of systemic lupus erythematosus (SLE), a systemic autoimmune disease affecting multiple organs, but can also occur in the absence of systemic disease. Cutaneous lupus erythematosus (CLE) significantly impacts patients' quality of life, socioeconomic status, and can result in permanent scarring and dyspigmentation. Therefore, more effective therapies are critically required. However, our current understanding of CLE pathogenesis is limited, making the development of targeted therapies difficult. As a consequence, patient care can be negatively impacted as optimal treatment regimens cannot always be achieved. Therapies can improve the skin, systemic disease, both, or neither. Therefore, it is of critical importance that a better understanding of the basic immunologic underpinnings of CLE pathogenesis be achieved to meet this clinical need. This proposal aims to investigate the role of IL-23R expression on CD4+ T cells in the development of CLE. The proposed project will directly address this vital question while overcoming current limitations in the field. Aim 1 will examine the mechanisms by which the IL-23R confers pathogenicity to CD4+ T cells. Aim 2 tests whether the IL-23R confers pathogenicity to CD4+ T cells, which can then drive spontaneous skin inflammation in a mouse model of lupus erythematosus. Aim 3 leverages cutting edge genomic technologies and analysis to identify novel, transcriptionally distinct, pathogenic CD4+ T lymphocytes in the CLE lesional skin. Taken together, this project combines traditional molecular and cellular approaches with emerging genomic technologies and analysis to address a critically unmet need in cutaneous autoimmune disease.

NIH Research Projects · FY 2024 · 2021-07

Project Summary/Abstract There is growing societal and scientific interest in using genomic sequencing (GS) as screening to identify genetic predispositions for disease early in life to prevent or mitigate future illness. There is, however, skepticism about the clinical utility of GS in infants and concerns that it could lead to psychosocial harm, unjustified health expenditures, and unnecessary healthcare utilization, with associated iatrogenic morbidity. Over the past five years, within the NIH-funded NSIGHT Consortium, our team launched the “BabySeq Project,” the first randomized controlled trial (RCT) of GS in newborns. We implemented a clinical workflow for whole exome sequencing, created criteria for returnable gene/variant selection and interpretation, curated a list of 1,514 disease-associated genes with favorable validity, age of onset and penetrance; and designed novel reporting formats. We enrolled and randomized 325 families to a family history (FH) arm or a FH+GS arm, completed sequencing in the FH+GS arm, disclosed results to families and placed reports in the infants’ medical record. Our results were striking. Medically, we identified and disclosed unanticipated monogenic disease risks in 11% of infants randomized to GS, and through follow-up testing revealed previously undiscovered signs of underlying disease and unexplored family history in over half of these. We found no increased distress or disruption to the parent-child relationship in response to receiving GS results and no significant increases in downstream healthcare costs. Healthcare providers (HCPs) were able to constructively manage the information reported. The BabySeq Project created a template for studying the psychological impact, medical utility, and cost effectiveness of GS in healthy newborns. However, our BabySeq population was not diverse and thus our findings not generalizable. In order to disseminate this technology equitably, it will be crucial to understand its impact on ethnically and racially diverse populations. The goal of this study is to build on what we learned in BabySeq to study GS as screening in a population of underserved, primarily African American and Hispanic, infants. We will return pathogenic GS and copy number variation results and study the impact on families and HCPs, as well as the medical and economic impact. Through this research we will develop, implement, and evaluate a sustainable approach to GS as screening that leverages underserved community engagement to minimize distrust and maximize benefit. This novel study provides a unique opportunity to determine medical, behavioral and economic outcomes in an under-represented population of infants at three diverse CTSA sites, modeling the vision of GS as a part of healthcare implemented early in childhood. This project is significant because it proposes to generate much-needed evidence of the value of GS infants, innovative in its design as the first RCT to explore the impact of WGS in a diverse population of healthy infants, and feasible because this team of experts has experience in enrolling participants and the infrastructure to rigorously collect and analyze outcomes.

NIH Research Projects · FY 2024 · 2021-06

Discovery of Drugs that Modulate Neuroinflammation for the Treatment of Alzheimer's Disease Project Summary/Abstract (30 lines) Alzheimer’s disease (AD) is the primary cause of dementia in the elderly. At present, approximately 36 million people worldwide suffer with AD, and that number is expected to increase to about 120 million by 2040. Despite decades of intense research, currently there are only four FDA-approved drugs to treat AD symptoms. These drugs, however, do not prevent, stop or slow the progression of the disease. Inflammation is considered a crucial link between Aβ plaques, NFTs and AD. Therefore, the modulation of pro- inflammatory cytokines may be a viable approach to treat AD. In a screen to identify small molecule modulators of inflammation, we identified a promising lead that has modest affinity for both the GABAA and TSPO receptors. The preliminary SAR and data suggest that the anti-inflammatory effect derives from a combination of both GABAA and TSPO activities. Continued optimization of both the pharmacodynamic and pharmacokinetic properties of the lead will result in a significantly improved molecule that has the potential to treat both (i) cognitive deficits and (ii) anxiety and aggression in AD. The specific aims to achieve this goal are: Aim 1. In vivo proof of concept studies of etifoxine in two mouse models of AD. Etifoxine has demonstrated beneficial effects in several neurodegenerative disease models; however, it was not tested in mouse models of AD or in human AD patients. Therefore, we will evaluate the efficacy of etifoxine in (i) the rTG4510 (Tau pathology) and (ii) the APP/PS1 (amyloid plaque) mouse models of AD. Aim 2. Medicinal chemistry optimization and characterization of novel analogs of etifoxine. Single enantiomer analogs of etifoxine will be designed, synthesized and characterized in biological assays. The most promising compounds will be evaluated in drug-like property and PK studies. Compounds with appropriate PK and brain exposure will advance into in vivo studies to measure target engagement (e.g., stimulation of pregnenolone in mouse brain). Lead compounds also will be tested for sedative effects, and those that have sedative potential will be deprioritized. Aim 3. In vivo efficacy of the lead molecule in the rTG4510 mouse model of AD. We will evaluate the effects of three different doses of the lead compound in the rTG4510 mouse model (as described in Aim 1), Treatment will begin at 2 months (onset pathology), and end at 5 months (start of cognitive decline). The goal is to demonstrate efficacy on multiple measures including inflammation, synaptic integrity, neurodegeneration, tau pathogenesis, memory and learning. Aim 4. Pre-IND enabling studies; scale-up synthesis, multi-species PK, and rodent toxicity. The goal is to determine if the lead compound has any liabilities that would preclude its further development. The lead will be tested in a battery of industry standard in vitro DMPK and in vitro toxicity studies (e.g., CYP inhibition, metabolite identification, and safety panels). Finally, a 10-day, toxicity study will be performed to de-risk the lead compound. 1

NIH Research Projects · FY 2026 · 2021-06

The overall goal of this P01 is to determine how cells differentiate into states unique to human patients and animal models with autoimmune diseases, how these cells interact with other cells in their environment and how they contribute to disease pathogenesis. Project 1 will focus on the regulation and function of regulatory T cells (Tregs) through the identification of factors and cellular interactions that induce or block Treg acquisition of a dysfunctional AREG+ state in the RA synovium. A key question will be the cross-talk between Tregs and fibroblasts and myeloid cells. Project 2 will determine how fibroblasts differentiate into inflammatory vs invasive states, focusing on the role of the transcription factor, ARID5B, in epigenetic regulation of state transition in RA, and its impact on disease pathology. This project will collaborate with other groups to study the interactions of Treg with fibroblasts via glucocorticoids and AREG and of myeloid cell states with fibroblasts via cytokines. Project 3 will address how plasma cells, which are critical in SLE and RA, adopt diverse states with the potential to interact with other cell types in the tissues via key inflammatory/anti-inflammatory cytokines that impact tissue inflammation, damage and repair. Project 4 will study injury-associated myeloid cells found in patients with LN or RA as well as models of lupus nephritis, and determine their tissue localization, their interactions with fibroblasts, plasma cells and Treg and their roles in autoimmune disease. The computational systems immunology core will carry out analysis of single-cell RNA-sequencing, spatial imaging, lymphocyte repertoire analysis, and genetic variant function. It will also build key data resources that enable cross comparison of RA and SLE tissue cell states. Each project will utilize high-dimensional single-cell genomics in cells or tissues and will be enhanced by computational expertise of the core using integrated and consistent pipelines. It will serve as a cross-disease atlas repository making available all of the cell and molecular data types from RA and SLE collected or analyzed in each project thereby facilitating cell-cell interactions and cross-disease similarities and differences. Our capacity to study the interactions among Tregs, fibroblasts, plasma cells and myeloid cells, which are central to the immunopathology of these diseases, depends upon synergistic interactions enabled by the program project mechanism. If successful, this P01 will enable an integrated multicellular view of Treg dysfunction and recovery, fibroblast-mediated tissue inflammation and damage, plasma cell-regulated inflammation, damage and repair, and the impact of injury-induced myeloid states on tissue homeostasis. The identification of cell states, pathways and cell-cell interactions should provide valuable targets for future therapies for lupus nephritis and rheumatoid arthritis.

NIH Research Projects · FY 2025 · 2021-06

PROJECT SUMMARY Further characterization of longitudinal lung function (LLF) throughout adulthood in asthmatics is critically important, as low lung function correlates with increased exacerbations, morbidity, and mortality. Precise genomic and metabolomic profiling of the biological mechanisms underlying LLF trajectories will be instrumental in understanding and ameliorating lung function deterioration. MicroRNAs (miRs; short non-coding RNAs) exhibit broad impact on inflammatory cascades, leading to airway remodeling and chronic airway obstruction, and specific metabolites provide a measure of real-time inflammatory changes that reflect both genetic and environmental influences. Therefore, the combined use of miRs and metabolites has great potential to provide critical insight into disease physiology and identify mechanisms to regulate, diagnose, and prognosticate LLF. The objective of this proposal is to identify miRNA and metabolomic determinants of LLF patterns, classified using longitudinal spirometry measures from electronic medical records (EMRs), that accurately identify individuals with asthma at the greatest risk of progression to more serious chronic lung obstruction. Our central hypothesis is that LLF trajectories are regulated by specific sets of genes, miRNAs, and metabolites that can 1) inform on underlying biological dysregulation and 2) serve as biomarkers to distinguish clinically actionable patterns of LLF, enabling personalized medicine approaches through the identification of multiomic therapeutic targets. We will explore this hypothesis by generating the novel and unique Biobank of Asthmatics with Longitudinal Lung Function (BALLF) cohort; which includes rigorous LLF phenotyping generated from electronic medical records (Aim 1a) and global metabolomics profiling and miRNA sequencing (Aim 1b) supplementing existing genetic and phenotypic data. We will identify metabolites (Aim2a) and miRNAs (Aim2b) associated with these LLF; capitalizing on our rich preliminary data implicating sphingolipid and eicosanoid biosynthesis to guide our analyses. Finally, we will leverage our extensive systems biology expertise to integrate this multiomic data to improve our biological understanding of LLF (Aim3a) and to develop clinically translatable biomarkers (Aim 3b). Crucially, we have the ability to both validate these findings and to assess their generalizability in two existing independent cohorts of asthmatics. This will represent the first integrative omic study of LLF trajectories in asthma focusing on the unique combination of miRs, metabolites, and genes; as such the findings of this innovative proposal have tremendous potential to elucidate the biological mechanisms of lung function decline and to influence the management of asthmatics at risk of this devastating complication.