Icahn School Of Medicine At Mount Sinai

NIH Research Projects · FY 2025 · 2023-08

Project summary: In the human body, the small molecule chemical space originates from 1) the exposome( natural or synthetic exogenous compounds) and the metabolome (functional readout of metabolic pathways of host and commensal microbiota genomes). Studying this chemical space has provided new insights into the initiation and progression of cancer, neurological, cardiovascular and respiratory diseases and biomarkers for exposures to industrial chemicals, nutrients, drugs and bioactive internal molecules. Targeted biomonitoring and untargeted chemical analysis assays generate core datasets for exposomics projects to study the chemical space and its impact on human health. Inter-chemical correlations are ubiquitously observed in these core datasets. However, interpretation of these correlations has been limited to metabolic pathway and reaction contexts which do not cover the origin, source, transformation and interaction among exposome chemicals. We propose to develop the Exposome Correlation and Interpretation Database (ECID), a new biomedical knowledgebase that will systematically catalogue and curate inter-chemical correlations and their interpretation for the core datasets in exposomics. ECID will have three main informatics resources 1) Chemical Correlation Database (CCDB), a curated, trustworthy, and FAIR compliance database of inter- chemical correlations from biomonitoring and untargeted chemical analysis assays (aim1). In the prototype version, 56 datasets have been included and by end of the project, over 250 datasets (human-only) will be covered by the CCDB. We will curate the inter-chemical correlations that are observed across multiple studies. 2) Exposome Data Interpretation Resource (EDIR), an integrated database of structural and functional relationships among chemicals (aim 2). Aim 2 will utilize text mining, cheminformatics, database fusion, ontologies and chemical network mapping methods to create an atlas of functional and structural relationships among exposome chemicals. EDIR will be used for annotating curated inter-chemical correlations with plausible interpretations. and 3) Exposome WorkSpace, an online space to explore the CCDB and EDIR information and to interpret user-provided datasets (aim 3). We will re-engineer the established data exploration and analytics methods to provide an integrated, focused and relevant framework for exploring inter- chemical correlations in core exposomics datasets. ECID portal will provide self-guided tutorials and online data exploration tools for the exposomics and metabolomics researchers. ECID will leverage and complement the HHEAR program's data center, targeted and untargeted laboratory components at the Mount Sinai Exposomics Hub. We will utilize HHEAR studies (post-embargo) as validation studies to showcase the application of ECID in exposome research. ECID will make significant contributions towards expanding our understanding about small molecules chemical space within the human body by revealing exposure chemical's health effects, new metabolic and xenobiotic transformation pathways, and exposure groups.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY In this proposal we want to understand the metabolic factors that are essential to tissue-resident macrophage (TRM) development and function. New advances in metabolomics technology have helped to decode how cellular metabolism helps to shape immune cell form and function, but these developments have so far generally stopped short of meaningfully probing the metabolism of immune cells within the tissues themselves. For cells like TRMs, that exclusively reside within the tissues, a full understanding the biology of these cells is missing until we can identify how they utilize cellular metabolism to support their tissue-specific identity and function. Given the important roles TRMs play in maintaining tissue homeostasis and shaping pathogenic environments, it is essential we begin to probe the biochemistry of these cells. We present an approach for exploring TRM metabolism in vivo. Through the use of metabolic tracers in vivo and rapid isolation of TRMs from the tissue, we detail how this approach will be used to identify metabolic programs essential to TRM development and function within the tissues. We show how proof of principle testing of this framework reveals the polyamine-hypusine axis as a novel metabolic node active in differentiating monocytes and TRMs. We implement in vitro and in vivo validation studies laid out in our framework, which include bone marrow chimera, parabiosis and novel mouse model creation, to show that this pathway is essential for the development and maintenance of TRMs across a multitude of organs. We also propose a highly novel approach to studying TRM metabolism in humans. Using normathemic perfusion machines, we will perfuse human organs with metabolic tracers to gain an understanding of human TRM biology in situ. Crucially, we will employ this approach to experimentally test the pathways identified as important in mouse TRMs in a human setting. Finally, a major focus of this proposal is to explore TRM metabolism within tumors. Using similar approaches outlined above for TRMs during homeostasis, we will evaluate the metabolic activity of TAMs using well defined murine tumor models. We will use our innovative human system that allows us to experimentally manipulate human organs to probe the metabolism of human hepatocellular carcinoma lesions and of the TRMs that reside inside them. Through these orthogonal approaches across species, we expect to build up a detailed picture of tumor macrophage metabolic activity that can be used to identify novel pathways that can be targeted to modulate these cells within tumors for therapeutic benefit.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY Sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (RYGB) are the most effective weight (wt) loss procedures for severe obesity. Our lab recently showed decreased brain reward activation to high energy dense (HED) vs low energy dense (LED) food cues following both SG and RYGB. The reward activation changes, however, have not been correlated with changes in actual intake of HED or LED foods. There is also recent concerning evidence of increased alcohol intake and new onset alcohol use disorder (AUD) by 2 y postsurgery. Although there are overlapping neural reward pathways underlying food intake and alcohol use, the mechanisms behind increased alcohol intake postsurgery remain unknown. There is, however, evidence of more rapid alcohol absorption in both SG and RYGB, which could be a factor in increased alcohol intake. Alcohol absorption, however, has not been studied over time postsurgery to link it to increased alcohol intake or AUD. To investigate the neurobiological mechanisms, we will conduct a study of three groups of 70 each: SG, RYGB, and a nontreatment (NT) group, matched for baseline BMI, sex, age, and alcohol intake, at presurgery, 1 y (when body weight tends to stabilize), and 2 y postsurgery (when alcohol intake increases). Although weight loss is similar for SG and RYGB, the surgeries differ anatomically, yet lead to similar increased drinking, making them both worthwhile to study. Primary Aim 1: a) Determine neural responses to visual cues of alcohol (ALC) and non-alcohol (NA) drinks as well as HED and LED foods. From pre to post surgery, cue reactivity in 9 common reward ROIs to alcohol and food is expected to increase in response to cues of ALC vs NA and decrease to HED vs LED. The changes are expected to manifest at 1 y and strengthen at 2 y postsurgery. b) Relate changes in neural responses to ALC vs NA cues with changes in alcohol intake, # AUD symptoms, and AUD status at 1 and 2 y. c) Test whether baseline reward activation to ALC vs NA cues predicts increased postsurgical alcohol intake at 1 and 2 y. d) Compare for the above, the effects of (SG + RYGB) vs NT (primary) and RYGB vs SG (secondary), expecting greater effects for RYGB than SG. Primary Aim 2: a) Determine pharmacokinetics (PK) after 1 alcohol drink equivalent from blood alcohol concentrations (BAC) at pre-drink, 2, 5, 15, 25, 35, 50, 65, 80 min post-drink. We expect that the surgical groups will exhibit higher and sooner BAC peaks than NT, and that RYGB will result in higher and earlier peak BAC than SG. b) Correlate changes in brain activation to ALC vs. NA cues in the common reward areas with changes in BAC peak and time to peakpredict alcohol intake and AUD based on changes in BAC peak and time to peak. The study results should enhance knowledge of neural mechanisms underlying the postsurgical changes in alcohol and food intake, in association with changes in alcohol PK. This knowledge could lead to development of new surgery procedures which do not lead to increased alcohol intake.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY / ABSTRACT Hepatocellular carcinoma (HCC) incidence and mortality is increasing in the US and worldwide. Around ~50- 60% of HCC patients will receive systemic therapies. After a decade of primacy of sorafenib, the combination regime of immune checkpoint inhibitor (ICI) atezolizumab (anti-PDL1) with bevacizumab (anti-VEGFA) demonstrated superior clinical benefits (median survival of ~19 months) and has become the standard of care. However, the rate of objective response remains at ~30%. In parallel, our group demonstrated that 1) HCC etiology differentially impacts outcome with patients with HCC deriving from non-alcoholic steatohepatitis (NASH) benefitting significantly less from immunotherapy; 2) Dysfunctional CD8 cells are implicated in the underlying mechanism of resistance in NASH-HCC; 3) Newly generated gene signatures predict response to ICI; and 4) The immune excluded class is driven by Wnt signaling/CTNNB1 mutations in HCC and, thus discovered KIT/MAPK/Wnt inhibitors combined with ICI are adequate strategies to rescue this mechanism of immune- evasion. Our central hypothesis is that such decreased response to ICIs in patients with NASH-HCC can be reverted therapeutically using combinations of ICI and KIT/MAPK/Wnt signaling blockers; and candidate biomarkers of response can be identified and validated. Thus, the overarching goal of this proposal is to gain further insight into mechanisms of both NASH-HCC immune response and resistance via state-of-the-art single cell technologies, so as to identify biomarkers and overcome resistance through the rational testing of combinatorial immunotherapeutic strategies, which could eventually increase the number of HCC patients deriving clinical benefit from immunotherapy. To accomplish this goal, we seek to achieve the following specific aims: 1) To map the immune cell microenvironment in human NASH-HCC by using single cell-based approaches and high-resolution spatial transcriptomics; 2) To identify biomarkers predicting response and resistance to the combination of atezolizumab plus bevacizumab in human NASH-HCC by testing identified gene signatures and molecular markers of response (using transcriptomics and mutational profiling), as well as spatial transcriptomics; 3) To develop therapeutic strategies to overcome ICI resistance in NASH-HCC using specific patient-derived organoids with immune component and mouse models that recapitulate the human NASH-HCC microenvironment. These hypothesis-driven strategies include testing drugs blocking key pathways of immune evasion (Wnt) in combination with ICI. The pursuit of these aims will be coupled with our expertise in NASH- related hepatocarcinogenesis, genomics and transcriptomics, single-cell based technologies, immuno-oncology, generation of organoids reconstituted with TILs and mouse modeling. We expect that our proposal will bring precision immune-oncology closer to the clinics, will promote clinical trials including KIT/MAPK/WNT inhibitors with promise of significant benefit to the outcomes of HCC patients. Overall, our discoveries will create a paradigm shift in the field of NASH-HCC.

NIH Research Projects · FY 2025 · 2023-08

ABSTRACT. Intradialytic hypotension (IDH) and major adverse cardiovascular events (MACE) are common in patients on maintenance hemodialysis (HD) and contribute significantly to morbidity and mortality in this vulnerable patient population. Although strategies to decrease these adverse outcomes exist, the lack of accurate and actionable predictive risk models has led to overall low and non-targeted utilization of these strategies. Electrocardiography (ECG) is ubiquitous, cheap, simple to perform, and it provides an immediately accessible, non-invasive insight into cardiovascular reflexes and health. The raw waveform data can be leveraged by advanced deep learning for accurate determination of various cardiac features as well as prognostication of key outcomes. In our prior published work, we demonstrated the utility of deep learning to determine both right and left heart function and the utility of transfer learning to improve outcome prediction in patients on HD. In recent preliminary analysis, we also show utility of waveform data to predict in hospital IDH and association with 30-day mortality using retrospective data. However, prospective development and validation on IDH and MACE are critical to clinical deployment. Thus, extending our prior work, we propose the largest prospective study on utilizing ECGs for prediction of key outcomes in patients on HD. We will recruit 1000 diverse patients on HD from dialysis units in New York City (derivation) and 150 patients from North Carolina (validation) and obtain standard duration, 12-lead ECGs at baseline and 4 weeks after baseline. In addition, a subset of participants will undergo continuous waveform monitoring during 3 consecutive HD sessions in an exploratory sub-study. We will then use deep learning and transfer learning (using pre-trained models from our approximately 11 million archival ECG database) and use this to predict IDH at the same session and within 30 days (Aim 1) and a composite outcome of MACE at 1 year of follow up (Aim 2). The results of this proposal are of high clinical importance for the prediction of both short- and long-term cardiac outcomes. Positive results will prompt studies testing deployment of our predictive models into HD units for detection and prevention of IDH and MACE as well use of novel wearables for IDH and cardiac risk prediction.

NIH Research Projects · FY 2025 · 2023-08

PROJECT SUMMARY 40% of the population over the age of 60 experiences a rotator cuff tear. The high failure rates of rotator cuff tear after surgical repair or non-surgical treatment make it a major clinical challenge. The outcome failures accompany the formation of scar tissues at the tendon-to-bone insertion (tendon enthesis) with disorganized architecture and deteriorated function. Development of effective therapeutics has been hampered by limited knowledge of enthesis development biology and mechanobiology and an incomplete understanding of endogenous mechanisms governing enthesis pathogenesis and healing. To bridge this knowledge gap, the current proposal seeks to elucidate how tendon enthesis responds to its mechanical and biochemical environment during development and healing processes. It is known that a combination of mechanical force and distinct pathways, including hedgehog (Hh) signaling, drive enthesis formation, promote remodeling of mature enthesis, and affect enthesis healing. Recently, our studies have indicated that the primary cilium, a solitary antenna protruding from mammalian cell surface, potentially functions as a hub for mechanotransduction and Hh signaling. Building on our previous work, the objective of this proposal is to gain a mechanistic understanding of the role of primary cilia in concentrating and synchronizing mechanical and Hh signals during enthesis development and healing. To achieve this objective, we will determine identities and activities of ciliated enthesis cells during enthesis development and mechanical adaptation (Specific Aim 1) and evaluate the regenerative capacity of ciliated enthesis cells for improving enthesis healing (Specific Aim 2). The approaches we will use include cilia-labeled and cilia-deleted transgenic mouse models, different established loading models, cell transplantation, and transcriptomics analysis, combined with structural, compositional, and biomechanical evaluation assays. At the conclusion of this project, we expect to identify new cilia-regulated mechano- transduction pathways during in vivo enthesis mechanical adaptation and suggest novel mechanisms by which cilia convert mechanical cues to cellular signaling events. The new findings of the role of primary cilia in enthesis healing will guide the development of novel pharmacological and mechanobiology therapeutics for treating rotator cuff tears.

NIH Research Projects · FY 2025 · 2023-08

SUMMARY Cancer is a leading cause of morbidity and mortality among aging people with HIV (PWH) and prostate cancer is now one of the most common cancers among PWH. Despite this, prostate cancer remains the least studied tumor in terms of its natural history and clinical outcomes in the context of HIV. Our findings suggest that HIV infection is associated with rapid carcinogenesis, increased adverse treatment events, and elevated mortality risk. However, there are very limited data on the impact of HIV on treatment selection (versus active surveillance) on key short- and long-term outcomes, including cancer control, quality of life, and mortality particularly for PWH with clinically localized prostate cancer (the most commonly diagnosed stage). These include tradeoffs in toxicity profiles and oncologic control among therapeutic modalities, as well as competing risks of death from non-cancer causes. Quantifying the downstream harms and benefits of different management strategies for localized prostate cancers is critical to aid decision-making, maximize treatment benefits, and reduce harms. Despite compelling need, treatment of localized prostate cancer has never been investigated in the context of HIV in clinical trials, and extrapolating results from clinical trials in HIV uninfected persons is inappropriate due to differences in treatment complications and tolerability. Furthermore, unique HIV-related factors may substantially alter prostate cancer natural history, comorbidities, functional status, risk of second primary cancers, life expectancy, and quality of life. This project will determine the role of HIV on localized prostate cancer natural history and outcomes. We will synthesize a disease simulation that will be used to perform comparative assessment of common treatment pathways to guide treatment decision-making. Our Specific Aims are: (1) To evaluate the impact of immune dysfunction and specific ART regimens on a) active surveillance (AS) for low-risk disease, and definitive treatment for intermediate- and high-risk disease and b) outcomes and adverse treatment events for all stages of prostate cancer among PWH; (2) To create and validate a microsimulation model (HIv Prostate Treatment [HIPR-T]) of prostate cancer natural history and treatment outcomes for localized prostate cancer in PWH; and (3) To use the HIPR-T model to compare the benefits vs harms of optimized AS and definitive treatment for localized prostate cancer over the lifetime of PWH. To achieve these aims, we will use data from large, representative HIV/cancer cohorts (>3,000 PWH prostate cancer survivors) and a validated HIV natural history simulation framework. We will synthesize and validate a novel prostate cancer-HIV simulation model capturing AS, treatment initiation and definitive therapy outcomes. Then, we will use the enhanced model to assess the optimal management of PWH with localized prostate cancer that will maximize survival and quality of life. The findings from this study will transform the clinical decision-making process for early-stage prostate cancer, maximize benefits and reduce harms, reduce uncertainties and treatment disparities, and will inform treatment recommendations for managing prostate cancer among PWH.

NIH Research Projects · FY 2026 · 2023-08

PROJECT SUMMARY: Our laboratory has, for many years, studied the essential process of mRNA decay in the model Gram-positive bacterium, Bacillus subtilis. We have identified several ribonuclease (RNase) enzymes of B. subtilis and have elucidated the role they play in mRNA turnover. The viability of a B. subtilis strain lacking all of the known 3’-to-5’ exoribonucleases prompted us to pursue identification of additional RNase activities. Using classic protein biochemistry, we recently identified a novel RNase, named YloC. YloC is an endoribonuclease with a hexameric structure, an unusual characteristic that is shared with only one other RNase: the Nsp15 protein of the SARS-CoV family. Initial experiments suggest that, although YloC has ribonuclease activity in vitro, it may function as an adapter for RNA interactions in vivo. Although proteins with significant homology to YloC are widespread in bacterial species, there is no published information on the structure of any member of this protein family. The current proposal seeks to elucidate the structure and function of YloC, as follows: • Mutagenize highly conserved residues of YloC to determine the effect on several properties – including ribonuclease activity, RNA binding, and structure – and to clarify functional domains of the protein. • Identify high-affinity RNA ligands of YloC via SELEX procedures with random-sequence oligonucleotides and with genomic RNA sequences. • Characterize how the strong interaction of YloC with E. coli polynucleotide phosphorylase (PNPase) acts in small RNA (sRNA) regulation in E. coli and possibly in B. subtilis. • Determine the three-dimensional structure of the highly homologous E. coli YicC protein bound to an RNA substrate, as well as the structure of YloC and/or its homologs from thermophilic bacterial species. This work will build on an initial determination of the structure of YicC. RELEVANCE: Ribonucleases play essential roles in RNA turnover and processing. A thorough understanding of the proteins that bind to and act enzymatically on RNA molecules will enable design of antimicrobial agents that disrupt such proteins and thereby interfere with bacterial cell growth.

NIH Research Projects · FY 2026 · 2023-08

ABSTRACT T cell activation initiates a program of differentiation that generates a continuum of different memory T cell states with diverse functional and molecular profiles. Activated T cells upregulate the inhibitory receptor programmed cell death protein 1 (PD-1) to prevent excessive T cell inflammation, autoreactivity and tissue damage. Upon binding to its ligands, PD-1 interferes with the phosphorylation cascade that modulates the quality and quantity of T cell signaling. Cancers evade T cell recognition by engaging PD-1 and consequently PD-1 blocking antibodies restore anti-tumor T cell responses and improve the survival of patients with various malignancies. Unfortunately, the majority of cancer patients do not respond to PD-1 blockade and up to 30% develop inflammatory toxicities highlighting the critical role of PD-1 in the maintenance of immune tolerance. Research into basic PD-1 biology, together with the clinical picture of cancer patients treated with PD-1 blocking antibodies, converge to emphasize that PD-1 engages complex signaling networks to support T cell homeostasis, differentiation and immune responses. Therefore, elucidating the signaling cascades and molecular pathways triggered by PD-1 are paramount to fundamental T cells biology and will lay the foundation for advancing the development of PD-1 targeting therapies. Nevertheless, our knowledge as it pertains to the molecular programs that support PD-1 inhibition in functionally diverse human T cell populations is limited. Furthermore, PD-1 has two ligands with distinct tissues expression patterns and binding affinity, yet the functional consequences of these differences are unknown. Our preliminary data highlight that PD-1 engages unique signaling cascades in ligand specific-manner across the trajectory of naïve to memory differentiation, and that the molecular programs underlying functional, phenotypic and developmental T cell heterogeneity also guide pathways of resistance to PD-1 inhibition. Here we will leverage: (1) quantitative phosphoproteomics to reveal PD-1 ligand specific phosphorylation cascades triggered in functionally distinct T cell populations; (2) functional immuno-assays in combination with scRNA-seq and cellular barcoding to identify transcriptional regulators of PD-1 responsivity across the trajectory of naïve through memory and effector T cell generation; and (3) functional genomics to identify cellular and molecular mediators of resistance to PD-1 inhibition. Successful completion of this proposal will reveal how functional T cell diversity shapes and guides PD-1 triggered cellular and molecular pathways and their associated PD-1 ligand specific dependencies. Collectively, understanding the cellular and molecular etiologies associated with PD-1 responsivity and the mechanisms driving T cell resistance to PD-1 inhibition will further our understanding of the fundamental functions of this critical inhibitory receptor in immunological tolerance and advance novel therapeutic directions targeting PD-1 with implications in cancer, infection and autoimmunity.

NIH Research Projects · FY 2026 · 2023-07

Project Summary Human immunodeficiency virus type 1 (HIV-1) infection affects more than 38 million people worldwide and remains incurable due to the early establishment of reservoirs where the virus remains latent. HIV-1 enters the brain within the first two weeks of infection, and neurologic symptoms have been observed with accompanying central nervous system (CNS) biomarkers in acute HIV disease. The seven billion microglial cells in the CNS are the primary cell type infected by HIV in the adult human brain, and in the central nervous system represents a large potential reservoir site. Additionally, the brain is one of the organs with the highest burden of HIV-associated disease. HIV-associated neurocognitive disorder (HAND) affects 20-50% of people with HIV (PWH), with the milder forms of HAND predominating in the era of combined antiretroviral therapy (cART). Importantly, intact HIV proviruses persist in the brain despite viral suppression with cART. Despite this, little is known about the unique regulatory mechanisms governing HIV activation and latency in the brain. According to our recent cell studies in human postmortem brain, inflammation-associated reprogramming of microglial transcriptomes and 3D genomes (chromosomal conformations) is a key factor linked to viral infection and integration in brain cells during advanced stages of infection associated with encephalitis. However, non-encephalitic infected human brain, other than showing transcriptomic signatures indicative for disrupted interactions of microglia with the neuronal synapse, provides little information about the epigenomic and other determinants governing viral activation and latency in the brain. Here, as a first step towards understanding molecular mechanisms governing HIV latency in the humanized mouse brain, we will explore an extremely innovative molecular toolbox differentiating, on the single cell level, infected microglia and other myeloid cells actively expressing HIV, and separating them from infected cells not expressing HIV (latent). We will use this toolbox for advanced experimental approaches to quantitatively test molecular, epigenetic, and pharmacological interventions aimed at reducing the reservoir of humanized HIV+ brain, spleen, and blood. We will employ a novel genetic approach called enhanced HIV- induced lineage tracing (E-HILT) to reveal the frequency and kinetics of the establishment of latency in the CNS at the single cell resolution. We will define, in cell culture, and in humanized mouse brain and spleen/blood at single cell level resolution, the proportional representation of productively infected versus latently infected microglia and lymphocytes and other peripheral myeloid cells subject to genetically or pharmacologically induced disruption of chromatin-bound silencers, including the Human Silencing Hub (HUSH)/CTIP2- KAP1/KMT1E/SETDB1 repressive histone methyltransferase complex and more, broadly, histone H3-lysine 9 methylation (H3K9me)-associated repressive chromatin remodeling. The study will uncover the degree of latency in primary microglial cells in vivo, explore the transcriptome, epigenomic and chromatic 3D architecture that supports latency and explore the effects of chromatin modulating drugs on these cell states.

NIH Research Projects · FY 2026 · 2023-07

Depression is a devastating public health problem, yet the pathophysiological mechanisms underlying distinct aspects of the disorder remain largely unknown. Convergent evidence from animal and human studies have strongly implicated functional perturbations in the subgenual anterior cingulate cortex (sgACC) in depression. However, it is not known how dysfunction within specific sub-circuits of this heterogenous structure map to specific depression-related symptom domains. This gap in knowledge concerning the pathophysiology of depression is a major impediment to the advancement of diagnostic and therapeutic approaches to this disabling disorder. To address this gap, we propose a rigorous translational neuroscience study to define the distinct circuit-specific mechanisms of anhedonia and anxiety in humans with depression, building upon work in non- human primates, and converging human evidence from our laboratories. In marmosets, selective over-activation of Brodmann Area 25 (BA25) within the sgACC via glutamate re-uptake inhibition causally leads to deficits in anticipatory arousal – an established analogue of anhedonia in humans. Critically, these behavioral deficits are selectively reversed by peripheral administration of the glutamate NMDA receptor antagonist ketamine. Pilot work from our laboratory show a remarkable degree of inter-species convergence, pointing towards conservation of a glutamate-sensitive sub-circuit within the sgACC/BA25 that controls hedonic responses to environmental stimuli. We show that the sgACC/BA25 is specifically overactive in response to positive (but not negative) incentives in individuals with major depressive disorder (MDD) compared to unaffected health control (HC) individuals. We also show that the magnitude of activation specifically within BA25 (but not more rostral prelimbic area 32 [PL32]) is positively associated with degree of self-reported anhedonia, as predicted by primate work. Finally, we show that a single intravenous infusion of ketamine specifically reverses overactivation of the BA25 to positive stimuli; the degree of reduction in BA25 following ketamine correlated with improved in self-reported anhedonia (but not anxiety), as predicted by primate work. The overall goal of the proposed work is to define the distinct circuit-specific mechanisms of anhedonia and anxiety in humans with depression. To complete Aim 1, we will enroll N=60 medication-free adults with MDD and N=60 HC adults. All individuals will undergo clinical and behavioral assessment of anhedonia, anxiety, and other depression-relevant domains and both resting-state and task-based acquisitions with a validated reward task using ultra-high-field 7-Tesla (7T) MRI. To complete Aim 2, the N=60 medication-free adults with MDD from Aim 1 will be randomized to either a single IV infusion of 0.5 mg/kg racemic ketamine (KET) or placebo (PBO, saline) and undergo repeated clinical and behavioral assessments and 7T MRI at 24 hours post treatment. To complete Aim 3, all MDD participants from Aim 2 will undergo follow up clinical and behavioral assessments and 7T MRI at 7 days post-treatment. Participants will complete mobile digital health measures over the 7-day follow up time, and for a total of 4 weeks from dosing.

NIH Research Projects · FY 2025 · 2023-07

The goal of our Tisch Cancer Institute (TCI) Mentored Medical Student Summer Scholars (TCI-MMSSS) Program is to inspire medical students to pursue careers in cancer research through engagement in an innovative, highly structured program of strongly mentored research and interactive curricular activities. Our program builds upon the foundation of a successful 10 week pilot initiative of a summer mentored research experience for medical students in which 69% of participants (rising second year medical students) have either already completed or have committed to pursuing an additional year of research with their mentors. Our proposed 15 week rigorously mentored research experience is designed to recruit exceptional, and highly motivated students interested in cancer research and enriched by novel pedagogical approaches to foster an innovative and nurturing learning environment using a strategically crafted Cancer Research Fundamental 101 (CRF 101) curriculum to advance research knowledge, analytical mindset and career skills. Our program leverages the seasoned mentoring capacity and scientific strengths of the TCI scientific programs including Cancer Immunology (CI), Cancer Mechanisms (CM), Cancer Clinical Investigations (CCI), and Cancer Prevention and Control (CPC), as well as our acknowledged expertise in Community Outreach and Engagement. Our program is also informed by excellence in basic, translational, clinical and population research in community-recognized catchment-relevant cancers including Liver, Lung, Multiple Myeloma, HIV-related malignancies and Prostate Cancer as well as Breast, Gastrointestinal and Myeloproliferative Neoplasms. Our program Multi-PI Leadership team reflects complementary expertise in pre-doctoral education and medical student research to ensure the realization of potential for cancer research by each student participating in the TCI-MMSSS Program. We propose a holistic valuation process that incorporates validated tools to evaluate students, mentors, and the overall program to achieve continuous quality improvement and propose to follow program alumni over several years to obtain longitudinal outcomes to assess integration of cancer research into medical careers.

NIH Research Projects · FY 2025 · 2023-07

The coronavirus disease 2019 (COVID-19) pandemic caused by the betacoronavirus “severe acute respiratory syndrome coronavirus 2” (SARS-CoV-2) represents an unprecedented public health emergency. Most patients with COVID-19 clear the virus upon resolution of the acute infection but ongoing, persistent, SARS-CoV-2 replication has been documented in immunocompromised individuals. In these chronically infected patients, recovery of replication-competent virus over several weeks to months is linked to stepwise acquisition of mutations within and outside of spike. Our preliminary data show that such prolonged intra-host viral evolution plays a role in the emergence of new, antigenically distinct, SARS-CoV-2 variants. We propose to systematically elucidate the determinants of persistent SARS-CoV-2 infections using an integrated translational research approach combining real-world clinical metadata with bioinformatics, genomics and molecular virology. We will leverage an existing large surveillance dataset covering two and a half years of SARS-CoV-2 spread in New York City going back to the beginning of the pandemic in the spring of 2020 when the NY metropolitan area emerged as one of the early epicenters of the pandemic. Specific Aim 1 will dissect the clinical features and therapeutic interventions associated with persistent SARS-CoV-2 replication using existing longitudinal data from electronic medical records. These studies will be complemented by the analysis of the B and T cell populations of persistently infected patients. Specific Aim 2 will dissect the viral genotypes representative of intra-host evolution of prolonged periods with a special emphasis on co-circulating viral variants. Specific Aim 3 will examine the phenotypic properties of persistent SARS-CoV-2 variants with an emphasis on convergent evolution within and outside of the spike region (susceptibility to neutralization, fusogenicity, spike processing and interferon antagonism). Altogether, the proposed studies address a critical knowledge gap regarding the biological drivers and viral dynamics fueling the selection of SARS-CoV-2 viral variants during persistent SARS-CoV-2 infection. This knowledge will provide the scientific basis needed to treat and prevent such chronic infections thereby limiting the emergence and spread of increasingly neutralization-resistant yet transmissible SARS-CoV-2 variants.

NIH Research Projects · FY 2026 · 2023-07

PROJECT SUMMARY Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder with dozens of highly penetrant risk alleles and yet no effective pharmacological treatment. Mutations in the X-linked gene DDX3X are a high-risk factor for ASD. Affected individuals are predominantly females, so studying DDX3X might offer insights into sex differences in brain development and function. DDX3X encodes a DEAD-box RNA helicase critical for mRNA metabolism. DDX3X is broadly expressed, and its functions in the brain are just beginning to emerge: Ddx3x regulates cortical neurogenesis, hindbrain development, and synaptogenesis. However, we do not know the circuit-level determinants of DDX3X mutations. There is a critical need to fill these gaps because, until we do so, deciphering the complexity of ASD and developing effective therapeutics remain out of reach. To address this unmet need, a mouse with construct and face validity for DDX3X mutations was generated in our laboratory (Ddx3x+/- mice). The long-term goal is to understand the cellular and circuitry biology of ASD and identify new targets for therapeutic intervention. The overall objective is to capture the neural mechanisms of mutations in the ASD risk gene DDX3X with multimodal and holistic profiling. The central hypothesis is that Ddx3x regulates the molecular identity, connectivity, and activity of corticofugal circuits subserving complex behaviors. The rationale is that, once we identify reliable neural substrates, mechanism-based therapeutics can be developed and tested pre-clinically. The hypothesis will be tested by pursuing three Specific Aims: 1) Identify the cortical populations and the molecular signatures affected in Ddx3x+/- mice; 2) Map brain-wide neural ensembles with altered connectivity and/or activity in Ddx3x+/- mice; and, 3) Dissect and manipulate corticofugal circuits driving abnormal behavior in Ddx3x+/- mice. Under Aim 1, the major molecular and cellular ensembles affected by Ddx3x mutations will be identified using single-cell transcriptomics and 3D cellular mapping. Under Aim 2, activity-based neural substrates that are disrupted by Ddx3x mutations will be dissected using 3D mapping of immediate-early genes expression after behavior. Under Aim 3, circuits will be manipulated with chemogenetics approaches. The proposal is innovative because it uses cutting-edge methods to map the 3D landscape of defined neuronal populations and whole-brain activity through the entire brain of a novel ASD mouse model. It is also innovative because DDX3X is a high-confidence risk gene for ASD just recently discovered, and its role on shaping brain circuits is still completely unknown. The application is significant because it will advance our understanding of ASD complexity by reaching whole-brain, circuitry-level resolution, while propelling the development of a robust platform to probe convergences across models and developmental stages. These results are expected to have a positive impact because they will pave the way for novel therapeutic interventions for ASD.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder with dozens of highly penetrant risk alleles and yet no effective pharmacological treatment. Mutations in the X-linked gene DDX3X are a high-risk factor for ASD. Affected individuals are predominantly females, so studying DDX3X might offer insights into sex differences in brain development and function. DDX3X encodes a DEAD-box RNA helicase critical for mRNA metabolism. DDX3X is broadly expressed, and its functions in the brain are just beginning to emerge: Ddx3x regulates cortical neurogenesis, hindbrain development, and synaptogenesis. However, we do not know the circuit-level determinants of DDX3X mutations. There is a critical need to fill these gaps because, until we do so, deciphering the complexity of ASD and developing effective therapeutics remain out of reach. To address this unmet need, a mouse with construct and face validity for DDX3X mutations was generated in our laboratory (Ddx3x+/- mice). The long-term goal is to understand the cellular and circuitry biology of ASD and identify new targets for therapeutic intervention. The overall objective is to capture the neural mechanisms of mutations in the ASD risk gene DDX3X with multimodal and holistic profiling. The central hypothesis is that Ddx3x regulates the molecular identity, connectivity, and activity of corticofugal circuits subserving complex behaviors. The rationale is that, once we identify reliable neural substrates, mechanism-based therapeutics can be developed and tested pre-clinically. The hypothesis will be tested by pursuing three Specific Aims: 1) Identify the cortical populations and the molecular signatures affected in Ddx3x+/- mice; 2) Map brain-wide neural ensembles with altered connectivity and/or activity in Ddx3x+/- mice; and, 3) Dissect and manipulate corticofugal circuits driving abnormal behavior in Ddx3x+/- mice. Under Aim 1, the major molecular and cellular ensembles affected by Ddx3x mutations will be identified using single-cell transcriptomics and 3D cellular mapping. Under Aim 2, activity-based neural substrates that are disrupted by Ddx3x mutations will be dissected using 3D mapping of immediate-early genes expression after behavior. Under Aim 3, circuits will be manipulated with chemogenetics approaches. The proposal is innovative because it uses cutting-edge methods to map the 3D landscape of defined neuronal populations and whole-brain activity through the entire brain of a novel ASD mouse model. It is also innovative because DDX3X is a high-confidence risk gene for ASD just recently discovered, and its role on shaping brain circuits is still completely unknown. The application is significant because it will advance our understanding of ASD complexity by reaching whole-brain, circuitry-level resolution, while propelling the development of a robust platform to probe convergences across models and developmental stages. These results are expected to have a positive impact because they will pave the way for novel therapeutic interventions for ASD.

NIH Research Projects · FY 2025 · 2023-07

SUMMARY Alterations in cell metabolism support rapid growth and proliferation of cells in pathologies such as cancer, au- toimmune disease, and heart ischemia, resulting in increased reliance on the metabolism of amino acids such as glutamine and leucine. Nutrient Solute Carrier (SLC) transporters play a major role in reprogrammed meta- bolic networks by supplying cells with nutrients that are used to build biomass, serve as signaling molecules that enhance cell proliferation and differentiation, or regulate cell death. Our broad goal is to describe the sub- strate and inhibitor specificity determinants in disease-related nutrient SLC transporters and develop unique strategies to modulate their functions. We take an integrative approach that includes computational chemistry methods, coupled with biochemical and biophysical approaches and disease-related cell lines, to char- acterize two amino acid transporters that play a key role in metabolism of rapidly-growing cells: the Alanine- Serine-Cysteine Transporter (SLC1A5, ASCT2), a Na+-dependent amino acid exchanger that modulates intra- cellular glutamine levels, and the Amino Acid Transporter B0+ (ATB0+, SLC6A14), a neutral and cationic amino acid transporter, driven by Na+ and Cl- co-transport. In Aim 1 of this project, we will continue characterizing ASCT2, a well-validated drug target for various patholo- gies (eg triple negative breast cancer and prostate cancer). Despite recent advancements in our understanding of ASCT2 structure and function made by us and others, many aspects of its biology are highly unexplored. We will rationally design chemical tools that modulate the activity of ASCT2 using unique mechanisms, including: (A) allosteric inhibitors interacting with a recently identified allosteric site; (B) covalent inhibitors targeting a unique cysteine residue in the substrate binding site of ASCT2; and (C) conformation-specific small molecule modulators targeting specific subpockets in the substrate binding site. In Aim 2, we will characterize SLC6A14, an understudied transporter involved in cancer and metabolic diseases. We will develop structural models of SLC6A14 in different conformations. We will describe biophysical features of the models’ substrate binding site, including electrostatic potential, size, shape, and hydrophobicity, to develop hypotheses for the substrate and inhibitor specificity determinants in SLC6A14. We will use this knowledge to guide the development of inhibitors and substrates, including photoactivatable compounds, to directly test inhibitor-binding site interaction(s). Successful completion of this project will provide a greater understanding of mechanisms of transport and inhi- bition of nutrient transporters, as well as novel chemical tools to further characterize their role in disease. Notably, we will test an emerging and innovative approach to transporter drug discovery that targets allosteric modulation and covalent inhibition via small molecules, to deprive hyper-proliferating cells of nutrients, potentially expanding future applications to treat other diseases that involve SLCs.

NIH Research Projects · FY 2024 · 2023-07

Modified Project Summary/Abstract Section In this study, I seek to understand how common and rare genetic variation influences the risk of developing obsessive-compulsive disorder (OCD). OCD is a disabling psychiatric disorder with an unclear underlying pathophysiology, which has hindered the development of new treatments and interventions. While there is a clear genetic contribution to OCD risk, decades of investigations have yet to yield reproducible, statistically significant findings that identify high-confidence risk genes. In other neurodevelopmental psychiatric disorders (NDDs), including schizophrenia, attention-deficit/hyperactivity disorder, and autism, genome-wide association studies (GWAS) and whole exome sequencing (WES) in large numbers of subjects are now identifying risk genes and loci, paving the way for novel therapeutics. Increasing sample sizes in OCD and applying multi-omic approaches will lead to similar advances. Of note, in spite of advances in NDDs, studies to date have been primarily carried out in samples of European ancestry (EA), so we know comparatively less about the genetic architecture of these disorders in non-EA populations. To address these gaps, with the ultimate goal of studying the role of common and rare deleterious variation in OCD risk. I will work on emerging, large-scale WES studies in OCD, collaborate in ongoing common variant studies, and collect and analyze Latin American (LA) OCD samples. To achieve these goals, during the K99 phase, I will first be trained on, and make use of, relevant statistical genetic methods using suitably powered samples of autism, schizophrenia, and other psychiatric disorders, while building a LA OCD cohort. The R00 phase will focus on meta-analyses of OCD genetic data, including the LA cohort, using well-established pipelines. This will increase power to identify OCD risk genes and loci and will enable functional approaches using gene findings to study pathways, cell types, and developmental stages implicated in OCD risk. Furthermore, since studies of cross-disorder risk are an opportunity to enhance gene discovery by combining datasets, in the R00 phase shared risk between psychiatric disorders will be leveraged in exploratory analyses in the OCD gene and locus discovery efforts. Ultimately, these efforts will begin with OCD, using genome-wide techniques across populations, and expand into other NDDs.

NIH Research Projects · FY 2024 · 2023-07

Project Summary In adults, the skin constantly renews itself and the stem cells (SCs) of the basal layer (EpSCs) of the interfollicular epithelium and the hair follicle stem cells (HFSCs) residing in the hair follicle bulge are responsible for maintaining tissue integrity, structure, and reepithelization following an injury. However, over an organism’s lifetime these SC pools of the adult skin either lose their vigor or diminish in numbers which manifests into aging- related phenotypes that include epidermal atrophy, fragility, hair loss disorders and delayed wound healing. The fundamental mechanisms that drive SC aging in the adult skin remain largely unknown. To date research in invertebrate and cellular models of aging have shown that there is a change in global occupancy of many histone methylations, and modulation of methyltransferases and demethylases increase organism longevity. While most of these studies have paved the way for us to understand how epigenetic mechanisms influence the aging process, there is a need for addressing if these mechanisms also contribute towards aging of a mammalian tissue. My preliminary in vivo loss-of-function studies indicate that the conserved epigenetic regulators, Polycomb repressive complexes (PRCs), may be functioning differentially in the HFSCs and EpSCs to maintain their longevity in the adult skin. This is particularly intriguing in light of the fact that genome-wide studies have implicated that the modulation of chromatin accessibility in aged HFSCs establish a transcriptional landscape that promotes aging. The goal of this proposal is to add to these correlative observations and elucidate if epigenetic regulators and their corresponding histone modifications have a functional role in safeguarding SC longevity in the skin. To this end, the Specific Aims of this Proposal seek to combine functional in vivo genetic models with state-of-the-art multi-omics approaches to: 1) Characterize the age-dependent changes in transcriptional and chromatin landscape of the various SC pools of the adult skin; 2) Test the functional role of Polycomb-dependent mechanisms in maintaining the longevity and regenerative capacity of adult skin SCs; and 3) Establish a functional correlation that age-dependent changes in the SC chromatin state promotes aging- associated phenotypes. The results of this Proposal will significantly enhance our understanding of how age-dependent changes in epigenetic mechanisms establish a transcriptional landscape that promotes SC aging and will provide new scientific avenues for translational research application in the treatment for aging-associated conditions and disorders.

NIH Research Projects · FY 2024 · 2023-07

Project Summary Bladder cancer is the most expensive cancer per capita to treat in the US. Non-muscle invasive bladder cancer (NMIBC) which accounts for 70-75% of all newly diagnosed tumors only has a single FDA approved first-line treatment option, Bacillus Calmette-Guérin (BCG). BCG has been the only approved first-line therapy for intermediate and high-risk NMIBC for more than 40 years. While BCG can induce durable responses, ~50% of patients have recurrence or progression of their disease. No clear mechanism of action behind BCG’s anti- neoplastic activity in NMIBC has been delineated. Studies have demonstrated that PD-L1 showed significant increases following BCG administration, supporting the use of PD-1 or PD-L1 blockade in settings of BCG resistance. These finding have led to Pembrolizumab monotherapy, a PD-1 inhibitor, becoming the first FDA approved treatment for BCG refractory NMIBC in over 20 years. In KEYNOTE-057 (n = 101), 41% of BCG resistant patients had complete response at 3 months, but only a 19% durable response at 12 months. As we can see from KEYNOTE-057 inhibition of PD-1 has modest activity against BCG resistant tumors even though the tumor has upregulation of PD-1. The failure of PD-1 blockade to yield a more complete response in BCG- resistant patients suggests that our understanding of immune resistance mechanisms in NMIBC is incomplete. The HLA-E/NKG2A axis is a novel immune checkpoint that has shown significant preclinical promise as a target including in the setting of PD-1 resistance. This axis has been studied in several other tumor types. Significant data has also accumulated identifying the ability of tumor cells to modulate the tumor microenvironment leading to anti-tumor immunity. We have demonstrated that HLA-E BRIGHT tumors are highly activated and produce chemokines, CXCL9/10/11, leading to recruitment of NK and CD8 T cells (including regulatory T cells (Tregs)) within proximity of HLA-EBRIGHT tumor nests. This recruitment leads to immune dysregulation allowing for continued tumor growth. Together this data describes a dynamic process of tumor cell and immune cell interactions, which can be altered under certain pressures. Our central hypothesis is that BCG resistance occurs in the setting of HLAE-EBRIGHT tumor cell causing recruitment and dysregulation of immune cells allowing for HLA-EDIM cells to grow. We seek to capitalize on spatial transcriptomic sequencing (STseq) and immue mass cytometry (IMC), novel technologies with the potential to revolutionize our understanding of NMIBC at the tissue-architecture level.

NIH Research Projects · FY 2026 · 2023-07

PROJECT SUMMARY. Maintenance of an intact intestinal barrier is critical to prevent microbial activation of mucosal immunity. In inflammatory bowel disease, this barrier is compromised, thus exposing the mucosal immune system to the contents of the intestinal lumen. A substantial increase in the shedding or extrusion of epithelial cells into the lumen has been shown to be a predictor of relapse in Crohn’s disease (CD) patients. gd intraepithelial lymphocytes (IEL) migrate extensively within the epithelial compartment to serve as a first line of defense against invasive microorganisms and facilitate apoptotic cell shedding. Although gd IELs are protective in mouse models of colitis, the involvement of these sentinel lymphocytes in the pathogenesis of chronic ileitis is less clear. Published reports provide conflicting evidence regarding the contribution of gd IELs in the pathogenesis of chronic ileitis; however, we now show that inducible depletion of gd T cells prior to disease initiation increases lethality. Further, detailed immunoprofiling of the IEL compartment in mice that develop spontaneous CD-like ileitis indicates that the loss of gd IELs coincides with the histological onset of ileal inflammation, suggesting that loss of gd IELs may be an initiating event. In support of this, we observe a reduction in the frequency of CD39+ gd Tregs, while less activated, peripheral Vg1+ T cells infiltrate the IEL compartment prior to disease development. Therefore, we propose to interrogate the contribution of gd IELs in the pathogenesis of chronic ileitis and elucidate the cellular and molecular mechanisms involved in the dysregulation of the gd IEL compartment during the development of CD-like ileitis. To address these questions, we will take advantage of unique gd T-cell-specific mouse models and intravital microscopy to define how gd IEL motility and effector function are regulated in the events leading up to the onset of chronic ileitis. By combining temporal and cell-specific gene targeting, cutting-edge live imaging techniques, and novel models to analyze gd IEL function ex vivo, we expect to clearly elucidate the contribution of gd IELs to the development of ileal disease and further define the functional dysregulation within gd IEL subpopulations in the context of chronic inflammation. Developing a better understanding of the cellular and molecular mechanisms involved in gd IEL immunosurveillance and immunoregulation may elucidate additional targets for future therapies designed to reinforce the epithelial barrier and prevent disease relapse.

NIH Research Projects · FY 2025 · 2023-07

Project Summary/Abstract Locally advanced cervical cancer (LACC) associated with human papillomavirus (HPV) infection continues to be a significant source of morbidity and mortality in the US and globally. In particular, patients with evidence of metastases to lymph nodes have a dismal 3-year overall survival of 39%, despite treatment with the current standard of care of chemotherapy combined with radiation (CRT). There is thus a critical need to develop new therapeutic strategies for patients with high-risk LACC. Combinations of CRT with immune checkpoint blockade (ICB) drugs targeting PD-L1 (durvalumab) or PD-1 (pembrolizumab) are being studied in global prospective trials CALLA and KEYNOTE A18, respectively. Unfortunately, the results of the CALLA trial failed to demonstrate substantial improvement in 24-month survival with addition of durvalumab, highlighting several critical knowledge gaps in combination of CRT and ICB in LACC. First, optimal sequencing of CRT and ICB is unknown, and there are clear concerns that concurrent initiation of CRT and ICB carries a potential to kill activated proliferating T cells in tumors and tumor-draining lymph nodes, leading to tolerance. Second, predictors of long-term outcomes for the patients treated with ICB and CRT are unknown. In this application, our key study objectives are to examine the evolution of blood and tumor microenvironment (TME) immune parameters in response to differential ICB-CRT sequencing and to establish the predictors of long-term outcomes. To achieve these goals, we conducted and completed an NCI-sponsored clinical trial of PD-L1 inhibitor atezolizumab in combination with CRT in patients with high-risk LACC, randomizing patients to atezolizumab administration prior to and concurrent with CRT vs. concurrent with CRT in 36 patients. The study incorporated comprehensive collection of pre- and on-treatment tumor biopsies and blood and PET scans that will enable us to address the knowledge gaps above. In Aim 1 we will determine how the tumor immune microenvironment evolves as a function of differential immunotherapy and CRT sequencing. By using multi-parameter fluorescence microscopy, we will determine how activation of T cells and their interaction with other cells in the tumors change in response to therapy and how these changes predict long term outcomes. In Aim 2, we will take advantage of T cell receptor (TCR) repertoire sequencing as well as advanced bioinformatics techniques to evaluate how evolution of T cells in tumors and peripheral blood could serve as an indicator of anti-tumor immune response and long-term outcomes. In Aim 3 we will establish radiographic and blood biomarkers as predictors of outcomes in high-risk LACC patients by examining blood HPV DNA and post-treatment PET-CT as markers of disease burden pre- and post-therapy. Identification of early biomarkers predictive of outcomes will be critical for risk-stratification of patients with LACC in order to guide patient selection for clinical trials or maintenance therapy, while minimizing the potential clinical toxicities and financial burden in patients at low risk for recurrence.

NIH Research Projects · FY 2025 · 2023-07

Project Summary Our long-term goal has been to characterize the heterogeneous group of chronic lower airway diseases (LAD) observed in World Trade Center (WTC) workers and volunteers, uncover their risk factors and comorbidities, identify subgroups with adverse and favorable lung function trajectories and outcomes, and develop and deploy novel imaging approaches to the investigation of the lung injury underlying them. Such goal will in turn translate into better understanding of disease pathophysiology, more targeted, personalized, and perhaps disease modifying treatment approaches, and improved surveillance and prevention strategies. The goal of this project has been to characterize the transitions into chronic obstructive pulmonary disease (COPD) among former workers and volunteers at the WTC disaster site. Following our objective characterization of our COPD cases, our multidisciplinary investigative team proposes to establish the quantitative computed tomography (QCT) characteristics that may differentiate WTC-related from non- WTC-related COPD, investigate characteristics and longitudinal lung function trajectories of WTC patients with pre-COPD, and investigate lung mechanical strain (LMS) as an early QCT marker of lung injury associated with chronic disease and accelerated longitudinal lung function decline. This project will be conducted in the occupational cohort followed at Mount Sinai. To that end, we will utilize the WTC Pulmonary Evaluation Unit Chest CT Imaging Archive, a large repository with more than 3000 chest CT images on 1700 WTC workers, as well as linked datasets with disease symptoms, both pre- WTC and WTC-related occupational exposures, detailed pulmonary function and longitudinal spirometry measurements and body weight trends, visual imaging classification and grading, and quantitative computer tomography (QCT) measurements of airway, body composition, and pulmonary parenchymal and vascular abnormalities.

NIH Research Projects · FY 2026 · 2023-07

Project Summary: Chronic kidney disease (CKD) continues to be a significant factor in global morbidity and mortality. Patients experiencing repetitive acute kidney injury (AKI) are predisposed to CKD. Despite discoveries of novel biomarkers and increasing awareness of kidney health, the prevalence of CKD and end- stage kidney disease (ESKD) continues to rise. To date, the lack of therapeutic options halting progression from AKI to CKD still represents an unmet need. Our preliminary data suggest while activation of complement component 5 receptor 1 (C5aR1) promotes renal tubular epithelial cell (RTEC) damage, C5aR1 signaling on myeloid cells may confer renoprotective effects ameliorating AKI. This project will determine the roles of C5a- C5aR1 axis activation in 1) RTEC cellular senescence and kidney fibrosis (Aim 1), and in 2) myeloid cells responsible for AKI pathogenesis (Aim 2). These aims will test our central hypothesis that C5aR1 activation in kidney resident macrophage (KRM) mitigates the acute phase of AKI, whereas C5a-C5aR1 signaling in RTEC mediates their cellular senescence with subsequent CKD progression and fibrosis. Our findings will lay the fundamental knowledge of the potential clinical use of complement-regulating therapies for kidney diseases. Candidate and Training: The primary objective of this application is to support Dr. Mon-Wei (Sam) Yu's career development into an independent basic scientist in the fields of complement biology and kidney diseases by using novel murine models and immunological approaches. Dr. Yu's proposed training activities are in four areas: 1) Establish innovative scientific questions and design appropriate experiments to answer those questions; 2) Attain the necessary techniques, especially in the immunology field, to perform experiments; 3) Gain training and experiences for big data analysis, and 4) Refine the skills for grantsmanship and manuscript preparation. Environment: Division of Nephrology at Mount Sinai Hospital and the Icahn School of Medicine at Mount Sinai (ISMMS) are fully committed to junior faculty career and scientific development. Dr. Paolo Cravedi and Dr. John Cijiang He (Division Chief) are renowned experts in complement and tubular biology with a strong K Award trainees track record.

NIH Research Projects · FY 2025 · 2023-07

Racial and Ethnic Disparities in Liver Disease in the WTC General Responder Cohort: People of color experience persistent disparities in liver disease outcomes in the U.S. This project investigates how these dis- parities may affect members of the Mount Sinai WTC General Responder Cohort. Currently, the WTC Healthcare Program (WTCHP) covers liver cancer treatment, but it does not cover the diagnosis and treatment of other liver diseases or liver cancer surveillance These policies may create holes in the healthcare safety net that could disproportionately disadvantage African American Responders. Fortunately, WTC monitoring visits provide the data needed to calculate the Fibrosis-4 (FIB-4) score, a well-validated instrument for liver disease screening. We embedded a FIB-4 calculator in Mount Sinai’s EPIC electronic medical record (EMR). It is available to Mount Sinai WTCHP providers. In this project, we will introduce the calculator to Mount Sinai WTCHP providers. We will also analyze for disparities in mortality and study archived specimens to assess for toxins that were present in the WTC dust cloud. Environmental and workplace exposures to toxins can cause liver injury and cancer and they synergize with other sources of liver injury to magnify damage and liver cancer risk. The WTC dust cloud contained tons of debris and hepatotoxins, including particulates, polychlorinated biphenyls (PCBs) and other persistent organic pollutants (POPs). Adolescents exposed to WTC dust had elevated PCDD/F levels > 12 years after the attack, establishing that toxins in WTC dust remain detectable for long periods. Our research is expected to show that WTC exposure caused, aggravated, or contributed to liver disease (criteria for certification). Aim I: Disparities in mortality. The goal of SubAim1 is to collaborate with the WTCHP General Responder Data Center to rigorously identify all Mount Sinai WTC General Responders with cirrhosis and/or liver cancer. The goal of SubAim 2 is to test the hypothesis that among responders with cirrhosis and/or liver cancer, African American responders have higher all-cause and liver-related mortality than other responders. Aim II: A FIB-4 calculator to screen for liver disease in Mount Sinai General Responders. The goal of Aim II is to enable WTCHP providers to screen for liver disease. We will introduce the FIB-4 calculator to Mount Sinai WTCHP providers at some clinics and not others and test the hypothesis that education increases use of the calculator. We will also monitor for differences in rates of referral to hepatology between clinics in each arm. Aim III: WTC toxins in plasma and liver. The goal of SubAim 1 is to test the hypothesis that plasma levels of PCBs and other POPs are higher in GRC responders than in controls and are directly related to FIB-4 scores and inversely related to platelet counts. The goal of SubAim 2 is to compare particulates and granulomas be- tween archived liver specimens of WTC responders and controls matched for liver disease etiology. Impact: The long-term goals are to provide data to inform CDC/NIOSH decisions about whether liver diseases meet criteria for WTC certification and to address any disparities that may exist among General Responders.

NIH Research Projects · FY 2025 · 2023-07

PROJECT SUMMARY/ABSTRACT Background: Metastasis in distant organs years after treatment is the primary cause of cancer death. Late progression occurs through the reactivation of dormant tumor cells that disseminated early in the disease. To date, no therapy has been designed to target those cells and the lack of understanding on their biology prevents the development of selective strategies to kill them. We aim to gain molecular insight into the gene regulatory signature of the cancer dormancy state and use this information to devise a dormant cancer cell biosensor that will allow us to identify, profile, and genetically manipulate them in vivo. Hypothesis: We hypothesize that the application of intersectional genetics tools to define the unique transcriptional profile of dormant cells will reveal vulnerabilities that could be exploited to eliminate those cells. Specific Aims: Aim 1. To obtain and validate the enhancer activity profiles of dormant cancer cells in an in vivo context Aim 2. To develop a dormant cancer cell biosensor and test its in vivo potential to selectively identify dormant cancer cells. Study design/Methods: To increase the specificity of dormant cancer cell identification in vivo, reduce side- effects on non-target normal cells, and allow the systematization of the generation of dormant cell-specific biosensors and its downstream applications, such as targeted cell ablation therapies, we propose to develop a new dormant cell biosensor that bypasses cell-surface marker requirements distinguishing them instead via intracellular properties that can be harnessed to allow the precise and exclusive genetic manipulation of these cells within the body. We will validate our biosensor in vivo by using cellular dormancy models and intravital two- photon microscopy. Relevance: The mechanisms of cancer cell dormancy are poorly understood, hence the options available for their targeted treatment to prevent metastasis are limited. Here, we propose to use state-of-the-art genomic activity profiling technology to gain molecular insight into the genetic program that defines the cancer dormancy state in vivo. We will then couple our unique computational and synthetic biology know-how to define unique signatures of the dormancy program to engineer genetic sensors that can be systemically-delivered into the body to find dormant cancer cells. With this strategy, we hope to develop strategies to eliminate metastatic dormant cells, the source of metastasis.