Icahn School Of Medicine At Mount Sinai

NIH Research Projects · FY 2025 · 2022-09

Project Summary In early 2020, a new virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), generated headlines due to its unprecedented rate of transmission. SARS-CoV-2 caused the first reported cases of coronavirus disease 2019 (COVID-19) in December 2019 and continues to spread worldwide. As a family of RNA viruses, SARS-CoV-2 is prone to mutate at a rate up to a million times faster than its hosts1,2. These rapid genomic alterations have already generated highly transmissible variants, and have raised concerns that the virus will evade vaccine-induced immunity. In addition, a large percentage of the global population remains unvaccinated, due to the challenges of production and mass distribution, vaccine hesitancy, and pending approval status for patients under age 12. Therefore, an effective antiviral has the potential to relieve suffering for millions—not only helping individual patients recover and reducing the number of deaths, but also limiting the number of positive carriers and thereby curbing the spread of the pandemic. This proposal aims to develop an efficient antiviral to impede the virus’ entry into cells, specifically into lung alveolar type II (AT2) cells, the stem cells of the distal lung. Thanks to recent studies, we know which “door” (a receptor called ACE2) and “key” (a protease called TMPRSS2) the virus uses to enter cells. Our goal is to remove the key so the virus cannot open the door and enter host cells. We will use a conventional air-liquid interface (ALI) culture that is representative of the in vivo airway and a recently developed 3-dimensional (3D) in vitro lung organoid model that recapitulates many aspects of lung structure and the cellular environment and that has been used to study respiratory viruses, including SARS-CoV-2. These systems represent tissues better than cell lines, but offers the benefit of being less complex than tissue explants or animal models. In addition, we have generated a panel of highly sensitive and specific mouse monoclonal antibodies (mAbs) directed against TMPRSS2. In preliminary studies, the lead TMPRSS2 mAb, AL20, shows no signs of cytotoxicity with a trend towards inhibition of SARS-CoV-2 pseudovirus entry in cell lines and in lung organoids. Furthermore, we have identified at least two serine protease inhibitors (serpins) that form complexes with TMPRSS2, and the presence of these complexes is inversely correlated with the SARS-CoV-2 infection rate. These findings lead to our hypothesis that targeting TMPRSS2 can inhibit SARS-CoV-2 viral entry and spread. To test our hypothesis, we will first test the efficacy of AL20 for blocking the entry of SARS-CoV-2 into AT2 cells in lung organoids and in airway epithelial cells in ALI cultures, and elucidate the underlying mechanisms. We will then evaluate the effects of serpins on TMPRSS2 activity and SARS-CoV-2 viral entry and spread. Finally, to explore the feasibility of advancing AL20 to human trials, we will test humanized AL20 in a SARS-CoV-2 hamster model. Syrian golden hamsters are naturally susceptible to SARS-CoV-2 infection that recapitulates the clinical, virological, histopathological, and immunological characteristics of human disease, enabling study of its pathogenesis, transmission, and passive immunization effect. Transgenic human ACE2 is not required for SARS-CoV-2 infection, ensuring that the cell types infected are highly relevant. These studies will provide critical insights into the mechanisms whereby TMPRSS2 regulates SARS-CoV-2 entry, and suggest potential therapeutic candidates against COVID-19. The proposed work has the potential to impact the lives of millions of individuals affected by COVID-19 and other respiratory viruses, such as influenza A, that use TMPRSS2 to enter cells.

NIH Research Projects · FY 2025 · 2022-08

SUMMARY The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected over 233 million people globally. The US alone has reported ~126,000 coronavirus disease-19 (COVID-19) cases in pregnant individuals, not including many asymptomatic and unconfirmed cases. Thus, potentially millions of children worldwide may be impacted by the sequelae of prenatal SARS-CoV-2 exposure. Animal research has shown that various maternal viral infections during pregnancy are associated with impaired neurodevelopment in offspring. In line with these findings, epidemiological studies suggest that prenatal exposure to infections is linked to neurodevelopmental deviations, and an elevated risk for ASD. There is an urgent need for prospective, well-characterized birth cohorts to study the link between prenatal exposure to SARS-CoV-2 infection and risk for adverse child development, particularly in light of a global health crisis with potentially lifelong consequences for the child. Moreover, pregnant women are now being vaccinated against COVID-19 on a large scale. Vaccines elicit a brief immune response, ranging from mild to severe, with fever and increased cytokine levels. While studies have shown that these vaccines are safe during pregnancy, the long- term effects on the child's developing brain are unknown. This study aims to investigate the association of prenatal exposure to SARS-CoV-2 infection and COVID-19 vaccination with behavior, cognition, and brain functioning in the child at 3 years of age. We hypothesize that SARS-CoV-2 infection negatively impact child outcomes, mediated by changes to the fetal immune system. We further hypothesize that COVID-19 vaccines are safe, with little to no long-term effects on the child. We will leverage our on-going prospective pregnancy cohort `Generation C', which we established at The Mount Sinai Health System in New York City (NYC) in the early weeks of the pandemic (> 2,800 women enrolled). The cohort is racially/ethnically and socio-economically diverse. We obtained the following: 1) maternal blood samples during pregnancy, and at delivery; 2) maternal SARS-CoV-2 antibody titers for each blood draw; 3) demographic and clinical data; and 4) neonatal dried blood spots (DBS). In the proposed project, we will (i) follow-up SARS-CoV-2 exposed, vaccine-exposed and non-infected and non-vaccinated mother-child dyads 3 years after birth, combining (ii) existing information on maternal SARS-CoV-2 infection and COVID-19 vaccination status during pregnancy, with (iii) newly collected data on SARS-CoV-2 antibody and cytokine levels in neonatal DBS; (iv) childhood neurodevelopment including behavior, cognition, and motor development, and (iv) brain functioning using electroencephalogram (EEG).

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY Individuals diagnosed with schizophrenia and related psychotic disorders (SZ) exhibit a markedly elevated risk of premature mortality, with a 10–20-year shorter lifespan relative to the general population. Increased mortality rates in SZ are largely attributable to the early manifestation of medical conditions that normally occur later in life, a process known as ‘accelerated aging’. While unhealthy lifestyle behaviors, such as smoking and unhealthy diet, account, in part, for accelerated aging in SZ, the excess of physical comorbidities cannot be solely attributed to these factors. Remarkably, the direct adverse health effects of key clinical characteristics of SZ have rarely been considered. In the general population, the absence of social contact is known to pose enormous challenges for physical health, especially at older ages. Given that social isolation is a persistent and disabling feature of SZ, it is possible that this behavior may contribute to the premature manifestation of health conditions in SZ. Building on rich pilot data pointing to significant associations between social isolation and long-term perceived health in SZ, our overarching goal is to test whether and how social isolation contributes to the health challenges of individuals with SZ as they age. With participants from Europe (EU-GEI) and the US (Olin Neuropsychiatry Research Center), we will create a longitudinal database of 650 participants, including 500 individuals with SZ, and 150 of their unaffected siblings. We will apply an accelerated longitudinal design by re- assessing and by examining medical records of research participants who were first evaluated between the ages of 30-50 and are now 50-65 years of age, a period when many medical conditions and health problems tend to manifest. We will determine the age-related association between social isolation and adverse health outcomes in SZ, test for familiality, directionality, and factors moderating this association, and determine the extent to which the COVID-19 pandemic and the resulting imposed lockdowns impacted health in SZ. We will consider generalizability across countries, sexes, and race/ethnicities. The rationale for the proposed research is that in order to facilitate much-needed targeted therapies to prevent early mortality in SZ, we need to better understand factors that contribute to the excess of medical comorbidities in SZ. Our central hypothesis is that social isolation, a common and persistent characteristic of SZ, contributes to the excess of physical comorbidities in SZ. To meet our overall goal, we will pursue the following aims: (1) Determine the association between social isolation and adverse health outcomes in SZ; (2) Test for the directionality, and moderating factors, of the association between social isolation and health outcomes in SZ, and; (3) Examine whether the COVID-19 pandemic modified associations between social isolation and health outcome in SZ. This study will be the first to comprehensively examine the health impact of social isolation in SZ. The project may show that in SZ socialization in midlife can reduce the risk for poor health outcomes and ultimately facilitate much-needed preventive targeted therapies to reduce early-age mortality in SZ.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY Opiate use, dependence and addiction represent enduring public health issues, resulting in substantial financial and societal health burdens, as well as increasing numbers of overdoses. Drug addiction is characterized as a chronic, relapsing disease. However, to date, there remains insufficient data examining the molecular mechanisms underlying persistent opiate-induced neurobiological changes, which has led to a scarcity of effective therapies and interventions to treat and prevent relapse. Drug addiction has long been thought of as a disorder of dopamine (DA) signaling. However, therapeutic interventions targeting receptor mediated DA neurotransmission have not yet resulted in fully efficacious treatments. Therefore, an overarching goal of our laboratories – and the focus of this application – has been to investigate novel, non-canonical actions of DA involved in mediating addiction phenotypes. Our laboratory recently identified a novel signaling moiety for DA in brain, termed dopaminylation (dop), whereby DA acts as a donor source for the establishment of post-translational modifications (PTM) on substrate proteins (e.g., histone H3) via transamidation by the Transglutaminase 2 (TGM2) enzyme. In more recent efforts by our lab to unbiasedly identify additional substrates of these PTMs (focused now on synaptic proteins in nucleus accumbens/NAc, a key brain reward region), we developed a novel chemical tagging approach that, when coupled to mass spectrometry, allowed for the discovery of hundreds of dopaminylated proteins in brain, both in the context of normal neural function and in response to aberrant dopamine signaling following chronic heroin self-administration (SA) in rats. Among them, gCaMKII: 1) was found to be robustly dopaminylated at only a single amino acid residue located within its autoinhibitory helix [glutamine (Q)285], a site that exists only two amino acids away from a critical threonine (T) residue (287), which when phosphorylated directs Calmodulin (CaM) sequestration; 2) is upregulated in its dopaminylation following heroin SA, both during acute and prolonged abstinence, but not in response to natural rewards; and 3) represents a critical substrate involved in mediating long range signals from the synapse to nucleus in brain, ultimately promoting CREB activation and neuronal plasticity. Thus, this dopaminylation event on gCaMKII may represent a critical convergent mechanism linking altered dopaminergic signaling in response to heroin to CREB mediated transcriptional abnormalities. As such, we hypothesize that gCaMKIIQ285dop may play a direct role in mediating heroin relapse via aberrant modulation of CREB signaling in NAc. In Aim 1, we will fully characterize gCaMKIIQ285dop’s temporal effects on drug taking vs. relapse vulnerability in the context of heroin SA. In Aim 2, we will explore gCaMKIIQ285dop’s effects on CREB signaling/transcription following heroin SA, events that may precipitate relapse vulnerability. In Aim 3, we will investigate roles for gCaMKIIQ285dop mediated CREB signaling/transcription in D1 vs. D2 dopamine receptor-expressing MSNs during abstinence from heroin SA in the regulation of relapse behaviors.

NIH Research Projects · FY 2026 · 2022-08

The inability to visualize enzymes in action at atomic resolution constitutes a major technological barrier in biology, stalling mechanistic understanding and hindering the rational design of therapeutics for numerous human diseases. This project directly addresses this critical barrier by developing and generalizing a powerful, integrated methodology combining time-resolved X-ray crystallography with quantum mechanics/molecular mechanics {TRX-QM/MM) simulations. The power of this approach has been demonstrated through the fundamental reversal of the accepted paradigm for ATP hydrolysis in Hsp70 chaperones, a discovery built on an unprecedented dataset of time-resolved structures. The overarching goal of the independent R00 phase is to leverage this breakthrough to establish a broadly applicable platform for deciphering the mechanisms of challenging enzymatic systems. The central hypothesis is that mechanistically distinct enzymes require different catalytic strategies that can only be resolved by our integrated approach. The specific aims are: 1) To provide an atomic-level motion picture of Hsp70 catalysis by capturing key intermediates to define the energy landscape of its novel dissociative mechanism and the essential proton relay network. 2) To elucidate the chemomechanical gating of actin's contrasting associative ATPase mechanism, testing the general applicability of our platform on a fast, allosterically-regulated enzyme. 3) To engineer and disseminate a multi-scale platform for time-resolved enzymology by developing a next-generation mix-and-quench apparatus, integrating time-resolved MicroED to visualize proton dynamics, and implementing a novel QM/MM refinement protocol for modeling reactive intermediates. Successful completion of this project will deliver a transformative, validated toolkit for the scientific community, breaking a long-standing technological bottleneck and enabling the mechanistic investigation of a vast range of enzymes essential to human health and disease. This will provide the fundamental knowledge required to accelerate the development of next-generation, mechanism-based therapeutics.

NIH Research Projects · FY 2025 · 2022-08

The cannabis sociopolitical landscape has dramatically shifted in recent years leading to the decriminalization, medicalization, and legalization of cannabis use, which has contributed to the reduced risk perception of its harm. This transformational time, however, has health implications particularly for vulnerable populations related to neurodevelopment since cannabis is commonly used by pregnant women and women of childbearing age. Accumulating evidence from our long-standing research has clearly demonstrated that prenatal exposure to D9- tetrahydrocannabinol (THC), the major psychoactive component of cannabis, has long-term effects on behaviors — relevant to reward, motivation, negative affect and decision-making, and molecular disturbances linked to synaptic plasticity with profound epigenetic dysregulation that are exacerbated by stress. We have also identified specific epigenetic modifications linked to synaptic plasticity and behaviors associated with the protracted effects of developmental THC exposure. Recent results have highlighted the immune system as relevant to developmental cannabis/THC since preliminary gene expression analysis of the placenta from women who used cannabis during pregnancy revealed marked reorganization of the immune transcriptome that correlated with later childhood behavior. Immune-related genes were also altered in mesocorticolimbic structures of adult rats with developmental THC exposure, which enhances the correlation between immune- and synaptic-related genes. To gain neurobiological and mechanistic insights, we will conduct integrative and translational studies (human and rat models) to: (1) Determine the impact of prenatal cannabis/THC exposure on immune-related disturbances (placenta and brain); (2) Delineate molecular networks within distinct mesocorticolimbic cell populations through high resolution single-cell strategies altered by developmental cannabis/THC exposure relevant to immune function; and (3) Identify early biological disturbances (sustained into adulthood) predictive of long-term effects on brain and causally mediate behavior due to prenatal cannabis/THC exposure. The translational knowledge gained and the human and rodent databases generated from this project will significantly advance our understanding of psychopathology risk that often has its genesis during development.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY With the widespread use of combination antiretroviral agents, the incidence of HIV-associated nephropathy (HIVAN) has dramatically decreased in the recent years. Yet, the prevalence of chronic kidney disease (CKD) and end-stage kidney disease in patients living with HIV remains high, suggesting that HIV predisposes patients to increased risk for chronic kidney disease. Indeed, several lines of evidence from recent epidemiological and animal model studies indicate that concurrent HIV infection and age-related comorbidities, such as diabetes mellitus, have a synergistic effect on the incidence of chronic kidney disease, thereby necessitating an examination of mechanisms by which HIV infection even at low viral load accelerates the progression of CKD. Among the HIV-1 viral proteins, we previously showed that HIV viral protein R (Vpr) can induce cell cycle dysregulation, apoptosis, and polyploidy in renal tubular cells. However, the importance and consequences of Vpr-mediated cell cycle arrest and polyploidy has not been fully explored in the setting of kidney disease. In this proposal, we will further dissect the mechanisms dictating the cell fates of Vpr- expressing renal tubular using in vitro approaches (Aim 1). Similarly, using transgenic mice expressing Vpr in renal tubular epithelial cells, we will characterize the cell cycle dysregulation and gene expression at single-cell levels, and determine whether the pharmacological intervention of cell cycle dysregulation can attenuate kidney disease progression in this model, as well as in HIVAN mouse model, Tg26 (Aim 2). To complement the findings in Aims 1 and 2, we will assess the expression of genes and cell cycle regulators in kidney biopsy samples of HIV+ CKD patients (Aim 3). We will also perform transcriptomic profiling for comparative analyses with findings in murine kidneys. Our results will provide a better understanding of the underlying molecular mechanisms by which chronic HIV infection accelerates the progression of CKD and a proof-of-concept for novel target treatment for CKD in HIV patients.

NIH Research Projects · FY 2026 · 2022-08

ABSTRACT: Mal de Débarquement Syndrome (MdDS) is an under-recognized but nevertheless common balance disorder, which in most cases occurs after exposure to prolonged passive motion. MdDS, a chronic illness that can last for many years, is manifested by persistent false sensations of rocking/swaying or gravitational pull. MdDS is debilitating as these symptoms and signs are typically accompanied by other presumably secondary physical, cognitive, and affective problems. In addition to motion-triggered (MT) cases, the same or indistinguishable symptoms can occur without a specific trigger, identified as spontaneous-onset (SO) MdDS. Treatment options for MdDS are limited, and it was only recently that a breakthrough was made in our clinical laboratory with physiological readaptation of the vestibulo-ocular reflex (VOR). The premise of this treatment is that MdDS is caused by maladaptation of a functional component of the VOR called velocity storage, which shapes spatial orientation and the perception of self-motion. The treatment has been administered by maneuvering the head of the patient seated inside a cylindrical chamber during a full-field optokinetic stimulation (OKS). Our current success rates immediately after treatment of MT and SO MdDS are 75% and 50%, respectively. A follow-up study indicated that the success rates later fluctuate as well as that a significant number of patients remain sensitive to bright lights, movements of visual objects, and transportation, pointing to the treatment method's limitations. A primary hurdle is access to the treatment. Full-field OKS requires a specialized set-up in a dedicated room, making the treatment possible only in several laboratories around the world. We recently successfully pilot tested the efficacy of virtual reality (VR) goggles for MdDS treatment with the readaptation approach. In this proposed project, VR goggles will be tested on a larger group of patients, and the effects will be compared to those of full-field OKS. If proven to be effective, MdDS can be treated locally to patients in many vestibular therapy offices, not only for initial treatment but also for remedial or follow-up treatment when symptoms return. This proposal also addresses the weaknesses of the VOR readaptation approach by testing complementary approaches. We hypothesize that reducing (habituating) the velocity storage capacity decreases sensitivity to physical movement and improves MdDS symptoms as well as limits symptom recurrence. We further hypothesize that desensitization to visual stimuli can reduce visually induced dizziness frequently observed in patients with MdDS. We will verify whether these complementary treatments will provide a better outcome compared to the readaptation treatment by itself. Lastly, we hypothesize that OKS without head motion can reduce the false sensation of gravitational pull commonly reported by MdDS patients. Two hundred MdDS patients will be recruited for the study. Patients will be treated for 1-2 hours a day for 5 days. Patients will be followed up with for up to 12 months. The proposed study will facilitate improved outcomes for MdDS by broadening its treatment options.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY/ABSTRACT Studies find a substantial delay between the onset of psychosis and the initiation of specialty treatment for first episode psychosis (FEP), with the duration of untreated psychosis (DUP) typically over one year in the U.S. Better strategies are needed to improve identification of individuals with FEP and to rapidly engage them in Coordinated Specialty Care (CSC) aimed at restoring functioning. This study will investigate whether a U.S. adaptation of a successful detection approach from the Netherlands enhanced by an innovative model of communicating information about psychosis and treatment options to patients and families (ComPsych), can reduce DUP. Our collaborators in the Netherlands compared screening of a consecutive help-seeking population entering mental health services to clinician referral from mental health clinics and found that screening captured significantly more individuals at clinical high risk for psychosis (CHR) and with FEP. Based on the Dutch model, within the Mount Sinai Health System in New York, we have piloted and established the feasibility of screening help-seeking youth entering mental health services with the aim of improving early identification of FEP cases and rapid referral to specialty care (Early Stage Identification and Engagement to Reduce DUP study (EaSIE), supported by NIMH R34). Individuals entering services are screened with the Prodromal Questionnaire-Brief Version (PQ-B). Those who screen positive are assessed by Structured Interview for Psychosis Risk Syndromes (SIPS) and referred to stage-specific specialty care (FEP or CHR services). To facilitate service engagement we developed, piloted, and established feasibility of the ComPsych model. While our data showed that compared to clinician referral, systematic screening method (SM) can substantially reduce DUP by identifying a greater number of patients earlier in the course of illness, more research is needed to evaluate the impact of ComPsych on FEP treatment initiation and engagement in order to further reduce DUP. We will use a stepped-wedge cluster randomized controlled trial design to compare a systematic screening and communication method (SCM) to SM. Following a 6-month baseline period of SM, 12 mental health clinics will be randomized (2 clinics at a time) to transition from SM to SCM at 6-month intervals. In both conditions, individuals aged 12-30 who screen positive on PQ-B will be assessed with SIPS by trained clinicians in each clinic and referred to FEP and CHR services as appropriate. In SCM condition the ComPsych model will be used to facilitate initiation of CHR and FEP services. We will measure DUP for patients who meet psychosis criteria. We hypothesize that: (1) SCM will result in a higher number of individuals initiating CHR and FEP services compared to SM; (2) The mean DUP of FEP individuals in SCM condition will be lower than the mean DUP of FEP individuals in SM condition, due to the reduced time to initiate FEP services. We will also examine multi-level implementation factors that can inform the identification of implementation strategies for future deployment of SCM in routine practice.

NIH Research Projects · FY 2024 · 2022-08

PROJECT SUMMARY: IgE-mediated food allergy affects approximately 1 in 13 children in the USA and has continued to grow in prevalence in recent decades. For many, current immunotherapies are ineffective, making this is a lifelong disease with significant impairment in quality of life. Although IgE is central to the pathophysiology of food allergy, the mechanisms maintaining high affinity (pathogenic) IgE are not well understood. Previous work from our laboratory has shown that IgE memory in mice is contained within a population of antigen-specific IgG memory B cells (MBC) that can undergo class switching to IgE. However, strategies targeting a broad subset of IgG-expressing cells for treatment of food allergy is complicated by the need to retain protective immunity against pathogens. Therefore, it is important to identify the specific IgG MBC that have the ability to generate high affinity IgE responses. This proposal seeks to use mouse models of peanut allergy to identify immunophenotypic markers that can distinguish IgG MBC subsets with the ability to produce high affinity IgE plasma cells (PC). In addition, this application will address the plasticity of this cell fate and the external signals that are required for IgG MBC differentiation into IgE PC. Ultimately, we want to understand what it takes for an IgG MBC to become a pathogenic-IgE producing plasma cell and reveal targets that could be amenable to therapeutic intervention to improve the quality of life of patients who suffer from food allergies.

NIH Research Projects · FY 2024 · 2022-08

PROJECT SUMMARY/ABSTRACT Cardiovascular disease (CVD) due to atherosclerosis represents the leading cause of death worldwide. Progress in preventing CVD has been stalled by the growing epidemic of obesity, insulin resistance and type 2 diabetes (T2D), which increases the relative risk of developing atherosclerotic vascular disease and its complications four-fold compared to non-diabetic individuals. Despite this, the cellular and molecular mechanisms underlying the incidence of diabetic atherosclerosis are still unclear, as are appropriate strategies for the prevention and treatment of CVD in diabetic patients. We have recently developed an orally available, liver-directed controlled release mitochondrial protonophore (CRMP) that promotes oxidation of hepatic triglycerides by promoting a subtle sustained increase in hepatic mitochondrial inefficiency and shown that this agent safely reverses hypertriglyceridemia, fatty liver, insulin resistance and liver fibrosis in rodent and nonhuman primate models of obesity. Here, we will leverage the insulin-sensitizing effects of CRMP to directly assess the role of hyperinsulinemia and insulin resistance in driving diabetic atherosclerosis in a murine model of metabolic syndrome (Aims 1 and 2). We hypothesize that chronic CRMP treatment will reduce hepatic steatosis, insulin resistance and dyslipidemia due to increases in rates of hepatic mitochondrial fat oxidation, which in turn will reduce susceptibility to atherosclerosis. In addition, we will develop and utilize novel state-of- the-art metabolic tracer methods to characterize the regulation of macrophage immunometabolism during diabetic atherosclerosis (Aim 3), as the relationship between the inflammatory status and bioenergetic profile of plaque macrophages in vivo, as well as its impact on atherosclerotic development and stability, remains largely unknown. We hypothesize that obesity and T2D will increase glucose availability and utilization in macrophages which will initiate a feed forward loop that fosters inflammation and further aggravates atherosclerosis Collectively, this work will provide meaningful insight into the mechanisms regulating diabetic atherosclerosis and will be critical for understanding the therapeutic utility of liver-directed mitochondrial uncoupling agents for the treatment of cardiometabolic diseases. Therefore, we propose a focused career development training plan during which the applicant will be trained in the responsible conduct of research, learning all aspects of atherosclerotic plaque sectioning and characterization; the development and utilization of stable isotope methods to assess macrophage immunometabolism; and bioinformatics analysis of large data sets. This will be carried out under the supervision of the candidate’s primary mentor Dr. Gerald Shulman, co- mentor Dr. William Sessa, and collaborators Drs. Carlos Fernandez-Hernando and Rachel Perry. By completing the proposed training outlined in this application (K99), the applicant will obtain the knowledge and skills that will provide her with the initial steps towards scientific autonomy in the subsequent phase (R00) and transition successfully from the role of postdoctoral trainee to that of an independent researcher.

NIH Research Projects · FY 2025 · 2022-08

Different regions of the skin vary in their characteristics such as thickness, pigmentation, innervation, and presence, size and density of hair follicles and sweat glands, that are reflected in differential responses to injury and disease. As examples, androgenetic alopecia is limited to the scalp; acne predominates in facial skin; psoriasis is often most prominent in extensor regions; palmoplantar keratoderma is limited to palms and soles; and vitiligo can appear in symmetrical patterns. While regional characteristics of the skin are established during fetal development, positional information must be retained in the skin throughout life to allow for maintenance of regional characteristics and their re-establishment in wound healing. Positional information is known to reside in the skin dermis, but its molecular basis is poorly understood. To address this question, we propose the following Specific Aims. AIM 1: To identify candidate factors and areas of chromatin involved in establishing skin heterogeneity in embryogenesis we will analyze transcriptional profiles through single cell RNA-seq, and chromatin structure via single cell ATAC-seq, in distinct regions of developing skin to identify those that show region-specific expression or openness, respectively. AIM 2: (i) To determine which of these candidate factors and chromatin areas may also be responsible for maintaining regional skin heterogeneity in adult life, we will perform the same analyses on the corresponding areas of adult skin. (ii) We hypothesize that epigenetic mechanisms contribute to maintenance of regional skin characteristics. To test this, we will first identify patterns of DNA methylation and histone modifications that characterize developing dermis in specific skin regions by carrying out Bisulfite-seq to reveal sites of DNA methylation, and CUT&RUN for histone modifications that mark enhancers and active, repressed, or poised genes. We will then ask which of these patterns are maintained in adult dermal cells from the same regions. AIM 3: To test the functions of candidate regulators in directing and maintaining region-specific differentiation programs, we will use inducible genetic tools to delete the corresponding genes in developing or adult mouse dermis in vivo. Together, these experiments provide a comprehensive and unbiased approach to identify novel mechanisms that establish and maintain skin heterogeneity. Improved understanding of these mechanisms has potential to reveal new therapeutic targets in wound healing and in common and rare diseases that affect specific skin regions and have a major negative impact on quality of life; data obtained in this project will also inform strategies for generating specific skin types, including hair follicle- and sweat gland-bearing skin, for reparative skin grafting.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY/ABSTRACT The mechanism whereby RNA-binding proteins impact muscle function and disease progression is still largely unknown. Fragile X-related protein 1 (FXR1), an RNA-binding protein, is multi-functional and plays a role in regulating the temporal and spatial expression of RNAs in myocytes. It is becoming increasingly evident that FXR1 is essential for normal muscle function and is associated with both human cardiac and skeletal myopathies. Although global knockout of Fxr1 in mice results in perinatal lethality with cardiac and skeletal muscle defects, little is known regarding the fundamental mechanistic role(s) of FXR1. We discovered that FXR1 interacts with, and post-transcriptionally regulates, mRNAs that encode proteins essential for excitation-contraction coupling, including components that regulate phosphorylation of the myosin regulatory light chain (RLC). We also identified an interaction between FXR1 and the mRNA that encodes utrophin, a protein that can functionally substitute for the loss of dystrophin in Duchenne Muscular Dystrophy. Our extensive preliminary data, and data from others, reveal that FXR1 protein levels are significantly reduced in human DMD myocytes as well as in all DMD models tested including those from canine, pig, mouse and rat. Remarkably, restoring FXR1 levels in three different mouse models of DMD attenuates disease progression, resulting in structural and functional improvements in both cardiac and skeletal muscle. Utrophin expression is also enhanced in DMD mice in response to increased FXR1 levels. Thus, we hypothesize that FXR1 specifically regulates cellular components that are critical for proper muscle function and alterations in FXR1 levels/function contribute to disease progression, particularly in DMD. We propose a global, unbiased and multidisciplinary approach from single molecule to in vivo studies, including the use of human tissue, to allow us to accomplish three Specific Aims focused on determining the basic physiological function of a Fragile X protein and the role it plays in muscle pathogenesis. In addition, we will be among the first groups to assess gene-therapy strategies to prevent muscle dysfunction in DMD-rats (a model which closely resembles human DMD). We predict these discoveries will facilitate a unique RNA-level therapeutic approach to ameliorate muscle disease progression.

NIH Research Projects · FY 2025 · 2022-08

Project Summary / Abstract Despite significant advances in treatment, women are still dying from breast cancer, particularly triple negative breast cancer (TNBC). More than 50% of women with TNBC have elevated circulating triglycerides (TGs), and these elevated levels are associated with reduced breast cancer survival. While the link between hypertriglyceridemia (HTG) and TNBC is well described in epidemiology studies, checking and treating TG levels in women with TNBCs are not part of standard clinical care. To understand the biological links between HTG and TNBC progression, we employ pre-clinical models of hypertriglyceridemia in isolation from other metabolic abnormalities. In our preliminary studies, we have found that the mice with HTG develop more rapid growth and metastasis in murine models of TNBC. The HTG mice demonstrated lipid profiles with elevated very low density lipoprotein (VLDL), and high circulating of phospholipids associated with elevated VLDL. Examining RNA sequencing gene expression, we found that a number of genes associated with cholesterol synthesis and peroxisome proliferator activated receptor (PPAR) signaling were downregulated in the TNBC from our HTG models, while cytoskeleton related genes were upregulated. As these gene expression changes have previously been related to hypoxia signatures, we examined lipid peroxidation products and found higher levels of lipid peroxidation sterols in the tumors from the HTG mice. In addition, we found increased phosphorylation of p42/44 mitogen activated protein kinase (MAPK) and epithelial to mesenchymal transition (EMT) markers. VLDL binds to the VLDL receptor (VLDLR), which is part of a breast cancer gene signature that is associated hypoxia and is highly expressed on the basal-like subtype of TNBC. High VLDLR expression in breast cancer has been associated with cancer metastasis, and its expression in basal-like TNBC is associated with a 50% decrease in recurrence free survival. Therefore, we hypothesized that HTG promotes TNBC growth and progression by increased VLDL uptake through the VLDLR, which contributes to lipid peroxidation in hypoxic tumors. We hypothesize that lipid peroxidation increases cell signaling which enhances tumor survival in the setting of hypoxia, and also contributes to EMT, cytoskeletal changes and changes in the tumor immune microenvironment. In this project we will explore the importance of tumor VLDLR expression in HTG-driven TNBC growth and metastasis using patient derived xenografts. Secondly, we will examine the importance of an abundant lipid peroxidation product in TNBC. Finally, we will explore therapeutic strategies to lower TG, which if successful could readily be translated into clinical care to improve outcomes for women with HTG and TNBC.

NIH Research Projects · FY 2026 · 2022-08

This project will seek to define the relative risk contributions of microbial and genetic factors to the development of inflammatory bowel disease (IBD) within a cohort of high-risk multiplex (3 first-degree relatives affected) IBD families. Candidate: The primary objective of this application is to support Dr. Elizabeth Spencer’s career development into an independent, patient-oriented investigator in the field of prevention and personalized medicine for IBD patients. Dr. Spencer’s career goal is to become an independent researcher and leader in the application of risk stratification and prevention for IBD. Dr. Spencer’s proposed training activities are in five areas: 1) microbiomics, 2) metabolomics, 3) computational genomics and metagenomics, 4) longitudinal cohort building, and 5) leadership. To achieve this, she has assembled a mentoring team led by Dr. Marla Dubinsky, Co-Director of the IBD Clinical Center at Mount Sinai and Chief of the Division of Pediatric Gastroenterology, an expert in IBD risk stratification, Dr. Judy Cho, Ward-Coleman Professor, Vice-Chair of Genetics & Genomics & Gastroenterology, and Director of the Charles Bronfman Institute for Personalized Medicine (IPM) at the Icahn School of Medicine at Mount Sinai (ISMMS), an expert in the genetics of IBD, and Dr. Jeremiah Faith, Associate Professor of Genetics and Genomic Sciences and Clinical Immunology and Director of the Microbiome Translational Center, an expert in microbiomic analysis. Environment: The ISMMS has a strong tradition of outstanding research and is one of the top 20 medical schools in NIH funding. The Mount Sinai Division of Pediatric Gastroenterology is an international leader in IBD research and clinical care. Research: IBD is a heterogenous set of chronic inflammatory disorders that arise from the complex interplay of genetic, environmental and microbial factors, and immune responses. These complicated interactions arise before the identification of overt disease, making it difficult to tease out the causative factors behind disease inception given the need for a pre-clinical, high-risk cohort. The Multiplex Families Research Program at ISMMS provides a unique cohort of affected and unaffected members of multiplex families with IBD to examine the relative contribution of these factors. Dr. Spencer’s preliminary observations in this cohort have shown that siblings with IBD tend to cluster together in birth order, likely due to some environmental sharing, which could be attributed to microbial changes. We would like to explore this further by characterizing the microbial and genetic contributions to familial IBD to improve stratification of those at high-risk for developing both pre-clinical and overt IBD. Therefore, our specific aims are (1) to define the features of microbial and metabolomic profiles in sibling clusters of IBD and their association with genetic risk and (2) to develop an IBD risk score incorporating genetic, microbial, and metabolomic factors with validation in a similar, external cohort. The general approaches and skills developed during this award can be applied to further IBD risk stratification and continued exploration of possible inciting environmental triggers for those at high-risk for IBD.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY The COVID-19 pandemic prompted governments to implement a range of public health measures, including school closures, to slow the spread of SARS-CoV-2. However, the role of in-school transmission of SARS-CoV- 2, what mitigation levels and testing policies are needed, and the value of school closures have been contentious issues. In-person school closures or quarantine policies that prevent students from being in school can have immediate and long-lasting negative impacts on child development. In New York City, the calculated magnitude of student-level learning losses due to COVID-19 and the transition away from classroom-based instruction was on average 125 (69%) and 212 (118%) days of reading and math, respectively, relative to a typical 180-day school year. Across the United States, reduced educational attainment is estimated to translate into a loss of four to five percent of lifetime earning wages. Thus, opening schools to in-person learning is an important step in re-opening the economy and promoting development and success of students; however, it comes with the danger of increasing contact networks and transmission opportunities. To assess this trade-off and the potential for increased transmission, we will build models to incorporate school-level infection monitoring data along with community-level testing data, vaccination data, immunological and serological indicators among students and faculty, in addition to built environment indicators of school settings. These models will allows us to determine associations between community-level transmission rates and test positivity rates within schools (Aim 1), develop an epidemiological disease transmission model that identifies how to cost-effectively collect sentinel school surveillance data (Aim 2), and identify policy trigger points to predict when interventions should be implemented in schools to prevent disease transmission (Aim 3). Although I have the requisite engineering background and experience developing infectious disease models, additional training will maximize success of the proposed project and catalyze a robust independent research program. To accomplish these goals, I will obtain additional training in biological sciences and public health, particularly in community engagement, immunology, virology, and epidemiology. I will develop these skills through didactic training, independent study, and mentorship from experts in these fields: Drs. Maida Galvez, Rachel Vreeman, Jeffrey Shaman, Andrea Graham, Nicole Bouvier, and Chris Gennings. At the end of this training period, I will be uniquely positioned to comprehensively examine the effects of respiratory disease transmission in future research. Further, I will use the knowledge gained and the developed disease transmission models in future grant applications, establishing a crucial step toward my long-term goal of optimally designing infectious disease monitoring networks to reduce the spread of disease and improve the health of communities.

NIH Research Projects · FY 2025 · 2022-07

PROJECT SUMMARY Multiple Myeloma (MM) patients undergoing Autologous Stem Cell Transplantation (ASCT) experience clinically significant negative sequelae affecting disease prognosis, survival, and quality of life. These sequelae include increase in production of pro-inflammatory cytokines, higher occurrences of neutropenic fever and higher symptom burden (e.g., depression, pain) which are associated with circadian rhythm disruption (CRD). CRD involves disruption in naturally occurring 24-hour cycles of hormone secretion, temperature and activity. CRD raises production of pro-inflammatory cytokines unfolding a cascade of negative effects that include higher symptom burden and risk of developing neutropenic fever. CRD has been associated with poorer prognosis and survival. Our recently completed R21 study showed that morning circadian-effective illumination of patients' hospital rooms resulted in significantly higher nocturnal melatonin levels, reduced depression and production of inflammatory cytokines compared to the circadian-ineffective group (control). In the active group, an improvement in sleep and reduction in neutropenic fever was observed. Our R21 results also showed a strong negative relationship between melatonin levels and pro-inflammatory cytokines. Therefore, for the proposed multi-site randomized controlled trial (RCT) we hypothesize that circadian entrainment resulting from morning light exposure will lead to better sleep, lower levels of pro- inflammatory cytokines and symptom burden, as well as fewer occurrences of neutropenic fever. We will investigate if circadian-effective illumination, of patients' hospital rooms/outpatient settings during ASCT, promotes circadian entrainment and improves sleep, and if circadian entrainment reduces inflammation. We will also investigate whether better entrainment and lower levels of pro-inflammatory markers are associated with fewer occurrences of neutropenic fever and reduced symptom burden. The circadian stimulating light will be installed in the outpatient setting/hospital rooms since transplants are performed in both settings. A unique advantage of our intervention is that it does not require any patient effort because the circadian- active light is delivered throughout the entire room. The project will determine if: 1) circadian-effective light compared to circadian-ineffective light, delivered during ASCT results in circadian rhythm entrainment; 2) circadian entrainment reduces pro-inflammation cytokines and mediates the effects of circadian-effective light on the cytokines; and 3) reduced levels of inflammatory cytokines are associated with reduced occurrence of neutropenic fever and lower symptom burden in patients.

NIH Research Projects · FY 2026 · 2022-07

PROJECT SUMMARY The impact of mitochondrial biology on human cancers is broad because these organelles are critical regulators of metabolism, proliferation, metastasis, and cell death. Indeed, mitochondrial aberrations are common in multiple cancer types – not only do mitochondrial dysfunctions correlate with disease pathogenesis, but aberrant mitochondria also negatively impact upon chemotherapeutic success. Within a cell, mitochondrial homeostasis is maintained by a process referred to as “mitochondrial dynamics”, which is essential for efficient ATP generation, mitochondrial metabolites/substrates distribution, and mitochondrial DNA (mtDNA) integrity. Homeostatic mitochondrial dynamics result from the cumulative nature of complementary cycles of mitochondrial division and fusion. Work from my laboratory demonstrates: (1) the mitochondrial division machinery is essential for cellular transformation, (2) mitochondrial division is chronically activated in RAS-transformed murine cells and human cancer lines harboring oncogenic mutations within the MAPK pathway, (3) chronic mitochondrial division is sufficient to initiate mitochondrial dysfunction and cancer cell metabolism, and (4) FDA-approved targeted therapies that inhibit oncogenic MAPK signaling turn off the mitochondrial division machinery. While the above studies link chronic mitochondrial division to cancer biology, mechanistic explanations for how chronic mitochondrial division promotes organelle dysfunction and cancer phenotypes are scarce. In this R01 application, our goals are to (1) provide key mechanistic details into the process and contributions of mitochondrial dysfunction during oncogenic transformation, and (2) develop novel translational tools focused on the detection and inhibition of chronic mitochondrial division to enhance cancer prognosis and treatment. As our expertise and resources are in dermatology, we will focus on melanoma. The presence of mtDNA mutations and mitochondrial aberrations in cancer have been described for decades, but the molecular events that drive these changes and their impact on cancer biology remain speculative. To address this knowledge gap, we recently completed an unbiased screen using normal melanocytes and melanoma cell lines to understand how chronic mitochondrial division impacts on mitochondrial function, and identified that loss-of-function mtDNA mutations are essential for cancer cell metabolism, proliferation, and tumorigenesis. We hypothesize that oncogene- induced chronic mitochondrial division promotes mtDNA mutations and organelle heterogeneity to instigate transformation. Based on our data, chronic mitochondrial division is an early event during melanomagenesis, and provides strong prognostic value and therapeutic potential. This project emerged following years of effort to identify how chronic mitochondrial division impacts cancer mechanisms, prognosis, and treatment.

NIH Research Projects · FY 2025 · 2022-07

Project Summary Seasonal influenza epidemics, caused by influenza A and B viruses, result in 3–5 million severe cases and 300,000–500,000 deaths globally each year - especially in high-risk groups such as young children, pregnant women, obese individuals, individuals with a compromised immune system, and indigenous populations. The burden of influenza can vary widely between seasons, in part due to characteristics of the circulating viruses, the existing immunity in the population, and the effectiveness of seasonal influenza vaccines against the circulating virus strains. Disease morbidity and mortality increase when a new influenza strain reasserts or jumps the host and becomes capable of infecting humans. In this case, there is no (or minimal) pre-existing antibody-mediated immunity to the new viral strain at the population level, leading to millions of infections and a rapid global spread of the virus. In the absence of antibodies, the severity of the disease can be ameliorated by broadly cross-reactive cellular immunity. However, the precise mechanism of how immune cells mediate recovery in some individuals, but not others is far from clear. NIAID has made significant investments in the generation of data to improve our understanding of infectious diseases, their progression, risk, and severity as well as treatment and prevention. Not only subject of specific programs, such as CEIRS (Centers of Excellence for Influenza Research and Surveillance) and the ongoing efforts in CIVICs (Collaborative Influenza Vaccine Innovation Centers), but in particular, omics-related programs have generated high-throughput genomic, proteomic, and integrated "omic" data sets, and provided other related resources to the scientific community to promote basic and applied research in infectious diseases. We will make use of these open access datasets and resources available via the Bioinformatics Resource Centers (BRCs) in this application. In particular, we will utilize immune epitope, viral sequence and antiviral drug information from the Influenza Research Database (IRD) and combine these data with other public information from studies of human cohorts infected with the influenza virus. Single-cell data will provide sufficient cellular detail and will serve as “scaffold” in the case that only bulk data is available. In our view, a comprehensive and truly predictive model of these complex relationships can only be achieved through the systematic, integrative, and multi-dimensional OMICS approach that we offer. Host response to vaccination and to influenza infection is the result of complex traits that involve a combination of host factors along with entire networks of transcripts, proteins, glycans and metabolites. Together these responses impact cellular, tissue, and whole organism behaviors. Thus, the host responses to vaccination and infection are an emergent property of molecular networks. The goal of this integrated systems biology approach is to understand mechanisms of heterogeneous response to Influenza by determining how the interactions among biological components compare between high-risk and lower risk populations. Such findings will significantly improve therapeutic options in the fight against these threatening infectious diseases. All the models and the software tools developed through this project will be shared with the community.

NIH Research Projects · FY 2025 · 2022-07

PROJECT SUMMARY Bladder cancer is the fifth most common cancer in the United States, accounting for around 47 deaths per day. Promisingly, five PD-1/PD-L1 immune checkpoint blockade (ICB) therapies were approved for bladder cancer in 2016. Although these ICB treatments have achieved durable clinical responses in a subset of patients (15-25%), the majority of patients have still not benefitted from this therapy. This clinical urgency to extend the benefits of ICB to more patients has led to a need to investigate tumor intrinsic mechanisms underlying resistance. Tumor- promoting inflammation, a hallmark of cancer pathogenesis, is known to contribute to cancer growth in multiple ways including restraining antitumor immunity. We discovered a gene signature from pre-treatment tumor associating with myeloid cells that is enriched in inflammation and innate immune genes and predictive of poor ICB outcomes and survival in two ICB clinical trials. I plan to follow up on this work and dissect the innate immune landscape of bladder cancer and investigate mechanisms of myeloid-cell mediated resistance to ICB therapy. Aim 1 seeks to define the landscape of untreated bladder tumors and provide insight into the immune cell subsets underlying ICB resistance. I will construct a transcriptomic and molecular atlas of bladder cancer at a single-cell resolution, a resource that does not currently exist. I will build atlases of patients’ tumor, blood, and urine using single-cell RNA sequencing, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITEseq), spatial transcriptomics, and O-link proteomics and analyze them using Seurat and other R-based tools. I plan to resolve myeloid cells expressing this resistant gene signature and define their cellular interactions. In Aim 2, I will delve into the transcriptional pathways in myeloid cells that are contributing to ICB resistance. We have identified NLRP3 inflammasome activation and IL-1β signaling in tumor monocyte-macrophages (mono- MΦs) as candidate pathways promoting tumor inflammation and progression. I will model these mono-MΦs by differentiating peripheral blood monocytes into MΦ using GM-CSF and M-CSF under hypoxic conditions with IL- 1β and NLRP3 inflammasome activators., I will test effects on adaptive immunity by co-culturing these mono- MΦs with activated autologous CD8+ T cells. I will also use this model to test drug candidates known to modulate IL-1β and NLRP3 inflammasome activity as potential combinatorial treatments with ICB in bladder cancer. This proposal combines direct ex vivo single cell genomics with in vitro functional experiments for a thorough interrogation of the innate immune contribution to ICB resistance in bladder cancer. Combined, these aims will elucidate innate immune pathway driven resistance to PD-1/PD-L1 ICB therapy in bladder cancer, which can be used to identify critical predictive clinical biomarkers and inform new combinatorial treatment strategies.

NIH Research Projects · FY 2024 · 2022-07

PROJECT SUMMARY/ABSTRACT Immunotherapies such as checkpoint blockade have revolutionized cancer therapy, but responses are seen only in a subset of patients. Though tumor-intrinsic factors such as tumor mutational burden (TMB) or IFNγ “inflamed” signature partially predict sensitivity to checkpoint blockade, these correlations are limited—most patients with “inflamed” tumors or high TMB still fail to respond. A critical step for efficacy of T cell-mediated immunotherapies, including checkpoint blockade, is dendritic cell cross-presentation of tumor antigen (Ag) to CD8+ T cells. Cross- presentation in vivo requires Batf3-expressing type 1 dendritic cells (cDC1), though these DC have additional functions, including secretion of T cell-recruiting chemokines, driving tumor-reactive T cell (TRT) responses. Because patients with cDC1-enriched tumors have improved responses to anti-PD1, we developed an in situ vaccination (ISV) combining FLT3L, radiotherapy (XRT), and TLR agonism to enhance cDC1 cross-priming of TRT and observed that ISV potentiated anti-tumor effects of PD1 blockade and induced systemic tumor regressions in treated patients. Additionally, we have shown that adoptive transfer of tumor-specific T cells into syngeneic RAG-/- mice clears tumors, while transfer into allogeneic RAG-/- mice fails to control tumor growth, highlighting that APC cross-priming of CD8+ T cells is required for efficacy of antitumor T cells. Despite the critical role of cDC1 cross-priming of CD8+ T cells for effective therapy, there is no established method for measuring T cell cross- or direct-priming in vivo. Consequently, there is a critical need for methods to directly measure CD8+ T cell cross-priming for identifying novel therapeutic targets to enhance cross-priming, and to understand mechanisms of therapy resistance. We hypothesize that cross- and direct-primed T cells, and ISV-primed vs untreated T cells, will harbor distinct signatures, mirroring their differential antitumor efficacy. In Aim 1, we will develop mouse models of cross- and direct-priming using H2Kd knockout, H2Kb-transfected, GFP/OVA- expressing lymphoma and breast cancers and transfer of Ag-specific T cells into syngeneic and allogeneic RAG-/- mice. We will sort tumor-reactive T cells and perform bulk RNA-seq and spectral flow cytometry to identify a cross-primed CD8+ T cell signature. In Aim 2, we will use bulk RNA-seq and spectral flow cytometry to characterize the T cell response to ISV and checkpoint blockade across tumors (lymphoma, breast cancer), model antigens (GFP, OVA, luciferase), and endogenous tumor antigens. The outcome of this study will be elucidation of a cross-primed CD8+ T cell phenotype and a novel immune monitoring technique that allows targeted design of novel immunotherapies by targeting novel checkpoints or costimulators to increase cross- priming of tumor-reactive T cells.

NIH Research Projects · FY 2025 · 2022-07

The purpose of our NRSA TL1 Training Core is to develop, implement and disseminate innovative educational programs designed to catalyze and launch the careers of the next generation of transdisciplinary (TD) investigators in clinical and translational science (CTS). Our NRSA-TL1 pre- doctoral and postdoctoral trainees, equipped with clinical epidemiology skills, data science acumen and teaming capacity, will be prepared to embrace the scientific and medical challenges of tomorrow and pursue novel healthcare solutions. As medicine increasingly tackles previously intractable, yet common complex chronic diseases (e.g., Alzheimer’s, Diabetes, Cancer, Cardiovascular Disease), training in patient-oriented research (POR) needs to champion and catalyze trainee specific data science acumen and capacity. A deeper understanding of data science will enable emerging investigators to capitalize, learn from, harness the potential and realize the promise of Big Data (genetic, epigenetic, biochemical, administrative, quantified self and real world). Our program will catalyze the development of the next generation of leaders in CTS and TD research by building upon our previously established CTSA-funded competency-based educational initiatives, innovative data science curricular activities, novel training assessment toolkits, peer and near peer mentorship and our highly productive and impactful Patient Oriented Research Training, And Leadership (PORTAL) Program, that supports both medical students and PhD students. Our efforts to realize modern CTS through TD research training of physician and PhD data scientists is informed by and leverages our long-standing institutional commitment to big data research, as evidenced by our Biomedical Data Science Initiative, the Exposomics Institute, the PhD programs in Genomics, Data Science and Artificial Intelligence, the Hamilton and Amabel James Center for Artificial Intelligence, Biomedical Engineering and Imaging Institute, Clinical Informatics Fellowship, Center for Resilience and Personal Growth as well as our Resilience Accelerators. Our strategically aligned, stage- and learner-specific pedagogical approaches and educational forums aspire to propel the CTS workforce of tomorrow prepared to unravel and reduce chronic disease burden and advance collaborative team science capacity committed to improving the health of society.

NIH Research Projects · FY 2025 · 2022-07

There is an emerging workforce crisis in the number of scientists entering tranƒslational research careers. This shortage is occurring against the backdrop of increasing complexity in modern scientific research, where single discipline research studies simply cannot answer the challenges that face modern medicine today. The ever- growing complexity of 21st century translational science requires transdisciplinary (TD) team-based research that integrates and extends beyond discipline-specific concepts, approaches, and methods to accelerate the innovations that will solve complex real-world problems. The NCATS KL2 career development program is a key initiative designed to maintain and expand the pipeline of innovative, collaborative and productive clinical- translational scientists though implementation of customized individual development plans (IDPs), TD mentoring, and individualized curricula. Our goal is to develop a cohort of TD scientists who have the breadth and depth of skills necessary to navigate the critical future issues of health and disease in our increasingly complex world. In our newly envisaged ConduITS career development program, we will focus on training TD clinical translational research data scientists. The KL2 scholars will be trained in core competencies including epidemiology, study design, biostatistics/data science, informatics, clinical trials, and ethical/regulatory guidelines, as well as have broad exposure to the methodological steps of the translational process from discovery to community engagement via innovation, life course research, and workforce development. Moreover, we focus on training team-based clinical and translational researchers by leveraging our rich research environment of large-scale clinical datasets, well-established cohorts and biobanks, such as the BioMe Biobank and the Environmental Influences on Child Health Outcomes (ECHO) cohort among other big data resources. Our state-of-the-art programs in genomics and exposomics, and strong community engagement have helped Mount Sinai develop a number of highly innovative programs in drug discovery, entrepreneurship, and team-building, bringing together biomedical research stakeholders that reflect scientific expertise across the lifespan. Our workshops, short courses and advanced training seminars focus on strategic areas, such as informatics, big data, workforce development, team science, and community engagement, as well as academic skills including scientific writing, negotiation skills, conflict resolution, industry interactions, federal grant preparation and management, and the promotion process. We also offer a mentor training program aimed to teach mentors the skills that will help improve the mentoring experience, promote mentees’ growth and help build resilience and confidence. Furthermore, to provide our younger generation of scientists networking opportunities, we are building an institutional K-Club of successful junior faculty with career development grants, to serve as a communication hub for various career development activities.

NIH Research Projects · FY 2025 · 2022-07

In the past decade, Mount Sinai has invested significantly in the integrative translational initiatives needed to advance precision medicine. This included investments in genomics, high-performance computing, clinical informatics, smart technologies, and computational biology. In concert with institutional strategic goals and increasing community concerns around environmental toxins, ConduITS, the Mount Sinai Institute for Translational Science, has evolved its approach to precision medicine to include a precision public health framework integrating genomics with key public health domains such as environmental health, community-level determinants, and big data team science to more effectively address emerging health challenges. ConduITS will harness unique strengths in research informatics, digital health, genomics, exposomics (the study of all health relevant environment), and data science to transform the science of translation to accelerate discoveries into better health outcomes for all across the lifespan. We will augment ConduITS’ role in transforming the local, regional, and national translational research enterprise by developing and sharing innovative educational programs, incentivizing transdisciplinary team science in emerging data science fields (e.g., exposomics) and entrepreneurship, as well as training the workforce on emerging clinical and bioinformatics learning health system approaches that leverage big data. Our aims cut across the domains serving as organizing principles for our CTSA hub including: 1) Workforce Development. Evolve learning opportunities promoting transdisciplinary clinical data science and entrepreneurial activities; 2) Full-spectrum translational science. Advance full-spectrum translational science (from basic to dissemination science) across all training initiatives and leadership ranks in ConduITS to promote activities that drives sustainable health impact and promotes longevity,; 3) Collaboration and Engagement. Engage a range of stakeholders in all phases of translational research through accelerator models constituted to address priority concerns of the populations we serve and apply a life course and data science framework: 4) Informatics. Leverage data science to better coordinate health care delivery with translational research by integrating secure electronic health records (EHRs), patient reported outcomes, clinical trials management systems, and institutional biobanks and data repositories, enabling clinical data science research; 5) Methods and Processes. Innovate and streamline research administrative oversight and processes to minimize roadblocks, ensure quality and integrity; monitor outcomes and garner feedback from stakeholders to facilitate and enhance participation in clinical translational research supported by ConduITS, regional CTSA hubs, and the CTSA national network; and 6) Integration. Incorporate translational research across the lifespan, spanning from perinatal and pediatric participants to geriatric populations, accelerating inclusion of environment in life course precision medicine via our innovative Exposomics optional function.

NIH Research Projects · FY 2025 · 2022-07

PROJECT SUMMARY/ABSTRACT Mutations in DYRK1A, which encodes a ubiquitously expressed kinase that antagonizes the calcium- dependent calcineurin (CaN)/NFAT signaling pathway, have been reproducibly linked to neurodevelopmental disease. DYRK1A loss of function has been associated with syndromic intellectual disability and autism spectrum disorders (ASD), and increased DYRK1A activity is thought to underlie aspects of Down Syndrome pathophysiology. These genetic clues underscore DYRK1A dosage-dependent regulation of nervous system development; however, the precise mechanisms by which DYRK1A executes its roles in the developing brain remain poorly understood. Our long-term goal is to understand how DYRK1A acts in specific cell types of the embryonic cerebral cortex to influence the commitment of neural stem and progenitor cells to specific neural fates. In the proposed studies, we focus on NFAT-dependent transcriptional mechanisms as primary effectors of DYRK1A activity in neural stem cells and their progeny. We have found that deleting Dyrk1a specifically in the developing cortex differentially impacts calcium signaling in neural stem/progenitor cells and neurons of both the mouse and human. Loss of one or both copies of Dyrk1a results in dose-dependent cortical thinning, depletion of radial glia stem cells, reduced astrocyte abundance, neuronal cell death, and shifts in excitatory neuron differentiation. Our previous studies uncovered similar changes in the generation of excitatory neuron subtypes resulting from the mutation in the Cav1.2 calcium channel that gives rise to the syndromic ASD Timothy Syndrome. Imbalances in these same excitatory neuron types have also been linked to neuropsychiatric syndromes and channelopathies, hinting that calcium-regulated molecular mechanisms may represent a core substrate underlying cellular phenotypes in ASD and other neurodevelopmental disorders. In line with this idea, we have found that the effects of Dyrk1a deletion during cortical development are phenocopied by in vivo modulation of CaN/NFAT signaling, and we have used CUT&RUN sequencing to begin to identify NFAT transcriptional targets in the developing brain. Building on these strong published and preliminary findings, the central objective of this proposal is to define cell type-specific mechanisms by which DYRK1A regulates the development of the cortex. The proposed research tests the ideas that NFAT transcriptional targets underlie deficits in stem cell maintenance and differentiation resulting from cortex-specific Dyrk1a inactivation (AIM 1), that DYRK1A and calcium signaling through CaN/NFAT play key roles in cortical astrogliogenesis (AIM 2), and that cell type-specific NFAT targets contribute to DYRK1A signaling specificity (AIM 3). These studies will build a foundation for future research expanding our knowledge of how calcium signaling regulates brain development and how ubiquitously expressed disease-relevant genes exert specific functions in different cell types. Our results will also provide therapeutic entry points for convergent intracellular mechanisms driving neurodevelopmental disorders.