Icahn School Of Medicine At Mount Sinai

NIH Research Projects · FY 2024 · 2022-09

PROJECT SUMMARY/ABSTRACT The fundamental mechanisms by which acute intense stress affects energy homeostasis via brain substrates and sexual dimorphism of these processes are poorly understood. Environmental stressors induce fight-or- flight-or-freeze response via the locus coeruleus (LC) in the brainstem, a major sympathetic regulator in humans and animals that triggers energy metabolism. LC innervates the brown adipose tissue (BAT) and expresses high levels of PAC1 receptor for the neuropeptide PACAP (pituitary adenylate cyclase activating peptide). PACAP/PAC1 are critical regulators of stressors of all kinds, fear, appetite, feeding, and energy metabolism and genetically linked to stress-related disorders like post-traumatic stress (PTSD) in humans. Intriguingly, women with PTSD showing high blood levels of this neuropeptide and brain PAC1 receptors regulate fear in a sexually dimorphic manner in animals. To test the importance of PAC1 in acute intense stress and energy homeostasis, we used the stress-enhanced fear learning (SEFL) behavioral model in mice. Our preliminary data show that ablation of PAC1 receptors from the LC enhances SEFL expression, energy metabolism as assessed by indirect calorimetry measurement, and increases metabolic genes like uncoupling protein 1 in BAT in females than males. Thus, harnessing on the biology of PAC1 receptors, we aim to lay a mechanistic framework linking acute intense stress and energy metabolism in a systematic and sex-dependent manner via the LC. We hypothesize that PAC1 receptors in the LC are important for gating stress-associated metabolic information and BAT functions in a sexually dimorphic manner. Aim 1 will test a SEFL mediated loss of function of LC-PAC1 on whole body energy expenditure and on BAT functions. For this, we will test if viral cre-recombinase mediated PAC1 deletion from LC in mice with floxed PAC1 regulates SEFL-associated energy expenditure and induction of thermogenic genes in BAT in a sex-dependent manner (via transcript analysis, mitochondrial bioenergetics, and tissue lipolysis). Aim 2 will test if PAC1 expressing LC neurons project directly to BAT in a sexually dimorphic manner under SEFL. For this, we will use retrograde viral tracing to determine LC to BAT projecting cell populations combined with in situ hybridization for PAC1 in LC. We predict that female mice will show enhanced energy expenditure, BAT thermogenesis and increased LC projection to BAT. Overall, using state-of-the-art tools and techniques and rigorous systems biology approach of linking acute intense stress and energy metabolism, our studies will lay crucial groundwork for several future work. This will serve as a premise for studying central sympathetic control of metabolism in chronic stress- related conditions such as PTSD that are comorbid with metabolic diseases and increasingly prevalent in the US populations.

NIH Research Projects · FY 2025 · 2022-09

Project Summary: Sickle cell disease (SCD) is the most common inherited blood disorder in the United States, affecting 70,000- 100,000 Americans. SCD is caused by a mutation in the β-globin gene that leads to significant deformation of the red blood cell (RBC) membrane and promotes RBC adhesion to other cells, inducing vaso-occlusive episodes (VOE). Chronic SCD is accompanied by progressive, systemic multi-organ dysfunction and costs over $475 million annually in hospital admissions. Our recent work demonstrates that the depletion of microbiota in SCD mice by antibiotics reduces organ damage and iron overload. Our preliminary data show that organ damage is significantly improved in germ-free SCD mice compared to specific-pathogen-free SCD mice, confirming the importance of microbiota in organ damage development. Analysis by 16S rDNA sequencing uncovered a candidate bacterium—Enterococcus gallinarum (E. gallinarum)—that may promote organ damage in SCD mice. Additionally, we demonstrate that SCD mice fed an iron-restricted diet exhibit significant reversal of organ damage compared with SCD mice fed a control diet. In the current application, we propose a 5-year experimental plan to advance our understanding of the microbiota-mediated effects on SCD disease progression and to test the manipulation of microbiota as a potential novel SCD treatment. In Specific Aim 1, we will confirm whether E. gallinarum functions as a pathogenic bacterium to influence the progression of organ damage in SCD mice. Additionally, we will investigate whether an E. gallinarum–specific vaccine reduces organ damage burden in SCD mice. We will explore the microbiota- related mechanisms that induce organ damage in SCD mice. Specifically, we will study how microbiota can bypass the gut barrier by analyzing relevant gut permeability parameters such as tight junction and mucus layer integrity. We hypothesize that once E. gallinarum translocates from the portal vein to the liver, it upregulates T helper 17 (Th17) cells that recruit other inflammatory cells to induce the organ damage seen in SCD mice. In Specific Aim 2, we will explore the role of dietary iron in gut microbiota survival and whether dietary iron is involved in disrupting gut barrier integrity in SCD mice. These proposed studies, focused on strategies of microbiota manipulation in SCD, will allow us to identify the key microbial species that contribute to SCD pathophysiology and potentially provide novel, cost-effective approaches for managing SCD’s life-long complications.

NIH Research Projects · FY 2025 · 2022-09

ABSTRACT Tau normally regulates microtubules in neurons and glia, however during diseases pathogenesis, several post- translational modifications cause hyperphosphorylation of this protein which consequently is toxic to the cell. Primary age-related tauopathy (PART), a common pathology associated with human aging is estimated to effect 1-7 % of the of the population and patients with the disorder can be cognitively normal or exhibit a range of symptomology including mild cognitive impairment or dementia. Neuropathologically, those with PART have var- ying degrees neurofibrillary tangles in the medial temporal lobe, and an absence of amyloid plaques throughout the brain. Our goal is to deploy three independent approaches to understand how PART has convergent and divergent features from other primary and secondary tauopathies. The objective is to use novel high-throughput genetic and transcriptomic technologies combined with innovative computational methods including computer vision and AI to better characterize drivers of tau phosphorylation in PART. Our hypothesis is that machine learning classifiers (supervised and unsupervised) combined with single cell analysis will be able to accurately identify and quantify transcriptomic, genomic, clinical, and morphological features in PART to further understand the underlying amyloid independent mechanisms of tauopathy. Our rationale is that understanding the genetic transcriptomic and clinical architecture of PART will assistant in understand disease staging, diagnosis, and progression. We plan to test our hypothesis by pursing the following significant aims: (1) Quantify neurofibrillary tangle burden using supervised machine learning models and integrate this data in genetic and clinicopatholog- ical association studies (2) Model the sequential progression of neurofibrillary tangle degeneration in PART with unsupervised deep generative approaches. (3) Identify transcriptional alterations associated with neurofibrillary tangles in PART using single cell RNA sequencing. The proposed research is innovative as it applies novel transcriptomic and machine learning techniques to identify in an understudied group of elderly subjects with tauopathy lacking amyloidosis. This proposed research is significant as it addresses a critical unmet need to develop algorithms which can assist neuropathologists in their post-mortem diagnosis and provide better quan- titative phenotypic data which can aid in facilitating better neuroprotective strategies. The proposal builds upon the candidate's established interest in age-related tauopathy and his prior training in biomedical engineering and translational basic science research. The candidate’s primary mentor, Dr. John Crary, is an experienced neuro- pathologist and tau neuroscientist and will be supplemented by mentoring team consisting of Dr. Bin Zhang with specific expertise in computational genetics and transcriptomics and Dr. Thomas Fuchs, a prominent scientist in the field of computational pathology with a specific expertise in machine learning classifiers, AI, and computer vision. They will assure that the proposed research and training prepare the applicant to be an independent investigator in experimental computational neuropathology.

NIH Research Projects · FY 2025 · 2022-09

Project Summary Forty million Americans live with kidney disease and this number is projected to increase with rising rates of CKD comorbid conditions, including diabetes, obesity, and hypertension, superimposed on an aging patient population. A tremendous financial burden is imparted by dialysis therapy and kidney transplantation for end- stage CKD. At present, however, there are limited tools in existence to predict the progression of AKI and CKD, and development of therapies has been disappointingly restricted. The overall objective of this application is to establish the Mount Sinai Kidney Precision Medicine Project (KPMP) recruitment site in support of the larger consortium’s tissue interrogation and phenotyping activities. There is a tremendous need to utilize human kidney tissue as a research tool for the identification of AKI and CKD disease markers to elucidate molecular pathways that contribute to kidney disease development and progression. We have proposed three Specific Aims: Aim 1 will establish a robust system of patient centered oversight to recruit diverse patients into a kidney biopsy cohort while maintaining the highest standards of safety, quality and ethical research conduct. In Aim 2 we will recruit and retain a spectrum of patients with CKD in response to KPMP priorities. This includes leveraging existing institutional risk stratification tools and resources to identify and recall patients at risk for CKD progression due to diabetes, hypertension, prior COVID-19 infection and apolipoprotein L1 associated disease. Aim 3 will recruit and retain patients with AKI as well as those at high risk for AKI identified by a machine learning algorithm. These Aims overseen by a stakeholder board and executed by an experienced multidisciplinary team, will integrate with the KPMP consortium to accomplish its transformative aims.

NIH Research Projects · FY 2025 · 2022-09

ABSTRACT Depressive symptoms are present in up to 40% of individuals with Alzheimer’s disease (AD) and an ongoing debate regarding whether they represent a risk factor or a prodromal sign of AD. Chronic conditions such as depression impact the stress response and may accelerate biological aging further contributing to susceptibility to age-related conditions specifically cognitive decline. However, genetics of psychiatric traits and AD have been mostly studied separately. This proposal aims to identify coding and non-coding regulatory variants associated with shared genetic risk for depression and AD in multiple cohorts: UK biobank, Million Veteran Program, Alzheimer’s Disease Sequencing Project, National Health and Resilience in Veterans Study, and Yale-Penn study, and replicate findings in PsycheMERGE, cumulatively studying more than 1 million individuals. We will assess two major risk factors of AD - APOE-ε4 carrier status (Model-1) and parental history of AD (Model-2) with depression. Our previous findings from the genetically regulated expression study of depression in 1.2 million individuals using hippocampus-based expression quantitative trait loci (QTL) identified several genes which have roles in AD pathology (e.g. PARK2, NEGR1, HSPA1A, ITPR3, NLGN1, and DRD2). Therefore, we hypothesize that stratifying depression with AD phenotypes will uncover overlapping genetic contributions between depression and AD and elucidate the shared molecular mechanisms, and potential therapeutic targets. To test theses hypotheses, this proposal aims to develop a multi-modal framework to study neuropsychiatric comorbidities by investigating, Aim-1) whole exome profiles for coding regions associated with depression and genetic risk for AD (K99 phase), Aim-2) transcriptomic profiles to identify a shared molecular basis for depression and AD risk by integrating large-scale GWAS with brain tissue-based molecular QTL studies (R00 phase), and Aim-3) epigenome profiles to identify methylation sites associated with a combined polygenic score of depression and AD, and compare biological aging between depression and AD comorbidity, and either disorder alone (R00 phase). The accompanying training includes didactic courses in i) data analysis from multiple high throughput technologies, ii) developing biomarkers from large-scale datasets, iii) computational programming and iv) gerontological studies. The professional development training will include writing workshops, building mentoring portfolio, training opportunities to establish laboratory as an independent researcher. This training plan was developed under advisory team comprised of five members who are experts in AD, psychiatry, aging, large-scale genomics, and cohorts with electronic health records. Together they provide guidance on the proposed study and support a multidisciplinary neuropsychiatric research career for the candidate.

NIH Research Projects · FY 2025 · 2022-09

Project Summary/Abstract Amyloid-beta (Aβ) is a small piece of a larger protein called amyloid precursor protein. It accumulates in stages into microscopic amyloid plaques that are considered a hallmark of a brain affected by Alzheimer’s disease (AD). Positron emission tomography (PET) is an established technique to detect Aβ plaques in vivo. Some preclinical and postmortem data report an accumulation of redox-active iron near Aβ plaques. magnetic resonance imaging (MRI) of Aβ plaques has been attempted using various techniques, notably with susceptibility contrast. The non-invasive detectability of Aβ plaques in MRI has so far been largely attributed to iron deposition accompanying Aβ plaques. It is believed that the susceptibility shortening effects of paramagnetic iron are the primary source of contrast between plaques and surrounding tissue. We hypothesized that aggregations of iron associated Aβ would increase electron density and induce notable changes in local susceptibility value. Due to higher susceptibility at ultra-high field (UHF) strengths, induced iron susceptibility is large enough to generate contrast relative to surrounding normal tissues that can be visualized by quantitative susceptibility techniques at 7 Tesla (7T) MRI. The goal of this proposal is to bring forward an alternative platform for analysis of pathologic biomarkers in AD patients, thanks to ultrahigh field (7T) MR neuroimaging. The development of specialized sequences for 7T susceptibility MRI will enable the comparison and microstructural data in AD patients at an unprecedented resolution; this, in turn, will provide a deeper understanding of the in vivo pathophysiology of AD and allow us to potentially identify a set of susceptibility-based markers of disease pathology. Specifically, we expect our integrated approach to help us validate UHF MRI as a unique tool to improve AD diagnosis and prognostic measurements. Our central hypothesis is that UHF MRI provides a unique and powerful measure of changes associated with AD in the brain, and may be integrated with existing neuroimaging tools to achieve unprecedented visualization of the consequences of disease pathology. This career development project also includes a training plan designed to refine and address gaps in the applicant’s technical and scientific knowledge and experience, develop his research career skills, expose him to the neuroimaging and neuroscience communities, and lay the groundwork for his career as an independent scientist. The training plan encompasses: coursework in neurological disorders, clinical neuroscience, research grant applications, and budget management; presentation of his work at technical MRI and neuroscience conferences; delivery of formal classroom lectures and small-group teaching sessions; mentorship of research volunteers; organizing a research symposium; and hands-on training during the conduct of the research project.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY Autism spectrum disorder (ASD) affects 1 in 54 children in the US, however the modifiable risk factors for this disorder remain unknown, creating a pressing public health need. As ASD likely arises early in prenatal development, efforts in identifying such modifiable factors have focused on maternal exposures in pregnancy, including medications. While some medications have been shown to be associated with ASD, major critical knowledge gaps remain, including: (1) the underlying mechanisms have not been elucidated, and (2) the effects of most maternal medications on ASD risk are still unknown — despite pervasive use of prescription and over- the-counter (OTC) medications in pregnancy, most of which cross the placenta, with unknown effects on the fetus. In response, the key objectives of the proposed study are to identify medications taken by pregnant women that influence offspring ASD risk, elucidate confounding factors in these associations, and benchmark their generalizability and specificity. To achieve these objectives, we propose independent, but synergistic aims: Aim 1: Systematically investigate the effects of the full range of maternal prescription and OTC medications used in pregnancy on ASD offspring risk, using well-powered sample of 1.2M live births from Israel with full demographic, prescription, medical and pedigree information. We will test if the observed effects on ASD differ depending on the timing or duration of the exposure, concurrent use of other medications, indication or offspring sex. Aim 2: Test the mechanisms underlying the associations between maternal medication use and ASD, 2A: examining familial confounding, using sibling comparisons and negative control of paternal exposure; and 2B: identifying clinical confounding by (i) examining risk of ASD associated with clusters of medications defined by their pharmacological features (target(s), chemical structure) vs indication, (ii) adjustment for maternal health proxies; (iii) discontinuation analysis. Aim 3: Establish the specificity and generalizability of maternal medication effects on ASD, by 3A: examining the range of other (neuro)developmental outcomes affected by the same maternal medications as ASD, and 3B: performing a replication study in Sweden, Finland and the US. The innovation of this project is four-fold: (1) it can identify novel, potentially modifiable risk factors for ASD; (2) it triangulates orthogonal approaches to discern causal vs confounded effects of medications on ASD risk; (3) it leverages pharmacological and pharmacokinetic data on medications to unambiguously define exposure; and (4) it provides new insights into shared and distinct risk factors in different adverse developmental outcomes. Upon completion, our multi-dimensional approach, rigorous methods and unprecedented study power in the hands of our expert team will deliver a systematic list of the maternal prescription and OTC medications in pregnancy associated with ASD, and robust evidence regarding the role of the confounding factors in these effects. This will help identify potential modifiable risk factors for the disorder, contribute high-quality evidence about the risks associated with maternal use of certain medications during pregnancy, and delineate the etiology of ASD.

NIH Research Projects · FY 2025 · 2022-09

Pulse oximeters provide indirect evaluations of blood oxygen concentration (SpO2) and are widely used throughout the medical professions for diagnosing and monitoring respiratory anomalies in patients. Research shows that commercially available pulse oximeters systematically overestimate true arterial blood oxygen saturation (SaO2) due to the concentration of melanin in the skin. This overestimation in SpO2 puts patients at a greater risk for not meeting the criteria for hospitalization or initiation of ventilator support, which increases risk for mortality or morbidity. No published explanations exist for this well-documented observation and, indeed, the available literature often contrarily states that pulse oximeter measurements are not affected by skin pigmentation. Our theoretical analysis and pilot research, however, demonstrate that the overestimation is due to the use of broadband light-emitting diode (LED) light sources. The broad spectral bandwidths of these LEDs interact with the spectral absorption of melanin concentration in skin to systematically shift the oximeter calibration. This shift causes artificially high values of SpO2 at low blood concentrations of O2, particularly in skin with high melanin concentration. The 3 proposed aims will extend our efforts to date, providing a scientific foundation for eliminating this error and to foster development and promotion of simple, inexpensive, and accurate pulse oximeters. In Aim 1, we will: (a) determine if there are other spectrally-dependent constituents in the finger that change with each pulse; (b) determine how light-source bandwidth interacts with melanin, including whether there are other pulse-dependent changes in spectral transmission through the fingers, and how sensitive SpO2 measurements are to light source bandwidth; (c) specify the practical peak wavelength and spectral bandwidth needed for bias-free pulse oximetry; and (d) fabricate an optimized light source that provides bias-free pulse oximeter measurements for testing in Aim 2. In Aim 2, we will demonstrate that the finger probe developed in Aim 1d provides bias-free pulse oximeter measurements (SpO2) that do not overestimate true arterial oxygen saturation measurements (SaO2) at low blood concentrations of O2. In Aim 3, which will not employ human subjects as in Aims 1 and 2, we will translate our findings (i.e., print, in-person, and social media) to physicians, hospitals, and health care facilities. As part of Aim 3, we will reach out to healthcare professionals to ensure they are aware of the problems with existing commercial pulse oximeters and introduce them to bias-free pulse oximeters once they are available. Finally, we will license the technology to major manufacturers of pulse oximeters to facilitate translation.

NIH Research Projects · FY 2025 · 2022-09

This proposal studies two fatal, neurological lysosomal storage diseases, Type A/B and Type C Niemann-Pick disease (NPA/B and NPC, respectively). NPA/B is due to an inherited deficiency of the enzyme acid sphingomyelinase (ASM), leading to the accumulation of the sphingolipid, sphingomyelin (SPM), in cells and tissues of affected patients. In contrast, ~95% of patients with NPC have a defect in the cholesterol transport protein, NPC1, leading to a primary defect in cholesterol storage. Despite their distinct genetic and protein defects, the pathological and clinical presentation of NPA/B and NPC overlap. For example, ~50% of NPA/B patients and all patients with NPC suffer from debilitating and life-threatening central nervous system (CNS) complications, and no effective therapies exist. To address this important unmet medical need, in preliminary studies we have generated a range of data supporting the use of a novel endocannabinoid (ECB)-based treatment for these disorders. For example, we have found that inhibitors of the enzyme fatty acid amide hydrolase (FAAH), which elevate several ECBs, significantly lowered SPM in cultured neurons and tissues of Type A/B NPD mice, leading to CNS improvements and extension of lifespan. We also found a significant down-regulation of the type-1 cannabinoid receptor (CB1R) expression on the surface of neurons from these mice and in brain tissue from a patient with NPA, due to entrapment of the receptor within the lysosome. This abnormality was corrected by FAAH inhibition. Similarly, treatment of NPC mouse neurons with FAAH inhibitors led to a reduction of both SPM and cholesterol, and there was a down-regulation of CB1R expression on the surface of these cells as well. Based on these preliminary findings, we propose that FAAH inhibition could be a novel and highly effective treatment for the CNS disease in both NPA/B and NPC, and that repurposing existing FAAH inhibitors that cross the blood brain barrier might be rapidly translatable to patients. To pursue this goal and further understand the relatedness of these disorders, three specific aims are proposed: 1) Characterize the molecular mechanism(s) underpinning the protective effects of FAAH inhibition in NPA/B cells and mice; 2) Investigate the function of the ECB system in NPC, and further explore FAAH inhibition as a potential treatment for this disease, and; 3) Use system biology and multi-omic approaches to compare the pathways and networks impacted in NPA/B and NPC, and to obtain a global picture of the molecular changes resulting from FAAH inhibition. We also hope to provide further insights regarding the relatedness of these ultra rare diseases to common neurologic diseases with which they share significant CNS pathology, including Alzheimer's and Parkinson's disease.

NIH Research Projects · FY 2025 · 2022-09

SUMMARY Individual responses to vaccinations are a critical public health issue and mounting evidence suggests that early life environmental factors may program immune dysregulation that manifests years later. This developmental origins of health and development (DOHaD) theory posits that dose and timing of early life immunotoxic environmental exposures can have long-lasting consequences on the trajectory of immune system function. The immune system begins to develop in utero and, as children age and experience infections and vaccinations, an ever-expanding repertoire of antibodies become part of their lifelong immune memory. Yet research on child immune function and its response to ubiquitous immunotoxic metal exposures—experienced in utero and early in life (0–5 years)—has been largely overlooked.We will address this knowledge gap in the Mexican PROGRESS study, which has measures of immunotoxic metal exposures [arsenic (As), cadmium (Cd), manganese (Mn), and lead (Pb)] at several key developmental time windows and from multiple biomatrices (tooth, blood, and urine). We will assess child immune function by measuring antibody levels at 4, 6, 8, 10–11, and 13–15 years of age in response to scheduled childhood vaccinations (i.e., measles, mumps, rubella, diphtheria, tetanus, and pertussis). Our preliminary data show that (i) exposure to individual metals (Cd, Pb) and a metal mixture (As, Cd, Mn, Pb) may result in poorer antibody responses at age 4 years and that (ii) there are critical windows of susceptibility to As, Mn, and Pb exposures. Additionally, metal exposures induce systemic oxidative stress (OS) leading to suboptimal immune system function. Given the pro-oxidant role of metals, we will also quantify cumulative OS via a novel biomarker—mitochondrial DNA (mtDNA) heteroplasmy, which reflects OS-induced mtDNA mutation counts accumulating over time. Our initial data show that prenatal metal exposures are associated with mtDNA heteroplasmy counts at birth. We will measure mtDNA heteroplasmy at birth and at 8 and 13–15 years of age as a predictor and mediator of antibody responses. In Aim 1, we will determine the association between exposure to individual metals and metal mixtures with child antibody responses to vaccination at specific ages and antibody response trajectories over time. In Aim 2, we will determine critical windows of susceptibility to immunotoxic metals exposure on child immune system at specific ages and over time. In Aim 3, we will investigate associations between mtDNA heteroplasmy levels and (i) exposure to individual metals and metal mixtures and (ii) child antibody response to vaccination at specific ages and antibody response trajectories. We will apply statistical causal modeling strategies to evaluate the mediating role of mitochondrial biomarkers on the metal–immune system relationship. Completion of these aims will drive interventions that may help prevent lifelong immune system dysregulation and related adverse health consequences.

NIH Research Projects · FY 2025 · 2022-09

Project summary In low- and middle-income countries ~2.8 billion people are exposed daily to smoke from cooking fires, termed household air pollution (HAP), resulting in an estimated 2.3M deaths and 91.4M DALYs in 2019. The largest proportion of HAP-attributable deaths are due to cardiovascular disease. Establishment of cardiovascular health in childhood is critical to reduce risk for future cardiovascular disease. We hypothesize that early life (prenatal to age 1) exposure to HAP alters cardiovascular development and programs future disease risk. We further hypothesize that the metal composition of air pollution drives toxicity. We propose to build on an existing pregnancy cohort in Ghana – the Ghana Randomized Air Pollution and Health Study, or GRAPHS – to assess how early life air pollution exposure and metals exposures affect cardiovascular health through age 12 years. We will use well-established, validated methods to assess these outcomes. In the long run, our research will help build the evidence base for cost effective interventions to improve health by reducing HAP exposure.

NIH Research Projects · FY 2025 · 2022-09

The prevalence of type 2 diabetes (T2D) is increasing, and etiological factors promoting the T2D epidemic are not fully understood. Growing experimental evidence shows that exposures to endocrine-disrupting chemicals (EDCs), such as per- and polyfluoroalkyl substances (PFAS), promote T2D development, likely in synergy with known risk factors such as genetic variations. PFAS are ubiquitous and persistent chemicals that perturb metabolism. However, few prospective studies examined the association between PFAS and T2D risk, and those were in small and not fully representative samples. Previous studies also lacked clinically ascertained T2D diagnosis, investigated only a few of the many potentially hazardous PFAS, and did not examine potential effects of PFAS mixtures or gene–PFAS interactions. State-of-the-art integrated omics approaches can overcome these limitations to advance the field. We propose the first integrated metabolome–genome approach to (1) characterize the associations between PFAS concentrations (individual PFAS and mixtures) in prediagnostic plasma samples and incident T2D risk and potential effect modification by genetic predisposition to T2D using polygenic risk scores as an innovative solution for studying interactions, (2) identify underlying dysregulated metabolic pathways, and (3) identify metabolic signatures in prediagnostic plasma samples defined by EDC exposures and endogenous metabolites associated with T2D risk. We will perform a nested case–control study leveraging BioMe, an ongoing electronic health record-linked biobank with >55,000 participants enrolled while seeking primary care at Mount Sinai Hospital (NY) since 2007. Incident T2D cases are matched (1:1) to BioMe T2D-free controls (N = 1,700), with ~6 years average time between blood draw and T2D diagnosis. We will use prediagnostic plasma to measure PFAS and metabolic pathways using state-of-the-art high-resolution metabolomics (HRM) approaches. We will replicate findings among incident T2D cases and matched controls from an existing population-based study in Los Angeles and Hawaii with extant genome data and prediagnostic plasma concentrations of PFAS and HRM measured at the same lab as BioMe samples. In contrast to prior studies, we incorporate a wide suite of legacy and emerging PFAS, exposure-mixture effects, and gene–environment interactions by leveraging state-of-the-art metabolome–genome approaches and a rigorous discovery–replication design in two unique, well-phenotyped US cohorts with prediagnostic plasma samples to identify early biomarkers associated with T2D. This research relies on a multidisciplinary team of seasoned investigators with expertise in environmental/genetic epidemiology, PFAS and T2D research, and state-of-theart HRM, genomics, and biostatistical exposure–mixture methods. Findings will inform precision medicine approaches for T2D prevention and treatment in US populations.

NIH Research Projects · FY 2025 · 2022-09

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. Our previous studies established valid clinical diagnoses and have demonstrated markedly diverging longitudinal lung function trajectories in the largest and most diverse WTC occupational cohort. Besides our expertise with longitudinal lung function analyses, we were uniquely able to demonstrate associated quantitative chest computer tomography (QCT) metrics that have helped validate and characterize the disease processes that have been associated with WTC occupational exposures. QCT has revolutionized respiratory research, and has contributed important and novel information on interstitial, proximal and distal airway, and vascular changes that underlie the process of inflammatory remodeling and disease progression. Our observations in this cohort have also identified a subgroup who has experienced unexpected and significant lung function gain in adult life, suggesting a process of resolution in need of improved understanding. Our studies have been on the forefront of occupational respiratory research. We propose three specific aims to deploy novel QCT and spirometric markers to investigate early interstitial and airway injury and remodeling in subjects who have experienced accelerated lung function decline or developed chronic obstructive pulmonary disease while on longitudinal and clinical surveillance.

NIH Research Projects · FY 2024 · 2022-09

PROJECT SUMMARY The treatment of recurrent Clostridioides difficile infection (rCDI) by fecal microbiota transplantation (FMT) is the defining success amongst therapeutics aimed to manipulate the microbiome with cure rates typically exceeding 80% of recipients. This success has facilitated numerous clinical trials yielding important insights that have advanced clinical care including the quantification of the durable stability of frozen fecal slurries that enabled stool biobanks, the studies of fecal slurry administration that compared efficacies across administration routes of oral, colonoscopic, and nasogastric, and the application of FMT in other conditions including ulcerative colitis where it appears to have modest efficacy. However, the use of complex fecal slurries as a therapy is a challenge due to our inability to completely determine the safety of a product that varies with each FMT donor, including some that have transmitted opportunistic pathogens that led to serious adverse events. The scaling of FMT is also a challenge, as the drug material is sourced from individual human donations that are finite in supply and labor intensive to process into the final product. We propose to administer live biotherapeutic products (LBP) as an alternative to FMT. We have isolated the strains for this LBP from known-successful FMT donors allowing us to compare (Aim 1) the clinical response and (Aim 2) the microbial engraftment of the FMT with that of the LBP. The LBP was specifically designed to contain prevalent human gut microbes that have engrafted in a majority of recipients and that are not associated with severe adverse events in prior FMT studies. The results from this pilot and feasibility clinical trial (60 subjects, N=30 FMT and N=30 LBP) will provide important safety data, clinical insights, and basic science results to advance the potential of LBPs as novel therapeutics.

NIH Research Projects · FY 2025 · 2022-09

ABSTRACT The proposed training grant is designed to advance the academic career of Dr. Vaishnavi Kundel, MD, by building upon her strong background in clinical sleep medicine to engage in patient-oriented research, and develop expertise in exploring the role of sleep in cardiometabolic disease risk. Through this proposal, she will obtain multidisciplinary training to investigate chronic sleep deprivation and sleep irregularity as potentially modifiable risk factors for atherosclerosis and visceral adiposity measured using multi-modality imaging - hybrid 18fluorodeoxyglucose (FDG) PET/MRI. Research plan: The proposed research builds on Dr. Kundel's pilot studies funded by the AASM. The aims are to determine whether habitual short sleep duration and sleep irregularity are associated with increased vascular inflammation and visceral adiposity (which is strongly linked to increased CVD risk), independent of OSA (often a confounder in these associations). We will utilize multi-day actigraphy to collect objective sleep metrics, and PET/MRI to measure vascular inflammation and visceral adipose tissue (VAT) metabolic activity (a novel marker of adipose tissue inflammation) in the recruited patients. With successful completion of the proposed training and research, we hope to underscore the role of chronic sleep deprivation and sleep irregularity in cardiometabolic risk, establishing an index of imaging biomarkers for future research. Moreover, the results will provide direction for future (R01) proposals - laying the groundwork for developing multidisciplinary collaborations to elucidate mechanisms by which sleep modulates inflammation, with a long-term goal of identifying biomarkers of early cardiovascular risk in this subset of patients, and designing sleep extension studies. Career Development: Dr. Kundel's training plan features an outstanding research environment at the Icahn School of Medicine at Mount Sinai along with nationally renowned mentors and advisors with complimentary expertise. Her primary mentoring team comprises of (a) Dr. Neomi Shah, MD, MPH, MS (expert in obstructive sleep apnea [OSA] and cardiovascular (CV) diseases, and application of advanced cardiovascular imaging in OSA) (b) Dr. Indu Ayappa, PhD, (recipient of a mentored K-24 award, with expertise in OSA, sleep physiology, and use of actigraphy for objective sleep assessments) (c) Drs. Zahi Fayad and Philip Robson, PhD (experts in use of multimodality imaging for assessment of atherosclerosis and organ system biology). Her training features a combination of carefully designed coursework and practical experiences in 1) actigraphy for comprehensive assessments of objective sleep metrics 2) multi-modality cardiometabolic imaging 3) clinical study design and patient-oriented research 4) training in biomarker science for future proposals. Together, her mentors and advisors have a successful track record of mentoring junior faculty in career development awards, with extensive collaborations and grant portfolios to provide a solid foundation for Dr. Kundel's present proposal, and ultimate success in developing into an independent investigator.

NIH Research Projects · FY 2025 · 2022-09

SUMMARY Many cancer-related independent studies that employ bulk and single cell RNA-seq remain under reused due to their lower findability, accessibility, interoperability, and reusability. The data from these studies can be found in the Gene Expression Omnibus (GEO) but it is provided mostly as raw FASTQ files with non-uniform metadata annotations. While some studies provide aligned reads files, these are processed non-uniformly. This shortcoming makes it difficult to query and integrate this data across studies and with additional external data. To bridge the gap that currently exists between RNA-seq data generation and RNA-seq data processing and reuse, we developed the resource All RNA-seq and ChIP-Seq Sample and Signature Search (ARCHS4). ARCHS4 provides processed RNA-seq data from GEO to support retrospective data analyses and reuse. ARCHS4 caters to users with different levels of computational expertise and has been already employed for many post-hoc analyses and projects. The goals go far beyond just providing cancer researchers with direct access to RNA-seq data through a web-based user interface. We plan to transform other transcriptomics data into RNA-seq-like profiles with Deep Learning, identify pathogenic sequences in human RNA-seq samples, identify short variants from RNA-seq reads, predict gene function from co-expression data including ways to modulate the expression of long non-coding RNAs with small molecules, and most importantly, using the ARCHS4 cost-effective infrastructure, continue to provide a free FASTQ alignment service to the community.

NIH Research Projects · FY 2025 · 2022-09

Project Summary In this new and unfunded study, we will capitalize on the lessons from the past 15 years of psychiatric genomic. Based on these lessons, we propose an exceptionally novel and important set of aims to further knowledge of the genetic architecture of mental illness. We propose to perform whole-exome sequencing and SNP-array genotyping on >150,000 cases with severe psychiatric disorders along with a similar number of controls. It will be large, transdiagnostic, based on patients seen in clinical psychiatry, and comprehensively analyze ultra-rare exonic, rare copy number, and common variation. Because assay costs are prohibitive (on the order of $US 80 million), we are partnering with Regeneron Genomics Center (RGC) that will conduct all genomic assays. NIMH funding is within the $500K direct cost cap at each site. We will: (1) Acquire samples with clinically severe psychiatric disorders. Cases will have lifetime diagnoses of schizophrenia (SCZ), schizoaffective disorder (SAD), bipolar I disorder (BD1), or severe major depressive disorder (sevMDD). Roles: UNC is responsible for data coordination; the sampling sites are ISMMS (the Americas and East Asia) and Cardiff (Europe, Africa, and South Asia) and each will collate samples (i.e., MTAs, ethical approvals, individual consent, harmonize phenotypes, QC DNA). Phase 1 (Years 1-2) will focus on existing samples (N=100K cases). Phase 2 (Years 1-4) will focus on obtaining new samples (N=50K cases), and will enable colleagues from low-income countries to obtain genetic data that would otherwise be impossible. This will help those investigators and greatly increase diversity in genomics research. 2) Genomic assays (Years 1-4). Samples will be sent to RGC in batches from ISMMS and Cardiff. RGC will generate whole exome sequencing and SNP array data. UNC and RGC will jointly conduct alignment, QC, variant calling (SNVs, indels, SVs), and array processing (common SNPs, imputation and CNVs). QC includes assessment of multiple biases and comparison to independent datasets. Deliverable: analysis-ready data frames for rare exonic, rare CNV, and common genetic variation. 3) Analysis for substantive scientific aims. Briefly, the main analytical themes are to identify genetic variation associated with: (a) severe mental illness, (b) specific disorders, and (c) cross-cutting clinical features (e.g., psychosis, treatment resistance, mania, ID). All analyses will be conducted using robust methods/bias control, formally compared to relevant prior studies, and evaluate the impact of all types of measured genetic variation across diverse genetic ancestries. 4) Data sharing will align with NIMH policies via the NIMH Data Archive. Successful completion of the proposed work will markedly increase the number of genes pinpointed by burdens of rare coding variation, rare CNVs, as well as less specific GWAS associations–we will markedly increase knowledge of the genetic architectures of these critically important and burdensome disorders.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY / ABSTRACT Persons with advanced Alzheimer’s disease and related dementias present unique challenges for the healthcare system; they typically have complex chronic illness trajectories that encompass both cognitive and functional impairments. They are also subject to inadequate symptom control. Caring for a patient at home with dementia poses particular challenges for family caregivers who may suffer depression, increased caregiver burden, and may ultimately be dissatisfied with the care their loved ones receive. Palliative care, which is not the same thing as hospice or end-of-life care, is suited to meet the needs of these patients and their caregivers. “Palliative Care at Home for Patients with Dementia” (PCAH) will be a four-hospital, single-blinded, randomized-controlled, clinical trial of an innovative model of home-based palliative care for older adults with dementia and their caregivers. Intervention patients will be cared for by a pyramid of palliative care focused providers, the core of which comprises specially trained community health workers (CHW), social workers (SW), and registered nurses (RN). These providers are supported by a palliative care advanced practice nurse (APN) and physician (MD). This innovative model is more generalizable than traditional palliative care teams, which are centered on the scarce and expensive resources of specialty-trained MDs or APNs. Our model is unique in combining traditional medical (MD, APN, RN) and psychosocial/community-focused providers (CHW, SW) to provide specialized care within a palliative care context, strengthen connections to resources in patients’ local environment, and is highly responsive to the cultural context in which the patient/caregiver dyad make their decisions about healthcare. Intervention patients will receive regular and comprehensive assessments by the community health worker, nurse, and social worker. Together, the team will use these assessments to create comprehensive, individualized, care plans to address patients’ physical, psychosocial and functional needs; caregivers’ needs; improve understanding around illness, medications, and goals of care; and help coordinate services. The PCAH team will continue to work with the patient / caregiver though face-to-face visits (in person or via video) and (at least) weekly phone calls for 12 months. We will enroll and randomize 150 dyads of patients with advanced dementia and their caregivers (total 300 subjects) to receive either the intervention or an augmented control (visits to the caregiver from a CHW without training in dementia or palliative care). Patients with advanced dementia (defined as a global deterioration scale >6) with recent ED or hospital visits and poor functional status will be eligible for enrollment. We will determine if the intervention: improves symptom control in persons with dementia; decreases hospital admissions and patient days in the hospital; and decreases caregiver burden and depression while improving caregiver satisfaction with care. In exploratory analyses we will determine if the intervention decreases costs. Our model has the potential to improve care for thousands of Americans with dementia and their caregivers.

NIH Research Projects · FY 2024 · 2022-09

Project summary Social memory impairment is one of the most debilitating symptoms of autism spectrum disorder (ASD). Although the hippocampus has been well established to be the key player in social memory, hippocampal input regions that may regulate social memory have not been explored. The septum sends strong direct and indirect projections to the hippocampus and has been heavily implicated in emotional processing and social interactions. However, it is unclear which synaptic changes and cell-types drive the septum’s role in social memory. Further, the impact of the septum in social memory-related disorders such as ASD is understudied. Therefore, investigating the mechanism of social memory and the associated synaptic and cellular changes will be critical for creating additional and potentially improved treatment options. My long-term goal is to use integrative approaches to study the mechanisms of social dysfunction. The overall objective is to identify circuit and synaptic underpinnings of social memory regulation by the septum and develop rescue strategies for social memory deficits in mouse models with social memory impairments. Based on my preliminary results, I hypothesize that synaptic plasticity in certain septal cell-types occurs after social exposure and that these synaptic changes are likely to be the critical factor in enhancing social memory. Therefore, I will pursue two specific aims: 1) Dissect the circuit and synaptic mechanisms of social memory modulation by the septum; and 2) Develop rescue strategies for social memory deficits in ASD-associated mouse models with social memory impairment. In the first aim I will systematically identify the septal cell-types involved in social memory using a combination of viral tracing and immunohistochemistry. I will then determine social memory- induced input changes from septal neurons onto hippocampal neurons with ex vivo slice electrophysiology in FosTRAP2 mice. Finally, I will determine the septum’s role in social memory acquisition, consolidation and recall via in vivo optogenetics. In the second aim, I plan to identify the synaptic alterations in two ASD-associated mouse models, Neuroligin-3R451C and SynGAP1het lines, which display social memory deficiency. Moreover, I will develop strategies for the improvement of social memory in these mouse lines via in vivo optogenetic stimulation and micro-infusion of neuromodulators. The approach detailed in this proposal is innovative, because it harnesses new technological advances by integrating viral-tracing with in vivo and ex vivo optogenetics to examine the mechanisms governing social memory. Preliminary studies suggest that the septum to hippocampal projection plays a role in regulating social memory and that the control of social memory by the septum is bi-directional. The proposed research is therefore highly significant, as the bi-directional control of social memory offers immense therapeutic potential. Ultimately, the outcome will likely provide a framework for translational research towards the improvement of social memory deficits.

NIH Research Projects · FY 2024 · 2022-09

Project Summary This project summary pertains to the Supplement. Rhinosinusitis (RS) is one of the most prevalent airway diseases, effecting approximately 15% of the U.S population. With symptoms of sinonasal mucus hypersecretion and plugging, severe facial pain and breathing difficulties, RS significantly affects both quality of life and socioeconomic burden. Despite these dire outcomes, the etiology of RS is completely unknown, severely hampering the development of preventative or curative treatments. In the parent grant, we investigate how aberrant patterning of the nasal submucosal glands (SMGs), may be causative for chronic RS (CRS, > 12 weeks). Based on the high penetrance of CRS in patients with mutations in cystic fibrosis transmembrane conductance regulator (CFTR) gene (Cystic Fibrosis) and studies showing aberrant SMG morphology and function are common to this disease, this proposal tests the hypothesis that dysfunction in CFTR leads to aberrant SMG patterning and thus, CRS. This hypothesis will be tested via three specific aims. (1) Define cell identities, lineage dynamics and cell-cell signaling networks during SMG development. In this Aim, transcriptomic techniques and quantitative measures of morphological changes will be employed to uncover processes governing human SMG development, which can then be utilized to delineate mechanisms of disease SMG patterning. (2) Elucidate CFTR dysfunction in SMGs as an underlying cause of CRS. This Aim will use the murine mouse model to test the hypothesis that mis- regulation in CFTR is a cause of tissue remodeling and CRS. (3) Identify molecular and cellular signatures of SMG remodeling in human adult CRS. This final aim will examine morphological and transcriptomic gland phenotypes common to healthy, eosinophilic CRS without polyps, and eosinophilic CRS with nasal polyps, providing insight into alterations in gland structure and function, and thus contribution to different CRS pathologies. In this Diversity Supplement application, we build on our subsequent studies that have established the emergence of nasal ionocytes during early SMG morphogenesis, with an enrichment of these cells in SMG ducts. We confirm that Cftr expression is highly expressed in embryonic ionocytes and epithelial specific deletion of Cftr significantly reduces ionocyte identity regulator genes. To this end, we hypothesize that CFTR regulates ionocyte differentiation and SMG development. To test this, we will build on our AIM 1 and AIM 2 of the parent grant and scrutinize the role of CFTR in ionocyte specification and airway SMG signaling mechanisms, at a single cell resolution. Outcomes will determine how CFTR mediates ionocyte emergence and how this contributes to aberrant SMG morphogenesis.

NIH Research Projects · FY 2025 · 2022-09

PROJECT SUMMARY In this K23 proposal, I outline a comprehensive 5-year training program that will support my transition towards an independent investigator focused on the development and rigorous testing of interventions for dyads (i.e., pairs) of persons living with dementia (PWDs) and their informal care-partners, with an emphasis on early intervention. In this application, I propose a significant and innovative proposal that is directly tied with my proposed training and career development goals. Background: Alzheimer's disease and related dementias (ADRD) produce a host of stressors for PWDs and their spousal care-partners (SPs), who both experience substantial emotional distress after diagnosis. Emotional distress is interdependent within dyads and – without treatment—becomes chronic and negatively impacts both partners' health, quality of life, and their ability to navigate the short and long-term challenges associated with ADRDs. Addressing emotional distress early, when PWDs can still meaningfully participate, is an unexplored opportunity to prevent chronic emotional distress and preserve quality of life for both partners. Specific aims and research design: I aim to develop the first version of the live video Resilient Together for Dementia (RT-D) intervention and methodology via 1) interviews and quantitative surveys (N=20) of PWD-SP dyads, with additional feedback from 2) focus groups with ADRD medical stakeholders (N=4) (Aim 1). Next, I will explore, via an open pilot (N=5 dyads) with exit interviews and pre-post self- report assessments, the initial feasibility, acceptability, and credibility of the live video RT-D and procedures, and to further refine RT-D as needed (Aim 2). Finally, I will establish, via a pilot feasibility RCT of the RT-D versus control (N= up to 50 dyads), the feasibility, acceptability and credibility of RT-D following predetermined benchmarks (Aim 3). Findings will inform a hybrid efficacy-effectiveness trial through the R01 mechanisms and future studies extending this work to include additional family members and other care-partners. Training and mentoring: My aims are supported by 3 training goals to develop expertise in: 1) qualitative and mixed methods assessment to inform intervention adaptation; 2) specialty training in geriatrics and ADRD clinical care; 3) clinical trial methodology to facilitate dyadic intervention development and refinement. I will obtain mentorship from an exemplary team led by my primary mentor Dr. Ana-Maria Vranceanu, a clinical health psychologist with expertise in mixed-methods research and live video dyadic intervention development, and my co-mentor Dr. Christine Ritchie, a geriatrician and palliative care physician with decades of work improving the treatment of ADRD. My training goals are supported by 1) a team of expert mentors, 2) a rich institutional environment at Massachusetts General Hospital and Harvard Medical School, and 3) targeted coursework, scientific meetings, seminars and planned publications. Relevance to the NIA mission. This K23 is in line with NIAs priorities to develop interventions to the maintain health and wellbeing and reduce the burden of ADRDs. Impact: I am a clinical psychologist with expertise in couple and family interventions for neurological populations. The experience gained will serve as the foundation for an independent career in dyadic interventions for ADRDs, with a focus on early intervention.

NIH Research Projects · FY 2024 · 2022-09

PROJECT SUMMARY / ABSTRACT Persons with advanced Alzheimer’s disease and related dementias present unique challenges for the healthcare system; they typically have complex chronic illness trajectories that encompass both cognitive and functional impairments. They are also subject to inadequate symptom control. Caring for a patient at home with dementia poses particular challenges for family caregivers who may suffer depression, increased caregiver burden, and may ultimately be dissatisfied with the care their loved ones receive. Palliative care, which is not the same thing as hospice or end-of-life care, is suited to meet the needs of these patients and their caregivers. “Palliative Care at Home for Patients with Dementia” (PCAH) will be a four-hospital, single-blinded, randomized-controlled, clinical trial of an innovative model of home-based palliative care for older adults with dementia and their caregivers. Intervention patients will be cared for by a pyramid of palliative care focused providers, the core of which comprises specially trained community health workers (CHW), social workers (SW), and registered nurses (RN). These providers are supported by a palliative care advanced practice nurse (APN) and physician (MD). This innovative model is more generalizable than traditional palliative care teams, which are centered on the scarce and expensive resources of specialty-trained MDs or APNs. Our model is unique in combining traditional medical (MD, APN, RN) and psychosocial/community-focused providers (CHW, SW) to provide specialized care within a palliative care context, strengthen connections to resources in patients’ local environment, and is highly responsive to the cultural context in which the patient/caregiver dyad make their decisions about healthcare. Intervention patients will receive regular and comprehensive assessments by the community health worker, nurse, and social worker. Together, the team will use these assessments to create comprehensive, individualized, care plans to address patients’ physical, psychosocial and functional needs; caregivers’ needs; improve understanding around illness, medications, and goals of care; and help coordinate services. The PCAH team will continue to work with the patient / caregiver though face-to-face visits (in person or via video) and (at least) weekly phone calls for 12 months. We will enroll and randomize 150 dyads of patients with advanced dementia and their caregivers (total 300 subjects) to receive either the intervention or an augmented control (visits to the caregiver from a CHW without training in dementia or palliative care). Patients with advanced dementia (defined as a global deterioration scale >6) with recent ED or hospital visits and poor functional status will be eligible for enrollment. We will determine if the intervention: improves symptom control in persons with dementia; decreases hospital admissions and patient days in the hospital; and decreases caregiver burden and depression while improving caregiver satisfaction with care. In exploratory analyses we will determine if the intervention decreases costs. Our model has the potential to improve care for thousands of Americans with dementia and their caregivers.

NIH Research Projects · FY 2025 · 2022-09

No Abstract

NIH Research Projects · FY 2025 · 2022-09

ABSTRACT Structural Mechanism for Gating of Mechanosensitive Channels Mechanical force sensation mediated by mechanosensitive channels underlies an array of fundamental physiological processes, including hearing, touch, proprioception, osmoregulation, and morphogenesis. Dysfunctional force sensation is associated with numerous diseases including deafness, atherosclerosis, chronic pain and cancer. The prokaryotic mechanosensitive channel of small conductance (MscS) protects bacterial cells from rupture under hypoosmotic downshock. A variety of MscS-like channels, found in many organisms including bacteria, fungi, algae, and plants, form an exceptionally diverse superfamily of channels that are crucial for management of osmotic pressure. MscS homologs are absent in animals, and thus targeting MscS channels in pathogenic microorganisms such as bacteria and fungi could lead to new antimicrobial treatment strategies. Current mechanistic understanding, primarily inferred from studies of the prototypical prokaryotic channel, E. Coli MscS, remains limited. Structural, biochemical, and biophysical analyses of complex membrane proteins such as eukaryotic MscS channels and multi-domain prokaryotic MscS homologs have proven challenging owing to major difficulties in producing sufficiently large quantities of biochemically stable protein samples. We have overcome these critical barriers through recent developments in large-scale protein production and structural and functional analyses of a variety of MscS family members with distinct membrane topologies and domain organizations. Our recent structural and functional studies of a eukaryotic channel MSL1 have uncovered a `flattening and expansion' gating mechanism stemming from a non-planar transmembrane domain at the resting state, which is reminiscent of the evolutionarily and architecturally unrelated mammalian mechanosensitive Piezo channels. These results lead to our central hypothesis that `flattening and expansion' in the transmembrane region may be a unifying gating mechanism. With these exciting developments, we are now able to combine structural biology and electrophysiology to address one of the central questions in mechanobiology: how do mechanosensitive channels gate? Specifically, we aim to reveal gating transitions of a diverse set of MscS channels with distinct membrane topologies to further evaluate this potentially universal gating mechanism. Detailed understanding of the mechanisms will provide critical information that will ultimately lead to development of new antimicrobial reagents and new treatment strategies for a broad spectrum of diseases associated with altered mechanical force sensation.

NIH Research Projects · FY 2024 · 2022-09

Project Summary Title: Tracing and targeting the epigenetic heterogeneity in breast cancer metastasis. Metastasis is major cause of cancer-related death and is the most challenging to treat. Besides the well-studied genomic mutations in cancer, our understanding of non-genomic alterations remains limited. The proposed approach is to dissect the mechanisms of non-genomic intra-metastasis heterogeneity in breast cancer. Recently, we demonstrated that osteoblasts (bone forming cells) promote a global alteration of chromatin organization which associates with increased stemness, epithelial to mesenchymal transition, and overexpression of multiple receptor tyrosine kinases included FGFR1 and PDGFRβ. Ultimately, estrogen signaling was inhibited while endocrine resistance was increased. Mechanistically, we identified FGF2/PDBFβ/ EZH2 axis as a novel regulator of epigenetic reprogramming in breast cancer bone metastasis. However, several outstanding questions remained unanswered: (i) what mechanisms drive phenotypic variations between neighboring cells in bone metastasis, (ii) are epigenetic traits inheritable during metastasis progression, and (ii) if yes, how do they influence therapeutic response? In this project, our goal is to understand the mechanisms of intra-tumor heterogeneity in bone metastases and determine how epigenetic heterogeneity affects therapeutic response beyond the genetic heterogeneity that has been extensively studied. We aim to trace and dissect the epigenetic intra-tumor heterogeneity (eITH) using a cutting-edge barcoding strategy (K99 phase), identify epigenetic modulators by integrating single cell multi-omics (K99-R00 phase), test new therapeutic approaches and eventually expand our findings to other breast cancer metastasis sites (R00 phase) including lung, liver, and brain. Baylor College of Medicine (BCM) is an internationally renowned institution for breast cancer research, which gives me the opportunity to closely interact, exchange ideas, and share my findings with leading scientists, clinicians and patient advocates. For my career transition, I assembled a team of senior scientists and experts including my mentor, Professor Xiang H-F Zhang, who is well-established in breast cancer bone metastasis. My co-mentor, Professor Jeffrey Rosen, is a distinguished scientist in mammary gland development and breast cancer modeling. Because of the clinical relevance of the project, I also included Professor C. Kent Osborne, founding director of the Dan L. Duncan Comprehensive Cancer Center (DLDCCC), Professor Matthew J. Ellis, a world-renowned oncologist and director of the Breast Center, Dr. Bora Lim, an expert in aggressive subtypes of breast cancer (e.g. inflammatory breast cancer), Professor Susan G. Hilsenbeck, a distinguished biostatistician, and Dr. Zhandong Liu a computational biologist and statistician with expertise in single cell analysis. Adding the expertise of my advisory team to the rich intellectual resource and cutting-edge technology available at BCM will facilitate my successful transition into an independent position at a top research institution.