Yale University

NIH Research Projects · FY 2026 · 2023-03

Invasive and proliferative phenotypes are vital cancer hallmarks, and these phenotypes are distinguished by the fact that invasive cells lead the path for dividing cells as the tumor grows. Glioblastoma multiforme (GBM) treatments, specifically chemotherapies, fail because cancer cells invade and proliferate beyond tumor boundaries. But neither phenotypes can be tracked with existing imaging methods. We will develop 1H/23Na MRSI technology to differentiate and track these phenotypes, and which will have major clinical relevance. Compared to normal cells, cancer cells possess unique chemical and electrical properties. Interstitial fluid's acidity and salinity are crucial for cell survival. Many cellular mechanisms help regulate essential cellular functions by maintaining hydrogen ions (H+) and sodium ions (Na+) in the interstitial milieu, which is saline and near neutral pH. Research from us, and others, reveal that acidity and salinity of interstitial and intracellular spaces are altered in cancer, e.g., sodium-hydrogen exchanger 1 (NHE1), which aids H+ efflux and Na+ influx, is upregulated in GBMs and contributes to altered transmembrane ion distributions. Research on GBM models reveals an acidic interstitial fluid, vital for reshaping the interstitial matrix for cancer cell proliferation and to guide cancer cell invasion. Similar work on human-derived GBMs shows that interstitial Na+ is also altered, but this change supports a depolarized cell membrane - vital for cancer cell proliferation. These novel results suggest that the combination of interstitial pH (pHo) and transmembrane Na+ gradient (ΔNa+m) maps can help generate independent biomarkers of invasive and proliferative phenotypes. While 1H-MRI with gadolinium agents tracks tumor size, we and others have shown that agents with other lanthanides can be used for pHo mapping with 1H-MRSI and ΔNa+m mapping with 23Na-MRSI. These 1H/23Na maps are currently obtained individually, requiring lengthy acquisitions with separate agent injections. To explore the relationship between dysregulated pH and electrolyte imbalances regulating cancer cell invasion and proliferation, pHo and ΔNa+m maps must be spatiotemporally compared during tumor growth/therapy. Our goal is to test the hypothesis that invasive cells lead dividing cells as the tumor grows, and explore how their patterns change with treatment. First, we will interleave 1H and 23Na acquisitions to enable rapid pHo and ΔNa+m mapping with a single agent infusion. Next, proliferative and invasive maps from combination of pHo and ΔNa+m maps will be validated in nodular vs. invasive patient -derived xenografts (PDXs) using IHC and ICP-MS. For clinical relevance, we will test potential of NHE1 inhibitor as an adjuvant chemotherapy to improve GBM outcome. We will compare pHo and ΔNa+m maps with two different therapies (i.e., first-line GBM standard of care chemotherapy temozolomide alone vs. temozolomide + cariporide) to capture fates of invasive and proliferative phenotypes in nodular vs. invasive PDXs.

NIH Research Projects · FY 2026 · 2023-03

ABSTRACT Alcohol use disorder (AUD) reaches peak levels during young adulthood, making it critical that we understand person-specific alcohol risk profiles in young adults to prevent AUD or intervene before this disorder becomes chronic. The National Institute on Alcohol Abuse & Alcoholism’s (NIAAA) neurobiological framework, the Addictions Neuroclinical Assessment (ANA), offers an innovative approach for understanding AUD in this population. The ANA posits that individual differences in 3 neurofunctional domains can help differentiate the substantial clinical heterogeneity in AUD. The ANA builds upon the NIMH Research Domain Criteria (RDoC), a dimensional framework for investigating mental disorders in terms of varying degrees of dysfunction in 6 core biological/psychological systems. As a starting point, NIAAA endorsed an initial 3-domain ANA model, which aligns with most RDoC systems. Two RDoC systems, not in the initial ANA, include sleep/circadian and social processes and are highly relevant to young adult alcohol risk. The 3-domain ANA model has been validated in research with adults and predicts treatment outcomes, including work by our team. It has yet to be investigated in young adults. We propose to study the ANA model, expanded to include sleep/circadian and social processes, in young adults (non-college/college, ages 18-25) (N=350), who report recent moderate to heavy drinking. Specifically, young adults will participate in a 12-month longitudinal study, which involves completing self-report questionnaires, neuropsychological tasks, and engaging in passive and active smartphone data collection. These assessments include recommended/similar ANA measures, RDoC-relevant sleep/circadian and social measures, and novel smartphone measures to improve ANA scalability. Smartphone data collection is rigorous, unobtrusive, scalable, and highly relevant for young adults given their extensive smartphone use. Smartphones can generate rich moment-by-moment neurobehavioral data (e.g., mobility, sociality) passively through embedded sensors and phone usage logs and actively through survey prompts. These digital behavioral indicators show promise for predicting psychiatric disorder symptoms, course, treatment response, and functional brain activity. We will use data from study participants to achieve the following aims: For Aim 1, we will validate an ANA model for young adults (ANA-YA) using baseline self-report and neuropsychological measures related to the 3 ANA domains and RDoC sleep/circadian and social processes. We will then examine baseline associations between the ANA-YA model and baseline drinking measures. We will also explore longitudinal change in ANA-YA phenotypes and test whether these changes predict 12-month alcohol outcomes. For Aim 2, we will examine the baseline associations of smartphone data to ANA-YA domains and then examine longitudinal change in smartphone data and whether these changes predict 12-month ANA-YA phenotypes. Our results will advance the science of young adult AUD neurobiology and identify efficient, valid assessments for distinguishing alcohol risk in this group.

NIH Research Projects · FY 2026 · 2023-03

SPECIFIC AIMS: Obesity-induced metabolic inflammation results in the transition of nonalcoholic fatty liver disease (NAFLD) to steatohepatitis (NASH) [1-3]. Myeloid cell populations such as macrophages have been established as the main driver of metabolic inflammation [4-10]. Single-cell RNA sequencing (scRNA-seq) studies have provided a high-resolution fate map of myeloid diversity in NAFLD associated with distinct epigenomes, transcriptomes, and functions [9-11]. Recent advances emphasize the importance of post-transcriptional regulation of gene expression at the RNA level in obesity-driven hepatic inflammation [12, 13]. N6-methyladenosine (m6A) methylation represents the most prevalent and abundant epigenetic modification of eukaryotic mRNA. m6A methylation is dynamically installed, erased, and recognized by m6A methyltransferases (writers), m6A demethylases (erasers), and m6A specific binding enzymes (readers) [14, 15]. Highly m6A modified transcripts generally result in lower mRNA stability leading to reduced mRNA levels and thus greatly influence diverse cellular and biological responses [16-18]. The reader proteins recognize the m6A-modified sequences and determine the fate of the target mRNA. We recently identified that myeloid lineage-restricted deletion of m6A writer protein methyltransferase like 3 (METTL3) results in differential expression of m6A modified mRNA transcripts, particularly DNA Damage Inducible Transcript 4 (DDIT4) that negatively regulates mTOR/NFkB activation resulting in decreased immune cell infiltration, recovered liver homeostasis, improved hepatic metabolic abnormalities, and reduced inflammation during diet-induced obesity/NAFLD [19]. Although macrophage METTL3 plays an essential role in obesity-associated NAFLD, how it competes and collaborates with distinct m6A readers has not been identified, nor has the specificity of the methylation reaction and RNA structural motif determined. The molecular and cellular effects of m6A methylation in myeloid cell subsets, in addition to reducing mRNA stability, have yet to be elucidated in advanced fibrosis. DEAD-box RNA helicase DDX21 plays multifaceted roles in ribosome biogenesis, RNA editing, RNA transport, and transcription. DDX21 has been reported to interact with m6A writer proteins. Analysis of publicly available RNA-CLIP sequencing data indicates the overlap between DDX21 binding regions and m6A methylation sites on target mRNA molecules. Our preliminary results showed that mice with DDX21 deficiency in myeloid lineage, analogous to METTL3 deficiency, resulted in significant prevention of diet-induced steatohepatitis and fibrosis. The scRNA-seq analysis revealed two distinct myeloid populations, liver-resident (KC-H) macrophages and monocyte-derived macrophages (Mo-M), that have opposite proportional mobilization between chow and diet-fed mice. The lack of DDX21 restored the proportion of KC-H in diet-fed mice while reducing the proportion of Mo-M along with reduced inflammatory markers, indicating DDX21 plays a novel role in liver myeloid cells during obesity-associated NAFLD. Therefore, we hypothesize that mRNA m6A methylation in myeloid cell subsets, in association with DDX21, leads to hepatic inflammation during obesity-associated NAFLD (Fig.1). Aim 1 Establish the role of METTL3 in myeloid cell-driven hepatic inflammation during obesity-associated NAFLD. 1.1) Determine the contributions of METTL3 in KC-H and Mo-M subsets to hepatic inflammation. 1.1.1) Obtain the transcriptome-wide map of dynamic mRNA m6A at single-nucleotide resolution in METTL3-deficient KC-H and Mo-M cells during diet-induced NAFLD. 1.1.2). Identify the myeloid subset in which METTL3 deficiency results in protection from metabolic inflammation. This aim will identify the m6A pathway in myeloid subsets and downstream genes that contribute to hepatic inflammation during obesity-associated NAFLD. Aim 2 Determine the mechanistic relationship between the RNA helicase DDX21 and the m6A methylation to myeloid cell-driven hepatic inflammation. 2.1) Determine DDX21 recognition of m6A methylation on mRNAs. 2.2) Determine the role of DDX21 in myeloid lineage to promote obesity-associated steatohepatitis and fibrosis. This aim will mechanistically uncover DDX21 as a novel m6A regulator, and potential therapeutic target for obesity-associated NAFLD. This application will elucidate novel regulatory organisms underlying the role of m6A methylation in hepatic inflammation under obesity-associated NAFLD. The identification of DDX21 as a key role in liver myeloid subpopulations to prevent hepatic inflammation will provide the rationale for manipulating DDX21 and the basis for applying small molecules targeting m6A modulators in metabolic liver disease.

NIH Research Projects · FY 2025 · 2023-03

Expanded use of telemedicine for buprenorphine prescribing may reduce barriers to buprenorphine prescribers. However, federal regulations that require prescribers to conduct in-person medical evaluations to induct patients on buprenorphine and limit maintenance visits to real-time, two-way, interactive audio-visual communication (i.e., telehealth) has prevented research on the potential role of expanding telehealth for buprenorphine prescribing. The initial surge of COVID-19 cases in the US in March 2020 led federal agencies to ease the in-person evaluation requirement, allowing providers to use telemedicine or telephone-only visits for medical evaluations to start patients on buprenorphine. We propose a study that leverages these COVID-related regulator reforms to answer important clinical and policy questions regarding the regulations governing the use of telehealth for buprenorphine initiation and treatment among Veterans Administration (VA) patients. Serving ~5,000,000 patients each year, we will leverage the VA electronic health record data to answer three important clinical and policy questions. (1) What was the effect of the relaxed buprenorphine prescribing guidelines on buprenorphine treatment rates change during the COVID-19 pandemic overall and by treatment stage (new patients vs. long- standing patients)? (2) What is the effect on treatment outcomes of more flexible telehealth regulations on patients initiating buprenorphine treatment? (3) What is the effect of telehealth use on treatment outcomes on patients in long-standing buprenorphine treatment (in care ≥6 months)? We will answer these questions in three steps: (1) We will use time-series methods to model the monthly counts of VA patients in buprenorphine treatment prior to March 2020, predict the monthly count in treatment from April to December 2020 and compare it to the observe counts to quantify the change in buprenorphine treatment rates associated with more flexible treatment regulations; (2) Test whether: (a) clinical treatment outcomes in patients initiating buprenorphine via telehealth post-Policy changes differ from patients initiating treatment in the year before the outbreak and (b) Investigate individual, facility, and area-level modifiers of the policy effects on clinical treatment outcomes; and (3) Among long-standing patients: (a) Examine the relationship between telehealth use and clinical treatment outcomes and (b) Determine individual, facility, and area-level differences in telehealth buprenorphine treatment. Determining the effects of more flexible telehealth regulations will provide critical information on a potential policy lever to increase access to critical life-saving medications for OUD. The complementary training program comprising of formal courses, workshops, directed readings, and experiential learning will let me develop the skill and expertise to launch my career as a substance use epidemiologist and prepare me to successfully compete for R01 funding as an independent investigator with a focus on understanding the causes of addiction and policy evaluation to inform interventions, prevent, and treat OUD and its related harms.

NIH Research Projects · FY 2026 · 2023-03

PROJECT SUMMARY/ABSTRACT The dorsal lateral geniculate nucleus (dLGN) of the thalamus routes visual signals from the eye to the visual cortex and provides critical support for conscious visual sensation. Rather than being a simple relay station, a growing body of evidence is revealing that the mouse dLGN plays an active role in shaping visual information flow to the cortex by selectively converging and integrating diverse streams of inputs. Studies of retinal inputs to the dLGN have provided rich knowledge about the organization and development of neural circuits for mammalian species. However, much less is known about the non-retinal inputs although they contribute to ~90% of total inputs to the dLGN. How the visual and behavioral state information conveyed by non-retinal inputs combines with information from the retina to impact thalamic visual processing remains a topic of great experimental and theoretical interest. Direct functional characterization of inputs to the dLGN in awake behaving animals has been hindered by the difficulty in performing high-resolution recording of subcortical brain regions. To address this challenge, we established a chronic, high-resolution, deep-brain two-photon calcium imaging platform to simultaneously measure visual responses in hundreds of retinal axonal boutons. Here, we have further expanded our imaging capacity to simultaneously record signals from calcium indicators of two different colors that are expressed in retinal and non-retinal inputs respectively. With these innovations, we will determine how the diverse inputs from the midbrain superior colliculus coordinate with retinal inputs at multiple levels to reinforce or broaden channels of visual information in the dLGN. The highly conserved colliculogeniculate axons possess several synaptic properties that resemble those of retinogeniculate axons, including comingling axonal boutons on the proximal dendrites of dLGN neurons and providing strong synaptic inputs that can elicit neural firing in target neurons. However, it remains unclear how the collicular inputs combine with retinal inputs and contribute to visual responses of dLGN neurons. In Aim 1, we will determine the functional and spatial relationships between retinal and collicular inputs to the dLGN. In Aim 2, we will reveal the modulation of colliculogeniculate inputs by behavioral states. In Aim 3, we will determine the contribution of collicular inputs to visual responses of dLGN neurons. These experiments will reveal rules for functional convergence between retinal and collicular inputs and demonstrate how they act in concert or in competition to sculpt thalamic visual computation. Our findings will also contribute to the understanding of how afferent visual signals are transformed into visual feature selectivity in the dLGN and how behavioral states impact this process, providing the foundation for the understanding and treatment of neurological disorders involving improper neural circuit connectivity and signal integration.

NIH Research Projects · FY 2026 · 2023-03

PROJECT SUMMARY: Social disconnection (SDC) and suicide deaths are major public health concerns for the aging population. SDC is one of the strongest risk factors of suicidal ideation, attempts, and deaths in older adults, and is a modifiable target for suicide prevention efforts in this population. While accumulating evidence has established an association between SDC and late-life suicide risk, the neural mechanisms that underlie this association remain unknown. Consequently, our understanding of how to optimally intervene to mitigate the adverse effects of SDC on suicide risk in older adults is limited. To address this gap, we propose to conduct the first in vivo molecular imaging study of a potential neural mechanism – corticolimbic synaptic density – that may mediate the link between SDC and late-life suicide risk. Given a higher prevalence of suicide death in older men than women, we will also examine whether sex moderates this association. Converging evidence from human magnetic resonance imaging and postmortem studies and preclinical work suggests brain alterations in SDC and suicidality, with robust evidence implicating lower corticolimbic synaptic density. In animal models of SDC, socialization appears to reverse some of these synaptic losses. These studies have also observed sex differences in synaptic changes in interventions designed to reverse SDC- related synaptic losses. Thus, it is critical to conduct in vivo human studies to evaluate molecular mechanisms that may confer risk for suicide in older adults with SDC in order to identify who is at greatest risk and how to mitigate burden of suicide to older adults, their families, and the community at large. In vivo quantification of synaptic density in humans is possible with the radioligand 11C-UCB-J, which quantifies the density of synaptic vesicle glycoprotein 2A (SV2A), a ubiquitously expressed marker of synaptic density, using positron emission tomography (PET) imaging. Our preliminary data from a diverse sample of older adults confirm preclinical findings of lower corticolimbic synaptic density in SDC and suggest sex-specific differences. In the proposed study, we will recruit a transdiagnostic cohort of older adults presenting with the full range of SDC and evaluate whether lower corticolimbic synaptic density mediates the relation between SDC and longitudinal trajectories of late-life suicide risk in a sex-specific manner. We will employ a novel, data-driven approach to model predominant trajectories of late-life suicide risk, which will include measures of suicide depressive and death ideation, symptoms, loss of personal and self-worth, executive control, and perceived meaning in life. Results of the proposed study will provide the first human in vivo data on the role of synaptic density alterations as a putative neural mechanism linking SDC to late-life suicide risk. They will also inform the development and testing of targeted interventions to enhance synaptogenesis (e.g., medications such as ketamine or psychosocial interventions such as peer support), as well as public policies to promote social connection among older adults who may suffer from illness or other issues that lead to SDC.

NIH Research Projects · FY 2026 · 2023-02

PROJECT SUMMARY Although new variants may contribute to surges, we expect SARS-CoV-2 to transition to a new phase where the virus continues to circulate but at lower levels. Sequential immunizing exposures, whether due to infection or vaccination, have transformed the immune status of populations by cumulatively increasing antibody levels and increasing the breadth of antigenic targeting of SARS-CoV-2 by antibodies. The relative role of increased magnitude of antibody responses or broadening of antigenic recognition of SARS-CoV-2 in protecting populations from infection is not known. Strikingly, though mucosal responses have been found to play key roles in protecting individuals from infection, SARS-CoV-2 literature has focused almost exclusively on serological responses. Effective policy and investment in public health measures as the pandemic continues will require information on the relative importance of specific immune responses. Gathering evidence in diverse settings including low and middle income countries (LMIC) is particularly important as the immunizing exposure history in these settings has been different (in terms of infections and vaccine use) and a smaller evidence base is available from these settings. Our proposed work seeks to continue to interrogate SARS-CoV-2 immunity in a cohort residing in an urban slum community in Brazil which we have followed since 2003. We identified an extraordinarily high SARS-CoV-2 attack rate (75%) during two epidemic waves with D614G and Gamma variants. Subsequent vaccination has generated hybrid immunity in a large proportion of our cohort. Our proposed study would investigate the relative role of antibody magnitude and breadth within systemic and mucosal compartments in protecting this population from infection. To accomplish this, we propose to conduct serologic and virologic surveillance in this community and develop tools to interpret serological measures of infection that address a key epidemiological challenge for the world in continued characterization of infection during the next phase of the pandemic. Our proposal leverages a 27-year scientific collaboration with the Brazilian Ministry of Health, an extensive track record of interrogating SARS-CoV-2 immunity, novel assays and analytical methods to infer infection histories and characterize multi-antigen immune responses. Our study will generate key evidence to inform the development of novel vaccines (intranasal, multi-antigen) and a new approach to tracking SARS-CoV-2 infections in populations with pre-existing immunity where symptom-based virologic surveillance may give an insufficient view of viral transmission.

NIH Research Projects · FY 2026 · 2023-02

Project Summary Genomics data sharing is of paramount importance to accelerate biomedical research and facilitate higher power in analysis. However, privacy and security concerns can hinder large scale data sharing across institutions and nations. Human genomics data contain unique information that is identifiable, and inappropriate sharing would put individual’s privacy at risk and potentially lead to leakage of sensitive personal information. Also, patients’ consents are crucial for genomic studies, and therefore novel sociotechnical methods are also essential for researchers to consider while conducting human genomic research. We intend to close the technology gap and bring advanced enabling technology to support human genomic research. We have organized a series of competitions to evaluate state-of-the-art privacy and security models with real-world motivated analysis tasks with companion workshops. As an emerging interdisciplinary community, we are pushing the frontiers of genomic privacy and security research. Motivated by our previous successes, we are proposing to continue the effort. We plan to engage and support researchers from nationally underrepresented groups to participate in our competitions and attend the workshops.

NIH Research Projects · FY 2026 · 2023-02

The objectives of the proposal are to determine, for the first time, how developing meningeal lymphatic vessels (MLVs) impact neuroimmune communication in early postnatal life, and if MLV- dependent neuroimmune communication can be harnessed by VEGF-C signaling in young mice at steady state and in a model of pediatric brain tumor such as medulloblastoma, the most common tumor affecting children. Our previous work and preliminary data show that MLVs develop during early postnatal life, that their growth requires Vascular Endothelial Growth Factor-C (VEGF-C) and the VEGF-C co- receptor Neuropilin2 (Nrp2), and that enhancing MLV growth enables adaptive immune responses against glioblastoma in the adult. These findings prompt us to investigate mechanims how MLV-mediated neuroimmune connection establishes and to characterize the transport of antigen-presenting cells (APCs) to CNS-collecting lymph nodes (cLNs) and the MLV-dependent education of T cells in developing cLNs. Experimental approaches to successfully complete this project include new lymphatic-specific knockout lines, new procedures of three-dimensional whole-head imaging by light sheet fluorescence microscopy, and unbiased molecular analysis by mass spectrometry and single cell- RNA sequencing. This multidisciplinary study will bring together complementary expertise in the fields of meningeal lymphatics (Jean-Leon Thomas, Yale), developmental angiogenesis (Anne Eichmann, Yale), and immunology (Akiko Iwasaki, Yale), with additional advisors in pediatric oncology (Asher Marks, Director of Yale Pediatric Neuro-Oncology), liquid-chromatography mass spectometry (Tukiet Lam, Director of Keck MS & Proteomics Resource at Yale), and TCR repertoire analysis (Le Zhang, Yale Neurology). We expect to characterize the development of MLV-dependent neuroimmune communication, to identify Nrp2 as a new mandatory regulator of MLV sprouting, identify APC subpopulation(s) required for CNS antigen transport into cLNs, and to determine, as a proof of principle, the potential of VEGF-C-driven MLV growth to promote early T cell education against abnormal CNS antigens, with perspectives for the treatment of aggressive pediatric brain tumors.

NIH Research Projects · FY 2025 · 2023-02

Abstract Background: De nova haplotype-resolved genome assembly not only plays a critical role in the studies of novel species, but also is the most comprehensive solution to discover structural variants and understand repeat-rich regions of the human genome. Moreover, haplotype-resolved assemblies are the fundamental infrastructures for various pangenome references. Recent advances in accurate long-read sequencing technologies open the opportunity to faithfully build high-quality haplotyperesolved assemblies, but most assembly algorithms could not take full advantage of the emerging accurate long-read data. To this end, I have developed a graph-based haplotype-resolved genome assembly algorithm, called hifiasm, which combines accurate long reads with the additional data providing long-range phasing information. Hifiasm has been widely used by multiple large-scale sequencing projects, such as the Human Pangenome Reference Consortium (HPRC), the Genome in a Bottle (GIAB), the Vertebrate Genomes Project (VGP), and the Darwin Tree of Life project. Based on hifiasm, this proposal focuses on developing a set of new haplotype-resolved assembly algorithms to further improve the assembly quality for complex regions and genomes, as well as substantially reduce the assembly cost. Research: My first aim is to develop a hybrid algorithm to produce high-quality haplotype-resolved assemblies for diploid genomes, especially focusing on resolving highly repetitive regions like centromeres. The proposed algorithm will combine the advantages of length and accuracy from different types of long-read data to automatically reconstruct the last unexplored repeat-rich regions of the genome. In the second aim, I will develop a haplotype-aware scaffolding algorithm to achieve chromosome-level haplotype-resolved assemblies for diploid genomes. In the third aim, I will propose different strategies to reduce the sequencing cost and the computational cost of the haplotype-resolved assembly, making it feasible for populationscale studies. I will also develop assembly algorithms to resolve complex genomes including not only two haplotypes. Upon completion, the proposed studies will offer efficient assembly tools for large-scale sequencing projects, and will pave the way to personal genome assembly for genomic research and clinical applications. Career development and training: My long-term career goal is to lead an independent research group focusing on developing novel computational methods for haplotype-resolved assemblies and the relevant applications. In addition to further enhancing my training in computational method development with my mentor Dr. Heng Li, I will obtain systematic training in biomedical research from the advisory committee (Dr. Erich D. Jarvis and Dr. Scott V. Edwards for human and non-human genomes, Dr. Evan E. Eichler and Dr. Karen H. Miga for repeats and structural variations, as well as Dr. Matthew Meyerson for complex genomes including not only two haplotypes). The training in career development, including laboratory management, grant-writing and leadership, will also be carried out during the K99 phase. My experience in computational method development, especially in genome assemblies, as well as the rigorous mentored support from my mentoring and advisory team, puts me in a unique position to establish an independent lab studying haplotype-resolved genome assembly algorithms.

NIH Research Projects · FY 2026 · 2023-02

SUMMARY While significant progress has been made in the past decade with immunotherapy for metastatic melanoma and renal cell carcinoma (RCC), not all patients respond, and others develop resistance over time. Hundreds of novel regimens are being developed to overcome primary and acquired resistance. Some combinations increase the infiltration of cytotoxic T cells in the tumor to kill cancer cells, while others modulate tumor-associated macrophages (TAMs) to enhance the T cell activity in the tumor microenvironment. However, toxicity to patients is an important limitation to immunotherapy regimens. Non-invasive imaging techniques are needed to determine response to combination therapy to save potential non-responders from unnecessary toxicity. Current imaging techniques do not assess the dynamic changes in the levels of T cells and TAMs at the same time. The overall hypothesis is that imaging the infiltration of cytotoxic T cells and TAMs concurrently can better determine response to immunotherapy regimens. The goal of this proposal is to develop non-invasive imaging probes for single photon emission computed tomography (SPECT) imaging of T cells and TAMs concurrently to determine response to combination therapy. We anticipate that SPECT will accurately recapitulate pathology and may ultimately replace on-treatment biopsies in patients who might have pseudoprogression. SPECT may also complement tissue-based analyses to further interrogate the tumor microenvironment through digital spatial profiling (DSP), an in situ profiling method that preserves spatial information. DSP can quantify multiple biomarkers simultaneously in immune cells responsible for the tumor’s sensitivity to combination therapy. In our preliminary work we developed the tools to implement the tracking of CD8+ T cells and CD68+ TAMs in vivo with radiolabeled antibodies. We will test our SPECT agents in established murine tumor models of melanoma and RCC in mice with intact immune systems. We will characterize their binding properties to CD8+ T cells and CD68+ TAMs in vitro (Aim 1). We will image tumoral T cell and TAM infiltration in vivo by SPECT imaging in syngeneic tumor models of melanoma and RCC and assess activation status of immune cells by DSP after immunotherapy in murine and patient tissues (Aim 2). These studies will lay the foundations for future clinical trials of dual-isotope SPECT in immunotherapy-treated patients.

NIH Research Projects · FY 2026 · 2023-02

The Yale-Metropolitan Emergency Trial network to advance patient Outcomes (Yale-METRO) is anchored by Yale New Haven Health System (YNHHS) as the Hub and 5 leading partner integrated health systems (1) Hartford Healthcare, (2) Rhode Island/Brown University Health System, (3) Mount Sinai Health System, (4) New York Presbyterian/Weill Cornell Medicine, and (5) Montefiore Health System. Yale-New Haven Hospital is the 7th largest hospital in the U.S. and in collaboration with YNHHS and the Spokes with their respective networks these geographically proximate institutions, cover a densely populated catchment area including more than 8 million people throughout Connecticut, Rhode Island, Southeast NY, Southern MA, and 4 boroughs of New York City, with 1,739,027 Emergency Department visits offering access to a large and diverse population of acutely ill adult and pediatric patients. Principal Investigators Dr. Gail D'Onofrio (Emergency Medicine) and Dr. Kevin Sheth (Neurology) bring a complementary set of leadership skills, high-level clinical trial experience, and an excellent organizational framework. Each have demonstrated expertise in leading and conducting multicenter trials, and a proven track record of high-quality ED and pre-hospital recruitment, and retention in studies, even during the COVID-19 Pandemic. They have collaborated and are actively engaged in multicenter trials with the Spoke institutions and investigators. These interactions include leveraging successful contributions currently in place for NIH networks such as NeuroNEXT and Stroke Net. They have access to a cadre of impressive multispecialty faculty, creating a highly collaborative environment focused on the emergency care related to presentations and diagnoses of interest including, neurological, cardiovascular, respiratory, hematology and trauma. Finally, they have created mechanisms to facilitate enrollment 24 hours, 7 days a week that are already in place. The proposal is strengthened by a: (1) Pool of talented investigators with nationally recognized researchers and MPIs with experience implementing multicenter trials (2) Large diverse patient population (3) Informaticist and analytic team bringing innovative technological strategies and processes for rapid uptake of Spokes, recruitment, data collection, monitoring and quality; (4) Robust track record of mentoring junior investigators and (5) Expertise in developing future proposals for SIREN research. Yale-METRO offers all the components for conducting high-quality research and unique opportunities to use innovative technology advances for disease detection, patient enrollment, data collection and high-quality assurances procedures. Thus, Yale-METRO offers unique opportunities to strengthen the SIREN Network, designing, testing, and discovering interventions and therapies improving patient outcomes.

NIH Research Projects · FY 2025 · 2023-02

PROJECT SUMMARY GAPs (GTPase activating proteins) play an essential role in the GTPase cycle, allowing for the regulation of complex processes such as signal transduction; consequently, their dysfunction has significant ramifications. In the case of p120RasGAP (RasGAP, p120; RASA1), the first GAP described, dysfunctions have been linked to vascular diseases such as capillary malformation-arteriovenous malformation syndromes (CM-AVM) and vein of Galen malformations (VOGM). The protein consists of an N-terminal Src homology 2 (SH2)-SH3-SH2 cassette, followed by pleckstrin homology (PH), C2, and GAP domains. Despite its importance and relatively long history as a target of study, p120RasGAP has not been adequately analyzed at the structural and biochemical levels. In particular, although full-length p120RasGAP has been shown to have greater activity than the GAP domain alone, the contributions of the PH and C2 domains have not specifically been isolated. I hypothesize that the GAP activity of p120RasGAP is controlled through conformational changes induced by the protein’s regulatory domains, which are in turn affected by lipid head groups and/or other binding proteins. Specifically, my preliminary data demonstrate that the C2 domain may play a role in GAP regulation. I will test these mechanisms in two aims. In Aim 1, I can already express and purify constructs of the GAP, C2, and PH domains of p120RasGAP, and preliminary enzymatic analysis suggests that the C2 domain accelerates enzymatic activity. I will conduct detailed enzymatic studies in vitro using GAP assays to assess the roles of these domains. I will then assess the effect of disease-causing mutations on enzyme activity. Additionally, I will quantify the affinities of the PH and C2 domains for different lipid head groups and assess C2 calcium sensitivity. These data will then be used to conduct in vitro GAP assays using vesicle-bound Ras to test the role of membrane association in PH and C2 regulatory behavior. In Aim 2, I have already obtained and am refining the first crystal structure of the C2-GAP region of p120RasGAP. This crystal structure demonstrates that the C2 and GAP domains are connected by a flexible linker and illustrates that the C2 domain is ideally positioned to interact with the allosteric lobes of Ras in an “opposable thumb” formation. I will also obtain a crystal structure of the C2- GAP region in complex with HRas to observe this binding directly. Based on analysis of these structures, I will validate interactions made by the C2 domain via site-directed point mutagenesis and GAP assays. Taken together, these aims will provide a comprehensive analysis of the roles of the PH and C2 domains in regulation of p120RasGAP and reveal interactions responsible for the observed changes in activity. These studies will elucidate molecular bases for vascular diseases including CM-AVM and VOGM.

NIH Research Projects · FY 2026 · 2023-02

ABSTRACT Saccular intracranial aneurysms (IA) represent a significant health issue in the US and worldwide. IA rupture leads to intracranial hemorrhage, with devastating outcomes: 30% of patients die within a month of the initial event, and 50% of survivors are left with severe neurological deficits requiring long-term care. IA is a multi- factorial disorder underlain by genetic and environmental risk factors. In a series of genome-wide association studies we identified multiple common variants that contribute to IA risk. To discover rare coding variants with large-effect size, we conducted whole exome sequencing analysis of a cohort of >250 patients from 58 families, each with at least 3 members diagnosed with IA. This analysis identified heterozygous rare and deleterious mutations in two novel genes, WBP11 and PPIL4, which collectively explain more than 10% of familial IA cases in our cohort. In preliminary experiments, we demonstrated that loss- of-function ppil4 and wbp11 zebrafish and mouse models display dramatic and similar changes in cerebrovascular morphology and cerebral hemorrhage, suggesting convergent action, and uncovered a specific requirement for both genes in endothelial cells (ECs). We also determined that depletion of WBP11 or PPIL4 in human ECs induces a pathological transcriptional reprogramming towards a senescent cellular state. Collectively, these findings led to the hypotheses that a) PPIL4 and WBP11 are critical components of a network that regulates cerebrovascular morphology and EC homeostasis; b) pathological EC reprogramming is the underlying mechanism in IA associated PPIL4 and WBP11 variants; and c) PPIL4 and WBP11 convergent action to the Wnt signaling pathway is mediated through binding partners and disrupted by IA-associated mutations. In this proposal we apply experimental and functional genomics approaches to test these hypotheses, aiming to establish the converging role of WBP11 and PPIL4 in cerebrovascular ECs, following the discovery of rare- deleterious coding mutations associated with familial IA. The expected outcome of this work is to define and integrate multiple facets that underpin the function of WBP11 and PPIL4: 1) the morphologic and histologic consequences of global and EC-specific deficiency of WBP11 and PPIL4 for structural integrity of the cerebral vessels in model organisms; 2) the impact of WBP11 and PPIL4 depletion and IA-associated variants on EC function at the cellular and molecular level; and 3) the convergence of WBP11 and PPIL4 in ECs via activation of Wnt signaling. These outcomes will inform a framework implicating pathological EC reprogramming as an overlooked contributing factor in IA etiology, while providing a novel conceptual framework for IA pathophysiology, with the long-term goal to develop precision medicine strategies to improve diagnosis and molecularly informed therapeutic interventions for IA patients.

NIH Research Projects · FY 2025 · 2023-02

PROJECT SUMMARY/ABSTRACT Opioid use disorder (QUO) is a public health challenge that affects millions of people worldwide. Evidence supporting the efficacy of three FDA-approved medications for OUD (MOUD), including methadone, buprenorphine and naltrexone, is well established. MOUD also constitutes an important intervention in patients who are dually diagnosed with OUD and HIV infection; successful use of MOUD is associated with improved HIV viral suppression. However, most patients with OUD remain untreated. Expanding access to MOUD has been hampered by various challenges in the cascade of OUD care (i.e., diagnosis, treatment initiation and retention, and recovery). Important questions remain about which factors may enhance retention in treatment and reduce both dropout from and cycling on and off MOUD therapy. Furthermore, enhancing knowledge about real-world effectiveness and guiding optimal use of MOUD in the clinical care of patients is also of critical importance. This proposal will use data from the Veterans Health Administration, the largest integrated healthcare system in the United States, along with rigorous analytic techniques, to address this urgent knowledge gap centering around OUD care. In Aim 1 (K99), I will characterize dynamic cascades of care among patients with OUD and among patients with both OUD and HIV, and identify predictors of treatment engagement, disengagement, and re-entry into treatment. In Aim 2 (K99/R00), I will evaluate real-world effectiveness of clinical management strategies on OUD and HIV, including the effect of buprenorphine prescription in primary care settings versus in substance use specialty settings on OUD outcomes, and the effect of MOUDs on HIV viral suppression among patients with both OUD and HIV. In Aim 3 (R00), I will estimate optimal treatment strategies for MOUD to guide personalized treatment decisions. This proposed research will provide a structured model for evaluation and optimization of OUD care. I received my Ph.D. in Epidemiology from the University of North Carolina Gillings School of Global Public Health, with research focus on HIV/AIDS. I am currently a postdoctoral associate in the Department of Epidemiology of Microbial Diseases at the Yale School of Public Health. The career development plan, which aligns with the research proposal and a multidisciplinary mentorship team, outlines a comprehensive strategy for acquiring expert knowledge and analytical skills for my research career. Specifically, I will receive training in: 1) science in substance use research and pharmacoepidemiology, 2) expert knowledge on the intersection of OUD and HIV, 3) skills in dynamic modelling and stochastic processes, and 4) integration of machine learning methods and causal inference theory. Successful completion of this training plan will provide me with skills and knowledge necessary to become an independent investigator and epidemiologist studying infectious diseases and substance use with advanced causal inference and big data analytics.

NIH Research Projects · FY 2026 · 2023-02

Project Summary The dominant and increasingly evident role of the central nervous system in glucose metabolism regulation remains an attractive therapeutic target for diabetes. Brain stem and hypothalamic coordinating centers of feeding and glucose homeostasis have been well characterized over the years, yet uncertainty over the vari- ous afferent autonomic pathways relaying information from the GI tract to the brain remains. While animal stud- ies indicate that neuronal sensors relaying information about changes in glucose levels and other nutrients are situated within the hepatic portal vein, less is known about these factors in humans. In fact, constrained by a lack of non-invasive tools to interrogate these regulatory circuits in humans, clinical translation of much of the recent advances in our understanding of feeding and glucose control in rodent models remains an active area of investigation. To overcome this critical limitation our group has recently identified neuromodulation via pe- ripheral focused ultrasound (pFUS) as a promising new tool to non-invasively and selectively alter autonomic nervous system afferents to the brain. Exciting preliminary studies in several rodent models of diabetes have revealed that transient application of ultrasound pulses to the hepatoportal plexus can enact long-lasting nor- malization of the hypothalamic glucose setpoint to restore euglycemia in an insulin-independent manner. The experiments under this proposal are designed to build upon this work to characterize the effect of pFUS di- rected towards the hepatoportal neuronal plexus in humans with newly diagnosed type 2 diabetics. We will quantify pFUS's impact on insulin sensitivity, as measured by euglycemic clamps, hepatic glucose disposal and glycogen synthesis by carbon13 NMR and the durability of these responses by long-term CGM glucose recordings. These studies will be augmented with preclinical diabetes models to identify additional sensory fields relevant to glycemic control. One site that holds great promise is the abdominal superior mesenteric plexus, which we found when combined with hepatoportal stimulation has the capacity to enhance the durabil- ity of the glucose-lowering response, likely by engaging the incretin axis. We will conduct additional transla- tional studies in human subjects to determine whether this encouraging dual site pFUS stimulation response indeed can be reproduced in type 2 diabetic subjects. As such ultrasound neuromodulation by pFUS repre- sents a paradigm shifting new tool to investigate the role of the autonomous nervous system in homeostatic glucose control in human subjects which if confirmed by our studies might lead to entirely new non- pharmaceutical treatment options for patients with diabetes.

NIH Research Projects · FY 2025 · 2023-02

PROJECT SUMMARY/ABSTRACT Hematopoiesis is responsible for producing the varied cell types found in blood. In adults, this process primarily takes place in the bone marrow and is characterized by successive rounds of differentiation beginning with the hematopoietic stem cell through to lineage commitment. This process involves progressive narrowing of lineage potency as progenitors eventually commit to the production of a single cell lineage. Disruption of hematopoiesis can lead to benign and malignant pathologies. We focus on the bipotent megakaryocytic-erythroid progenitor (MEP), which has the potential to differentiate into a lineage committed erythroid progenitor (ErP) or a lineage committed megakaryocytic progenitor (MkP). MEP fate specification has been studied to a limited extent, uncovering only a small number of influences that contribute to this process. One understudied aspect of human MEP fate specification is the role of epigenetics. KDM1A (LSD1) is known to be important for erythroid maturation, but its role in MEP fate specification is unknown. Preliminary data using primary human cells show that inhibition of LSD1 in primary human ErP results in the ability of erythroid committed progenitors to undergo granulocytic-monocytic and megakaryocytic commitment. In contrast, LSD1 inhibition does not affect MkP commitment to the megakaryocytic fate. This suggests that LSD1 only antagonizes alternative lineage potential during erythropoiesis, and not megakaryopoiesis, even though LSD1 mRNA is expressed at similar levels in MEP, ErP, and MkP. The goal of this proposal is to establish the mechanism by which LSD1 promotes erythroid commitment while silencing alternative myeloid and megakaryocytic lineage potential. I will achieve these goals utilizing a mix of functional (cell culture), genetic and epigenetic approaches to determine where and how LSD1 regulates gene expression and fate specification in MEP, ErP, and MkP. Computational analyses will determine candidate gene targets, and potential genomic sites to force epigenetic modifications using different fusion proteins based on the catalytically inactive Cas9 endonuclease (dCas9). These results will establish the epigenetic mechanisms that govern erythroid lineage commitment mediated by LSD1. They will also shed light on the distinct lineage-specific epigenetic mechanisms that mediate and maintain fate specification in hematopoiesis.

NIH Research Projects · FY 2025 · 2023-02

Project Summary Age-related diseases are among the leading causes of morbidity, mortality, and healthcare expenditure both in the United States and the world at large. Age-associated declines in fertility are one of the earliest and most common symptoms of aging in both men and women, and almost one-fourth of couples between the ages of 18 and 45 suffer from impaired fertility or infertility. Although assisted reproductive technology can help couples with impaired fertility produce viable offspring, it can be very expensive and does not treat the root of the problem: germline aging. Existing literature on aging is relatively sparse, focusing on conventional model organisms with relatively short lifespans and how various treatments can slow their decline rather than prevent it entirely, or even reverse aging. The negligibly-senescent, highly-regenerative, hermaphroditic planarian S. mediterranea presents a unique model system to study germline aging because it is one of the few species to actively reverse an aging phenotype. I have observed that S. mediterranea experiences an age-related decline in its fertility that can be reversed by bisecting the planarians and allowing them to regenerate. The overall goal of my project is to determine how aging impairs fertility in S. mediterranea, and how regeneration overcomes this impairment. Based on preliminary data, I hypothesize that age-associated molecular damage accumulates in late gonadal precursor cells of the testes and (especially) ovaries, compromising the production of mature germ cells, and that during regeneration these impaired cells are replaced by functional equivalents to restore fertility. To evaluate this hypothesis, I will seek to address the following specific aims. Aim 1: I will assay changes in markers of gametogenesis to determine how germ and niche cell population are affected by aging and rejuvenation. Aim 2: I will use a panel of molecular biomarkers on isolated gonads to determine if age-associated biomarkers accumulate in the gonads over time, and if regeneration restores the gonads to a more youthful state. Aim 3: I will use selective mating experiments to determine if impairments in fertility are due to defects in the testes, ovaries, or both. From these experiments, I will learn more about the cellular, molecular, and physiological causes of germline aging in S. mediterranea, and how regeneration manages to reverse them. These results will also help us understand why other organisms are unable to prevent age-related gonadal degeneration, and potentially lay the groundwork for more robust fertility treatments that extend or even restore fertility in humans.

NIH Research Projects · FY 2026 · 2023-02

PROJECT SUMMARY Supravalvular aortic stenosis (SVAS) is a developmental cardiovascular disease, occurring alone or in Williams Beuren Syndrome (WBS), and results in excessive arterial smooth muscle cell (SMC) proliferation and lumen obstruction. Our long-term objective is to elucidate how this pathology can be attenuated. Heterozygous loss-of-function mutations or deletions of the elastin gene ELN cause SVAS. Eln(-/-) embryos and Eln(+/-) neonatal mice develop arterial disease with features similar to human SVAS4-6. Elastin forms the major component of the elastic lamellae in arteries. Defective lamellae are associated with excessive developmental SMC proliferation in SVAS. If untreated, SVAS results in heart failure and an increased risk of sudden death, and major surgery, which carries substantial risk, is the only treatment. Medical therapies are lacking because mechanisms linking defective elastin and SMC hypermuscularization are incompletely defined. We aim to elucidate molecular and cellular mechanisms underlying elastin aortopathy. The Notch pathway is critical in regulating SMC biology, and we recently reported a role for Notch in SVAS pathogenesis (JCI, 2022). Signaling via Notch ligand Jagged1 (JAG1) and NOTCH3 receptor in SMCs activates proliferation. Our studies reveal that JAG1-NOTCH3 pathway components are upregulated after elastin depletion. Importantly, we determined that inhibiting the NOTCH3 pathway in Eln(-/-) embryos attenuates aortic hypermuscularization and stenosis and reverses established hypermuscularization in Eln(+/-) pups. Epigenetic modifications influence gene expression by altering chromatin accessibility but prior to our JCI paper, have not been explored in elastin deficiency. Our initial data indicate that elastin deficient aortas and SMCs display reduced DNA methylation, elevated histone acetylation and reduced expression of DNA methyltransferase 1 (DNMT1) and histone deacetylase 1 (HDAC1). We hypothesize that elastin deficiency attenuates DNMT1- and HDAC1-mediated repression of Notch pathway genes to promote aortic hypermuscularization and stenosis. The proposed studies use cell culture, mouse models, de-identified human samples and advanced genomic and epigenetic techniques to uncover mechanisms of SVAS that can be therapeutically targeted. We will test our hypothesis in two aims. Aim 1 will determine how elastin deficiency alters epigenetic mediators and the epigenetic landscape in human and murine SMCs, including 1a) identifying elastin-regulated epigenetic enzymes, 1b) determining mechanisms by which elastin deficiency modulates epigenetic regulators, 1c) an integrated genome-wide epigenetic and transcriptomic analysis to identify new regulatory mechanisms and 1d) characterization of epigenetic enzymes and marks in human samples. Aim 2 will elucidate the relationship between elastin, chromatin remodeling and the Notch pathway, including 2a) identifying causal epigenetic mechanisms, 2b) kinetics and 2c) testing HAT inhibition as a therapy in mouse models of SVAS. These studies promise to yield new treatments for this lethal genetic disease.

NIH Research Projects · FY 2026 · 2023-02

Enter the text here that is the new abstract information for your application. This section must be no longer than 30 lines of text. The overarching goal of the Yale MMPC-Live is to provide extramural investigators access to the unique metabolic phenotyping services provided by the Yale MMPC-Live and empower them to harness the power of mouse genetics to its fullest potential to metabolically phenotype their mouse models of obesity and diabetes. The Yale MMPC-Live consists of three highly interactive Cores that have an established (>20 yr) track record of working together in close harmony: 1) The Yale MMPC-Live Administrative Core oversees the operation of the Yale MMPC-Live, facilitates research with the other MMPC Centers and the MMPC Coordinating Unit to standardize key methodologies, and coordinates the efficient workflow through the Yale MMPC-Live cores and access to the Yale MMPC-Live Animal Core and the Yale MMPC-Live Phenotyping Core, 2) The Yale MMPC-Live Animal Core provides a centralized facility for coordinating receiving, screening and monitoring mice from outside investigators and 3) The Yale MMPC-Live Phenotyping Core empowers Yale MMPC-Live clients with access to unique metabolic phenotyping services that provides them with the means to characterize the metabolic changes in their particular mouse models of complex metabolic disease using established state-of-the-art methodology. The Specific Aims of the Yale MMPC-Live are to: 1) serve the US academic research community to study diabetes and obesity in their mouse models by providing metabolic, physiologic, and behavioral phenotyping on live mice, as well as expert advice in mouse models, experiment design, data analysis, and data interpretation at similar cost whether inside or outside Yale without bias and, and collaborate to provide a wide array of tests and expert advice while avoiding unnecessary overlap, 2) Promote rigor and reproducibility in research by: a) developing and sharing validated protocols for phenotyping live mice; b) providing difficult experimental tests conducted by experts with a high degree of standardization and quality control, to PIs who would otherwise not be able to conduct or afford them; and c) sharing technologies and providing web-based tools for gold-standard approaches in experimental methods and data analysis, 3) Develop standardized data formats and storage guidelines for complex data, including metadata, for sharing with clients and the public as appropriate, and employ unique Research Resource identifiers (RRID), Digital Object Identifiers (DOI), and other best practices directed by DKNet.

NIH Research Projects · FY 2026 · 2023-01

Ongoing analyses from our laboratory and others have identified novel properties of self proteins, namely posttranslational protein modifications (PTMs) that may be identified as early proteomic and immunologic biomarkers of Type 1 diabetes as well as alter metabolic pathways. An emerging number of self proteins acquire PTMs and become targets of B and T cell autoimmune responses leading to inflammation and pathology in the pancreas. Some examples of critical modifications to self proteins include citrullination, oxidation, deamidation reactions, and isoaspartyl modification, all responses of self proteins within cells that undergo inflammatory stress. Key PTM candidates have already been identified from human beta cells and other key candidates will be identified from beta cell derived exosomes, recently identified as a peripheral marker of beta cell health. As importantly, these PTMs within cells may alter the biological properties of proteins within beta cells. In the present proposal, we will define how modified self-proteins may alter enzymatic pathways of glucose sensing and insulin secretion in the pancreatic beta cell. The proposal will utilize MultiOrdinate Spectral Analysis (MIMOSA), a technology pioneered at Yale University. MIMOSA is a major innovation that provides an internally cross-validated as well as NMR-validated, direct, rigorous, comprehensive integrated analysis of metabolic fluxes. The “multi-ordinate” aspect of MIMOSA incorporates the flow of stable isotope from metabolite to metabolite along intersecting metabolic pathways. The “mass isotopomer” aspect uses MS/MS-based ion fragmentation analysis of stable-isotope-labeled metabolites to identify the carbon-specific position of label. The significance and innovation of the present studies is in identifying pathways that may restore beta cell functions, via pharmaceutical correction of the aberrant modification, as well as link autoimmune biomarkers with pathways of beta cell dysfunction.

NIH Research Projects · FY 2026 · 2023-01

Schizophrenia and other psychotic disorders are typically thought of as disorders of adolescence and early adulthood: the peak incidence of new psychotic disorder diagnoses is from 15 to 19 in men and 20 to 24 in women. However, women also demonstrate a second peak of incidence and vulnerability to the illness in their 40s and early 50s. Theories have been proposed to explain this second peak, including appeals to the neuroprotective effects of estrogen and other reproductive hormones, which wane in the years preceding menopause. Despite these observations and theoretical groundwork, very little evidence exists to identify risk factors for development of psychosis in women experiencing the menopause transition. This is partly because development of psychosis in this population is relatively rare and is thus difficult to observe. In response to the NIMH funding opportunity announcement entitled, “Mood and Psychosis Symptoms during the Menopause Transition”, we propose a two-pronged approach to identify risk factors for development of psychosis during the menopause transition. In our first aim, we propose to recruit from established local and national sources 179 individuals who have developed a first episode of psychosis during the menopause transition and to retrospectively identify elements of medical, reproductive, psychiatric, and family history that predispose to the development of psychosis when compared to 144 matched controls who developed depression in the same period. We hypothesize that women who developed psychosis during the menopause transition will report a prodromal period of attenuated symptoms preceding the development of frank psychosis, that factors generally predisposing to psychosis onset will be relatively over-represented in the psychosis cohort, and that psychiatric disorders tied to hormone fluctuations will be elevated in both cohorts relative to population rates. In our second aim, we propose to leverage our team’s established expertise in identifying risk factors for psychosis to prospectively study women who have attenuated psychotic symptoms, elevating their risk for developing psychosis. From established sources, we will identify 196 women who are at clinical high risk for psychosis during the earliest phases of the menopause transition. We will then follow these women and 98 matched healthy controls over 2 years, collecting clinical, behavioral, computational, endocrinological, and (in an exploratory subset) imaging and electrophysiological data as they transition toward menopause. We hypothesize that baseline psychotic and cognitive symptom severity will predict conversion to psychosis and that the worsening of these symptoms will correspond to specific clinical and hormonal markers of the menopause transition. We also hypothesize that candidate psychosis biomarkers will predict conversion and functional decline and will be impacted by markers of the menopause transition. Together, these studies will be the first to identify definitive risk factors for psychosis development in aging women. Our goal is to use the data generated to develop specific interventions to mitigate risk for psychosis in this vulnerable population.

NIH Research Projects · FY 2025 · 2023-01

Among youth, major depressive disorder (MDD) and bipolar disorder (BD) represent two of the top ten causes of disability and confer heightened risk of suicide. Since BD often initially presents as a MDD episode, youth with BD are frequently misdiagnosed and thus receive ineffective treatment. Family history of mood disorders is a robust predictor of early-onset MDD and BD as well as other psychiatric disorders. Prior studies have identified neurobiological differences between healthy youth at high familial risk for BD or MDD relative to low familial risk, and one study has identified neural circuit differences between youth at high familial risk for BD versus MDD. Relatedly, there is preliminary evidence for neural markers that predict later onset of psychopathology among youth at high familial risk for BD and MDD. These studies suggest that there are markers of vulnerability that can be detected in the brain, prior to symptom onset, which may further increase risk for poor mental health outcomes among these susceptible youth. However, extant research has been limited by small sample sizes and a lack of multiple longitudinal symptom measurements over time, which have hindered the identification of robust biomarkers that distinguish risk profiles among youth with a family history of BD versus MDD. The identification of brain-based signatures of BD and MDD risk in youth would advance understanding of distinct mechanisms underlying heightened vulnerability, which may ultimately inform approaches for earlier and more accurate identification of these disorders. The present study aims to uncover unique neurobiological profiles of high familial risk for BD and MDD among healthy youth, and to investigate whether these biomarkers predict the subsequent onset and longitudinal course of psychopathology across adolescence. This study will include healthy youth at low (LR, n=3,915) or high familial risk for MDD (HR-MDD, n=1,564) or BD (HR-BD, n=407) with longitudinal data up to 3 years, derived from the landmark Adolescent Brain Cognitive Development (ABCD) Study. Aim 1 will examine dissociable patterns of resting-state functional connectivity (FC) in emotion- and reward-related networks at baseline between healthy HR-BD, HR-MDD, and LR youth, using a whole-brain seed- to-voxel approach with the amygdala, ventral striatum, and dorsal striatum as seed regions of interest. Aim 2 will ascertain longitudinal trajectories of dimensional psychiatric symptoms across adolescence over 3 years in high familial risk youth using group-based trajectory modeling. Aim 3 will investigate whether alterations in baseline FC within emotion- and reward-related networks predicts the presence of a clinical diagnosis in later adolescence and/or a more severe longitudinal course of dimensional symptoms across adolescence. This research will reveal critical insight into the mechanisms that contribute to risk versus resilience in vulnerable youth, potentially serving as key biological targets for interventions. This knowledge may also potentially inform early detection and intervention programs, which will help to alleviate the immense burden of BD and MDD.

NIH Research Projects · FY 2026 · 2023-01

This research program focuses on the systems developmental biology, biophysics and biomechanics of early spinal column development. The research program utilizes zebrafish as model for understanding the mechanisms of human development and causes of birth defects such as scoliosis and spina bifida. The experimental approach is driven by the idea that quantitative in vivo analysis will lead to fundamental insights into the emergence of biological organization from the collective interaction of its constituent parts. The research program combines genetics, embryology, in vivo biophysics, live imaging and systems level data analysis and computational modeling to study pattern formation and morphogenesis. The proposed research program will address a number of questions regarding biological order and the reproducibility of embryonic development. The program will follow-up on the lab’s recent finding that a dynamically stable pattern of cell state transitions underlies the reproducibility of development to understand the mechanisms maintaining dynamic stability during zebrafish body elongation. The research program will also examine the mechanism of mechanical information regulating the flux of cells through a developmental trajectory. The program will address how tissue-tissue interactions constrain cell behavior during body elongation. At the molecular and cellular level, the program will utilize newly developed methods for in vivo single molecule biophysics to study cell adhesion protein dynamics and their relation to cell state transitions and cell morphology. Overall, this is multi-scale research program that considers the roles of molecules, cells and tissues in the genesis of order in the developing embryo.

NIH Research Projects · FY 2025 · 2023-01

Food allergy is associated with a hypersensitive type 2 immune response that develops following sensitization to food proteins. Allergic sensitization elicits the development of adaptive immune memory, characterized by antigen specific Th2 cells and B-cells which produce antibodies of the IgE and IgG1 isotypes. IgE antibodies bind to tissue resident mast cells, and these IgE-mast cell units enable a rapid and exuberant recall response to low quantities of food antigen. Pre-clinical and clinical studies underscore the importance of IgE antibodies in the gastrointestinal manifestation of food allergy, such as abdominal pain, nausea and vomiting, however what mast-cells induce to initiate these symptoms is poorly understood. GDF15 is a stress- induced TGF-b cytokine that mediates anorexia, conditioned taste aversion, and vomiting through its receptor, GFRAL, located on the area postrema. GDF15 can be induced by type 1 and type 2 inflammation, however its role in the context of food allergy is unclear. The objective of this proposal is to study the role of GDF15- GFRAL signaling in driving avoidance behavior to food allergens in allergic mice. Preliminary data in in vivo food allergy models demonstrates GDF15 is rapidly induced upon allergen challenge in a manner largely dependent on IgE, FceR1a expressing cells, and leukotrienes. Using qPCR and FISH of the small intestine and colon from food allergen challenged mice, we find that colonic, but not small intestinal, crypt epithelial cells are enriched in GDF15 transcripts. Interestingly, acute pharmacological blockade of GDF15 ameliorates food allergen aversion in a two-bottle preference test behavioral paradigm. This data suggests that IgE- mediated mast cell activation elicits colonic epithelial GDF15 production, potentially through leukotrienes, to drive allergen aversion. To test this hypothesis two aims will be pursued. Aim 1 will examine the effect of genetic deficiency of GDF15 and GFRAL on food allergen avoidance in vivo using newly generated KO mice on the food allergy susceptible BALB/cJ background strain. GDF15 and GFRAL deficiency’s effect on mast- cell mediated immune responses in experimental food allergy will also be characterized. Aim 2 will examine how IgE mediated mast cell activation initiates GDF15-GFRAL signaling in experimental food allergy using mice genetically or pharmacologically deficient in IgE, mast cells, and leukotrienes. Mast-cell dependent changes in the transcriptome of colonic epithelial cells will too be quantified. Together, these studies will enhance our understanding of how type 2 immune responses in the gastrointestinal tract lead to allergen induced malaise, and may reveal novel targets to prevent complications of oral immunotherapy (OIT). Alongside these studies, the applicant will complete a program of advanced technical and theoretical coursework, clinical electives, and scientific skill building. The research and training detailed in this application will prepare him to pursue a clinically relevant basic science career as a physician scientist.