University Of Southern California

NIH Research Projects · FY 2025 · 2021-08

Project Summary In each of our trillions of cells, genetic information is stored on meter-long chromosomes spatially organized inside micron-scale nuclei. In the past decade, large-scale efforts have built increasingly detailed atlases of transcription, regulatory elements, and genome folding across ever-expanding sets of cell types and tissues. Still, these beautiful maps do not by themselves reveal the sequences or molecular mechanisms acting in these diverse cellular contexts. Drawing on approaches from biophysics, bioinformatics, and machine learning, this project will develop novel computational approaches to determine the DNA sequences and mechanisms underlying 3D genome organization, and how this in turn relates to genomic functions. Drawing on the latest breakthroughs in machine learning, we will model how individual nucleotides contribute to genome folding. We will apply these models to characterize cell-type specific genome folding, develop methods to engineer DNA sequences in silico, and model enhancer-promoter influences. Concurrently, we will build biophysical models to understand deeply conserved mechanisms of genome folding. Using meiotic chromosome folding as a model system, we will develop models to learn new rules governing cohesin dynamics and loop extrusion. To uncover how extrusion interfaces with other mechanisms, we will build models of synaptonemal complex assembly, as well as models of meiotic chromosome organization across species. By honing in on the sequences most crucial for locus-specific genome folding and characterizing the mechanisms driving genome- wide folding, the computational models we develop and the mechanisms we discover will enable new approaches to precision genome engineering. This will include how to re-wire gene-regulatory circuits, not only by targeting enhancers and promoters, but also by modulating their cell-type specific communication. At the same time, the aims described here will bridge fundamental insights into 3D chromosome organization with clinical genomics, and greatly improve the interpretability of non-coding DNA variants.

NIH Research Projects · FY 2025 · 2021-08

Radiation therapy (RT) is known to exert direct cytotoxic effects on tumor cells; however, recent research is revealing its influence on the immunogenicity of tumors, thus affecting the overall outcome of RT. While RT alone is usually insufficient to overcome the immunosuppressive tumor microenvironment (TME), strategies to boost immune-stimulating effects of RT are under intensive investigation. To date, most of the focus has been placed on immunomodulation after RT, in particular in combination with immune checkpoint inhibitors. Little is known about how manipulation of the TME before RT can impact on immunogenicity and therapeutic efficacy of RT. A growing body of evidence reveals that Batf3-dependent conventional type 1 dendritic cells (cDC1) rarely found within the tumor myeloid compartment have the important capacity of cross-presenting tumor-associated antigens (TAA) to CD8+ T cells, and act as `master regulators' for the T cell response in cancer. We hypothesize that in situ induction and activation of cDC1 enhances the therapeutic efficacy and immunogenicity of RT. To test this hypothesis, we developed a combinatorial in situ radioimmunotherapy comprised of in situ administration of: 1) Flt3L to mobilize cDC1 to the TME; 2) RT to promote immunogenic death of cancer cells and maturation of DC; and 3) dual TLR3/CD40 stimulation to activate antigen-loaded cDC1 for priming of tumor-specific CD8+ T cells. Our new data using multiple syngeneic orthotopic murine models of poorly immunogenic tumors insensitive to anti-PD-L1 therapy reveal that in situ radioimmunotherapy elicits de novo adaptive T cell responses that are characterized by novel clonotypes and stem-like Tcf1+ Slamf6+ phenotypes, renders tumors responsive to anti-PD-L1 antibody, mediates durable complete responses, and develops tumor-specific systemic immunological memory. Compelling evidence suggests that immunogenicity of RT can be enhanced by in situ induction and activation of cDC1; however, immunomodulatory effect of in situ radioimmunotherapy against distant metastatic tumors remains unclear. cDC1 prime CD4+ T cells as well as CD8+ T cells, but the role of CD4+ T cells in in situ radioimmunotherapy remains elusive. In addition, it remains unknown whether in situ radioimmunotherapy overcomes poor T-cell infiltration in human non-T cell-inflamed tumors. In this proposal we will elucidate the roles of CD4+ T cells in augmenting antitumor efficacy of in situ radioimmunotherapy (Aim 1). Additionally, we will seek to better understand the mechanisms underlying the immunomodulatory effect of in situ radioimmunotherapy targeting non-irradiated distant metastatic tumors (Aim 2). Finally, in Aim 3, we will seek to determine the alteration of the human TME in patients with unresectable and metastatic breast cancer treated with in situ radioimmunotherapy. These studies will add essential mechanistic understanding to how RT and the immune system interact, and provide insight into the clinical potential of in situ radioimmunotherapy against non-T cell-inflamed tumors insensitive to anti-PD-L1 therapy.

NIH Research Projects · FY 2025 · 2021-08

Project Summary / Abstract Both environmental and genetic factors contribute to disparity in disease risks between populations. The genetic causes of differences between populations are intimately tied to the evolutionary histories of these populations. Therefore, a better incorporation of evolutionary thinking will help explain the disparity among diverse populations today and improve clinical practices and personalized care. To this end, the Chiang Lab will continue to develop an integrative framework combining evolutionary population genetics with genetic epidemiology in humans, utilizing both empirical data analysis and quantitative methods development to better probe into the genetic architecture of complex traits within and between populations. This integrative framework consists of three main foci: (1) the genetic architecture of human complex traits, (2) the demographic history, and (3) the adaptive history of human populations. Research in the first topic informs the genetic consequences on our phenome today, while research in the latter two explains the evolutionary mechanisms through which variation arise within and between human populations. More importantly, research from the Chiang Lab focuses not solely on these topics, but also leverages information on one to inform the other. Within this paradigm, the Chiang Lab will focus on the following three goals over the next five years. First, we will execute a comprehensive genetic research program to address the health disparities in Native Hawaiians. Specifically, we will generate the genomic resources necessary to accelerate genetic research in this population. We will then characterize the demographic history of the Native Hawaiians to illustrate the benefit of conducting genomic studies in understudied populations, perform large-scale meta-analysis in Polynesian populations to identify population- specific alleles associated with diseases prevalent in Native Hawaiians, and engage the Native Hawaiian community for future partnership and collaborations. Second, we will investigate the evolutionary etiology for elevated risk in present-day populations. Using Latino population as an example, we will examine if the elevated risk in childhood leukemia in this population is due to the selective pressure introduced during European contact in the 16th century. Third, we will revolutionize the current concept of genetic relatedness by introducing a new genetic similarity matrix among individuals that incorporates information from the genealogical tree of the population. This matrix will improve the performance of a number of statistical genetic applications, such as heritability estimation and phenotype imputation. While we used Native Hawaiians and Latinos as example populations in this proposal, this integrated framework of genetic epidemiology and evolution will also benefit future research in other understudied ethnic minorities. We are uniquely positioned to achieve these goals because of our expertise in combining population genetic principles with medical genetic analysis and statistical genetic development.

NIH Research Projects · FY 2025 · 2021-08

PROJECT SUMMARY/ABSTRACT Alzheimer’s disease (AD) is a progressive neurodegenerative disease that spreads across the brain from its origin in the medial temporal lobe. The hippocampus is one of the earliest and most affected brain regions in AD and hippocampal atrophy has been linked to the severity of the behavioral symptoms. Although numerous theories have been put forth, the molecular underpinnings of hippocampal neurodegeneration remain unclear. This lack of understanding has stymied AD drug development from translating animal research into human treatment. I believe that a translational cellular atlas that bridges the gap between mouse and human AD research is needed to determine which specific hippocampal cell types are affected by AD. My previous research creating the mouse Hippocampus Gene Expression Atlas (HGEA) lays a strong foundation for this effort (Bienkowski et al., Nature Neuroscience, 2018). The HGEA defines 20 distinct genetic subdivisions of the hippocampus and subiculum based on mapped gene expression patterns, delineates each region’s input/output pathways, and demonstrates how each region contributes to brain-wide networks. Overall, I found that hippocampal gene expression patterns were highly related to specific anatomical connectivity patterns. Among many new insights, I discovered that subiculum gene expression patterns revealed hidden lamina of pyramidal neurons and demonstrated how this laminar architecture underlies a columnar organization similar to the cerebral cortex. Altogether, the HGEA demonstrates the multiscale organization of the hippocampus from individual genetic cell types to neuronal networks regulating animal behavior. I established a number of resources and tools on the Mouse Connectome Project website so that other hippocampal scientists around the world could use the HGEA to guide their own research experiments. The funding of this K01 Mentored Research Scientist Career Development Award application will provide me with training and expertise I need in order to develop a human version of the HGEA as a translational resource to understand AD neurodegeneration. Building on the mouse HGEA, the proposed research uses a cutting-edge spatial transcriptomics approach in thick optically-cleared tissue sections (STARmap) to reveal multiplexed gene expression patterns, build a human HGEA that can be registered to MRI data, and investigate changes to HGEA-defined neuronal cell types caused by hippocampal neurodegeneration within an AD mouse model (5XFAD mice) and humans with AD. To guide this project and my career development, I have assembled a world-class team of supportive mentors (Drs. Arthur Toga and Berislav Zlokovic) and collaborators (Dr. Carol Miller) to provide me with new training to investigate Alzheimer’s disease in both transgenic mouse models and human post-mortem tissue. Ultimately, the funding of this K01 proposal will complete my career development toward leading a translational neuroscience laboratory studying the relationship of gene expression, connectivity, and behavior in neurological disease.

NIH Research Projects · FY 2026 · 2021-07

PROJECT SUMMARY In the US, prostate cancer (PCa) is the second leading cause of cancer death in men, with men of African ancestry having the highest incidence and mortality rates. Indeed, men of African ancestry who develop PCa have more aggressive and lethal prostate tumors on average, compared to their non-African ancestry counterparts. While the reasons for this health disparity are unknown, evidence suggests that genetics is likely a contributing factor. Indeed, large-scale genome-wide association studies (GWAS) of PCa have identified 300 genomic risk variants; however, the vast majority are in non-coding regions, which makes identifying the proximal target gene challenging and hinders translational efforts. A large body of works have demonstrated that PCa risk is highly enriched in functional regions of the genome, which indicates that risk is mediated through perturbed regulatory action on relevant susceptibility genes. Multiple lines of evidence have shown that integrating omics with large-scale genetic data increases statistical power to identify novel genomic risk regions and uncovers target molecular mechanisms of risk. These analyses rely on first identifying associations between genetics and various omics data (i.e., molecular quantitative trait loci, or molQTLs) and then using these associations to impute or predict omics into large-scale PCa GWAS data. However, to date, analyses have been limited for three primary reasons. First, previous integrative analyses with PCa risk relied on diverse omics data measured across tissues other than prostate, where translation to prostate-specific results may be inaccurate. Previous omics datasets measured in prostate together with genotype have been limited to small sample sizes, resulting in less accurate prediction when compared with larger sample size datasets. Second, prior omics datasets have been measured primarily in men of European ancestry. Multiple recent works find that genetic-based omics prediction translates poorly across populations, which limits the utility of existing omics data to non-European men. Third, previous studies have shown the importance of integrating omics data beyond gene expression with PCa risk, thus demonstrating that multi-omics investigations facilitate a more unbiased approach to provide biological insights into disease mechanisms. To date, the majority of imputation-based approaches have been applied to large- scale GWAS, however recent works have made crucial discoveries in cancer biology by imputing cancer risk from GWAS into molecular cohorts. Here, to understand the genetic regulatory mechanisms in prostate tissues across the molecular cascade, we propose to assay methylation, transcriptomic, proteomic, and metabolomic data in prostate tissue to perform large-scale molQTL mapping for African- and European-ancestry men. To elucidate the underlying mechanisms responsible for PCa risk and identify novel genetic risk factors, we will integrate identified molQTLs with the largest-available PCa GWAS. Overall, our proposal aims to characterize the genetic regulatory landscape of prostate tissue, its effect on PCa risk, and health disparities of this disease.

NIH Research Projects · FY 2025 · 2021-07

Project summary Although single-molecule sequencing (SMS) technologies have advanced in recent years to enable routine sequencing and assembly of human genomes, new software is required to utilize the potential of SMS in human genetics. The long term goal is to help improve our understanding of complex variation in human diversity and its role in disease. To achieve this, we will develop methods to (1) detect variation in SMS reads, (2) assemble duplicated sequences missing from SMS de novo assemblies, and (3) genotype complex variation in large HTS datasets using lightweight data structures. While several years of algorithm development for SMS data have resulted in an software ecosystem to detect variation in SMS genomes, the rationale for the need to continue development is that sensitivity and specificity are not yet sufficient for disease studies, important classes of variation are not resolved by current assembly approaches, and the knowledge gained from sequencing SMS genomes must be used to improve what can be discovered in large disease studies that rely heavily on short read data such as those conducted under TOPMed. The algorithmic innovations we will provide for SMS data are an alignment algorithm that explicitly optimizes over rearranged sequences, an assembly approach that exploits minor differences between duplication copies to resolve genome function. Software will be supported through Bioconda installation and distributed test cases. Once a variant is discovered by SMS, it may be more easily genotyped in short read data. We will develop methods to generate databases of SMS variation that may be queried with short read data. To aid in development of assembly algorithms for duplicated sequences, we will generate a public resource of SMS data for individuals with known copy number polymorphisms. The significance of this work is to enable SMS genomes to be used in disease studies, both by uncovering previously hidden variation, and by increasing the amount of variation found in large short-read datasets.

NIH Research Projects · FY 2026 · 2021-07

DESCRIPTION (provided by applicant): Functional magnetic resonance imagining (fMRI) has revealed two major principles of the functional organization of the ventral temporal cortex (VTC) in human adults. First, some regions of VTC respond selectively to a specific category of stimuli, such as the fusiform face area (FFA) which responds more to faces than to any other stimulus category. The second principle of organization is that different categories of stimuli have systematically distinct patterns of response across the entire VTC. How do these two key aspects of VTC functional organization in adults arise in development? The goal of my research program is to discover if these organizing principles are present in the infant brain (Aims 1 and 2) and design computational models to test different theories of cortical development (Aim 3). The dissertation work in this proposal will provide invaluable data toward the goal of refining theories of cortical development. In addition to innovations that enhance the quality of awake infant fMRI data, Aim 1 provides the first evidence that like adults, infants have face-selective responses in the FFA, scene-selective responses in the parahippocampal place area (PPA), and body-selective responses in the extrastriate body area (EBA). Aim 2 directly follows this up by asking if infants have systematically distinct patterns of response across higher- level visual areas that are similar to those found in the adult brain. The F99 phase of this proposal will provide training to optimize machine learning (ML) techniques that can withstand the unique challenges of infant fMRI data – specifically unbalanced and missing data. The F99 phase will be conducted at MIT, an intellectual environment with access to leaders in the fields of ML, cognitive neuroscience, and computational neuroscience. Finally, Aim 3 of this proposal is to build computational models designed to test current theories of cortical development. The K00 phase of this proposal will provide training on the design and implementation of artificial neural networks (ANNs) models as well as training on the best methods to test ANN models using infant fMRI data. Research for the K00 phase will provide a new mentorship experience with an established investigator in computational neuroscience and will take place at an institution with a thriving intellectual environment that has access to an MRI scanner and the computational resources necessary to build a variety of ANN models. In summary, the objective of the proposed research is to determine if the principles of functional organization in the adult brain are present in infants. Insights from this proposal will advance and refine theories of cortical development and have the potential to be applicable to other domains such audition and language. Further, by combining my predoctoral training in awake infant fMRI with my proposed postdoctoral training in computational modeling, the proposed research will enable me to become an independent investigator and leader in the field of computational developmental neuroscience.

NIH Research Projects · FY 2025 · 2021-07

PROJECT SUMMARY/ ABSTRACT Cancer drug resistance occurs not only by selection of genetically resistant clones, but also through phenotypic plasticity via rapid induction of transcriptional programs that allow some cells to adapt and persist. In bladder cancer (BC), phenotypic plasticity is observed in a model established in our lab, in which two subpopulations of tumor cells reversibly and spontaneously transition from one to the other. Isolated and studied by Hoechst staining and flow cytometry, these subpopulations consist of a “side population” (SP) of highly tumorigenic, cisplatin-resistant, stem-like cells, and a “non-side population” (NSP) of cells lacking these properties. A potential contributing epigenetic factor to this plasticity is N6-methyladenosine (m6A) RNA modification. Deposited by m6A writers and removed by m6A erasers, m6A dynamically and reversibly regulates key cellular functions and essential features of cancer cells. Deregulation of m6A modifications and m6A effectors (writers, erasers, readers) has been implicated in drug resistance in various cancer types. To study the role of m6A modifications in BC, I set up and validated in our lab the gold standard epitranscriptomic assay, methyl-RNA-immunoprecipitation followed by high-throughput sequencing (MeRIP-seq). I used this assay to compare the SP and NSP subpopulations and identified differentially methylated candidate transcripts. I also found that pharmacological inhibition of a key m6A eraser, fat mass and obesity-associated protein (FTO), potentiates a shift to the SP state. Based on these preliminary data, I propose to test the hypothesis that m6A modifications regulate expression of transcripts that promote transition to a drug-resistant state in BC in vitro and in patient-derived samples. I will accomplish this with the following aims: Aim 1: I will use MeRIP-seq and RNA-seq to systematically identify differentially methylated and differentially expressed transcripts that drive the shift to and from a drug-resistant state. I will genetically modulate these targets, and measure the impact on cisplatin resistance, SP-NSP interconversion, colony formation, migration and invasiveness. Aim 2: I will define the function of FTO, a key m6A eraser that affects plasticity in our model by genetically and pharmacologically modulating FTO. I will measure the impact on cisplatin resistance, SP-NSP interconversion, colony formation, migration and invasiveness, and use MeRIP-seq and RNA-seq to identify transcripts that are both differentially methylated and differentially expressed. Aim 3: I will use RT-qPCR to test which candidate transcripts and m6A effectors are associated with clinical progression to cisplatin resistance using BC patient-derived solid and liquid biopsy samples. Characterizing this novel epitranscriptomic mechanism will provide strong evidence for new biomarkers and therapeutic targets aimed at short-circuiting BC drug resistance. The proposed research study will offer rigorous physician-scientist training in an outstanding environment offering top notch research facilities integrated with translational patient tissue resources and diverse mentoring expertise.

NIH Research Projects · FY 2025 · 2021-07

Abstract This application for a Mentored Patient-Oriented Research Career Development Award proposes training and research designed to provide the candidate with a foundation to establish a successful career as an independent investigator with expertise in affective, neurocognitive, and neurological mechanisms underlying eating psychopathology and obesity. The candidate seeks advanced training in three areas, each of which build upon her prior knowledge and experience with ecological momentary assessment (EMA) and emotion dysregulation in eating disorders and obesity: (1) neurobiological mechanisms of eating behavior and obesity, including functional magnetic resonance imaging (fMRI) methodology; (2) neuroscience of self-control in relation to eating; and (3) design and analysis of multi-method ambulatory assessment and intervention approaches. Training will be guided by an interdisciplinary team (mentors and collaborators) and will involve formal (e.g., coursework, workshops) and informal (e.g., directed readings, mentoring meetings) activities across the funding period. The research plan harnesses these training experiences and proposes a multi- method study to examine how biobehavioral self-regulatory processes predict momentary binge eating and short-term weight change. Specifically, this study will examine the extent to which affect, attention bias to food cues, and impulsivity (measured via EMA, behavioral tasks, and fMRI) interact to predict real-time binge eating symptoms and subsequent weight change among a sample of 75 adults at risk for obesity (i.e., those with overweight body mass index who endorse regular binge eating). Participants will complete interviews, self- report measures, an fMRI protocol that includes response inhibition and delay discounting tasks, a two-week EMA protocol that includes ambulatory task-based measurement of attention bias, and a six-month follow-up assessment to assess weight change. Importantly, results of this research will identify biobehavioral mechanisms underlying binge eating and obesity risk, which will help to inform novel prevention and interventions. Taken together, the proposed study will advance the understanding of binge eating psychopathology in the context of obesity, and will set the stage for the candidate's future program of research. The training and mentorship provided by the award will further facilitate the candidate's success in becoming an independent investigator, with particular expertise in multi-method ambulatory strategies to identify and target mechanisms contributing to eating and weight disorders.

NIH Research Projects · FY 2025 · 2021-07

PROJECT SUMMARY / ABSTRACT Craniosynostosis is a craniofacial disorder characterized by the premature fusion of cranial sutures with defective mesenchymal stem cells (MSCs). Patients with severe craniosynostosis often have intellectual disabilities (IDs). Both genetic mutations and environmental factors have been linked to craniosynostosis coupled with MSC depletion. We propose to determine gene-environment interaction mechanisms in craniosynostosis by addressing how craniosynostosis disease genes Twist1 and Tcf12 interplay with an environmental risk factor, namely maternal usage of the antidepressant citalopram. Importantly, we aim to establish a MSC-based therapeutic strategy to mitigate both skull dysmorphology and neurocognitive dysfunctions in craniosynostosis. This is innovative and significant because we have little understanding of environmental factors and gene-environment interactions in craniosynostosis, and new treatments for this devastating disorder are urgently needed. Neurocognitive functions have been largely neglected in studies of animal models of craniosynostosis, although cognitive abnormalities such as IDs have been frequently observed in craniosynostosis patients. The only current treatment option for craniosynostosis is complex surgery, which is invasive and often requires re-operation due to the calvarial bones fusing again. Our MSC- based cranial suture regeneration approach is less invasive, avoids re-fusion, corrects skull dysmorphology, restores elevated intracranial pressure, and reduces neurocognitive dysfunctions later in life in a clinically relevant Twist1+/- mouse model of craniosynostosis. Gli1+ MSC depletion is observed both in Twist1+/- mice and in those with maternal exposure to citalopram. Citalopram is a selective serotonin reuptake inhibitor (SSRI), which is the most commonly prescribed class of antidepressant drugs. Maternal SSRI usage is also known as an environmental risk factor for craniosynostosis in humans. These results lead to the hypothesis that Twist1 and Tcf12 mutations may interplay with citalopram in exacerbating skull and neurocognitive defects in craniosynostosis, which will be tested in Aim 1. Aim 2 will determine cellular and molecular mechanisms by which gene mutations and maternal citalopram exposure act together to cause craniosynostosis. Aim 3 will use our newly developed MSC-based suture regeneration approach to determine whether and how MSC implantation mitigates skull and neurocognitive dysfunctions in craniosynostosis caused by gene mutations, citalopram, and their interactions. Collectively, our proposed studies build upon our previous discoveries, and our findings will be highly significant for improving the understanding of mechanisms underlying gene- environment interplay in craniosynostosis; it offers a unique opportunity for improving treatment of infants with craniosynostosis.

NIH Research Projects · FY 2025 · 2021-07

To address the widely recognized decline in the physician-scientist workforce, new approaches are needed to recruit talented physicians to pursue research as an integral part of their medical training and future careers. The Stimulating Access to Research in Residency (StARR) initiative provides a new point of access to research by accelerating the entry of residents into meaningful research pursuits during residency. The USC-StARR Program will draw the most promising Resident Investigators from the General Surgery, Integrated Vascular Surgery, and Integrated Cardiothoracic Surgery Residency Programs. We have designed an intensive, 24-month, contiguous StARR program. The goal of the USC-StARR program is to recruit, train, and mentor a group of exceptional Resident Investigators in acquiring rigorous research skills, conducting high-impact, clinically relevant research projects, and launching promising careers as surgeon-scientists in cardiovascular and pulmonary science. Our program will include two research tracks: 1) Basic and Translational Research and 2) Health Outcomes, Community Engagement, and Dissemination and Implementation Research. Our goals will be accomplished through the following specific aims: 1) recruit and train three Resident Investigators annually with the potential and commitment to become successful surgeon-scientists in cardiovascular or pulmonary science; 2) guide these Resident Investigators in obtaining more advanced methodological, analytic, and collaborative research skills appropriate for their level of training; 3) create and support effective, influential, and long-lasting mentor relationships during and after residency; and 4) guide Resident Investigators in successfully competing for other forms of clinical and translational research support that will pave the way for them to pursue long-term careers as surgeon-scientists. A Multi-Program Director structure will provide Administrative, Educational/Career Development, and Science/Research leadership for the program. The Resident Investigators will have access to a cadre of 32 carefully selected Research Preceptors with sustained NIH funding coupled with successful track records of mentoring early career scholars. A group of four highly dedicated and accomplished senior scientists will serve on the Internal and External Advisory Committees of the program. Each Resident Investigator will work with their primary Research Preceptor, Internal Advisory Committee, and Science/Research Director to achieve their individual and program goals, to provide independent evaluation of their progress, and to develop, advise on, and track their Independent Career Development Plan. The impact of this innovative proposal will be to increase the ability and capacity of the USC General Surgery, Integrated Vascular Surgery, and Integrated Cardiothoracic Surgery residency training programs to foster the development of surgeon-scientists in the field of cardiovascular and pulmonary science. Through this program, we will increase the ability of these surgeon-scientists to transition to other forms of research and career development support.

NIH Research Projects · FY 2025 · 2021-07

PROJECT SUMMARY / ABSTRACT Formation of the head and face is a complex process that is highly susceptible to disturbance as evidenced by the high incidence of craniofacial birth defects. Dysregulation in genetic and environmental factors are the main causes of craniofacial defects. However, less than 50% of craniofacial defect cases have identified genetic causes, and mechanisms of gene-environment interaction remains poorly understood. Therefore, molecular investigation is needed to increase understanding of craniofacial development. We recently identified a new regulator of craniofacial morphogenesis that interacts with environmental stress. This regulator, Protein Arginine Methyltransferase 1 (PRMT1), is an enzyme that methylates histone to generate a transcriptional activation mark H4R3me2a and methylation non-histone proteins on arginine residues. Prmt1 ablation in neural crest cells caused cleft palate and skull malformation. We further uncovered a role for PRMT1 in guarding against environmental toxin TCDD-induced cleft palate. In this proposal, we aim to determine PRMT1-dependent transcription and epigenetic mechanisms that regulated TCDD-induced cellular changes and developmental defects, using mouse genetic models, biochemical and cell biology approaches, RNA-seq, ChIP-seq and bioinformatic analysis.

NIH Research Projects · FY 2025 · 2021-06

Abstract There are stark differences in the burden of certain cancers across racial/ethnic populations. For example, in comparison to individuals of European ancestry, African American men have a ~67% higher incidence rate of prostate cancer and Asian/Pacific Islander men and women have a 70% and 95% higher incidence rate of liver cancer, respectively. These disparities in the burden of cancer across racial/ethnic groups have been attributed to an interplay of genetic, environmental, and social factors. Despite such disparities, a majority of genetic research has focused on individuals of European ancestry. While genome-wide association studies (GWAS) have successfully identified >1000 risk loci for cancer, they have focused primarily on individuals of European ancestry. The inadequate representation of diverse racial/ethnic populations limits the translational potential of GWAS findings to the world's populations. Applying PRS developed in European ancestry individuals to other populations may result in biased risk prediction, and further exacerbate health disparities due to inaccurate assessment of individuals at high risk of disease. Here, we propose to address the drastic need for appropriate PRS construction and evaluation across multiple race/ethnic groups by applying new PRS approaches to the following six large-scale, longstanding cohorts: the Multiethnic Cohort (MEC); the Kaiser Resource for Genetic Epidemiology Research on Aging (GERA) cohort; the Women's Health Initiative (WHI); the Harvard Nurses Health Studies (NHS); the Harvard Health Professionals Follow-Up Study (HPFS); and the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO). Together, these cohorts include over 300,000 individuals (100,000 non-Europeans) and 91,000 incident cancer cases (24,000 non-Europeans). The individuals in these cohorts are from five racial/ethnic groups: African Americans, Latinos, Japanese, Native Populations, and European ancestry. While focusing on cancer outcomes, we will utilize these unique and extensive resources to develop methods to construct and evaluate PRS, and importantly for translation, estimate absolute and excess relative risk of cancer jointly for PRS and established risk factors in multiethnic populations. To facilitate access to developed pipelines and data resources, we will follow F.A.I.R. analytic principles while participating with the Coordinating Center and other study sites. Ultimately, constructing and evaluating risk models in non-European ancestry populations is essential to broaden the impact of genomic medicine on human health.

NIH Research Projects · FY 2025 · 2021-06

Abstract Fluorescent proteins (FPs) and their derived biosensors based on fluorescence resonance energy transfer (FRET) have revolutionized biology/medicine by allowing the visualization of dynamic molecular activities in live cells with high spatiotemporal resolutions. Optogenetics has enabled the perturbation of specific molecular events in living systems, however, there is a lack of methods to manipulate cells and tissues deep in the body. I propose here to develop acoustothermogenetics as a general method to allow the direct, remotely-controlled, non-invasive manipulation of live cell functions in deep body sites for the correction of pathological processes and the control of specific therapeutic interventions. I will first engineer molecular sensors and genetic transducers which will allow the engineered cell to perceive the ultrasound signals directly and transduce them into genetic activation for the production of desired protein regulators. I will then use cell-based immunotherapy, particularly chimeric antigen receptor (CAR)- expressing T cells, as my initial test target to establish, in principle, the practical utility of this new method. CAR-T immunotherapy is becoming a paradigm-shifting therapeutic approach for cancer treatment, but its broad application has major challenges. I propose to develop ultrasound-sensitive CAR-T cells for their control from a distance by ultrasound transducers to target and eradicate solid tumors. Lastly, I will extend this remotely-controlled acoustothermogenetics approach to develop a general system that would allow the control of, in principle, any genetic or epigenetic modulation in live cells for the reprogramming of cellular functions under in vivo situation. This approach should allow the remotely-controlled cell activation with a high spatiotemporal precision in a non-invasive manner for a broad range of therapeutic applications. This novel approach should also provide a general paradigm to dynamically control molecular and cellular functions for biological studies and clinical applications.

NIH Research Projects · FY 2025 · 2021-06

Abstract Allogeneic hematopoietic stem cell transplantation (HSCT) is the only curative treatment for patients with high- risk acute myeloid leukemia (AML). However, HSCT is affected by graft-versus-host disease (GvHD) and graft- versus-leukemia (GvL) effects, both are mediated by donor T lymphocytes and significantly impact treatment success and thus overall outcome. AML patients commonly harbor FLT3/internal tandem duplication (FLT3-ITD), a mutation in the receptor tyrosine kinase FLT3 that is associated with poor prognosis. FLT3 targeted therapies have proven clinical benefit particularly when used in combinational approaches. Midostaurin (a kinase inhibitor) was recently approved for pre-transplant patients with FLT3-ITD in combination with standard therapy. In addition to their direct leukemia suppressive effects, FLT3 inhibitors activate leukemia antigen-specific T-cell responses. T-cell receptors (TCRs) are proteins expressed on the surface of T cells that recognize antigens presented by MHC molecules. We recently characterized the TCR repertoire in patients who underwent matched donor or haplo-cord HSCT. We demonstrated that GvHD and relapse (exclusive of each other) are associated with lower TCR repertoire diversity and expansion of certain T-cell clones. Our data suggest that individual variations in the immune repertoire significantly impact the clinical outcome in AML patients and underscore the need for comprehensive quantitative, functional, and mechanistic analyses of the TCR repertoire in a large cohort of AML patients. Here, we hypothesize: 1) TCR repertoire (diversity, clonal expansion, and V-segment utilization) affects clinical outcome (GvHD or relapse) and can therefore be used to identify GvL- and GvHD- associated clones; 2) Somatic mutations in leukemic cells (e.g., FLT3-ITD) affect the TCR repertoire and subsequent expansion of specific T-cell clones; and 3) FLT3 inhibitors (e.g., midostaurin) modulate the TCR repertoire and function and enhance GvL effects in patients undergoing HSCT. We will conduct a prospective longitudinal cohort study characterizing the TCR repertoire and mutational landscape of leukemia cells in ~250 patients (~ 60–80 with FLT3-ITD). GvHD or relapse will be predicted using a proportional hazards model for competing risks based on TCR repertoire characteristics. TCR sequences and somatic mutations will be analyzed using a structure based prediction algorithms we developed to predict candidate leukemia neoantigens and associated TCR clones. Neoantigens will be validated using in vitro and murine models. Finally, functional analyses will examine the effect of midostaurin on TCR repertoire and function. Our findings will establish the TCR repertoire as a useful tool for predicting clinical outcomes of HSCT and identify responsible TCR clones. The identification of TCR clones associated with the GvL effect against FLT3-ITD+ cells will facilitate the development of engineered T cells expressing GvL-associated TCR clones. Modifying the TCR repertoire composition via therapies targeting specific somatic mutations will facilitate development of optimized combinational therapeutic approaches, such as the addition of targeted therapy to post-transplant regimens.

NIH Research Projects · FY 2025 · 2021-06

PROJECT SUMMARY The COVID-19 pandemic has had sweeping effects on pregnant women and their partners. The need to adhere to social distancing guidelines has altered the social connectedness of expectant parents, with effects on stress, loneliness, reduced access to in- person prenatal care, and childbirth support. Social support during pregnancy is known to buffer stress and predict better postpartum outcomes for both new parents and their infants. For example, greater prenatal support has been linked with decreased risk of parental postpartum mood and anxiety disorders, lower incidence of preterm birth and low birth weight, calmer infant temperament, and healthier infant development. Given this evidence, pandemic-induced changes to social connectedness during pregnancy may have long-term effects for new parents and their children. The current proposal leverages the unique natural experiment of the COVID-19 pandemic to examine the maternal and infant health effects of social connectedness among pregnant women and their partners. The CHIRP (Coronavirus, Health, Isolation and Resilience in Pregnancy) study launched in spring 2020 and has enrolled 710 expectant parents who reported on their feelings of social connectedness and support during pregnancy. We will follow up with this cohort three, six, and 12 months after the birth of their child. In addition to collecting self-report data, we will gather hospital birth charts to measure gestational outcomes, and hair cortisol to measure neuroendocrine stress exposure. We also plan to use geocoding to model the social, economic, and health impacts of the pandemic and explore how these impacts shape postpartum outcomes. Our lab has already collected data from another cohort of 200 expectant parents recruited during pregnancy and followed over the transition to parenthood, constituting a pre-pandemic comparison sample with the same measures and timing. We will also conduct a five-year follow-up with children from our pre-pandemic dataset that will incorporate behavioral and neuroimaging measures of neurodevelopment. Our pilot data indicates significantly higher ratings of psychological distress and lower ratings of social support among expectant parents affected by the COVID-19 pandemic. We expect that this project will make important contributions to the study of stress and resilience during pregnancy and its long-term effects on both maternal and infant well-being.

NIH Research Projects · FY 2025 · 2021-05

Project Summary Hispanics are diagnosed with melanoma at later stages than their non-Hispanic white (NHW) counterparts, leading to increased likelihood of metastasis and worse survival. Hispanics are the largest ethnic group in the United States and have rising rates of melanoma, and in particular, increases in tumors with the worst prognosis. Hispanics represent an underserved and understudied population when it comes to melanoma occurrence and outcome. In our recent analysis, while the risk of presenting with a late stage melanoma was higher for Hispanics (OR:1.65 [95% CI:1.52-1.79]) than NHW, the overall risk of death from melanoma after accounting for stage at diagnosis was similar for Hispanics and NHW (HR: 0.99 [95% CI: 0.94-1.04]), implying that the overall poorer prognosis for Hispanics is due almost entirely to their later stage of disease at diagnosis, rather than response to treatment or other factors (e.g. ability to access treatment) once they are diagnosed. A later stage of diagnosis among Hispanics could be due to a multitude of factors all of which are modifiable: a lack of access to appropriate screening, lack of adherence to screening recommendations, lack of understanding of appropriate screening approaches in the primary care setting (among both patients and physicians), or a combination of these factors. The key question remaining to be answered is WHY Hispanics are diagnosed at a later stage: without answering that question, we cannot begin to design, test and implement effective interventions to improve earlier detection and reduce melanoma-related disparities for Hispanics. We will investigate modifiable factors related to diagnosis at later stage in Hispanics compared to NHW. Aim 1: Determine the roles of patient-perceived risk and knowledge of melanoma, perceived barriers to melanoma screening and diagnosis, patient access to screening and diagnosis, and cultural factors in determining the later stage at diagnosis of melanoma in Hispanic compared to NHW melanoma patients. Aim 2: Determine how, when and by whom melanomas are diagnosed (among Hispanics and NHW) and what factors are related to time delays in the diagnosis of melanoma. Aim 3: Develop, deliver and test a clinic-based health education telenovela intervention designed to achieve earlier diagnosis of melanoma among Hispanics. We will obtain data from multiple sources for this study in order to minimize the potential impact of selection, response and survival biases all of which would compromise the scientific rigor of our Approach. We will identify the key factors resulting in late diagnosis of melanoma among Hispanics to provide truly population- based data on HOW to develop targeted patient-and-systems level interventions to reduce the melanoma burden among Hispanics. We will then test targeted patient-and-physician level interventions carried out in low income primary care setting ensuring that we intervene at the earliest possible stage.

NIH Research Projects · FY 2025 · 2021-05

Project Summary Pursuant to my long-term research interest, understanding the transmembrane (TM) signaling of cell surface receptors, the present proposal aims to elucidate the signaling mechanism of CD33, a key immune modulator of amyloid-β (Aβ) peptide clearance by microglia. The response of microglia, the resident phagocytes of the central nervous system, to Aβ aggregates can be either phagocytotic and neuroprotective or inflammatory and cytotoxic. This influence makes the innate immune response a major determinant of Alzheimer disease (AD) pathogenesis. The activation state and phagocytosis capability of microglia correlate with signaling by the CD33 cell-surface receptor. CD33 inactivation promotes phagocytosis and mitigates Aβ pathology, identifying CD33 inhibition as a promising therapeutic AD avenue. CD33 belongs to the family of sialic acid-binding im- munoglobulin-like receptor (Siglecs) and consists of two extracellular immunoglobulin-like domains (IgV and IgC2), a single-pass transmembrane (TM) domain and a cytosolic (CS) domain. Here, we hypothesize that the IgV-IgC2-TM domain-domain orientations and couplings change upon ligand binding, which transmits a signal (structural change) to the CS domains. Aim 1 lays the structural and biochemical groundwork to test this hy- pothesis. It establishes expression systems to produce isotope-labeled, glycosylated domains, determines their structure, oligomerization state and membrane immersion by NMR spectroscopy. Aim 2 traces the structural changes upon ligand binding from IgV to the CS domain in full-length CD33 reconstituted in phospholipid bicelles to directly test our signaling hypothesis. Specifically, ligand-induced changes in structure, domain- domain orientations and couplings will be established using NMR. The CD33 activity state will be verified in cultured macrophages and structure-based point mutations will be examined to provide target sites for phar- macological CD33 inhibition. Aim 3 examines the link between the CS domain and downstream signaling. The binding motif and affinity of established CD33-binding proteins will be determined by ITC and NMR. This or- ganizes the binding hierarchy of cytosolic ligands, identifies binders whose binding sequences overlap with se- quences that experience structural perturbations upon receptor activation, and identifies additional CD33 can- didate sequences for pharmacological intervention. While fragments of cell surface receptors with extracellular ligand-binding domains have been studied at atomic resolution, the relatively small size of CD33 allows the first study of an entire such receptor in solution. Delineating its complete signaling mechanism at atomic resolution establishes a paradigm for receptor biology and provides novel insight into Siglec biology. The direct targeting of Aβ amyloid as AD therapy has been largely unsuccessful and we provide CD33 target sites verified by cell biology that can be translated to therapeutics to harness the great potential of optimizing the innate immune response to combat AD.

NIH Research Projects · FY 2025 · 2021-05

PROJECT SUMMARY/ABSTRACT Neurodegenerative disorders of the aging population are characterized by the progressive accumulation of proteins such as α-synuclein (α-syn), amyloid beta (Aß) and microtubule associate protein (tau). Misfolded and aggregated α-syn has been implicated in neurological disorders with Parkinsonism including Dementia with Lewy Body, Parkinson’s disease (PD), and Multiple Systems Atrophy. Accumulation of α-syn has even been confirmed in over 50% of Alzheimer’s disease (AD). Recent evidence points to a role of α-syn accumulation in the aggregation of tau and Aß in AD. Thus, regulation of α-syn expression may be crucial to the therapeutic control of numerous neurodegenerative diseases. Short interfering RNA molecules (siRNA) can bind specifically to target RNAs and deliver them for degradation; however, RNA molecules do not cross the blood- brain barrier so the only method for delivery is repeat intra-thecal injections. We recently developed a peptide (ApoB11) that binds oligonucleotides for transport across the blood-brain barrier following systemic administration. Using this peptide, we showed that we can deliver a si α-syn to reduce expression of α- synuclein in a mouse. We recently converted the ribonucleotide backbone of this siRNA to a 2’-MOe anti-sense oligonucleotide to increase half-life and affinity to the mRNA target. We plan to examine the pharmacokinetics and toxicology of systemic ApoB11:2’-MOe si α-syn following intra-peritoneal delivery in an α-syn tg mouse model of DLB. Then we will examine the ability of the ApoB11:2’-MOe si α-syn to reduce α-syn and improve survival of neurons and improve cognitive ability and motor coordination in an α-syn tg mouse model of DLB. Finally, we will examine the ability of the ApoB11:2’-MOe si α-syn to reduce the accumulation of α-syn in an in vitro model of human DLB neurons derived from iPSC cells in a blood-brain barrier model. We believe this may represent a new method of therapeutic delivery for DLB and other neurological disorders.

NIH Research Projects · FY 2025 · 2021-05

Americans of low socioeconomic status (SES) are less healthy than those of high SES. Understanding the causes of these health disparities is one of the most important research questions social scientists face today. I propose to investigate an understudied cause of such health disparities: economic uncertainty. Income volatility has been rising in the US, making it an increasingly important source of economic uncertainty. For 92 percent of Americans, having financial stability is more important than moving up the income ladder. The income swings are often unpredictable, making them impossible for families to anticipate and prepare accordingly. When income dips, low-SES families, who often lack a cushion of savings, may struggle to make ends meet. The prospect of this scenario of financial distress may cause anxiety, worry, and stress. The anticipation and concern about an aversive and uncertain event can cause anxiety and worry while the uncertainty about how one might cope if the event occurs may cause stress. According to the allostatic load framework, the stress increases the risks of cardiovascular disease and of age-related metabolic diseases, promotes cognitive decline and dementia, and accelerates cellular aging. I propose to analyze the relationship between income volatility, psychological health, and physiological aging. This project is interdisciplinary. I am an economist and can analyse and measure income volatility. However, I lack the skills to conceptualize and measure anxiety, worry, and stress; to understand the biological processes through which uncertainty and stress may accelerate aging; and to know how to use biomarkers to measure physiological aging. The K01 will provide training – under the guidance of two outstanding mentors and an expert advisory committee – that will give me such skills. My mentors, Profs. Arthur Stone and Eileen Crimmins, are leading experts in the areas where I need training and have experience in mentoring K01 awardees. The award will provide protected time for me to develop this agenda. The specific aims of this proposal are to: 1) Measure the extent of income volatility and document how it is distributed in the population. 2) Investigate the relationship between income volatility and psychological health. 3) Examine the relationship between income volatility and physiological aging. 4) Study populations at risk, such as those without a buffer of savings. My long-term career goal is to become an expert on how economic uncertainty affects health and aging. I am confident that this sustained period of career development and training will enable me to launch an independent research career and emerge as a leading researcher in this area.

NIH Research Projects · FY 2025 · 2021-05

Our long-term objective is to understand the principles that orchestrate skin morphogenesis in development and wound regeneration. The understanding of biochemical signaling is well advanced. Yet, research into the roles of non-neural bioelectricity lags behind, although evidence for a role of bioelectricity in development, regeneration (McLaughlin and Levin 2018 16; Li et al., 2020 5) and wound healing (Zhao et al. 2012 32) is growing. Our research objective is to study the mechanisms underlying the development and regeneration of skin appendages. In two of our recent research papers, we were inspired to see bioelectricity in action in two tissue patterning processes. First, the orientation of elongating feather buds is regulated by synchronization of oscillating calcium channel activities in bud dermal cells, which is controlled by epidermal Shh signaling (Li et al., 2018 11). Second, the skin frequently shows pigment stripes along the body. The size and spacing of longitudinal pigmentation stripes in Japanese quail was recently shown to be controlled autonomously within melanocyte progenitor populations in a gap junction-dependent manner (Inaba et al., 2019 12). At the time these periodic black/yellow stripes form in embryos, the spacing is in millimeters, a large-scale patterning process that cannot be explained by the classical Turing reaction-diffusion mechanism (patterning in micrometer range). The results led us to think hard about how large-scale tissue architecture is built. While localized signaling centers involving morphogens (e.g., WNT, BMP, FGF) were shown to initiate periodic patterning of feather/hair buds, some unidentified mechanism capable of spanning large distances dynamically must work together to transduce the information over the long-distance scale (Inaba and Chuong, 2019 15). Bioelectricity work here provides a clue. Thus, we organized a multi-disciplinary team to analyze the mechanisms on how biochemical and bioelectric signals integrate to achieve the large-scale tissue patterning. We hypothesize, among other possibilities, transient bioelectrical signaling across gap-junction-coupled cell collectives may allow rapid, long-distance signaling with minimal decrement. Electropotential gradients are harnessed to propagate signals rapidly over the long distance (millimeters in milliseconds) to regulate intracellular messengers and pattern the much larger morphogenetic field. The developing avian skin explants provide an excellent model because of the quantifiable distinct patterns, planar topology for easier channel activity visualization, electric current perturbation and optogenetic gene activation – not easy in the mouse model. Experimentally, we will first gauge the endogenous bioelectric landscape and evaluate the importance of bioelectricity in these two tissue patterning processes (Aim 1A, 2A). Then we will study how ion channels / gap junctions cross-talk with biochemical signals to achieve tissue patterns (Aim 1B, 2B). The work is likely to produce new findings and insights for future applications to use bioelectricity to benefit wound regeneration.

NIH Research Projects · FY 2024 · 2021-05

Neuromodulators regulate addiction, attention, cognition, mood, memory, motivation, sleep, and more through their influence on brain circuits. Classic tools for measuring neuromodulation in the brain have poor spatial and temporal resolution. This has hampered the discovery of the diverse and complex functions neuromodulation plays during behavior. Over the past few years, new indicators for imaging neuromodulator dynamics have begun to dismantle these barriers. However, all existing neuromodulator indicators have significant limitations. The goal of this proposal is to optimize our GPCR-activation-based (GRAB) genetically-encoded fluorescent indicators of four major neuromodulators: dopamine (DA), acetylcholine (ACh), norepinephrine (NE), and serotonin (5-HT). We will make their responses bigger and more specific, create red versions for multiplexed imaging, and make them easier for end-users to successfully deploy in vivo. In Aim 1, we will optimize GRAB indicators for DA, ACh, NE, and 5-HT by iteratively screening libraries via high-content confocal imaging and FACS. We will vary insertion site, linkers, cpGFP, FP-GPCR protein surface interface, and thermostabilizing GPCR residues on a range of chimeric GCPR sensor backbones. Library generation will be prioritized by computational prediction of function from GPCR structures. The dimensions of optimization will be brightness, dF/F0, ligand selectivity, affinity, and non-disruption of endogenous signals. Top hits will be validated following long-term expression in mammalian brain slice and behaving mice. Our targeted performance levels are: 1000x ligand selectivity across all neuromodulators (3rd gen), >5x SNR improvement over 2nd generation indicators in vitro and in vivo (3rd gen), and reliable single-trial subcellular resolution of graded responses with in vivo 2-photon imaging of cortex during behavior for all neuromodulators (4th gen). In Aim 2, we will use the same approach as Aim 1 to develop and validate in vivo 1st and 2nd generation red GRABs for the same neuromodulators to enable simultaneous imaging of multiple signals. Our targeted performance levels for second generation, spectrally orthogonal red GRABs are 10x dF/F in vitro, >50% dF/F in vivo responses. We will also engineer out any photoactivation of red GRAB fluorescence, demonstrate multiplexed imaging and optogenetic stimulation with zero opsin excitation crosstalk from imaging light. In Aim 3, we will optimize GRAB packaging and distribution for maximum end-user ease of use. We will quantify the best FPs for in vivo coexpression with GRABs, engineer viral-genetic strategies for robust, brain- wide GRAB expression from systemic AAV injection, and make cre-reporter mouse lines for the best green GRAB of each neuromodulator. Optimized plasmids, AAVs, and mice will be broadly disseminated. Successful completion of our Aims will yield an optimized suite of powerful molecular tools packaged for maximum utility and ease of use. Since these probes are well-suited for a large number of investigators, they will have a multiplicative impact on our understanding of neural circuit function and dysfunction.

NIH Research Projects · FY 2025 · 2021-05

PROJECT SUMMARY/ABSTRACT Cognitive decline is considered the greatest risk factor for financial exploitation in old age; yet, the financial defrauding of cognitively-intact older adults is well-documented, and the reasons for this are poorly understood. We believe that financial exploitation due to poor decision making in old age may be an early functional harbinger of cognitive decline, mild cognitive impairment, and Alzheimer’s Disease. Alzheimer’s Disease is defined neuropathologically by accumulation of beta amyloid plaques and neurofibrillary tangles, and a network of medial frontal, temporal, and parietal brain regions identified as the Default Network is particularly susceptible to this age-associated neuropathology. Cortical deterioration in the posterior Default Network (parietal and temporal lobes) occurs early in Alzheimer’s Disease, and since these regions subserve episodic memory functions, these also decline early in the disease. However, it is also known that neuropathological accumulation occurs early in medial frontal brain regions, the anterior portion of the Default Network. Although medial frontal brain regions do not deteriorate structurally until later in the course of the disease, neuropathological accumulation has been shown to impact functional connectivity of brain regions, and correspondingly brain function, ahead of brain structure. Thus, early neuropathological accumulation in the medial frontal brain networks may impact associated functions, and importantly, these medial frontal networks are integral for financial decision making. In practice, clinical neuropsychological assessment batteries have traditionally neglected consideration of medial frontal brain network functions, despite the fact that in preclinical Alzheimer’s Disease changes in these medial frontal network functions may coincide or even precede noticeable episodic memory changes. Behavioral economic preference measures in relation to time, risk, and trust are tools that appear particularly sensitive to medial frontal brain network functions, and the use of these in combination with common neurocognitive measurement approaches may offer a more sensitive and comprehensive approach to assessing early brain changes leading to Alzheimer’s Disease. The overall goal of this study is to examine the association of financial exploitation in old age with markers of Alzheimer’s Disease. We hypothesize the experience of financial exploitation due to poor decision making is associated with greater cognitive decline, greater change in behavioral economic preferences, greater deterioration in anterior Default Network (medial frontal network) functional brain imaging measures, and greater Alzheimer’s Disease genetic risk. Given significant heterogeneity in the causes, contextual factors, and consequences of financial exploitation in old age to consider, qualitative research approaches to phenotype exploitation episodes will be integrated with quantitative methods to more accurately identify exploitation experiences attributable to poor financial decision making as opposed to other reasons. Findings will inform early detection and intervention programs focused on cognitive health and wellbeing in old age.

NIH Research Projects · FY 2025 · 2021-04

Cerebrovascular dysfunction and blood-brain barrier (BBB) impairment are very common in neurological disorders, including age-related Alzheimer’s disease and related Dementia (AD/ADRD), head injuries including traumatic brain injury (TBI) and stroke. Microvascular injury and BBB breakdown often result in a cascade of events including extravasation of plasma proteins that are toxic to neuronal cells, parenchymal edema, hypoxia, metabolic stress including endoplasmic reticulum (ER) dysfunction, accumulation of metabolic wastes, activation of microglial and astrocytes, and eventually neuronal dysfunctions. Our central hypothesis is microvascular injury among different pathological conditions such as aging and AD can be attributed to an intrinsic molecular driver on BBB dysfunctions, which ultimately influence neuropathology and the development of cognitive impairment. Based on our preliminary data from comprehensive bioinformatic analysis and validations in multiple models of neurological disorders, we hypothesize that specific TMEM252 upregulation in BBB is a common molecular signature for microvascular injury. Mechanistically, TMEM252 may drive the microvascular injury endophenotype by inducing ER-dependent BBB dysfunctions. Hence, we propose to determine whether TMEM252 upregulation is a key event of microvascular injury and a common mechanism in aging and AD. More specifically, we will first provide a mechanistically understand TMEM252 functions in BBB (AIM 1), then understand the role of TMEM252 in age- and AD-associated microvascular injury using TMEM252-deficient mice (AIM 2), and finally examine the potential of targeting TMEM252 as an intervention for microvascular injury and BBB dysfunction in vivo (AIM 3). By phenotypically characterizing Tmem252 deficient model and its cross with Tg2576 model at multiple physiological levels, we hope to define a TMEM252-dependent link to vascular dysfunctions in aging and AD. As this molecular signature of microvascular injury was based on scRNA-seq analysis of multiple datasets obtained in TBI and aging mice, and cross-examined in human and mouse aging and AD samples, we expect that the propose project will provide very unique information regarding the common microvascular injury endophenotype across many neurological conditions. The data to be gathered from this study will expand our understanding of microvascular injury, as well as capture the nuance of the vascular changes between normal aging and AD. The successful completion of this study will provide new insights into the role of ER dysfunctions in microvascular injury, and novel molecular target for potential therapeutic intervention of microvascular injury in aging, AD and beyond.

NIH Research Projects · FY 2024 · 2021-04

Project Summary Recent advances in stem cell science have led to accelerated progress in cardiac regeneration. Our group successfully achieved large-scale re-muscularization of the infarcted hearts of macaque monkeys by transplanting human cardiomyocytes derived from pluripotent stem cells (hPSC-CMs). These cardiomyocytes restored ejection from ~40% to ~62%, the largest restoration of cardiac function of which we are aware. This therapy is complicated by the appearance of transient ventricular arrhythmias, which last for several weeks before disappearing. Our electrophysiological studies indicate that the arrhythmias result from pacemaking activity, which in turn results from the immaturity of the hPSC-CMs at the time of transplantation. The main goal of this proposal is to enhance the maturation of hPSC-CM to make them non-arrhythmogenic, using metabolic and transcriptional reprogramming. In Aim 1 we build on our observations that modulating metabolism has wide-ranging effects on maturation, including reducing automaticity, and increasing physiological hypertrophy, force production, and more adult-like calcium cycling. The most powerful metabolic interventions, substrate switching, metabolic hormones, and energy sensing, will be systematically optimized to enhance electrical maturity in vitro. Once optimized, we will explore the underlying mechanisms, and then test whether this maturation reduces arrhythmias by transplanting them into porcine hearts. Aim 2 takes advantage of a recently generated resource, where we performed RNA-seq on a timed series of human myocardial grafts in the rat heart as they matured to adult levels in vivo. By comparing these data to immature cardiomyocytes, we identified a set of transcriptional regulators that are candidate drivers of maturation. We will perform CRISPR-based gain-of-function studies to activate these factors in vitro. Using gene expression and electrophysiology analyses, we will then identify optimal combinations to enhance maturation. If successful, these studies will solve the greatest barrier to stem cell-based heart regeneration and bring us much closer to clinical trials.