University Of California, San Francisco

NIH Research Projects · FY 2025 · 2022-08

Project Summary Cervical cancer screening represents a remarkable success story that has led to profound reductions in cancer incidence and mortality in the United States (US), yet fundamental questions about screening cessation remain. For the last 25 years, the US Preventive Services Task Force (USPSTF) has recommended screening cessation at age 65 in those deemed to have been adequately screened. The increase in life expectancy over the last 25 years, however, raises questions about whether healthy, well-screened women over age 65 should continue screening. In fact, an estimated 21% of cervical cancer cases and 35% of deaths in the US occur after age 65. Screening older people for cancer, however, involves a judicious consideration of the balance between benefits and harms. For example, cervical cancer prevention through screening is only achieved by performing surgical procedures on the cervix, including hysterectomies, which may pose a higher risk of major medical complications for older women. Because up to 60% of women have not met the criteria to end screening at age 65, an estimated 1,700,000 women turning age 65 each year in the US can be expected to continue screening. In its most recent guideline, the USPSTF stated that research is needed to elucidate the balance of benefits and harms in various groups of women over age 65. The aims of this proposal will fill significant evidence gaps concerning the benefits and harms of cervical cancer screening after age 65. Aim 1 will involve a cohort study of about 280,000 women over 65 who were long-term members of two large health systems during 2005-2022 to investigate cervical cancer incidence, stage at cancer diagnosis, and cancer mortality by screening history documented ages 55 to 65. We will also use causal inference methods to emulate a randomized trial using observational data to estimate the effectiveness of screening after age 65 on cancer outcomes. Aim 2 involves a cohort study of women screened after age 65 to investigate harms, including the incidence and predictors of medical complications resulting from diagnostic procedures and surgical interventions. We will also conduct qualitative interviews in a sample of women to evaluate the personal experiences of women who continue with the screening process after age 65. Aim 3 will involve the enumeration of actual screening outcomes of 33,000 women screened after age 65 to inform a decision analytic model that will estimate benefits and harms of screening continuation after age 65 compared with screening cessation. We have assembled an ideal study team with expertise in obstetrics/gynecology, infectious disease, cancer epidemiology, cancer screening decision modeling, biostatistics, and geriatrics. Completion of this proposal’s aims will fill important gaps and move the field forward by providing evidence to make cervical cancer screening guidelines that better balance benefits and harms in older women.

NIH Research Projects · FY 2025 · 2022-08

ABSTRACT Animals build their multicellular bodies with diverse types of cells that perform and integrate distinct functions. Animals, however, are not unique in their capacity to generate distinct cell types. In fact, their closest living relatives, a group of aquatic, unicellular, bacterivorous protists called choanoflagellates, detect biotic and abiotic cues to differentiate into phenotypically and functionally distinct cell types in different environments. Choanoflagellates also possess critical genes that regulate animal cell differentiation during development, supporting the hypothesis that cell differentiation mechanisms evolved prior to the origin of animals and became integral in animal and choanoflagellate biology. Although nearly 800 million years of animal evolution has shaped human biology since we last shared a common ancestor with choanoflagellates, the commonalities in genetic toolkits and cytological characteristics indicate that choanoflagellates have tremendous potential as microeukaryotic models to investigate the core functions of genes that regulate cell differentiation. During my postdoc, I pioneered the first methods for gene delivery and genome editing in the choanoflagellate Salpingoeca rosetta to realize its full potential as a model system. My lab continues to propel those methods for the discovery of the molecular mechanisms that drive environmentally-triggered cell differentiation in S. rosetta. This proposal supports our research mission by using the molecular tools I developed to dissect putative regulatory pathways that emerge from functional genomic surveys. In particular, we focus on homologs of RNA-binding proteins that form the animal germline and and/or maintain pluripotency. Moreover, we strive to develop our nascent genetic tools into scalable, easy methods that enable genome-wide screens of cell differentiation regulators. Overall, this work will contribute a new, functional comparison to illuminate the origin and evolution of cell differentiation pathways in choanoflagellates and animals, which I anticipate will uncover core functions of biomedically important genes that originated before choanoflagellates and animals diverged.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY Hypoxic-ischemic encephalopathy (HIE) is a severe neurologic syndrome affecting more than 12,000 newborns in the United States each year. HIE results in death or neurodevelopmental disabilities in about half of affected neonates. The causes of HIE are heterogeneous and poorly understood. Chorioamnionitis, or intrauterine infection/inflammation, gives rise to a fetal inflammatory response syndrome that may reduce a fetus’ ability to tolerate hypoxia-ischemia during delivery. Chorioamnionitis has been associated with a 4-fold increased risk of HIE, and may also reduce the efficacy of therapeutic hypothermia, the only available therapy for HIE. However, chorioamnionitis is an imprecise clinical diagnosis that refers to a spectrum of conditions. Clinical evidence of inflammation (“clinical chorioamnionitis”) during labor and delivery relies on the presence of maternal fever which is non-specific. Fever occurs in 5% of laboring mothers and can be caused by other factors such as epidural analgesia. A better understanding of the relationship between chorioamnionitis, maternal fever and HIE is crucial to improving our ability to prevent and treat HIE. A recent NICHD consensus report recommended a more precise definition of clinical chorioamnionitis (“Chorio-NICHD”) based on specific cut-offs for maternal temperature, maternal white cell count, and fetal tachycardia. But how Chorio-NICHD relates to HIE risk is unknown. Whether the presence of Chorio-NICHD reduces the neuroprotective effect of therapeutic hypothermia has also not been studied. To fill these gaps in knowledge, I will test the hypothesis that Chorio-NICHD is independently associated with a higher risk of HIE in the child, and is associated with increased risk of HIE brain injury despite treatment with therapeutic hypothermia. By leveraging a large birth cohort with rich data spanning perinatal, neonatal, and childhood periods, I will: 1. Quantify the association between Chorio-NICHD, including clinical features such as height and duration of maternal fever, degree of leukocytosis, and degree of fetal tachycardia, and HIE. 2. Determine if chorioamnionitis defined by clinical or histologic criteria is associated with severity of MRI brain injury in neonates with HIE treated with therapeutic hypothermia. 3. Quantify the association between Chorio- NICHD and childhood neurodevelopmental impairment. As a neonatologist and clinical researcher, my career objective is to become an independent physician-epidemiologist generating actionable evidence that optimizes diagnosis and treatment of neonatal brain disorders. With this K23, I will pursue advanced training in neonatal brain disease epidemiology, develop skills in electronic health data management and longitudinal data analyses. I will receive training in the analysis of neonatal brain MRI findings and placental histology. This career award, with its rigorous training program and outstanding mentorship team, will allow me to become a leader in the field of neonatal neurology and an independent physician-scientist. In years 4-5 of this award, I will be poised to submit an R01 to study novel strategies for preventing and treating neonates with HIE in the setting of intrauterine inflammation. 1

NIH Research Projects · FY 2026 · 2022-08

Abstract Perinatal care continuity across the full continuum is essential for optimizing maternal and infant health; however, a stark gap occurs postpartum, with less than one half of Indian mothers receiving postpartum care due to significant logistical and sociocultural barriers, particularly for peri-urban and rural residents. To overcome these barriers and reduce women’s postpartum isolation, our international team of maternal and infant health clinicians and researchers developed and pilot-tested a culturally-tailored mobile interactive education and support group intervention: Maa Shishu Swasthya Sahayak Samooh (maternal and child health support group: MeSSSSage). MeSSSSage uses a provider-moderated group approach to increase women’s communication with providers, refer to in-person care, and connect them with a virtual social support group. Participants are recruited in late pregnancy and have 26 education and support sessions via audioconference facilitated by nurse-midwives (2 prenatal and weekly postpartum sessions through 6 months), plus engage in a text chat group. Pilot results indicated high acceptability and feasibility and suggest preliminary effectiveness. We propose to test the effectiveness of the MeSSSSage intervention compared to standard care on maternal and neonatal health-related behaviors and health outcomes in a randomized controlled trial among 2100 perinatal Indian women. Primary outcomes of exclusive breastfeeding, unmet need for postpartum contraceptives and postpartum depression will be assessed at 6 months. Our specific aims are to: estimate the effectiveness of a mobile interactive education and support group intervention (MeSSSSage) on postpartum behaviors for optimizing maternal and neonatal health in India (Aim 1), characterize the mechanisms of impact of the MeSSSSage intervention on maternal and neonatal health in India (Aim 2), and determine the cost-effectiveness of the MeSSSSage intervention in improving postpartum maternal and neonatal health as compared to the standard of care. We hope to positively impact women’s postnatal health knowledge and behaviors and improve health outcomes for women and their infants in the first six months postpartum. This study of a scaleable intervention will have an important contribution to the evidence base on mHealth for maternal and perinatal health and group care models for postnatal care, contributing to reducing disparities in women’s access to care through the removal of geographic and social barriers. 1

NIH Research Projects · FY 2025 · 2022-08

Project Summary/Abstract Biologic sex influences Alzheimer’s disease (AD). A major source of biologic difference between the sexes is that females have two X chromosomes and males have one. The sex-specific role of the X chromosome in influencing AD is largely unknown. This grant focuses on X-chromosome-derived mechanisms of sex difference using mouse models and primary neurons combined with genetic and epigenetic tools for molecular dissection. Understanding this understudied area may reveal new X-based pathways that could ultimately benefit both sexes. Sex differences in AD reveal differing vulnerabilities in men and women. In brief, male sex is a risk factor for rapid progression to death in AD. These findings support the fact that many more women have AD, due in part to their longevity and also to their increased risk or incidence in older age – which together contributes to a higher lifetime risk of AD in women. Using genetic models of sex biology, we found that the second X chromosome counters mortality, deficits and toxicity related to hAPP/Aβ in both male and female mice and primary neurons. Since one X inactivates in females, X dose is largely similar between the sexes. This raises a key question: why would having two X’s confer advantage to AD-related measures? Each female cell harbors two X chromosomes but one is silenced through random X chromosome inactivation (XCI). XCI independently silences one X chromosome in every XX cell to achieve dosage compensation of X expression between male and female cells. Thus, XX females are mosaics with their active X chromosomes being either maternally-derived (Xm) or paternally-derived (Xp), whereas males have a single maternal X (Xm). A potential benefit of having two X’s is that the diverse combination of maternal and paternal X chromosomes (Xm+Xp) could buffer deleterious cellular process related to AD. We hypothesize that Xm contributes functional deficits to AD pathophysiology in males through epigenetic mechanisms – and that mosaicism of the X (Xm+Xp) in females buffers deficits. Since Xm and Xp are genetically identical in our models, any differences between the two are attributed to epigenetics. We will pursue two aims: 1. In Aim 1, we will examine epigenetic, parent-of-X origin and its modulation of neural vulnerability to AD- related deficits in XX compared to XY mice and cells. We hypothesize that the maternal X chromosome worsens neural vulnerability to AD. 2. In Aim 2, we will define how silencing, or imprinting, of the maternal X chromosome impacts each sex in AD-related toxicity. We hypothesize that the maternal X silences select genes in a cell-type specific manner – and this contributes to sex-specific neural vulnerability. Answers to our questions in XX compared to XY mice and cells will fundamentally advance mechanistic understanding of how the X chromosome contributes to sex difference in AD, and will likely pave X-based paths toward urgently needed treatments in AD, personalized for men, women, or both.

NIH Research Projects · FY 2025 · 2022-08

ABSTRACT Tobacco use is the leading preventable cause of death and is responsible for a third of cancer deaths in the US. Tobacco-induced diseases and mortality are not equally distributed. Racial, ethnic, gender and sexual orientation minorities, as well as those living below the poverty line and with lower levels of education, have disproportionately higher rates of tobacco use and higher rates of tobacco-induced cancers. Tobacco control policies to date have not adequately addressed these inequities. The tobacco industry is the vector of tobacco- induced disparities. Therefore, reducing the burden of tobacco-induced disparities requires understanding how the industry targets minority communities and cultivates social, policy, and regulatory environments favorable to tobacco use. This understanding is ever more important as the landscape of tobacco products is evolving rapidly as tobacco companies expand their portfolio of products and reposition themselves as providers of tobacco harm reduction. The number and diversity of tobacco and nicotine products is increasing to include electronic cigarettes, electronic pod devices, heated tobacco products, and other nicotine vaporizers. Tobacco and the electronic cigarette companies are also expanding into the cannabis business. The impact of this expansion in exacerbating existing tobacco-related disparities is unknown. Policymakers face a new challenge in promoting tobacco-related health equity: responding to tobacco industry opposition to regulation while developing interventions appropriate for novel tobacco products, and increasingly, cannabis products sold by the same companies. However, local policy innovations are being implemented. We will explore how policymakers consider different policies in attempting to decrease health disparities. We will use industry documents, key informant interviews, publicly available policy documents (e.g., public hearings), published reports, and news media, to pursue three Specific Aims: 1)Analyze evolving tobacco industry strategies, in collaboration with third parties and allied industries, to influence public health policies and tobacco product regulations in ways that exacerbate health disparities; 2)Understand tobacco industry marketing strategies that seek to normalize nicotine use (including in new tobacco and nicotine products) and communicate claims of reduced risk, and how these target racial/ethnic minorities and other vulnerable groups; and 3) Analyze innovative local- and state-level tobacco and cannabis policies to understand how diffusion of these policies and interaction between them can support the reduction of tobacco-related health disparities and promote equity. This unique scientific contribution can inform future public health programmatic, policy, and regulatory strategies addressing the evolving industry and products while focusing on health equity.

NIH Research Projects · FY 2025 · 2022-08

The purpose of this Mentored Research Scientist Development Award (K01) is to provide the candidate with the training and expertise necessary to transition into an independent research career focused on developing and adapting intervention strategies to improve HIV treatment outcomes. This K01 integrates a robust career development plan with a research strategy designed to address gaps in HIV care engagement among adults living with HIV and recent substance use. The overall objective of the research component is to examine how multiple co-occurring social and behavioral factors influence HIV treatment outcomes and explore additional factors that may support engagement in HIV care among adults living with HIV and recent substance use in the United States. The findings will inform the selection and systematic adaptation of an established HIV intervention to support care engagement. This objective will be achieved through the following three specific aims: (1) To assess the association between adverse social experiences and differences in HIV treatment outcomes across substance use and racial categories among adults living with HIV in the United States, (2) To systematically adapt an HIV intervention to address social and behavioral factors that affect HIV care engagement among adults with HIV and recent substance use in San Francisco, CA, (3) To evaluate the acceptability and feasibility of the adapted intervention to support HIV care engagement among adults with HIV and recent substance use in San Francisco, CA. Dr. Jennifer Jain is well-positioned to conduct this research based on her strong foundation in epidemiological methods and HIV and substance use research. During the 5-year award period, Dr. Jain will pursue the following career development objectives: (1) Develop expertise in the application of advanced statistical methods and mixed methods for evaluating HIV care engagement among adults with HIV and recent substance use in the United States, (2) Gain experience in intervention adaptation and testing, including modifying established HIV interventions for use among adults with HIV and substance use histories, (3) Acquire training in intervention science, including the design and implementation of behavioral interventions to improve HIV care engagement, and (4) Build professional skills necessary for a successful independent research career, including grantsmanship, scientific manuscript preparation, and collaborative interdisciplinary research. These objectives will be accomplished through a diverse array of training activities, including mentor-directed learning, formal coursework, seminars, and hands-on research experience. The proposed research aligns with current NIH priorities to: (1) improve health outcomes among people living with HIV and substance use; and (2) advance scientific discoveries in HIV and substance use research. This project will directly support Dr. Jain’s long-term goal of establishing an independent research program focused on improving HIV care engagement through the adaptation and testing of behavioral interventions for adults living with HIV and recent substance use.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY/ABSTRACT Alzheimer’s Disease (AD) is a complex and heterogeneous neurodegenerative disorder, with numerous molecular and phenotypic features (e.g., sex) that have been identified as modifiers of disease risk, resilience, and progression. While single-omic (e.g. genomic or transcriptomics) contributions to the variability observed in AD have been studied, there have not been many integrative approaches to holistically understand precise mechanisms that link molecular pathways with clinical manifestations. With the abundance of longitudinal multi- modal clinical data (e.g., UCSF electronic medical records) and the development of integrative knowledge networks that link known relationships across multi-omic modalities (e.g., Scalable Precision Medicine Oriented Knowledge Engine), there is an untapped opportunity to derive further insights into the disease. I hypothesize that by utilizing integrative knowledge network representations on clinical datasets, I can characterize AD heterogeneity and apply predictive modelling to identify potential clinical and molecular features associated with AD risk, subtypes, and sex-specific differences. In Aim 1, I will characterize Alzheimer’s Disease heterogeneity through association analysis and utilization of unsupervised machine learning approaches. In Aim 2, I will develop predictive modelling approaches for identifying clinical and molecular features associated with AD progression. With this approach, I will aim to elucidate potential disease mechanisms underlying heterogeneous clinical manifestations, allowing for improved patient stratification and personalized therapeutic approaches. To pursue this project, I have the support of my sponsor Dr. Marina Sirota, an expert in integrative computational approaches and machine learning methods on clinical and omics data. I will also receive mentorship and support from my collaborators Dr. Sergio Baranzini, an expert in integrative networks and multi-omics integration, Dr. Kate Rankin, an exceptional and leading expert in neurodegeneration characterization, and Dr. Dena Dubal, an exceptional physician-scientist and expert in neurodegeneration sex-differences and resilience. Through this work, I will develop a variety of expertise across integrative computational and multi-disciplinary approaches that will allow for meaningful contributions to improve AD diagnosis and treatment and ultimately strengthen my training as an aspiring physician-scientist.

NIH Research Projects · FY 2025 · 2022-08

Project Summary/Abstract Juvenile myelomonocytic leukemia (JMML) is a hematopoietic disorder of childhood that is associated with a poor prognosis. The current standard of care involves hematopoietic stem cell transplantation (HCT), resulting in many short and long-terms side effects. However, despite the intensity of HCT, outcomes are still poor with event free survival (EFS) at three years of only 50%. Enigmatically, there are rare patients who are known to experience spontaneous resolution of their disease with little to no treatment. While robust biomarkers of favorable and unfavorable prognosis have historically been lacking in this disease, we have demonstrated that a hypomethylated DNA signature identifies patients most likely to experience spontaneous resolution without HCT. In contrast, the presence of a hypermethylated DNA signature portended a poor outcome even after HCT. Our earlier work also showed that the presence of more than one somatically mutated gene was predictive of exceedingly poor outcomes. Both these biomarkers have since been validated in additional studies. Therapeutically, azacitidine and trametinib have each shown promise in early phase clinical trials in this disease although neither is curative as a monotherapy. Our preclinical data demonstrates that the combination of azacitidine and trametinib is more effective than either agent alone.Our overall hypothesis is that risk stratified therapy will be feasible in patients with newly diagnosed JMML and will ultimately result in improved outcomes. We expect that combinatorial therapy with azacitidine and trametinib (“Aza-MEK”) will provide excellent disease control for those with lower-risk JMML, while Aza-MEK + chemotherapy will yield molecular responses prior to HCT for those with high-risk JMML, therefore leading to better outcomes post- HCT. We further hypothesize that dual inhibition of JAK/STAT and MAPK signaling will confer synergy and, as such, we will test these agents in pre-clinical models to inform future clinical trials. In Aim 1 we will implement the first risk-stratified trial in JMML. In Aim 1a we will determine the feasibility of avoiding HCT in lower-risk patients (defined as those with a low DNA methylation signature and only one mutated gene) by treating with azacitidine in combination with trametinib (Aza-MEK) for up to 12 cycles. Lower-risk patients will only proceed to HCT in the setting of disease progression. In Aim 1b we will determine if adding Aza-MEK to cytarabine and fludarabine for high-risk patients (those with multiple mutations or an intermediate/high methylation signature) will increase the number of patients achieving a molecular remission pre-HCT. Finally, in Aim 2 we will interrogate the JAK/STAT pathway as a therapeutic target in JMML. Our data from in-vitro and in-vivo testing revealed single-agent activity of JAK2 inhibitors. In Aim 2a we will harness genetically engineered mice and in Aim 2b, patient derived xenograft models to test the hypothesis that ruxolitinib will be synergistic in combination with trametinib. Collectively, these studies will improve outcomes for patients with JMML by expanding treatment options beyond just HCT.

NIH Research Projects · FY 2025 · 2022-08

PROJECT SUMMARY/ABSTRACT This proposed career development award will provide Dr. Diana Alba MD with targeted mentored training to ensure she develops into an independent researcher utilizing both experimental approaches and models, and “omics” coupled with bioinformatic tools, to probe the mechanisms linking obesity to adipose tissue dysfunction and diabetes. In certain individuals, adipose tissue is dysregulated in obesity, and this is an early mediator of diabetes pathogenesis. However, precisely what underlies this dysfunction is not well-defined. Subcutaneous white adipose tissue (sWAT) fibrosis is associated with insulin resistance, whereas the abundance of heat- generating brown-like adipocytes in sWAT (“beiging”) is linked to metabolic health. The proposed research plan aims to close key knowledge gaps regarding the reciprocal influences of sWAT fibrosis and beiging on insulin sensitivity. To do so, the PI will take advantage of an innovative human cohort containing individuals with widely divergent levels of both sWAT fibrosis and insulin sensitivity and use this resource to comprehensively probe key cellular constituents and molecular pathways that shift sWAT away from being influenced by beige adipocytes to developing fibrosis and insulin resistance. The PI aims to 1) identify transcriptional signatures across cell types in the sWAT that coordinately modulate WAT fibrosis, body fat distribution, and glucose homeostasis, 2) probe reciprocal influences of sWAT beige activity and fibrosis on insulin sensitivity via transcriptional regulation, 3 ) use the BXD panel of recombinant inbred mice as an orthogonal genetic reference to model divergent patterns of fat distribution and validate the mechanistic relevance of pathways and cell types identified in the humans studies. The proposed 5-year career development and training plan incorporates strategically designed didactic learning, mentored practical training, and career advising to complement the PI’s expertise in ways that are critical to completion of her research and career goals. The specific career development goals outlined in this application include developing mechanistic expertise in 1) adipose tissue biology through hands-on molecular and computational biology training; 2) metabolic assessment of mouse models; 3) the human translation of adipose tissue biology including multi-omics and metabolic phenotyping. She will be training at UCSF, a world- class center for basic and translational research and an excellent environment for physician-scientist training with experts in all aspects of the proposed training. She will be closely mentored by Dr. Suneil Koliwad, an expert in inflammation, nutrition, and glucose/energy metabolism, and Dr. Shingo Kajimura, an expert in adipogenesis and beige fat. The long-term goal is to provide Dr. Alba with the skills required to become an independent, R01- funded faculty member working to identify adipose tissue disease-relevant mechanisms and risk markers for diabetes, particularly in high-risk populations, and elucidate targets to specifically mitigate insulin resistance.

NIH Research Projects · FY 2025 · 2022-08

Behavioral and social sciences researchers continue to struggle to reach, sample, count, engage and retain participants from socially disadvantaged groups, or hard-to-reach (H2R) populations. Hard-to-reach populations are often those experiencing health disparities for many diseases and conditions. Such populations include individuals experiencing homelessness or housing insecurity, those living with chronic mental illness, out-of-school youth, gang-involved individuals, street children, people who use drugs, and many others. There are many reasons why these groups are not fully represented or included in behavioral, social sciences, and clinical research. One reason is the lack of training on state-of-the-art methodologies to sample hard-to-reach populations and the advance statistical skills to analyze complex survey data within formal training programs. Moreover, the advanced methods needed to estimate their numbers are not taught in conventional behavioral, public health, and social sciences degree programs. These fundamental skills are needed to advance multiple lines of research to end health disparities, to be more inclusive of all populations in research, and to efficiently obtain samples of hard-to-reach populations in large enough numbers necessary for statistically powerful study designs. Many innovations for engaging, recruiting, and sampling hard-to-reach populations originate from HIV research but remain underutilized in other areas of behavioral and social sciences research. This H2R training program will capitalize on our >15 years of research with hard-to-reach populations at risk for HIV, and a recent successful initiative, the Sampling Knowledge Hub at UCSF, to establish a core of short courses, strengthen mentorship, and initiate lines of research among hard-to-reach populations. Participants in the H2R program (both students and mentors) will be drawn from university students and researchers, public health practitioners in health departments, and colleagues at other institutions engaged in research or health service delivery.

NIH Research Projects · FY 2025 · 2022-07

Abstract Chlamydia trachomatis (Ct) infections are important causes of human disease for which no vaccine exists. An important gap in our knowledge is how this obligate intracellular vacuolar bacterium establishes a privileged niche--a membrane bound compartment termed the inclusion. Chlamydia encode a distinctive family of secreted effectors, the Incs (Inclusion membrane proteins), which are translocated from the bacteria through the type III secretion system and inserted into the inclusion membrane. We have discovered that an early expressed Inc, IncE, binds to two different host cell protein complexes that are involved in trafficking, sorting nexins (SNX)5 and 6 as well as two closely related Q-SNARES, Syntaxin(STX)7 and STX12, which are involved in late and early endosome trafficking, respectively. Our results support a model wherein IncE directly binds SNX5/6, which redirects the ESCPE-1 complex (SNX5/6 together with SNX1/2) to the inclusion membrane, potentially disrupting ESCPE-1-mediated trafficking. In preliminary experiments, we have defined the regions of IncE that are necessary for binding to STX7/12 and discovered that IncE encodes an additional distinct short motif separate from the SNX5/6 cargo binding motif that mimics the zero layer motif (ZLM) of the VAMP3 family of R-SNARE proteins, known binding partners of STX7/12. This exciting observation suggests that IncE may modulate STX7/12 vesicle fusion with the inclusion, either by stimulating it, inhibiting it, or functioning as a tether. Using RNAi, we have discovered that STX7 and STX12 serve distinct non-overlapping roles in Ct infection. We have created an IncE null mutant and complemented it with informative IncE variants. This heroic application of Ct genetics will allow us to separate IncE binding to SNX5/6 from its binding to STX7/12, and to test the role of a single Inc in an animal model of Ct genital tract infection. In this grant, we propose to employ a combination of Ct genetics, cell biology, advanced microscopy, and biochemistry to: Aim 1. Determine the role of IncE in the pathogenesis of Ct infections. We will characterize the phenotypes of the IncE in-frame deletion mutant strain and informative isogenic complemented derivatives using (A) cell-based assays and (B) a mouse model of upper genital tract infection. Aim 2. Understand the molecular mechanism and consequences of IncE:STX7/12 interactions. Using informative IncE mutant strains and proteins, we will (A) determine whether IncE:STX7/12 interactions modulate fusion, using live cell microscopy that employs novel fluorescent lipid probes (B) determine if IncE, and specifically its ZLM, is sufficient to modulate STX7 vesicle fusion, using an in vitro liposome fusion assay; (C) test the hypothesis that the IncE ZLM binds directly to STX7 and/or STX12, using purified proteins; ad (D) Test whether IncE can bind simultaneously to STX7/12 and SNX5/6; Aim 3. Decode the roles of STX7/12 in regulating the Ct intracellular lifecycle. We will investigate (A) how STX12 contributes to homotypic inclusion fusion; (B) how STX7 contributes inclusion formation and production of infectious progeny. Our studies will increase our knowledge of host cell biology and reveal how microbes subvert these processes.

NIH Research Projects · FY 2025 · 2022-07

Project Summary/Abstract Intracellular bacteria often secrete proteins (effectors) that hijack and rewire cellular pathways to establish their replicative niche. Studying the mechanisms by which these bacterial proteins function have frequently led to the identification of key cellular processes. Given that protein synthesis is essential to sustain cellular life and function, several bacteria manipulate host cell protein synthesis. We recently discovered that the intracellular bacterium, Legionella pneumophila (L.p.) secretes a eukaryotic-serine-threonine-protein-kinase (eSTPK) effector called LegK4, that translocates into the host cell cytosol and phosphorylates the chaperone HSC70 on T495 (pHSC70). Interestingly, this single phosphorylation causes a global block in protein synthesis. Often, bacterial proteins mimic the activities of host proteins to usurp their cellular function. Given that HSC70 plays diverse roles in the cell that includes the regulation of critical cellular processes such as protein homeostasis, we studied whether a host kinase was capable of phosphorylating HSC70 on T495. Indeed, we discovered that treatment of cells with methyl methanesulfonate, an alkylating agent that causes DNA damage, results in the accumulation of pHSC70. Global mRNA translation is blocked during the DNA damage response (DDR) and it is known that the type of stressor determines the mechanism of the block. For example, ionizing radiation and topoisomerase II inhibition leads to an inhibition of mTOR signaling, while UV exposure leads to the phosphorylation of eukaryotic initiation factor 2 by the kinase GCN2. However, the role of pHSC70 in inhibiting protein synthesis during the DDR has never been studied. Here, we propose to investigate the role of pHSC70 in response to DNA damage and elucidate the mechanisms by which pHSC70 leads to protein synthesis attenuation. In the first aim, we will use biochemical and fluorescence-based assays to determine how phosphorylation of HSC70 affects its chaperone function. In the second aim, we will perform polysome runoff assays to determine which step of protein synthesis is blocked when HSC70 is phosphorylated. In addition, we propose to identify the proteins that escape the protein synthesis block mediated by pHSC70. Finally, in the third aim, we will identify the kinases that phosphorylate HSC70 during the DNA damage response and the spatio-temporal regulation of signaling events that link the stress induced DNA damage response to pHSC70 and protein synthesis inhibition. Overall, the aims of this proposal will help elucidate the role of a multifunctional chaperone in mediating protein synthesis inhibition during DDR. The results of this study will not only be beneficial for the investigators studying HSC70, but also those that study the DNA damage response and host-pathogen interactions.

NIH Research Projects · FY 2026 · 2022-07

The mission of the Administrative Core is to support and promote the scientific and collaborative goals of the HARC Center. The Core will provide leadership that ensures strong oversight and representation of all stakeholders in decisions, facilitate the integration of research projects, and connect the HARC Center to the broader NIAID Centers for HIV Structural Biology. Day-to-day activities will be coordinated by a team co-lead by the HARC Center Director (Dr. Nevan Krogan), who has extensive experience leading and managing large research centers, and the Administrative Core co-Investigator (Dr. Lorena Zuliani-Alvarez). They will be supported by the UCSF Quantitative Biosciences Institute (QBI) administrative team. Evaluation of progress toward the Center's goals as well as budgeting and long-term planning of center activities will be performed by the HARC Center Executive Committee (EC), consisting of the Director, Project leads (Drs. Gross, Marson, and Frankel) and the Administrative Core (Zuliani-Alvarez). As a first task of the Executive Committee, a Scientific Advisory Board (SAB) will be formed to review the Center's progress and future plans. The Administrative Core will organize and manage a number of regularly scheduled meetings for the EC, the entire HARC Center, and the wider HIV research community to facilitate communication amongst members and provide ample opportunities to discuss overall research directions and specific experimental concerns. In collaboration with the Developmental Core, the Administrative Core will maintain the HARC Center website (harc.ucsf.edu) and shared file servers. To provide formal site review and involvement with NIAID staff, the Core will organize an annual SAB Meeting, in which the Pls and key personnel will meet with the SAB and NIAID program staff to review the Center's activities. The HARC Center's outreach activities will encompass workshops, podcasts, and internships for students and will be supported by the QBI Media & Events team.

NIH Research Projects · FY 2025 · 2022-07

Project Summary/Abstract Understanding the mechanisms of dental epithelial progenitor cell fate decisions will help to lay the long-term groundwork for clinical applications of stem cell biology in human dentition. In the continuously growing mouse incisor, cycling progenitor cells orchestrate incisor epithelium renewal during both homeostasis and injury- induced regeneration. The swift and well-orchestrated balance of progenitor cell self-renewal and differentiation into either enamel-producing ameloblasts or non-ameloblasts supports the continuous growth of the tooth. However, the mechanisms that control these rapid fate decisions remain unclear. To understand mechanisms of cell fate decisions, this proposal will examine how Polycomb Repressive Complex 2 (PRC2), through trimethylation of lysine 27 on Histone 3, represses gene expression to drive fate commitment of progenitor cells. This proposal will establish the role of PRC2 catalytic subunit Enhancer of Zeste Homolog 2 (EZH2) in the incisor epithelium and its specific chromatin targets during progenitor differentiation. Aim 1 will examine how EZH2 contributes to incisor epithelial progenitor cell fate decisions during homeostasis and injury-induced regeneration. This will be achieved by determining how loss of Ezh2 in progenitor cells affects cell fate decisions, such as changes to differentiation, self-renewal or apoptosis. Aim 2 will elucidate the specific targets of EZH2 in progenitor cells during homeostasis and injury-induced regeneration. Chromatin states of incisor epithelial cells during both conditions will be determined using state-of-the-art single-cell Assay for Transposase Accessible Chromatin sequencing (scATACseq) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) technologies. These analyses will show whether PRC2 targets in the incisor epithelium are similar to those in other self-renewing tissues. They will also identify the dental epithelial tissue-specific targets that contribute to ameloblast and non-ameloblast fates. This research plan will be conducted in conjunction with a comprehensive training plan designed to develop the applicant’s career as a dentist-scientist. The training includes structured mentorship from a highly qualified clinician-scientist sponsor, as well as scientific and technical training through attending seminars, journal clubs, classes, laboratory meetings, conferences, and more. Research and training will take place at the University of California, San Francisco, which offers both an outstanding research environment and an excellent dental school for clinical training.

NIH Research Projects · FY 2025 · 2022-07

Project Summary/Abstract Existing HIV care systems in the United States, usually based on scheduled appointments, are often inadequate for people living with HIV who have significant psychosocial and structural barriers to engagement in care (i.e. homelessness/unstable housing, substance use disorders, severe mental illness). Rather than connect these individuals to an incompatible system of HIV care, new approaches are needed that reduce barriers to care engagement and offer increased flexibility. In this study, we seek to implement an evidence- informed multicomponent clinical intervention that includes drop-in (i.e. no appointments) multidisciplinary HIV primary care, mobile HIV care, staged escalation/de-escalation of care intensity as needed, and active referral of patients from community-based clinical and non-clinical sites into this care model. This clinical intervention will be implemented at four diverse care sites in San Francisco and Alameda counties, both priority jurisdictions in the U.S. Ending the HIV Epidemic (EHE) strategy: an academic safety net HIV clinic, a needle exchange program, and two federally qualified health centers. Eligibility criteria include: 1) current HIV viral load ≥200 copies/mL or off antiretroviral therapy, 2) history of poor HIV care engagement, and 3) homelessness/ unstable housing, any mental health disorder, or any illicit substance. We use the Consolidated Framework for Implementation Research (CFIR) and RE-AIM implementation frameworks to guide implementation strategy selection and our implementation and clinical effectiveness evaluation. In Aim 1, we will use implementation mapping to assess barriers and facilitators of implementation and convene key stakeholders to contextually integrate the clinical intervention and finalize the implementation strategies. In Aim 2, we will conduct a hybrid type 2 implementation-effectiveness study to evaluate the effect of clinical intervention implementation on co-primary outcomes of Reach (any HIV primary care visit) and Effectiveness (any HIV viral load <200 copies/mL) among patients referred to the care model over 12 months of follow-up (n=400), comparing outcomes to two propensity score matched control groups (400 contemporaneous controls identified using Department of Public Health data and 400 historical controls identified at study sites). We will also assess clinic-level implementation outcomes. In Aim 3, we will evaluate and model the individual, clinic, and population-level impacts of the intervention approach using heterogeneity and health equity analysis, cost/ cost-effectiveness analysis, scenario modeling of optimal and reduced component scenarios and population- level impact. Our multidisciplinary study team has a strong track record of implementation research to improve HIV care engagement among vulnerable populations. The proposed study will provide robust evidence for a drop-in/mobile HIV care approach and strategies to support implementation at a diverse set of clinic sites. By codifying these implementation strategies to facilitate wider-scale implementation, we seek to contribute to improving EHE Treatment outcomes among those for whom traditional models of care are sub-optimal.

NIH Research Projects · FY 2025 · 2022-07

Project Summary The viruses that infect bacteria, called bacteriophages (phages), are robust killers. In response to the frequent threat of phage infection, bacteria have developed a suite of anti-phage immune mechanisms, such as restriction-modification and CRISPR-Cas enzymes. Phages have emerged as promising alternatives to antibiotics in our current “superbug” crisis, but immune systems are a barrier for successful phage replication. Broad-spectrum phages that evade immune detection and kill multiple isolates of antibiotic-resistant pathogens may prove essential in this fight. We screened 12 obligately lytic phages infecting the prominent antibiotic- resistant pathogen Pseudomonas aeruginosa to identify phages with the ability to broadly evade DNA-targeting immune systems CRISPR-Cas and restriction enzymes. Jumbophage ΦKZ evaded all six DNA-targeting systems tested, making it the strongest “anti-immune” phage identified to date. The mechanisms behind pan- immune evasion for this phage family will be investigated here, with the goal of making fundamental discoveries at the phage host-interface that could benefit phage therapies and other biotechnologies in the future. ΦKZ is a jumbophage with a 280 kb genome, has many relatives that infect other Gram negative pathogens, and is outstanding in its ability to evade bacterial nucleolytic immune systems. Immune evasion is enabled by the assembly of a phage-encoded proteinaceous nucleus-like shell (“phage nucleus”) that serves as a replicative compartment. However, it is unknown how this phage protects its genome prior to the phage nucleus being assembled and subsequently, how protein inclusion/exclusion is regulated. We have identified phage proteins that are ejected with the genome and hypothesize that an “injected structure” (IS) creates a DNA- containing organelle that occludes immune nucleases. Understanding how ejected proteins can rapidly shield DNA from numerous host nucleases, and how the host fights back against the IS with novel immune systems likely represents fundamentally new phage-host interaction paradigms. Next, the nascent phage nucleus assembles adjacent to the IS and receives the phage genome. Subsequently, the phage nucleus imports proteins involved in DNA replication and transcription, while excluding immune nucleases, through unknown mechanisms. A genetic screen in our lab has identified the first phage mutants defective in protein import, with mutations in a single gene. Structure predictions suggest that the encoded protein may be homologous to the conserved TRPV family of ion channels. We will determine its subcellular localization, interaction partners and in vitro properties with the goal of elucidating how a “nuclear pore” could work in a phage. In sum, our work here will unveil new phage biology driven by the co-evolution of host and virus, leading to innovative and potentially transferrable mechanisms for enhancing phage success in the fight against deadly pathogens.

NIH Research Projects · FY 2025 · 2022-07

Project Summary/Abstract Genomic medicine and U.S. healthcare have reached an inflection point, where the next wave of innovative technologies may alleviate or exacerbate existing health inequity. There are multiple ethical, legal and social implications (ELSI) of transitioning from precision diagnosis to preventive treatments for genetic disease in a societal context of significant scientific uncertainty and inequitable healthcare access. The implementation and ELSI research oversight of fetal gene therapy – until now a hypothetical exercise – will profoundly shape whether the NHGRI 2030 strategic vision for improved community stakeholder engagements and equitable genomic medicine can be realized. The proposed K99/R00 Award presents a significant opportunity to incorporate ELSI knowledge into the pioneering processes of fetal gene therapy by investigating three distinct levels of ethical concern for emergent fetal gene therapy: clinical, regulatory and societal. Through interdisciplinary training, mentorship, and collaborations with the University of California, San Francisco Center for Maternal-Fetal Precision Medicine (CMFPM), the Stanford Center for Biomedical Ethics (SCBE) and the UCSF-Stanford Center of Excellence in Regulatory Science and Innovation (CERSI), this project pursues an ethnographic and “embedded ethics” approach to fetal gene therapy at a critical juncture in preventive precision medicine and ELSI research. This multi-sited study on the ELSI of fetal gene therapy will connect what happens in the clinic, and its regulatory infrastructures, with the larger-scale societal values that will need to be incorporated to achieve greater social inclusion. The proposed five-year training and research program prepares the candidate for independent ELSI scholarship in the field of preventive genomic medicine, by harnessing ethnographic skills to complement a K99 acquired education in human genetics and genomics, bioethics and community engagement methods. Three barriers to social inclusion are identified: 1) tensions between clinical and social utility; 2) a lack of empirical data on decision-making processes given uncertainty; and 3) equitable stakeholder engagements. These problems inform three specific aims of this proposal: 1) to describe the processes that inform decisions about fetal gene therapy and its ‘utility,’ according to clinicians and patients who are directly involved in the most promising fetal gene and molecular therapies at CMFPM (K99); 2) to document how uncertainty is managed in the clinic and explore how this is shaped by social values and socioeconomic supports (K99); and 3) to account for diverse, non-patient community views and the extent to which fetal gene therapy developments are or are not socially inclusive (R00). Education and research to fulfill these aims will advance understanding about the scientific, regulatory, clinical, patient, and societal values that drive fetal gene therapy innovations. With unique ethnographic access to the clinical frontier of fetal gene therapy, it will provide an understanding of the importance of social inclusion during the process of knowledge translation, decision-making, and value-making.

NIH Research Projects · FY 2025 · 2022-07

PROJECT SUMMARY/ABSTRACT Hypertension is the leading preventable cause of morbidity and premature mortality globally and is a major driver of the rising burden of cardiovascular disease (CVD) in sub-Saharan Africa (SSA). Hypertension can be controlled with highly efficacious, cost-effective medications; however, of the over 100 million people with hypertension in SSA, 10% or fewer have controlled blood pressure, with similar low rates of control among people with HIV. There is a strong commitment both in SSA and globally to improve treatment for hypertension and other CVD risk factors by ensuring medication supply, by leveraging the HIV chronic care model, and via primary health system strengthening. As hypertension diagnosis and medication availability improve, strategies are needed to increase patient-centeredness of chronic hypertension care models in order to engage patients in the long-term care required to reduce CVD risk and achieve optimal health outcomes. In this K23 proposal, my overall scientific objective is to assess, and test interventions that overcome, patient- level barriers to hypertension treatment adherence in a chronic HIV-hypertension care model in Kenya. This proposal is nested within the NIH-funded SEARCH SAPPHIRE trial (U01AI150510) evaluating integrated hypertension-HIV care in East Africa. In Aim 1, I will use a theory-informed mixed methods approach to evaluate barriers to hypertension treatment adherence within the SEARCH integrated hypertension-HIV care model. In Aim 2, I will conduct a discrete choice experiment to assess patient preferences for strategies to improve care delivery, using findings to develop an implementation strategy to improve patient-centered hypertension care. In Aim 3, I will conduct a pilot study to assess feasibility and acceptability of this implementation strategy. My overall training objective is to develop expertise in implementation science approaches to improve the patient- centeredness and effectiveness of integrated care models for hypertension and HIV in sub-Saharan Africa. My research aims map to my specific training objectives to: (1) develop expertise in hypertension and CVD clinical research, (2) learn mixed methods applications in implementation science, (3) learn implementation science methods for intervention development and evaluation. This K23 proposal is responsive to NHLBI Strategic Objective 6, to optimize clinical and implementation research to improve health and reduce disease. My proposed training and research aims will equip me with the necessary skills to achieve my long-term goal of becoming an independent NIH-funded investigator with expertise in implementation science methods to improve CVD and HIV outcomes. Findings generated from this proposal will inform an NIH R01 application to test a multi- component strategy for improving hypertension treatment outcomes among people with and without HIV in SSA.

NIH Research Projects · FY 2025 · 2022-07

PROJECT SUMMARY/ABSTRACT Asthma, pneumonia, and bronchiolitis are the top causes of childhood hospitalization in the US, leading to over 350,000 hospitalizations and ≈$2 billion in costs annually. Poor guideline adoption by clinicians contributes to poor health outcomes for children hospitalized with these respiratory illnesses, including longer recovery time/hospital stay, higher rates of transfer to intensive care units, and increased risk of hospital readmission. General hospitals, such as community hospitals, primarily provide care for adults but also provide care for >70% of hospitalized children nationally. Unlike dedicated children's hospitals, community hospitals face unique challenges to achieving guideline adoption and high-quality care for children, including less access to pediatric services and limited resources for pediatric care and quality improvement. Pathways have been shown to improve clinicians' adoption of evidence-based practices/guidelines and health outcomes for children in community hospitals. Pathways are simple, visual diagrams that guide clinicians step-by-step through the evidence-based care of a specific medical condition (accessed via paper or electronically). Most hospitals implement pathways for a single medical condition at a time, but Seattle Children's Hospital developed an intervention for simultaneously implementing multiple pathways for multiple pediatric conditions. This intervention improved guideline adoption, decreased length of stay, and decreased costs; and these results were sustained. This multi-condition pathway intervention has not yet been studied in community hospitals, which face unique implementation barriers. Our objective is to identify and test pragmatic and sustainable strategies for implementing the multi-condition pathway intervention for children hospitalized with asthma, pneumonia, or bronchiolitis in community hospitals. In Aim 1 (R61), we will engage stakeholders from community hospitals in identifying barriers and facilitators of implementation and in refining the intervention. In Aim 2a (R33), we will conduct a pragmatic, cluster-randomized trial in 36 community hospitals (1:1 randomization to intervention vs. wait-list control) to determine the effects of the multi-condition pathway intervention. Our primary outcome will be adoption of 2 evidence-based practices for each condition over a sustained period of 2 years. We will also determine length of stay, ICU transfer, and readmission. During implementation, we will also measure fidelity (use of implementation strategies as intended) in hospitals receiving the intervention (n=18). In Aim 2b (R33), we will use multi-level models to determine if these strategies are associated with guideline adoption (measured in Aim 2a). Our expected outcomes will be a comprehensive understanding of how to pragmatically, sustainably implement the multi-condition pathway intervention in community hospitals and an assessment of its effects. These outcomes will have an important positive impact by providing evidence on an intervention that can leverage implementation resources by tackling multiple pathways and rapidly improve care and outcomes for children with respiratory illnesses.

NIH Research Projects · FY 2025 · 2022-07

SUMMARY Insulin resistance is a major risk factor for cardiovascular disease which in turn is the major cause of morbidity and mortality in diabetes. The prevalence of insulin resistance is increasing in the setting of a global obesity epidemic. The long-term goal is to understand the role of the integrin family of cell surface matrix receptors in regulating obesity and insulin resistance. The overall objective of this application is to elucidate the role of the αvβ5 integrin and its ligand, Milk Fat Globule Epidermal Growth Factor like 8 (Mfge8), in regulating skeletal muscle insulin resistance. The central hypothesis is that insulin accelerates movement of MFGE8 through the endoplasmic reticulum/Golgi network and subsequently to the outer plasma membrane where it binds αvβ5; αvβ5 subsequently interacts with a complex containing the insulin receptor leading to dampening of insulin receptor signaling and that disruption of the MFGE8-integrin pathway will ameliorate insulin resistance. These hypotheses are based on data showing that acute disruption of the MFGE8/αvβ5 pathway modulates skeletal muscle insulin-mediated glucose uptake and tyrosine phosphorylation/activation of the Insulin Receptor β subunit (IRβ) and the Insulin Receptor Substrate-1 (IRS1) coupled with evidence that the insulin receptor interacts directly with the αvβ5 integrin and that this interaction is strengthened by insulin as well as by MFGE8 (1). These hypotheses will be tested through 3 specific aims: 1) determining the cellular mechanism by which insulin induces cell surface enrichment of MFGE8; 2) investigating whether the MFGE8-αvβ5 pathway induces insulin resistance by regulating dephosphorylation of IRβ and IRS1; 3) investigating the contribution of skeletal muscle MFGE8/β5 signaling in regulating basal and obesity-induced insulin resistance. Aim 1 will determine how insulin promotes skeletal muscle plasma membrane Mfge8 localization and binding to αvβ5 which then activates downstream signaling leading to reduced insulin sensitivity. Aim 2 will examine how activation of the Mfge8-integrin axis leads to increase activity of the phosphatase PTP1β which subsequently dephosphorylates and inactivates the insulin receptor in skeletal muscle leading to reduced plasma membrane translocation of Glucose Transporter 4 and reduced glucose uptake. Aim 3 will examine the therapeutic potential of systemic blockade of the β5 integrin or MFGE8 in ameliorating insulin resistance in a mouse model of diet-induced obesity and insulin resistance and the relative contribution of skeletal muscle to this process. The proposed research is innovative, because it identifies a mechanism by which insulin activates an integrin pathway that subsequently feeds back to terminate insulin signaling. The proposed research is significant because it has the potential to inform the development of novel therapeutics that treat insulin resistance.

NIH Research Projects · FY 2025 · 2022-07

PROJECT SUMMARY/ ABSTRACT The long-term goal of this K01 Mentored Research Scientist Development Award is to advance Dr. Shannon Smith-Bernardin's development as an independent clinician-investigator focusing on novel treatment paradigms for people with alcohol-use disorders and acute alcohol intoxication. This proposed project has four training aims: advanced training in: 1) implementation science; 2) obtaining, merging and analyzing administrative data; 3) qualitative and mixed-methods research; and 4) grant writing. Dr. Smith- Bernardin has assembled a multi-disciplinary mentorship team including nationally recognized experts in implementation science, emergency medicine, alcohol use disorders, vulnerable populations, frequent utilizers of health care, mixed methods, and qualitative research. Alcohol use disorders are associated with significant morbidity and mortality worldwide. In the United States, emergency departments (EDs) and the ambulance system (EMS) provide the majority of acute care for alcohol intoxication. Between 2-12% of patients in medical or psychiatric EDs are acutely intoxicated. “Sobering centers” were designed to address the needs of people with acute uncomplicated alcohol intoxication who do not require ED care, so that these individuals could receive safe, high value care in an alternative care setting. If used appropriately, sobering centers can reduce the need for ED visits and reduce ED overcrowding. In Aim 1, Dr. Smith-Bernardin will characterize and define the incidence of patients with acute alcohol intoxication in the Sobering Center, the ED, and EMS system and compare the patient, provider, and environmental-level factors that influence the transport decision using administrative data. In Aim 2, using the CFIR framework, she will conduct and analyze in-depth interviews to determine modifiable factors influencing ambulance personnel's decision to transport patients with acute uncomplicated alcohol intoxication to an ED instead of the Sobering Center. The proposed study is the first to: 1) evaluate paramedic decision making in a community with an established sobering center alternative; and 2) recruit ambulance, ED, and Sobering Center personnel to examine the factors affecting triage in the field for uncomplicated alcohol intoxication. Both aims will use innovative implementation science methods to triangulate health related data from EMS, EDs, and the San Francisco Sobering Center. The training and research conducted in the proposed project will form the basis of a future R01-proposal hybrid type II trial to test the implementation and effectiveness of an intervention to reduce provider and environmental level variation in order to increase of appropriate use of sobering centers and reduce reliance on the ED for acute alcohol intoxication. The proposed project will provide Dr. Smith-Bernardin the support necessary to become an independent clinician-scientist using implementation science and mixed-methods research to develop, evaluate, and disseminate innovative, evidence-based treatment paradigms for individuals with alcohol-use disorders and acute alcohol intoxication.

NIH Research Projects · FY 2026 · 2022-07

PROJECT SUMMARY/ABSTRACT Approximately 1 in 7 women experience perinatal depression (i.e., during pregnancy or the postpartum period), making it the most common complication of childbirth. Perinatal depression is associated with long-lasting consequences, including increased risk of suicide, impairments in parenting, and immense societal costs. Prenatal insomnia is a robust risk factor for perinatal depression: nearly 1 in 4 women who experience prenatal insomnia develop postpartum depression. To date, depression prevention interventions mainly focus on pregnant women with elevated depressive symptoms or a history of depression, and no trials have investigated whether treating prenatal insomnia prevents perinatal depression. Digital cognitive behavior therapy (CBT-I) is safe and effective for treating prenatal insomnia and shows promise for preventing perinatal depression relative to standard care. Further, digital CBT-I may be of particular interest for pregnant women because it minimizes wait time, avoids burdensome traveling and scheduling requirements, and meets their preferences for flexible delivery options. The proposed project is a blinded randomized controlled trial to evaluate the efficacy of digital CBT-I for the prevention of depression during pregnancy and through 12 months postpartum among 498 non-depressed women with insomnia disorder relative to a credible, clinically-relevant control condition. Consistent with other research, sleep hygiene education will be the control condition, and will match digital CBT-I in delivery format (digital), frequency (weekly), and number of sessions (six). The proposed confirmatory efficacy trial addresses three specific aims: 1) To evaluate the efficacy of digital CBT-I for preventing perinatal depression; 2) To test whether the effect of digital CBT-I on perinatal depression is mediated through prenatal insomnia symptom improvement; 3) To test whether the effect of digital CBT-I on perinatal depression is moderated by baseline depressive symptom severity. By focusing on a low stigma target (i.e., prenatal insomnia) and using a scalable intervention, this approach has the potential to facilitate broad dissemination. The proposed project has high public health significance for reducing the burden of perinatal depression for mothers, families, and society.

NIH Research Projects · FY 2026 · 2022-07

ABSTRACT In this proposal we apply somatic cell gene editing strategies to enhance pancreatic beta cell replacement therapies for type 1 diabetes (T1D). We have formed a team that combines expertise in beta cell biology, synthetic and systems biology, and islet transplant immunology to address key impediments for efficient immunosuppression-free transplantation of pancreatic islets. We propose two orthogonal yet complementary aims to address two critical challenges in islet transplantation - islet survival and immune rejection. Most of the transplanted islets die before revascularization can occur, which limits the efficacy of the therapy. We have shown hypoxia and nutrient deprivation during ischemia independently and synergistically kill transplanted islet cells. Aim 1 of this proposal addresses the hypothesis that peri-transplant death can be alleviated by deleting negative regulators of beta cell survival or by over-expression of positive regulators. We will take both targeted and unbiased approaches to test candidate regulators and to identify novel regulators of human islet survival. Our team has already performed high-throughput screens using RNAi in primary human islets using in vivo transplant survival as a readout. We are ready to apply our expertise to CRISPRi and cDNA screens of primary human islets. Previous clinical islet transplant experiences show that stronger immunosuppression is associated with higher rate of insulin independence after islet transplantation. The immune system deploys multiple redundant mechanisms to eliminate transplanted foreign tissue. This, combined with the fragility of the transplanted islets and heightened immune functions in T1D recipients, forms a formidable immunological barrier to beta cell replacement therapy. We hypothesize that multipronged approach of minimizing islet cell immunogenicity, neutralizing inflammation in the graft, and blocking cellular infiltrate will shield the islets from immune rejection without the need for systemic immunosuppression. In Aim2, we will test this hypothesis by gene edit human islets to ablate the expression of polymorphic human leukocyte antigens. We will test dominant strategies that block innate inflammatory cytokines TNF, IL-1 and type 1 and type 2 interferons. We will also target adaptive immune cells by blocking their trafficking, activation and effector function. Successful confirmation of our hypotheses will provide proof-of-principle data to support efforts of clinical translation as next steps. We envision that these strategies may be applied to primary human islets, stem cell-derived beta cells, and even xenogeneic islets. While these CRISPR modalities are powerful research tools for screens and proof- of-concept experiments in the laboratory, base editing and/or prime editing may be preferred embodiments in the clinical setting. Our end goal is to generate game-changing strategies to address these key impediments, with a vision towards clinical translation.

NIH Research Projects · FY 2025 · 2022-07

PROJECT SUMMARY/ABSTRACT Background: Fms-Like Tyrosine Kinase 3 (FLT3) is the most commonly mutated gene in acute myeloid leukemia (AML) and mutations in FLT3 are associated with high relapse rates. FLT3 tyrosine kinase inhibitors (TKIs) are clinically active in FLT3-mutant AML but duration of response is limited by the development of resistance. Mutations in NRAS and other activation of the RAS pathway are major mechanisms of resistance to FLT3 inhibitors and other AML targeted therapies. Rationale: We have identified suppression of the Mediator/RNA Pol II pathway augments FLT3 TKI-induced apoptosis in the setting of RAS activation. The overall goals of this project are: (1) to prioritize therapeutic targets in the Mediator/RNA Pol II pathway; and (2) to determine the essential Mediator/RNA Pol II-dependent transcriptional targets relevant to FLT3 TKI resistance. Methods: We will identify essential components of the RNA Pol II pathway needed for TKI resistance in AML and evaluate the efficacy of existing RNA Pol II pathway inhibitors in MAPK-activated AML cells. We will determine RNA Pol II-dependent transcriptional changes induced by MAPK activation and FLT3 inhibition in pre-clinical models and patient samples. We will functionally validate the essential downstream transcriptional targets critical to RAS-mediated FLT3 TKI resistance in AML. Expected Results: These studies will rigorously evaluate RNA Pol II as a novel treatment strategy in AML with aberrant RAS/MAPK signaling. If successful, this strategy can be quickly translated to clinical trials in AML and this general approach may also prove efficacious in other RAS-mutant cancers.