Jackson Laboratory

NIH Research Projects · FY 2026 · 2020-08

PROJECT SUMMARY Anthracycline chemotherapeutics, such as doxorubicin (Doxo), are among the most effective and widely used antineoplastic drugs, yet their clinical application is limited by the damaging cardiac side effects that occur in many patients. Anthracycline-induced cardiotoxicity (AIC) can manifest acutely during cancer treatment but can also cause life threatening cardiomyopathy and heart failure (HF) that develops years after the cessation of chemotherapy. The underlying causes of AIC remain unclear. Thus, there is a critical need to identify the molecular mechanisms of AIC in order to stratify at-risk patients and develop therapies to improve survivorship. The overall objective of this proposal is to comprehensively define how Z-DNA Binding Protein 1 (ZBP1), a multifaceted innate immune sensor and cell death executioner, potentiates the cardiotoxic effects of Doxo chemotherapy. The central hypothesis is that Doxo induces the accumulation of Z-form nucleic acids that engage ZBP1 in multiple cardiac cell populations over time, driving a self-propagating cycle of mitochondrial dysfunction, cardiomyocyte (CM) death, and remodeling that are central features of AIC. In support of this hypothesis, ongoing studies have revealed that Doxo robustly induces Z-DNA accumulation CMs, which is stabilized by ZBP1. Strikingly, mice lacking ZBP1 are protected from Doxo-induced mitochondrial decline, myocardial remodeling, and left ventricle dysfunction. To gain additional insight this novel innate immune pathway shaping AIC, three related, but independent, aims are proposed. Aim 1 will utilize human induced pluripotent stem cell-derived CMs and cardiac mitochondrial immunocapture methods to test the hypothesis that Doxo induces mitochondrial DNA damage and Z-form nucleic acid accumulation, which activate ZBP1-dependent IFN-I signaling, mitochondrial dysfunction, and cell death. Aim 2 will employ ZBP1-deficient mice crossed to a novel IFN-I reporter strain, multi- parameter flow cytometry, spatial immunohistochemistry, and proteomics, to characterize the cellular origins and kinetics of ZBP1-dependent inflammation, cell death, and cardiac remodeling over a 10-week Doxo time course. Finally, Aim 3 will employ clinically relevant tumor-bearing models and novel cardiotropic adeno-associated viruses to determine whether silencing ZBP1 in CMs can reduce heart inflammation, cardiac remodeling, and systolic dysfunction while preserving the anti-cancer efficacy of Doxo. This proposal is innovative because it expands the current paradigms of AIC and defines the mitochondrial-ZBP1 nexus as a fundamental driver of Doxo-related HF. In addition, this research will contribute significant new information on how cardiac innate immune responses potentiate heart failure. In the long term, this work may positively impact human health by exploring ZBP1 as a therapeutic target in AIC, laying a foundation for developing new cardioprotective strategies to mitigate chemotherapy-related HF and other inflammatory cardiomyopathies.

NIH Research Projects · FY 2024 · 2020-07

PROJECT SUMMARY Addiction is an enormous economic, personal, and social burden, costing over $600 billion per year in the U.S. Understanding vulnerability to addiction, and developing effective therapies, requires identifying the genes and pathways that mediate the addiction process. Our long-term goal is to develop novel genetic models for addiction-relevant phenotypes, and use these models to characterize the genetic mechanisms of addiction. Here, we propose to extend our previous work that led to the cloning of a QTL that regulates addiction and the subsequent identification of Cyfip2 in mouse substrains as a regulator of cocaine acute and sensitized responses. We and others have since shown that this mutation regulates food reward, nicotine preference, and alcohol preference (preliminary data). In addition, we have shown that Cyfip2 regulates voluntary self- administration of cocaine in the IVSA assay, the gold standard in the addiction field. Cyfip2 is a hub for signal integration from multiple pathways, including the small GTPase RAC1, WIRS domain receptors, and Fragile X family signaling. We hypothesize that this signal integration by Cyfip2 is critical for reward behaviors. In response to PAR-19-278, we now propose to use precise genome engineering in mice to generate and functionally validate 5 variants in Cyfip2 (1-2 amino acid substitutions each) that specifically perturb each of these signal integration events. These mutations are designed using published biochemical data and in consultation with our Co- Investigator Dr. Chen, who is a leader in Cyfip biophysics and structure. In the R21 phase (Aim 1), we will leverage the mouse genetics expertise of the Jackson Laboratory to generate by CRISPR/Cas9 a set of 5 Cyfip2 signaling mutants. Specific milestones for progression to the R33 phase are (i) viability of the mutants, since the knockout of Cyfip2 is postnatal lethal, and (ii) the lack of functional off-target edits. We will then characterize these mutants comprehensively for cocaine and natural reward behavior (R33, Aim 2). To gain insight into mechanisms underlying these behaviors, we will determine the biochemical interactome of each mutant in mouse brain regions using a comprehensive mass spectrometry-based study (R33, Aim 3). The successful completion of this project will yield 5 preclinical mouse models of addiction transition for the scientific community, as well as information about specific signaling pathways that are critical for transition to addiction and that can be targeted for therapy.

NIH Research Projects · FY 2024 · 2020-07

ABSTRACT The annual Short Course on the Genetics of Addiction proposed in this application builds on the successes of the previous iteration of this Course and will provide students with an opportunity to learn about genetic applications and approaches to drug addiction research in humans and model organisms. The methodological instruction includes examples, literature and data sets drawn from studies of addiction-related phenotypes, plenary sessions on major progress in addiction genetics, and discussion sessions in which students each present their work on applications of genetic methods, and discuss general questions provoked by the lectures. Students will leave the course able to design and interpret genetic and genomic studies of addiction as they relate to their specific research question, to locate the opportunities and resources for extrapolation between human genetics and model organisms, and to utilize current online data resources to support their research. These aims will be accomplished annually over the next five years through an intensive five-day course to be offered in late summer at the Jackson Laboratory (JAX) in Bar Harbor, Maine. In 2020, the course will be held September 20-26, with arrivals and a reception on September 20 and departures on September 26. Participants will be chosen for their outstanding research potential in fields relevant to the course and will have the opportunity to interact with a group of prominent computational biologists, bioinformaticists, biologists, and geneticists from JAX and other institutions. A combination of didactic sessions and hands-on training will be offered during the day and informal discussions will be held in the evening. Student enrollment is deliberately kept small (35) to achieve a desirable level of student-faculty interaction. Food and lodging will be provided at the JAX-owned Highseas Conference Center, which creates an atmosphere highly conducive to interactions between students and faculty. A major emphasis will be placed on attracting promising young investigators to participate in this course and to actively promote the inclusion of women and under-represented minorities in an effort to cultivate diversity in the professoriate.

NIH Research Projects · FY 2026 · 2020-05

PROJECT SUMMARY/ABSTRACT The goal of the Precision Genetics of Neural Aging, Alzheimer’s disease, and Related Dementias Training Program (PGAD-TP) at The Jackson Laboratory (JAX) is to train the next generation of scientists to study the complexity and heterogeneity of neural aging and ADRD. Central to the PGAD-TP is training in the use of genetically diverse mouse strains to better reflect human aging and disease. In the first five years, the PGAD-TP included all aspects of aging and age-related diseases, with an emphasis on ADRD. Through leadership of co-directors Drs. Ron Korstanje (aging) and Howell (ADRD), in collaboration with JAX Genomic Education and scientific leadership, seven predoctoral and eight postdoctoral PGAD trainees received training in aging, neural aging, age-related kidney disease, blood disorders, neurodegenerative diseases of the eye, and ADRD. PGAD trainees were successful in obtaining independent funding through competitive internal fellowships (JAX Postdoctoral Scholar Award), federal (F30, F31, and F32) and foundation grants. PGAD trainees also contributed to publications in high tier journals including Nature Aging and Molecular Neurodegeneration. Based on feedback from trainees, preceptors, JAX leadership, and the external advisory board, the program continued to improve through modifications to the curriculum to ensure trainees received the best possible experience. For example, we developed the JAX/UK/IU T32 AD Network, a collaboration between T32 training programs at JAX, University of Kentucky (UK), and Indiana University (IU), that enabled cross-campus interactions between trainees and preceptors. Over the first five years of the PGAD-TP, JAX continued to grow its neuroscience program, particularly in the areas of neural aging and ADRD. For instance, JAX recruited three faculty focusing on neural circuit dysfunction in AD and stroke, and mitochondrial dysfunction and those faculty are now PGAD- TP preceptors. PGAD preceptors also received NIH funding to establish four new centers relating to ADRD (TREAT-AD, MARMO-AD, TOX-AD, VCID-CWOW). To capitalize on these investments, the PGAD-TP is now more focused on neural aging and ADRD. In line with this renewed focus, Dr. Kristen O’Connell has replaced Dr. Korstanje as co-director of the PGAD-TP. Dr. O’Connell is an expert in systems neuroscience, with a focus on neural aging and ADRD, and Drs. Howell and O’Connell have worked successfully together as executive members of the JAX Center for Alzheimer’s and Dementia Research (CADR). Both are active in the training and education mission of JAX, including both pre- and postdoctoral education, thus are well-suited to lead the PGAD- TP. Sixteen PGAD preceptors bring strengths in neural aging, ADRD, non-ADRD neurodegenerative diseases, technology development, cell modeling, and data sciences. The PGAD-TP will provide trainees (two predoctoral and two postdoctoral slots per year) with rigorous training in mouse modeling of human neurodegenerative diseases through course work, responsible conduct of research, grant writing and scientific communication, participation in the JAX/UK/IU T32 AD network, and preparation for an independent research career.

NIH Research Projects · FY 2026 · 2020-02

PROJECT SUMMARY/ABSTRACT Although chemotherapy has significantly improved the survival of breast cancer patients, treatment failure still remains a major clinical issue worldwide. Current knowledge about treatment failure is mostly derived from research on intrinsic and acquired chemoresistance in epithelial tumor cells. However, recent studies have implicated a critical role for host cells (i.e., the tissue microenvironment) in building a protective “niche” for tumor cells enabling their escape from chemotherapeutic treatments. Notably, the host regenerative response upon chemotherapy “injury”, which is regarded as a host intrinsic mechanism to repair damaged tissues, may be exploited by tumor cells for their local recurrence or distant metastases. The proposed study will build on our extensive experience in the study of tumor-stroma interactions in breast cancer metastasis, and will investigate the poorly explored question of how chemotherapy-induced changes in the lung stroma foster the early relapse of tumor cells in the lung. Based on our previous findings that tissue resident mesenchymal stem cells (MSCs) acquire a significantly higher potential to promote local tumor growth upon cancer therapies, we hypothesize that systemic chemotherapy treatment stimulates regenerative responses in lung resident MSCs, which are, in turn, utilized by drug-resistant disseminated tumor cells (DTCs) for their metastatic relapse in the lung. By designing different chemotherapy treatment scenarios in animal models mimicking clinical situations in human breast cancer patients, we will in Aim 1 determine how chemotherapeutic drugs cisplatin and doxorubicin modulate the lung resident MSCs using our newly established endogenous MSC modeling platform in mice. Subsequently, we will in Aim 2 delineate the molecular mechanisms underlying drug-activated lung resident MSCs to support metastatic tumor growth in the lung, with a focus on the TLR4 signaling pathway and the key wound healing cytokine osteopontin (OPN). Finally, we will in Aim 3 define the translational potential of stroma targeting approaches using both patient-derived xenograft models and breast cancer patient specimen analyses. We will specifically focus on the therapeutic efficacy of combining chemotherapy with TLR4 or OPN blockage in treatment of patient-derived human basal-like xenograft breast tumors. Further, by analyzing clinical plasma samples from human breast cancer patients, we expect to develop plasma OPN as a biomarker to predict early metastatic relapse of breast cancer patients after chemotherapy. Overall, our proposed study will energize an underdeveloped field of research that investigates the impact of cancer therapeutics on the pre-metastatic microenvironment. Findings from the proposed study will facilitate the development of clinically applicable strategies to improve treatment efficacy and prevent metastatic relapse of breast cancer by interfering with the tissue metastatic microenvironment.

NIH Research Projects · FY 2024 · 2019-09

PROJECT SUMMARY Alzheimer’s disease is the most common cause of dementia in the elderly, but there are a number of other related dementias that exhibit substantial overlap in the behavioral, cognitive, and neuropathological manifestations of the disease. In fact, the majority of dementia cases likely arise from the co-occurrence of one or more of these AD and AD-related pathologies, with very few individuals exhibiting ‘pure’ Alzheimer’s pathology (e.g., only amyloid plaques). This complexity makes diagnosis and therapeutic development challenging, a problem exacerbated by a paucity of accurate animal models for ADRD that faithfully recapitulate the full spectrum of the molecular, cellular, cognitive, and behavioral pathologies of these dementias. In response to PAR-19-167, we will create a panel of genetically diverse knock-in mice harboring known mutations associated with AD and several related dementias using precise genomic editing to ensure biologically-relevant gene expression patterns and levels. In Aim 1, we will use CRISPR/Cas9 to create mice carrying combinations of disease-causing mutations in App, Psen1, Mapt, Tardbp, and Snca to produce a set of ‘core’ strains we expect to better capture the complexity of ADRD. To capture the role of genetic background in disease risk, we will then cross these ‘core’ mice to four genetic backgrounds known to promote susceptibility or resilience of ADRD (DBA/2J, FVB/NJ, WSB/EiJ, and C57Bl/6J). We will then leverage our expertise in high-throughput mouse neurobehavioral phenotyping to screen 16 new ADRD strains to identify the lines that best model ADRD. In Aim 2, we will use our deep phenotyping pipeline to fully characterize our top strains across the entire spectrum of ADRD-related symptoms, including both cognitive and non-cognitive domains. We will also use high-field MRI, histopathological measurements, and molecular phenotypes to assess effects on brain structure, extent of neuropathologies, and impact on gene networks and pathways associated with disease. Finally, in Aim 3, we will validate our new models for use in basic science and preclinical studies by determining concordance between mouse and human data and use network modeling approaches to identify early drivers of disease that predict late-stage outcomes in humans. This project will produce much-needed new models for AD and related dementias that will greatly enhance our understanding of the pathological mechanisms underlying these diseases. Finally, all of the models produced here will be distributed to the community via the JAX Repository. We will also make all of the phenotyping data publicly available using resources such as Mouse Phenome Database, GeneWeaver, and Synapse.

NIH Research Projects · FY 2025 · 2019-09

PROJECT SUMMARY The NIA Interventions Testing Program (ITP) is a multi-institutional study investigating interventions with the potential to extend lifespan and delay disease or dysfunction in mice. Interventions are tested in parallel at three sites (The Jackson Laboratory, University of Michigan, and University of Texas) using identical standardized protocols. Such treatments include pharmaceuticals, nutraceuticals, foods, dietary supplements, plant extracts, hormones, peptides, amino acids, chelators, redox agents, and other compounds or mixtures of compounds. We propose to advance the Mouse Phenome Database (MPD) in response to emerging needs of the aging research community, specifically the ITP, to continue being a Data Coordinating Center (DCC) that curates ITP data, makes it available through a public database, and provides tools that enable users to visualize, analyze, and download the primary and summary data from these studies. Our objectives are to provide a central repository for data, documentation, and protocols, offering a unique and important venue for ITP investigators needing to make their data public; to continually refine and develop tools and features to best locate, present, and analyze those datasets; and to maintain, enhance, and promote this resource to further enable quantitative, standardized and predictive phenotype studies and, in turn facilitate new scientific advances in the field of aging. We have designed a publicly accessible website and data repository for the ITP. We have also curated and posted data from numerous ITP studies. ITP plans for the next five years include additional lifespan trials, detailed analyses of agents found to increase lifespan, and continued growth in data on health outcomes. To help support these goals, our specific aims are to: 1) maintain information on experimental designs, protocols, and SOPs, 2) create, maintain, and update a publicly accessible electronic inventory of samples in the Interventions Biospecimens Repository (IBR), 3) coordinate data collection among the three ITP Centers and members of the research community conducting focused, ancillary studies on specific interventions, 4) provide a statistical core for independent analysis of data collected by ITP, 5) implement interactive and dynamic visualization tools for statistical analyses and data reuse, and 6) maintain a public-access interactive website and machine accessible data repository for ITP. Successful completion of our Aims will yield a widely useful and sustainable system for public access to experimental details and analysis of ITP data. The resource will have a modern interactive environment and expose the data for many applications that support replication, extension, and interpretation of ITP studies in the context of lifespan, health span, and disease biology research. This will help maximize the value of these data and provide the traceability and reproducibility required for extension and translation of the outcomes of ITP testing.

NIH Research Projects · FY 2026 · 2019-08

PROJECT SUMMARY The overarching goal of my laboratory is to determine how natural genetic variation influences chromatin biology, cell fate, and, ultimately, phenotypic diversity. Since most disease-associated variants occur in regulatory elements rather than coding genes, delineating the role of regulatory variation in normal health and disease is a critical pursuit of modern genomics. Further, when variants disrupt gene regulation early in development, it can lead to lasting defects in the structure and function of adult tissues. Regulatory element function is determined by, and can be identified through, combinatorial sets of post-translational modifications on chromatin. To understand how genetic variation impacts chromatin modification and function and results in changes in development, we exploit the rich resources in mammalian diversity by deploying a novel cellular systems genetics approach using stem cells to model cell fate and differentiation. In the past 5 years, we established this innovative platform and developed a productive program to study how genetic variability in the epigenome shapes chromatin organization, subsequent gene expression, and cell identity. Specifically, we defined extensive trans-regulation of the pluripotent genome and identified genetically determined differentiation propensity. The Baker lab is continuing to harness these collective strategies and build on these findings to address the following gaps in our knowledge: What are the molecules and mechanisms underlying regulation of the chromatin landscape? How does genetic variation influence chromatin structure and function? How does variation in the establishment of the chromatin landscape impact differentiation and development? In the current proposal, we will determine how the trans-regulation of chromatin impacts developmental disorders and answer outstanding questions in the exaptation of transposable elements. We will develop tools to screen chromatin regulators for their modification of developmental disorders and transposable element regulation. We will also determine how genetic variation impacts expanded stem cell populations that contribute to extra-embryonic tissue, improving the fidelity and reproducibility of ex vivo models of development. Together, this research program will continue to shed light on the fundamental regulatory processes that shape genome function by combining discovery-based approaches through cellular systems genetics and hypothesis-driven mechanistic studies, which will be critical to fully realize the potential of regenerative medicine.

NIH Research Projects · FY 2026 · 2019-08

PROJECT SUMMARY The level and patterning of genetic diversity within populations reflects the interplay of mutation, recombination, natural selection, and demographic history. Knowledge of the intensity, frequency, distribution, and genetic regulation of these elemental evolutionary processes is therefore essential for understanding the evolutionary origins of disease-associated variation and predicting the evolutionary fate of genomes. This research program will unlock new basic biological understanding into the evolutionary mechanisms that give rise to genomic variation, with a particular focus on repeat-rich genomic loci. Our work will draw on the strengths of the mouse model system, including its translational relevance to humans, genetically diverse inbred and outbred strain resources, large whole genome sequence datasets from pedigreed populations, tools for functional discovery, and museum-archived samples for wild-caught mice. The proposed program is organized into three major research areas. The first research focus will pursue in-depth investigations of repeat-rich functional chromatin domains responsible for chromosome segregation, genome stability, and fertility. Using state-of-the-art long- read sequencing methods, we will generate high-quality de novo assemblies for diverse inbred mouse strains and pursue focused comparative genomic studies of two highly repetitive genomic loci: the Y chromosome and centromeres. We will complement these genomic investigations with hypothesis-driven studies to assess the functional consequences of diversity at these loci for male fertility and the fidelity of chromosome segregation, respectively. Second, we will retroactively mine laboratory mouse reference mapping populations as controlled evolution experiments. By monitoring the flow of genetic information over multiple generations, we aim to characterize variation in germline mutation rates, map mutation rate modifiers, and identify phenotypic correlates of mutation rate heterogeneity. Third, we will lead the development and analysis of a large-scale whole genome sequence resource comprised of ~1000 wild mouse genomes. Recognizing that deleterious variants are maintained at low frequency in the wild by the action of natural selection, we will identify variants in inbred mouse strains that are individually rare in wild mouse populations, and use allele frequencies in wild mice as a criterion for prioritizing likely deleterious causal alleles within legacy mouse QTL mapping datasets. Together, these investigations will make substantial inroads to our understanding of the mechanisms of genome diversity at structurally complex functional chromatin domains and the genetic and environmental controls on mutation rate. In addition, this program will create a new genome sequence resource that will empower biomedical and basic discovery in the mouse model system and solidify the PI’s leadership in the mouse genomics community. Crucially, the proposed program will also create meaningful hands-on research training opportunities in population and evolutionary genomics, computational biology, and mouse genetics at the undergraduate, postbaccalaureate, graduate, and postdoctoral levels.

NIH Research Projects · FY 2025 · 2019-07

The proposed renewal of the Summer Undergraduate Research Fellowship in the Molecular Biology and Genomics of Human Cancer at The Jackson Laboratory for Genomic Medicine (JAX-GM) in Farmington, CT, pledges to provide enhanced education in cancer research and genomics to the future biomedical workforce. This proposed program will function as a defined cohort within the existing JAX Summer Student Program (SSP). Under the larger umbrella of the JAX NCI-designated Cancer Center, JAX-GM constitutes a uniquely collaborative, highly innovative research environment that brings together scientists with diverse cancer expertise. The Specific Aims of our program are as follows: (1) Provide an authentic and mentored research experience. JAX-GM will recruit 10 students to join the laboratory of a program faculty mentor in a cutting-edge, collaborative research environment where they will use molecular and computational methods to investigate the etiology and evolution of human breast, ovarian, bone, and brain cancers, leukemia, cancer immunotherapy, and genome structural variation and instability. (2) Recruit students from across the country to experience cancer research training in the unique context of a biomedical research institution. The participants will be actively recruited through national outreach and chosen through a competitive application process. The program will admit undergraduates from varying academic institutions - from large research-intensive universities to primarily undergraduate institutions. Participation from across the country will be facilitated by the provision of each intern with a full fellowship, including subsistence, travel, research supplies, and funds to offset the cost of housing. These funds will also enable economically disadvantaged students to forgo summer jobs and participate in this life-changing educational experience. (3) Encourage careers in science and lifelong scientific literacy. Each participant will join the laboratory of a JAX faculty to design and conduct an independent, hypothesis-driven project using advanced analytic methods and tools as well as JAX-GM’s outstanding scientific resources. The Cancer Fellowship will include workshops on the fundamental ethical, legal, and social issues scientists face, as well as science communication and professional networking opportunities. Through JAX’s institutional commitment, students will have access to intellectual and research resources, including on-campus courses and workshops, state-of-the-art instrumentation and computational tools, dedicated program direction by JAX Genomic Education staff, housing in a college setting, and a professionally staffed residential program. The SSP––supported by institutional funds, private foundations, and federal grants–has well-established administrative procedures for recruitment and selection, mentor training, guidance, program design, management, and evaluation. JAX-GM offers a stimulating environment in which motivated, talented students can learn the fundamentals of scientific inquiry, contribute to real research progress, and make great strides in intellectual and personal growth and establishment of their science identity.

NIH Research Projects · FY 2026 · 2019-03

PROJECT SUMMARY OVERALL The main objective of our U19 proposal is to define the contribution of airway epithelial cells to age-related dysfunction of the tissue-resident immune system, particularly in the context of lung responses to viral infections. Indeed, age is a major risk factor for increased susceptibility to infectious diseases, including severe seasonal influenza virus infection. Recently, this risk was brought into even greater focus by the COVID-19 pandemic, with poor outcomes disproportionately affecting individuals over 65 years of age. While it is well documented that aging impacts both innate and adaptive immunity, the mechanisms underlying these effects, especially in lung tissue, are not well understood. In addition, little is known about how the aged airway epithelium contributes to functional immune alterations during respiratory virus infections. Based on our preliminary studies, we hypothesize that age-related epithelial changes contribute to chronic inflammation and altered tissue- resident lung immunity. This hypothesis directly builds upon our current U19 lung immunity research program that is advancing the concept that the lung epithelium, as the first site of respiratory virus infection and replication, acts as a critical pathogen barrier both as a modulator and an effector of the immune system. The workhorses of our program are primary human ex vivo air-liquid-interface (ALI) cultures, derived from airway epithelial progenitors, which closely resemble in vivo airway epithelial cell composition and responses to viruses. ALI cultures allow for 1) modelling, in time and space, of interactions between airway epithelium, pathogenic viruses (influenza and SARS-CoV-2), and immune cells; 2) genetically altering ALI genomes to study specific genes/pathways; 3) measuring the magnitude and kinetics of transcriptional responses to inflammatory insults that are difficult to measure in vivo; and 4) studying epigenetic regulation, RNA splicing, and impact of the microbiome in immune responses. Our findings will be validated using precision tissue slice assays from uninvolved lung tissue. We will also continue increasing the complexity of our 3D lung models, by incorporating alveolar space, integrating immune cells, and leveraging 3D bioprinting. To achieve our objective, we structured our Center around: two integrated research Projects focused on epigenetic, transcriptional, and alternative splicing mechanisms that we propose lead to a skewed isoform repertoire in aging lung epithelial cells and dysfunctional tissue-resident immunity; a Technology Development Project that will create sophisticated cellular models and gene editing tools to support research Project objectives; a Sample Core for storage and distribution of human tissues; and a Data Science Core for integrative analysis and data dissemination. The Center brings together clinicians and experts in lung immunology, bioengineering, genomics, and computational biology to maximize our scientific impact. An Administrative Core will provide coordination, communication, and oversight for the program. The proposed studies will enable us to uncover the molecular mechanisms underlying immune dysfunction in the lung of older adults, potentially identifying new targets for preventive intervention.

NIH Research Projects · FY 2026 · 2018-08

PROJECT SUMMARY/ABSTRACT Aging is associated with functional decline of the hematopoietic system and clonal hematopoiesis (CH), a poorly understood process by which long-lived hematopoietic stem cells (HSCs) and their progeny with certain somatic mutations undergo positive selection. Individuals with CH have increased risk of developing blood cancer, cardiovascular disease, type 2 diabetes, and all-cause mortality. Thus, CH is a healthspan-limiting condition. Understanding how and why CH occurs with aging, and defining effective interventions to extend healthspan, have strong potential to reduce the frequency or severity of CH-associated diseases in aged individuals. Our laboratory has recently made formative discoveries that the aging bone marrow microenvironment and impaired HSC mitochondrial function cooperate to cause HSC aging. These discoveries have inspired us to define the components of aging that contribute to positive selection of CH- mutant HSCs. The major goal of this proposal is to determine processes by which hematopoietic-intrinsic and -extrinsic factors cause age-associated CH. Using a mouse model of a common CH mutation in DNMT3A, our preliminary data demonstrate that both hematopoietic-intrinsic and -extrinsic adaptive mechanisms facilitate selective advantage of Dnmt3a-mutant HSCs in the context of aging. We hypothesize that Dnmt3a-mutant HSCs are adapted to survive and self-renew in an aging microenvironment through enhanced mitochondrial metabolism, and that they promote premature senescence of the microenvironment to further their selective advantage. In Aim 1, we will identify the specific mitochondrial alterations in Dnmt3a-mutant HSCs that functionally increase their competitive advantage in an aging microenvironment. In Aim 2, we will determine the mechanisms by which Dnmt3a-mutant HSCs induce senescence of mesenchymal stromal cells in the BM microenvironment. In Aim 3, we will determine the extent to which targeting mesenchymal stromal cell senescence will reduce the functional competitive advantage of Dnmt3a-mutant HSCs and progression to hematologic pathology. Successful completion of this project will determine the mechanisms by which hematopoietic-intrinsic and -extrinsic processes confer a competitive advantage to Dnmt3a-mutant HSCs during aging. We expect that understanding these mechanisms will allow prioritization of targets for therapeutic intervention to limit CH-associated pathologies including myeloid malignancies, cardiovascular disease, and type 2 diabetes.

NIH Research Projects · FY 2025 · 2017-09

PROJECT SUMMARY Patient-derived xenografts (PDXs) are a powerful model system to assess efficacy of anti-cancer agents and understand molecular mechanisms of drug resistance. By applying agent combinations against patient-derived models, it is possible to obtain evidence to determine the most promising combinations for advancement to clinical testing in defined sub-populations of cancer patients. However, integration of PDX drug response with molecular characterization data across diverse PDX collections is needed to enable this vision. A key aspect is the need for well-managed resources for community sharing and large-scale analysis of standardized datasets from PDXs and other patient-derived models. The Jackson Laboratory-Seven Bridges (JAX-SB) PDX Data Commons and Coordination Center (PDCCC) has addressed this challenge for the last 5 years, uniting the efforts of the data-generating (PDX Development and Trial Centers/PDTCs) and PDX model sharing (NCI’s Patient-Derived Model Repository/PDMR) components of the PDX Development and Trials Centers Research Network (PDXNet) into a cohesive, trans-Network whole. Using innovative cloud computing and bioinformatic approaches, our PDCCC provides administrative and computational infrastructure for PDXNet to enable PDX method standardization, model sharing, data sharing, and massive-scale data analysis. To date, we have built the PDXNet Portal, which currently contains PDXNet model information and data resources from 334 new models across 33 cancer types. Our PDCCC team has both facilitated and actively guided consortium collaborative projects, leading to several major publications and 10 Cancer Therapy Evaluation Program Letters of Intent. Here, we propose to enhance the PDXNet Portal and refine our organizational activities to address needs clarified by the NCI and PDX communities, including: faster translation of PDX studies to clinical trials; precise organization and sharing of multi-omic and treatment response data; and development of predictors of clinical treatment response. Our Specific Aims are: 1) To provide robust PDCCC support for PDXNet stakeholders through regular committees, personnel expertise, and project tools; 2) To enhance PDXNet Portal content, functionality, and data sharing; and 3) To develop and implement strategies that accelerate PDX translation to clinical trials. Through these Aims, we will coordinate the activities of the PDXNet to increase the value of patient-derived cancer model treatment studies and speed the generation of clinical trials.

NIH Research Projects · FY 2025 · 2017-08

Among the costliest diseases to society, and with rising prevalence in an aging population, neurodegenerative diseases pose a public health challenge. However, there are few options available for their treatment, and without pathomechanisms being sufficiently elucidated, one's ability to generate a rationale for interventions is greatly limited. Our studies are expected to address this barrier by establishing new etiological factors and molecular mechanisms of mammalian neurodegeneration. One such mechanism is Ribosome-associated Quality Control (RQC), that mediates the degradation of incomplete polypeptides produced by ribosomes that stall during translation. Key factors working in RQC are the Ltn1/Listerin E3 ubiquitin ligase and its partner, NEMF (Rqc2 in yeast). PI Joazeiro has previously found that Ltn1 mutation causes neurodegeneration in mice. PI Cox has more recently identified two independent mutations in mouse Nemf causing motor neuron disease and used this to knowledge to identify previously undiagnosed patients with a similar neuromuscular condition that inherited causative mutations in the human NEMF gene. In several ways, Ltn1-ENU and Nemf-ENU mice phenocopy each other, thus strengthening the connection between RQC dysfunction and neurodegeneration. The proposed studies are aimed at understanding molecular mechanisms underlying neurodegeneration caused by NEMF loss of function. We focus our analyses on a recently-discovered activity of NEMF that is conserved from bacteria to humans–the modification of aberrant nascent chains with C-terminal Alanine tails that have a proteolytic function. Based on our preliminary data, we hypothesize that NEMF-mediated Ala tailing protects neurons against degeneration. Results of these studies are expected to provide critical understanding of how defects in protein quality control lead to neurological disease.

NIH Research Projects · FY 2026 · 2016-12

PROJECT SUMMARY/ABSTRACT Deafness at birth frequently originates from defects in the development of sensory cells in the inner ear. Likewise, hearing degradation during life frequently follows damage sustained by these cells after normal development. In each case, a particularly susceptible cellular compartment is the hair bundle, a specialized structure in each sensory cell that detects and relays sound-borne vibrations. The hair bundle is an array of actin-based membrane protrusions, or stereocilia, precisely organized in rows of graded heights. Although the tiered architecture of the hair bundle is fundamental for sensory function, the molecular machinery required for its assembly during development and for the maintenance of its exact dimensions during life remains obscure. To address these open questions, we propose to exploit knowledge gained from our ongoing investigations of the GPSM2-Gαi protein complex in mouse. Absence of the scaffold protein GPSM2 or inhibitory G proteins (Gαi) result in defective hair bundle assembly, a likely etiology for congenital hearing loss in Chudley-McCullough syndrome. The GPSM2-Gαi protein complex is first enriched on one side of the nascent hair bundle only (the bare zone), and then enriched at the tip of stereocilia in the adjacent first row, a distribution required for proper stereocilia placement and elongation, respectively. We showed that the Myosin-15A motor transports GPSM2-Gαi to stereocilia tips, where in turn GPSM2-Gαi increases Myosin-15A amounts compared to other rows to define the tallest identity of the first row. Based on detailed preliminary data, we hypothesize that, 1) As yet unstudied Gαi regulators act as upstream cues to selectively enrich the GPSM2-Gαi complex only in the bare zone region of the apical membrane and only in a single row of stereocilia. 2) Prior GPSM2-Gαi enrichment on one side of the nascent hair bundle is the mechanism by which GPSM2-Gαi becomes restricted to abutting stereocilia in the first row, giving the hair bundle its tiered architecture. 3) Continued enrichment of GPSM2-Gαi at stereocilia tips after development has a role in maintenance of proper stereocilia height and girth in adult hair bundles. To test these hypotheses, we will: 1) Characterize the role of a negative Gαi protein regulator that we already established as a new deafness gene critical for GPSM2-Gαi complex localization and hair bundle morphogenesis. 2) Use a new chemical protein labeling technology and new reporter mouse models to track discrete pools of GPSM2- Gαi and follow their dynamic trafficking to the bare zone and stereocilia tips in time. 3) Inactivate GPSM2-Gαi function in structurally and functionally normal hair bundles in adults, and monitor stereocilia dimensions, stereocilia actin dynamics and mouse auditory function. A thorough understanding of the mechanisms that shape and preserve hair bundles will help interpret and design treatments for sensory cell dysfunction, the principal cause of hearing loss.

NIH Research Projects · FY 2025 · 2016-08

The Center for Systems Neurogenetics of Addiction (CSNA) leverages approaches and expertise in behavioral neuroscience, computational science, genome biology, mouse and human genetics, and genetic engineering to identify, contextualize and model shared and distinct biological mechanisms of biobehavioral risk for cocaine self-administration. Drug addiction is a devastating and complex disorder influenced by multiple etiological factors. Extensive evidence demonstrates the role of genetic variation on a range of addiction behaviors, from experimentation and initiation of drug use to compulsive drug-taking behavior. Yet discovery of predisposing genes and variants in human populations is limited by high sample size requirements, phenotyping capacity, and variability in drug exposure and other environmental factors. Advanced mouse genetic populations exhibit variation in addiction-relevant behaviors and offer an experimental platform to discover the neurobiological mechanisms by which predisposing traits predict the tendency to self-administer cocaine. The CSNA employs the Collaborative Cross mouse genetic reference population and Diversity Outbred mouse mapping population across three integrated research projects focused on three interrelated aspects of addiction susceptibility: impulsivity, cocaine sensitization and self-administration. These traits are evaluated using a multidimensional phenotyping platform in a mouse population exhibiting extreme genetic and phenotypic variation, enabling a replicable and extensible assessment of the shared and distinct biological mechanisms of addiction vulnerability. These complementary populations are derived from the same founder strains, allowing for extensive data integration across studies within and outside the CSNA. The CSNA develops data integration methods and produces multiple functional genomics and phenomics datasets, deposited in widely accessed and highly functional informatics resources for the global research community. The Center also extends its results into basic neurobiological and preclinical therapeutic research by integrating findings with human genetic and genomic studies, generating novel, validated mouse mutants and identifying vulnerable and resistant strains for mechanistic studies. Three research support cores provide state-of-the-art approaches to the CSNA research projects and the larger research community, including a sophisticated, large-capacity Behavioral Phenotyping Core, an Integrative Genetics and Genomics Core for statistical genetics, molecular profiling, biobanking, data integration and data dissemination, and a Mouse Resource and Validation Core for creating and delivering novel mouse resources for systems genetics, validation, and disease modeling. The Administrative Core coordinates, integrates, and disseminates research, education and outreach activities. Through its combined efforts, the CSNA will have a lasting impact on the study of addiction genetics through the holistic examination of biobehavioral risk, the generation of community data resources that we and others will expand and exploit in future studies, and through education and training.

NIH Research Projects · FY 2025 · 2015-04

PROJECT SUMMARY/ABSTRACT Our overarching goal is to discover the genetic and genomic mechanisms underlying behavioral predisposition and development of addiction. Addiction remains a substantial worldwide social and economic burden despite extensive efforts to curb drug availability and use. The high heritability of cocaine addiction, indicates that the propensity to develop a substance use disorder (SUD) after drug exposure is genetically influenced. Both human and animal studies indicate that behavioral traits such as novelty seeking are strongly correlated with the propensity to develop an SUD, but the biological basis of this relationship is unknown. We identify and characterize biological mechanisms of addiction and predisposing behavior by harnessing advances in mouse genetic resources, including the high-precision Diversity Outbred (DO) mouse population, validation in genetically modified mice, gene expression quantitation through RNA sequence analysis, and computational and statistical methods in systems genetics. In Aim 1 we will identify genetic mechanisms underlying predisposing novelty-related traits and drug self-administration through quantitative trait locus (QTL) analysis in a large set of DO mice. The most compelling and tractable of these will be validated in gene targeted mouse models. The intravenous drug-self administration (IVSA) paradigm, considered the gold standard for the assessment of addiction traits in rodent research, will enable quantification of the core features of addiction including initiation of drug use, poor extinction and enhanced reinstatement of reinforced drug taking. In Aim 2 we will quantify gene expression genetic variation in two connected addiction relevant tissues, the prefrontal cortex and striatum, map expression QTLs and identify genetic correlates of predisposing behavior using RNA- seq in a drug-naïve subset of DO mice, and disseminate these results through widely used informatics resources. Gene expression analysis in drug-naïve mice enables separation of the biological substrates of predisposition to addiction from the biological sequelae of drug exposure. In Aim 3, we will address the fundamental problem of evaluating coordinated gene expression across multiple components of the addiction circuitry to assess relative dysregulation toward the identification of global- vs brain region-specific factors in addiction vulnerability. This will be accomplished through the development of robust multivariate statistical methods for identification of relations across multiple high dimensional data sets. This strategy will make continued use of a common collection of phenotypes to relate disparate and incompatible measures across two independent sets of mice, while extending into multiple tissue co-expression networks. Development of this technique in the context of addiction research will extend a unifying data integration framework to multidimensional to human and mouse genetic and genomic studies for all disease areas. Synergy among the aims will reveal networks from polymorphism to addiction-related behavior.

NIH Research Projects · FY 2025 · 2014-04

Human and Mammalian Genetics and Genomics: the McKusick Short Course, developed through a six- decade long partnership between Johns Hopkins University and The Jackson Laboratory (JAX), trains the next generation of basic research and medical genetics professionals. The McKusick Short Course is purposefully an intense, two-week program that covers human and mouse genetic and genomics processes and the mechanisms of human disease. With graduate students, postdoctoral fellows, medical genetics residents, and faculty being the dominant audience, the course offers ~50 lectures, 10 workshops, multiple evening lectures by featured speakers, a poster session, and both formal and informal networking opportunities over a 12-day period, uniquely providing medical genetics, mouse genetics, and ethical, legal, and social implications of genomics content training. The content delivered by the Short Course would normally be covered by one or many more graduate-level, semester-long university courses. Additionally, the McKusick Short Course will be delivered in a hybrid format, with online/virtual access to the seminars and, where practical and feasible, the workshops. The hybrid format reduces barriers to participation for individuals who could not otherwise attend. Likewise, scholarships have been, and will be, provided to enable Course participation. Thus, JAX continues to be deeply committed to recruiting and training biomedical scientists from a breadth of backgrounds. Health care disparities will be discussed with regards to the initiatives, tools, and resources being generated to study the genetic basis of disease. This includes best practices for genetics and genomics research to address ongoing health care disparities, the need for studies of genetically representative models and populations, and representation of a breadth of backgrounds within genetic databases and samples.

NIH Research Projects · FY 2026 · 2013-09

PROJECT SUMMARY The characterization of the full spectrum of genetic variation from whole-genome sequencing (WGS) data is essential for genome research and precision medicine. Recent technological advances have led to substantially improved sensitivity in detecting and characterizing structural variants (SVs) and the generation of highly contiguous phased genomes; however, some genomic regions (e.g., short arms of acrocentric chromosomes, pericentromeric regions and regions containing complex SVs) remain extremely difficult to accurately assemble and genotype. The Investigators of this project are well qualified to tackle this problem. They have worked together for well over a decade to make substantial advances toward comprehensive SV discovery and improved genome assemblies by combining data from multiple technologies and developing new tools for analyzing and integrating these data. This competing renewal for a community resource has four aims. In Aim 1, computational methods will be developed to optimize SV discovery through accurate genome assembly - in the absence of parental sequencing data - and will be applied to 426 samples from all 26 populations of the 1000 Genomes Project (1kGP) where long-read sequencing data are available from both the Human Genome Structural Variation Consortium (HGSVC) and Human Pangenome Reference Consortium (HPRC) efforts. Aim 2 will develop pipelines that will provide the most comprehensive, rapid and low-cost genotyping of SVs in short-read datasets. This will be made possible from the incorporation of pooled Strand-seq data and inversions in 1000 individuals from the 1kGP. Aim 3 will develop pipelines and resources for SV imputation, genotyping, and functional characterization that can be used for future association studies. Proof-of-principle studies will be conducted on the 1kGP, and an autism spectrum disorder (ASD) cohort. Aim 4 will develop a fine-resolution SV resource containing precise breakpoint information and biologically relevant annotations. New visualization and analytical tools will be built into the International Genome Sample Resource (IGSR), making the data and tools acquired from this project widely available and in a manner that preserves the complexities of SVs. As a part of Aim 4, we also outline a plan to provide dedicated user training for our tools and datasets in different geographical locations and multiple times a year to maximize research community awareness and adoption. Taken together, our community resource project will provide valuable methods and tools for benchmarking SV discovery and genotyping across WGS datasets in the human genomic research and clinical domains.

NIH Research Projects · FY 2025 · 2013-04

PROJECT SUMMARY While the autoimmune destruction of pancreatic ß-cells causing type 1 diabetes (T1D) is ultimately a T-cell mediated process, it is clear in the NOD mouse model and also likely humans, that B-lymphocytes play an additional key pathogenic role. B-lymphocytes likely contribute to T1D by being the subset of APC most efficiently supporting pathogenic T-cell activation. This is due to the presence of B-lymphocytes expressing immunoglobulin (Ig) molecules that can efficiently capture and internalize ß-cell autoantigens. Thus, defects in mechanisms normally blocking the development or activity of autoreactive B- as well as T-lymphocytes contribute to T1D. Due to their role in supporting pathogenic T-cell responses there has been considerable interest in developing possible B-lymphocyte directed T1D interventions. Hence, the central hypothesis of this proposal is that gaining an increased understanding of the developmental and functional activity basis of T1D relevant B-lymphocytes in NOD mice could be of significance in identifying a means by which they could be effectively targeted. In this regards, current data indicate BAFF blockade may be a more effective B- lymphocyte directed T1D intervention than anti-CD20 treatment. Preliminary data now indicate a hypomorphic Ephb2 allelic variant may represent a T1D susceptibility (Idd) gene in NOD mice acting at the level of B- lymphocytes. Transgenically elevating Ephb2 expression inhibits T1D development through a B-lymphocyte dependent process. Aim 1 will address the currently unknown question if NOD B-lymphocytes with elevated Ephb2 expression have lost an ability to functionally activate diabetogenic T-cells, or alternatively have gained a capacity to functionally suppress such pathogenic effectors. We also previously found that a genetic and pharmaceutical approach inhibiting the ability of B-lymphocytes to undergo the processes of Ig somatic hypermutation (SHM) and class switch recombination (CSR) inhibits T1D development in NOD mice. Such T1D protection resulted from B-lymphocytes unable to undergo SHM and CSR converting to a regulatory phenotype (Breg) that inhibit pathogenic T-cells through increased activity of the immunosuppressive CD39/CD73 ecto-enzyme axis. More recent studies unexpectedly indicate ablation of the CD39 gene inhibits T1D development in NOD mice, and this is associated with a respective proportional increase and decrease in total B- and T-lymphocytes. Thus, Aim 2 is to determine if ablation of CD39 inhibits T1D development in NOD mice by expanding B-lymphocytes with a capacity to suppress pathogenic T-cell responses. We have also found T1D onset is accelerated in NOD mice with B-lymphocytes transgenically expressing an Ig specificity recognizing the peripherin molecule present in both pancreatic islets and neurons (NOD-PerIg mice), but this strain can also develop a potential multiple sclerosis (MS) relevant neurtitis syndrome. Aim 3 will determine the potential overlap in B-lymphocyte driven T-cell populations mediating T1D and neuritis development in NOD-PerIg mice, and assess if either of these pathologies can be attenuated by BAFF blockade.

NIH Research Projects · FY 2026 · 2012-04

The Jackson Laboratory (JAX) proposes to renew the existing Summer Research Experience in Neurobiology to continue supporting a focused neurobiology cohort within the existing JAX Summer Student Program, an internationally recognized research education program for undergraduates. Under the proposed renewal, six undergraduate students will conduct neurobiology research in the labs of 11 NIH-funded neuroscientists who lead cutting-edge, collaborative research programs in Alzheimer’s disease, peripheral neuropathies, motor neuron degeneration, synaptic development, retinal disease, epilepsy, addiction, Rett syndrome, stroke and sensory disorders. The 10-week residential internship will provide each participant with a summer salary plus funds to support research supplies as well as travel to national meetings to present their findings. The proposed program will offer an intense research internship in neurobiology with a focus on the laboratory mouse as an investigative tool to probe the basic mechanisms of human biology and disease. Students will be integrated into their mentor’s laboratory team and will collaborate with their mentor on experimental design and result interpretation during regular meetings. As the summer progresses, students will gain more independence in managing their day-to-day work of conducting experiments alongside their mentors. The defined research education curriculum will include asynchronous online learning modules, as well as workshops on the programming language R, animal care and use procedures, ethical conduct of research within historical and modern scientific contexts, and science communication. JAX institutional commitment includes student access to intellectual and research resources such as on-campus courses and conferences, state-of-the-art instrumentation and bioinformatics databases, dedicated program direction by JAX Genomic Education, and a staffed on-campus Living Learning Community. The neurobiology cohort will join the Summer Student Program, which is supported by institutional funds, private foundations, and federal grants and has well-established administrative procedures for recruitment and selection, mentor training and support, and program design, management, and evaluation. JAX offers a stimulating environment in which curious, motivated, talented students can learn the fundamentals of scientific inquiry, contribute to real research progress, and make great strides in intellectual and personal growth as researchers.

NIH Research Projects · FY 2025 · 2011-09

ABSTRACT Mice and humans share approximately 20,000 genes. To date, little data exists for more than a quarter of these genes and nearly one third have no functional annotation. Because of the high degree of similarity between the mouse and human gene set, genetic data generated in mice can often be extrapolated to human gene function. Mouse models of genes with common functionality between mice and humans can lead to new models of disease, which are useful for drug screening, preclinical studies, and deeper understanding of biological and disease mechanism. The goal of the Knockout Mouse Phenotyping Program (KOMP2) is to generate lines of mice that carry knockouts (KOs) for a genome-wide collection of mouse genes and subject the mice to broad based phenotyping. JAX KOMP2 phase 3 proposes to use cutting-edge and cost-effective Cas9 RNA-guided nuclease (Cas9 RGN, also called CRISPR/Cas9) technology to generate, breed, cryopreserve and phenotype 600 lines of mice during the project period. Continued effort will be made to improve the Cas9 RGN technology so as to reduce costs, increase targeting efficiency, and create more complex mutant alleles. Genes will be selected in coordination with our KOMP2 and IMPC partners and will focus on those that; have human orthologs, have not been previously knocked out, have no or poor annotation, have significant community demand and integrate with other NIH-support programs, or are predicted to function in select pathways. To guarantee ready access to the community, we will ship mice to outside investigators while they are alive on the shelf and deposit the lines into the Mouse Mutant Regional Resource Center (MMRRC) repositories for future use. Broad based phenotyping on young adult mice up to 17 weeks of age will be performed on all 600 lines of mice using International Mouse Phenotyping Consortium (IMPC)-required and JAX-specific protocols. We will assess body weight and composition, and behavior, cardiovascular, metabolic, ocular and physiological parameters. Based on data generated from the current phase of KOMP2, we expect about 30% of lines to be non-viable. We will characterize the non-viable mutants using high-throughput imaging modalities at three embryonic time points. Based on previous data we also expect approximately 7% of the lines to be infertile. Direct fertility testing to assess the fertility of each sex will be performed on all lines that fail to generate offspring from homozygous by homozygous matings. All data generated from embryonic and adult mice will be rapidly deposited into the Data Coordination Center (DCC) that supports KOMP2 and the IMPC. Lastly, JAX will work collaboratively with the KOMP2 Regional Network and with member organizations of the IMPC to share protocols, innovation, and new technology and to broadly and openly disseminate our findings to the international community through publication, presentations at meetings, web activities, and social media.

NIH Research Projects · FY 2025 · 2010-12

Abstract – OVERALL COMPONENT The goal of this application is the continued development and maintenance of the Gene Expression Database for Mouse Development (GXD). GXD is a well-established community resource. It integrates different types of expression data including biologically complex data, such as RNA in situ hybridization and immunohistochemistry results, and high-throughput expression data from RNA-seq experiments. It places these data in the larger biological context through integration with other Mouse Genome Informatics (MGI) resources and interconnections with many other databases, supporting complex queries that enable thorough biological and computational analyses. The specific aims of this proposal are (1) to continue and expand GXD’s curation of expression data and anatomical ontologies and ensure high-quality data annotation and integration. We will continue to curate data from RNA in situ hybridization, in situ-reporter knock-in, immunohistochemistry, RT-PCR, Northern blot and Western blot experiments; and expand our annotation of bulk and single-cell RNA-seq data sets. We will enhance the mouse anatomy ontology, and refine our expression annotations by combining anatomy and cell type terms. We will (2) maintain the GXD database and enhance GXD’s infrastructure and data entry interfaces to accommodate large volumes of expression data and to represent new types of data and relationships. We will enhance the database and software infrastructure to accommodate the expected increase in RNA-seq data. We will expand the database to represent anatomical differentiation pathways, as well as expression annotations to cell type terms. We will continue to modernize the editorial interface and expand the interface as needed for the annotation of new data types. We will automate more steps of the literature selection process to increase curation efficiency. We will (3) continue to evolve GXD’s user interface and develop advanced query and display tools. We will develop expression searches that allow the analysis of anatomical differentiation pathways and cell types. We will add support for quantitative expression analyses, comparisons and profiling. We will develop displays that superimpose expression data with molecular pathway and protein interaction data to support the analysis of molecular networks with co- expression information. We will (4) provide user support and promote use of GXD by the scientific community. We will continue to provide training and to solicit feedback on how we can improve GXD.

NIH Research Projects · FY 2025 · 2010-08

PROJECT SUMMARY / ABSTRACT OVERALL Healthy aging is a complex process influenced by genetic, environmental, and life history factors that may accelerate or delay aging and reduce or increase disease risk. Assessing the contribution of the myriads of factors affecting aging requires an experimental model system to control unwanted variation and isolate component effects while also reflecting the heterogeneity of human aging. The laboratory mouse has emerged as the mammalian model system of choice for aging research. With this proposal, The Jackson Laboratory Nathan Shock Center (JAX NSC) seeks to further develop and disseminate the next generation of genetic, phenotyping, and information resources necessary to enable a deeper understanding of healthy aging. Over the past 20 years, the JAX NSC has transformed aging research both at JAX and across the geroscience community by providing resources to support investigators. This resulted in 20 peer-reviewed publications in the current funding period. The Center has developed nascent regional and national resources for aging research, including aged mice and tissues that support collaborations with internal and external researchers. All JAX NSC data and protocols are disseminated through the Mouse Phenome Database and the JAX NSC website, ensuring that the resources generated and expertise acquired through the Center are readily available to the aging research community. In this renewal, we will build on the strength of past successes while also expanding the scope of our experimental strategies, for example, to examine reproductive life history interventions in aged mouse populations. We will develop and provide access to unique resources and tools, as well as provide support to geroscience investigators by enabling them to leverage JAX’s unparalleled expertise in the characterization of health and lifespan in aging mice. We will do this by providing effective Center administration and enhancing the utility of JAX NSC resources throughout the aging community (Aim 1); expanding the research focus on aging, late-life health and age-related diseases through a robust Research Development Core (Aim 2); increasing the diversity of mouse resources available for aging research, including a new study to investigate the effects of reproductive life history on the late-life health of female mice (Aim 3); strengthening the data and computational support available to the aging community (Aim 4); and expanding the use of machine learning technologies to the interpretation of aging pathologies (Aim 5). The Center will be led by a highly experienced team of Principal Investigators and Core Leads who, with oversight from our External Advisory Board, will provide effective management to facilitate the goals and objectives of the Center. The Center will leverage the world-class institutional resources, facilities, and expertise of The Jackson Laboratory, a globally renowned institution for mouse genetics research, to enhance its goals and maximize the utility of the resources it generates for the broader geroscience research community.

NIH Research Projects · FY 2026 · 2010-01

ABSTRACT/PROJECT SUMMARY This application proposes a renewal of the Mouse Mutant Resource and Research Center (MMRRC) at The Jackson Laboratory (JAX). Highly sophisticated genome engineering technologies, a well-characterized genome, mammalian physiology, and economical husbandry requirements make laboratory mice the mainstay of biomedical research on disease mechanisms and disease modeling. The NIH has recognized that the potential impact of genetically engineered mice for biomedical research cannot be fully realized without a centralized effort to identify, archive, evaluate, characterize, and distribute valuable strains of mice to qualified biomedical researchers. The MMRRC provides this centralized repository function. With over 94 years of mouse genetics and resource experience, JAX joined the MMRRC in 2009 and has since been a key member of the consortium. This proposal requests ongoing support for JAX as one of the four MMRRC core repositories. As a member of the MMRRC consortium, JAX will contribute to the development and improvement of consortium-wide standard operating procedures. The MMRRC at JAX will follow these mutually agreed upon standard operating procedures to fulfill the goals of importation, archiving (through cryopreservation of sperm and/or embryos), and distribution of biomedically important strains of mice and related materials. The MMRRC at JAX also provides related services on a fee-for-service basis and conducts high-risk, high-return research and model development projects that align with the overall goals of the consortium.