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NICHD - Eunice Kennedy Shriver National Institute of Child Health and Human Development

In the process of asymmetric cell division (ACD), two daughter cells with identical genetic information, but distinct fates, result from one cell division. Adult stem cells can undergo ACD to produce one self-renewed stem cell and one differentiating daughter cell. This process allows for important physiological processes including tissue development, homeostasis, and healing. Regulation of proper stem cell division can be lost in aging as well as cancer and other chronic diseases. How stem cells regulate ACD is not fully understood, but has broad implications for the study of cell fate determination and cellular reprogramming. To study ACD in an in vivo adult stem cell lineage, the Chen lab uses the Drosophila male germline. Germline stem cells (GSCs) in the Drosophila testis divide to generate both a self-renewed GSC and a differentiating daughter cell, called a gonialblast, which divides symmetrically to produce spermatogonial cells (SGs) that eventually undergo meiosis and terminal differentiation into sperm. Our group previously showed that histones that existed in the cell before DNA replication are retained in the self-renewed GSC, while newly synthesized histones are enriched in the differentiating daughter cell. The lab then discovered that during S- phase in GSCs, old histones are biased to the leading strand while new histones are biased to the lagging strand. Interesting, the catalytic subunits of both lagging strand enriched polymerase complexes, Polα and Polδ, are present at a lower level in GSCs as compared to SGs, while the leading strand enriched polymerase, Polε, shows comparable levels. Compromising Polα either pharmacologically (by an inhibitor) or genetically (polα+- flies), induces asymmetry in histone incorporation in SGs. However, how this differential expression of Polα and Polδ, but not Polε, is regulated is unknown. According to my preliminary data, polα and polε RNA levels reflect the protein level trend, and a stepwise increase in polα RNA across SG divisions was noted. I hypothesize that GSC transcriptionally repress polα, and this repression is lost as SGs divide. I will determine what cis-regulatory elements are responsible for this differential expression using a reporter assay. I will integrate transcription factor motif analysis, genomic data, and transcriptomic data to identify candidate trans-acting factors, which I can test further using molecular and genetic assays. In my second aim, I will investigate the functional outcome of reduced Polδ levels. The lab found that both polδ+/- and polα+/- flies display sustained fertility during aging. polα+/- flies also demonstrate enhanced regeneration in the germline. I will characterize the cell biology and morphology of polδ+/- testes during aging and test their regenerative potential using a genetic ablation experiment. The Chen lab has the expertise and resources necessary for me to carry out this proposed work. Between Dr. Chen’s mentorship and both academic and career support from the Johns Hopkins Department of Biology, I am confident I will have a successful doctoral research career and my findings will contribute to the NIH’s public health goals as well as benefit the broader scientific community.

NIGMS - National Institute of General Medical Sciences

PROJECT SUMMARY The endoplasmic reticulum (ER) performs many vital cellular functions, including protein and lipid synthesis and calcium storage, and importantly, the ER is a cell homeostasis sensor and signaling network. For example, when protein synthesis gets overloaded in the ER, the ER signals the integrated stress response. The ER also forms contacts with other organelles to signal and transport materials like calcium and lipids – ER health is therefore at the foundation of cellular health and disease prevention. In order to perform ER localized protein synthesis and signaling to other organelles, the ER network dynamically rearranges to form structures for dedicated functions. For instance, secretory cells are filled with expansive ribosome-studded sheets for protein synthesis, whereas cells which are constantly signaling, like neurons, are jam-packed with bundled tubules. So, what defines these functions and shapes? Changing ER protein levels alters both shape and function. I previously showed that ER-phagy, a process where ER membrane and attached proteins are selectively degraded, is required to set up the ER network as cells differentiate. Specifically, by deleting key autophagy and selective ER-phagy machineries in stem cells, I showed ER accumulation in axons and alterations in the ER proteome when they converted to neurons. These observations raise a key question: Are there similarities and/or differences in how these machineries function or are regulated in cell types with different functional outputs? In addition, we are missing key details about ER-phagy site formation and regulation, both under basal conditions in different non-dividing cell types and in post mitotic cells when stressors like antioxidant damage or protein misfolding occur. Thus, I will combine quantitative methods including ER protein turnover assays and mass spectrometry, with top-of-the-line imaging techniques including live-cell imaging and cryo-electron tomography, and functional assays to establish how ER clearance controls (i) the ER proteome landscape, (ii) ER structural rearrangements into tubules and sheets, and (iii) ER functions vital to cell-type establishment and homeostasis. In essence, the ultimate goal of my research program is to provide a blueprint detailing connections between the underlying ER proteome and how its regulation controls cellular function as cells specialize into unique types or respond to stress conditions. With extensive experience studying both ER-phagy and ER dynamics, I am well suited to achieve the goals of the proposed study, which lies at the intersection of the fields of organelle biogenesis and quality control. Defining the mechanisms driving the clearance of regions of the ER network and the specificity of these ER proteins in homeostasis and disease is essential to the field. In conclusion, the proposed work will lay the foundation for my laboratory, accelerating our research to the forefront of our field and deepening our understanding of key processes relevant to the areas of cell and developmental biology.

NIGMS - National Institute of General Medical Sciences

Abstract The Golgi apparatus is the central organelle in the secretory pathway, essential for processing and sorting of proteins and lipids, including receptors, hormones, and growth factors. In mammalian cells, multiple Golgi stacks are laterally interconnected into a continuous ribbon-like structure. Dysfunction and fragmentation of the Golgi ribbon are associated with various human diseases such as metastatic cancer, neurodegenerative disorders, or muscular dystrophies. Despite its essential function, the mechanism that regulate Golgi ribbon structure and function remain unclear. This lack of understanding stems primarily from limited knowledge of the molecules responsible for organizing and maintaining this structure. Our previous work showed that the ribbon structure depends on protein networks of Golgins; Golgi-resident membrane proteins defined by extensive coiled-coil domains that collectively form a matrix or scaffold. This matrix is crucial for both establishing the ribbon during interphase and for connecting Golgi membranes to the spindle during mitosis to ensure equal partitioning. However, the precise molecular mechanisms governing the organization of this scaffold or matrix remain unclear. In our recent effort aimed at identifying molecules that maintain the ribbon, we identified RNA an essential component of the Golgi matrix. The Golgin GM130 directly recruits RNA to the Golgi membrane to assemble a biomolecular scaffold or condensate that physically links Golgi stacks into a cohesive ribbon. Our central hypothesis is that RNA-Golgins assemblies function as a fundamental mechanism for organizing Golgi structure and function. We will employ a combination of biochemical, cell biological and microscopy approaches to elucidate the molecular mechanism by which RNA as a structural biopolymer scaffolds the Golgi ribbon. The objectives are to identify and characterize the dynamic organization of the RNA-Golgin scaffolds, and to define how this organization facilitates Golgi function at the molecular level. Furthermore, we aim to define the regulation of this scaffold to enable ribbon unlinking under stress conditions or during mitosis. Ultimately, this work will reveal the fundamental principles of how RNA as a structural biopolymer enables Golgi structure and function, define how cells use phase separation to organize organelle function, and provide novel mechanistic insights into neurodegeneration and cancer.

NIAID - National Institute of Allergy and Infectious Diseases

Our group recently identified a real-life model that uniquely illustrates the impact of the environment on asthma risk. Two populations of comparable Mexican ancestry living only 70 miles apart in Tucson, AZ, USA and Nogales, Mexico (MX) differ strikingly in their rates of childhood asthma, which are 4-fold lower in MX. The Binational Early Asthma and Microbiome Study (BEAMS-1, P01AI148104) was launched to test the hypothesis that MX or US residence impacts microbiome composition and metabolic capacity in pregnant mothers and their children, thereby shaping microbiome and immune responses and the child’s asthma risk. Initial findings from BEAMS-1 have supported this hypothesis. Asthma-predictive symptom (S) scores at 6-9 months (mo) were significantly higher in US than MX infants and were significantly associated with infant fecal microbiome composition and metabolome. Dietary lipids were the largest class of S-score-associated stool metabolites. Oleic, palmitic & linoleic acid metabolites were enriched in high S-score infants, while poly- unsaturated fatty acids were enriched in low S-score infants. These data linked dietary lipid stool metabolites to S-scores and infant asthma risk, but the underlying mechanisms remained unknown. Because asthma risk is associated with both early allergic sensitization and early respiratory viral infections, we now propose to define the mechanisms through which stool metabolites from BEAMS children with distinct S-scores differentially affect immune responses to airway viral infection and aeroallergens, and airway barrier integrity. Our plan stems from a rich set of preliminary data. Sterile fecal extracts (SFEs) from 1-mo-old infants with distinct S-scores 1) differed in their ability to reduce viral load and promote anti-viral responses in mice infected with human rhinovirus (RV), and 2) differentially affected aeroallergen-driven lung inflammation, in part through a novel B cell/IL17/neutrophil pro-inflammatory axis. 3) SFEs from 1-mo old MX infants more effectively promoted human airway epithelial barrier integrity compared to SFEs from their US counterparts. 4) Specific stool metabolites enriched in asthma-protected farm children protected mice from allergic inflammation and enhanced human airway barrier integrity. Therefore, we hypothesize that increased infant S-scores reflect the production of pathogenic microbial metabolites that dysregulate immune responses to respiratory viruses and aeroallergens, and impair airway barrier integrity, thus licensing the initiation of the asthma trajectory. Relying on extant BEAMS samples, we propose to expose mice to SFEs from 1- and 24-mo children with distinct S-scores and characterize the immune mechanisms and microbial metabolites that dysregulate responses to RV infection (Aim 1) and aeroallergen (Aim 2). (Aim 3) will characterize the transcriptional mechanisms that regulate human airway barrier responses to 1- and 24-mo SFEs from children with distinct S- scores, and their relation to SFEs metabolites. Our data will reveal mechanisms that connect gut microbial metabolites to asthma-predictive symptoms and inform approaches that target microbial metabolic dysfunction.

NIGMS - National Institute of General Medical Sciences

Project Summary: Cell migration is a critical aspect of normal development, as cells are often not born in the location of function, and migrate long distances to their final destination. But this process is often co-opted in disease states such as cancer. Much of our understanding regarding cell migration stems from work in 2D cell culture models, in which many types of cells exhibit a net forward movement through cell protrusion at the front and cell retraction at the back. Central to this form of migration is the ability of the cell to physically attach to its underlying substrate through the formation of focal adhesions. in vitro 2D and 3D approaches offer numerous advantages to dissect focal adhesion biology in terms of high-resolution image acquisition, control over matrix properties, and quantitatively assessing biophysical properties. While these studies have been immensely valuable, despite the years of research, it is still unclear what the organization and dynamic regulation of focal adhesions are during single cell migration in complex in vivo systems. Furthermore, pharmacological inhibitors have been developed against components of focal adhesion machinery for the treatment of disease without a clear understanding of how focal adhesions form and function during cell migration in animals. To meet this need, we developed a system in which we can directly visualize the formation and dynamics of focal adhesion structures of highly migratory single cells on a relatively planar surface of the zebrafish larval skin. Our recently published work challenges dogma established by in vitro studies, showing that phosphorylation of a key focal adhesion component, Paxillin, is greatly reduced in migrating cells in vivo, and that lack of Paxillin phosphorylation promotes focal adhesion disassembly rates and single cell migration in vivo, despite inhibiting cell migration in culture. This contradiction emphasizes the need for additional work in understanding focal adhesion regulation in complex in vivo environments (Aim 1). Furthermore, we found that the expression of the upstream kinase, FAK, is significantly reduced in cells in vivo compared to cells in culture. Given that FAK inhibitors are currently being developed in the clinic under the premise that part of FAK's function is for focal adhesion regulation, it is important to definitively determine whether FAK activity is required for focal adhesion regulation during single cell migration in vivo (Aim 2), and how Paxillin promotes cell migration in the absence of FAK phosphorylation (Aim 3). Identifying new proteins that interact with Paxillin in vivo will also begin to unravel why focal adhesion regulation is different in vivo versus in culture. Thus, our work has the potential to re-define the roles for focal adhesion proteins during single cell migration in vivo.

NIAID - National Institute of Allergy and Infectious Diseases

PROJECT SUMMARY/ABSTRACT CD8 T cells are important immune mediators central to protection against intracellular pathogens and cancer. Regulation of the delicate balance between T cell activation and quiescence is essential for mounting effective immune responses while preventing excessive inflammation. T cell dysfunction resulting from chronic antigen stimulation, known as “exhaustion”, leads to loss of protection against infections and cancer. In part related to this, chimeric antigen receptor (CAR)-T cell therapy has faced major challenges in eradicating solid tumors, with data demonstrating that the high antigen load contributes to chronic stimulation through the CAR, driving an exhausted phenotype. Conversely, an overactive and dysregulated T cell response can cause inflammatory disorders, including autoimmunity and graft-versus-host disease (GVHD), a deadly immune complications of hematopoietic stem cell transplant (HCT). Thus, effectively controlling T cell activation is key both to harnessing their potential to control infection and malignancies, and to managing pathologically inflammatory conditions. The transcription factor Hobit (ZNF683) has emerged as a novel central regulator for T cell activation and cytotoxicity. First identified as a lineage-specific marker of resident-memory T cells, Hobit has also been discovered across several cancer clinical trials to be expressed by exhausted anti-tumor T cells re-animated by PD-1 blockade. Hobit expression is lost in terminally exhausted T cells, suggesting a malleable role in T cell quiescence and re-activation. Compelling new work from our lab has deepened this paradigm shift: In the pivotal clinical trial that led to FDA approval of the CD28:CD80/86 co-stimulation blockade agent, abatacept, for GVHD prevention, we found that Hobit was significantly downregulated in the inflammatory proliferating T cells that normally precede acute GVHD (aGVHD), and that this downregulation was controlled with abatacept. Our goal is to uncover how Hobit governs T cell activation under chronic antigen stimulation and develop strategies to harness this pathway. We hypothesize that Hobit maintains antigen-experienced CD8 T cells in a state of revivable quiescence, which prevents terminal exhaustion and preserves their cytotoxic potential. To improve the outcomes of cellular therapies—by suppressing alloreactive T cells after HCT or enhancing persistence of CAR-T cells against tumor and antiviral T cells for chronic infections—it is critical to elucidate the molecular switches that control T cell cytotoxicity in the face of chronic antigen. We will approach this question through the following Aims: Aim 1: Determine if Hobit can preserve cytotoxicity in exhausted CD8 T cells. We hypothesize that Hobit can preserve cytotoxic potential in chronically stimulated CD8 T cells by inhibiting Blimp-1-mediated terminal exhaustion differentiation. Aim 2: Determine how Hobit expression regulates quiescence and cytotoxicity in transplanted CD8 T cells experiencing chronic antigen stimulation. We hypothesize that tuning Hobit expression can allow control over CD8 T cell activation during the chronic stimulation that occurs after HCT or after CAR-T therapy.

NCI - National Cancer Institute

TAL1 is a hematopoietic-specific member of the basic helix-loop-helix family of transcription factors (TFs) required for hematopoietic stem cell (HSC) function and the development of all hematopoietic lineages1-4. Aberrant activation of TAL1 oncogene associates with up to 60% of T-cell acute lymphoblastic leukemia (T-ALL) patients5-7. Its ectopic expression also led to development of leukemia or lymphoma in mice8,9. Deletion of TAL1 in T-ALL cells lost leukemic phenotype and induced apoptosis10. Furthermore, the TAL1 expressing (TAL1+) TALL subtype associates with poor prognosis and high rate of relapse indicating that dysregulation of TAL1 oncogene plays an important role in T cell leukemogenesis. In order to comprehensively understand the role of TAL1 domain structure in T-ALL pathogenesis, we employed unbiased sgRNA tiling library scanning of TAL1 exons for structural and functional domains in resolution of 3.9 base pairs (bp)/sgRNA. We identified that two lysine residues, K221 and K222, are critical for T-ALL cell function and survival. K221 and K222 sites of TAL1 are key targets for HAT mediated acetylation in vivo. The level of acetyl-TAL1 is lower in TAL1+ T-ALL cell lines than that of differentiated erythroid cells. Furthermore, we generated unacetyl-mimicking TAL1K221,222R (TAL1K2R) and acetyl-mimickingTAL1K221,222Q (TAL1K2Q) knock-in (KI) Jurkat cells and TAL1K2R and TAL1K2Q conditional KI (cKI) mice. While TAL1K2R Jurkat cells behaves similar to TAL1+ T-ALL cells that promote leukemic transcription profile for leukemia survival, TAL1K2Q cells facilitated T-cell differentiation and blocked leukemogenesis in xenograft mouse models, suggesting that acetylation status of TAL1 dynamically regulates TAL1 function in normal hematopoiesis vs leukemogenesis. In addition, IP-LC/LC MS revealed that TAL1K2Q mainly associates with HAT complexes while TAL1K2R interacts with HDACs and leukemic TFs. Based on these preliminary data, we hypothesize that acetylation status of K221 and K222 of TAL1 act as a molecular switch to control its ability to interact with TFs and epigenetic factors, as well as TAL1 mediated transcription circuit for normal hematopoiesis and T-ALL leukemogenesis. In this proposal, we will investigate: 1) key novel factors that are differentially associated with TAL1K2R and TAL1K2Q in controlling TAL1 transcription function in T-ALL; 2) the underlying mechanisms of TAL1 acetylation on TAL1-driven transcriptional regulation; 3) the biological function of TAL1 mutants in BM HSC regulation and T-cell leukemogenesis. To achieve this goal, we generated several mouse models of human T-ALL disease that are not only critical and essential to study how TAL1 acetylation alters HSC/LSC function during T-ALL development, but also potentially lead to the development of new therapeutic strategies targeting TAL1 modifications for T-ALL treatment. Success of the proposed studies, especially using our unique mouse models of human T-ALL disease, will lead to a better understanding of mechanism by which aberrant expression of TAL1 oncogene leads to T-ALL and how TAL1 acetylation status switches its ability to alter hematopoietic transcription regulatory networks in T-ALL.

NICHD - Eunice Kennedy Shriver National Institute of Child Health and Human Development

ABSTRACT Life begins with the fusion of unipotent sperm and egg, forming a totipotent zygote capable of generating an entire organism. The mechanisms governing totipotency during preimplantation development remain poorly understood. RNA modifications, such as methylation, play essential roles in post-transcriptional gene regulation. Here, we aim to explore the role of a putative RNA methyltransferase in regulating totipotency and early embryonic development. The zygote is initially transcriptionally silent, relying on maternal RNA and proteins. Its genome undergoes transcriptional activation through zygotic genome activation (ZGA), a pivotal process involving two phases: minor ZGA and major ZGA. This transition is characterized by a dramatic increase in gene expression, enabling further embryonic development. RNA modifications, including methylation by METTL proteins, play key roles in gene expression. Analysis of single cell sequencing data from mouse preimplantation embryos revealed that Mettl7a1, encoding a putative RNA methyltransferase, is highly expressed during 1-cell and early two-cell stage, coinciding with minor ZGA. Knockdown of Mettl7a1 in mouse embryonic stem cells (mESCs) downregulated totipotency markers and reduced the proportion of 2- cell-like cells (2CLCs), which exhibit features of totipotency. Based on these observations, we hypothesize that Mettl7a1 regulates ZGA and totipotency via its RNA methyltransferase activity. Aim 1 will investigate Mettl7a1’s role in minor ZGA and preimplantation development. Aim 2 will identify RNA targets and modifications catalyzed by METTL7A1. This work will uncover novel mechanisms of totipotency regulation, advancing knowledge in developmental biology, regenerative medicine, and epitranscriptomics.

NCI - National Cancer Institute

Project Summary. For proteins implicated in human diseases such as cancer, therapeutic advances arise not only from discovering ways to manipulate their function directly, but also through indirect approaches such as investigating their regulation by other cellular molecules. Heterotrimeric G proteins of the G12/13 subfamily provide a good example; the GTP-binding a subunits - Ga12 and Ga13 - are substrates for several chemical modifications after their translation. Two such mechanisms, covalent attachment of a specific fatty acid (S- palmitoylation) and a phosphate group (phosphorylation), were reported soon after discovery of these G proteins; however, follow-up studies of these modifications have been sparse. The specific enzymes that covalently modify the G12/13 a subunits have not been identified. Because Ga12 and Ga13 harbor potent ability to drive tumorigenic signaling and metastatic invasiveness in cells, and recently were implicated as conferring stem cell-like properties upon tumor initiating cells, methods of disrupting or manipulating their signaling could lead to useful therapeutics. My laboratory's undergraduates used mutagenic strategies to either nullify or mimic phosphorylation of Ga12 and Ga13 at selected amino acids, and recently obtained experimental results for Ga12 that point to a rarely observed cross-regulatory mechanism between its phosphorylation and S-palmitoylation. This putative mechanism, in which down-regulated S-palmitoylation of Ga12 disrupts its ability to drive tumorigenic signaling, has not been reported for any G protein. The first phase of this proposal describes a plan to “dissect” this cellular mechanism by i.) identifying enzymes that catalyze S-palmitoylation and phosphorylation of Ga12, ii.) revealing the contextual amino acids in Ga12 that allow its specific targeting, and iii.) developing assays to detect the S-palmitoylation and/or phosphorylation of recombinant Ga12 mutants expressed in cultured human cells. The second phase of this proposal also arose from a discovery by UNC Asheville undergraduates: a new mechanism in which activation of protein kinase A (PKA) drives a steep increase in the already potent tumorigenic signaling by both Ga12 and Ga13. A combination of mutagenesis, signaling assays, and molecular probes will be employed to investigate the components of this regulatory mechanism. Interestingly, the responses of Ga12 and Ga13 to PKA activation show several differences that will be investigated. An overarching goal of the proposed studies is to discover distinct features of tumorigenic signaling by the G12/13 subfamily, not only in comparison to other G protein a subunits but between Ga12 and Ga13 themselves. Such information should provide value toward developing therapeutics against cancers in which aberrant signaling by a specific G protein plays a role.

NIAID - National Institute of Allergy and Infectious Diseases

Project Summary Project Description: Viruses are obligate intracellular parasites, as they require access to cellular translation machinery for viral protein synthesis. The order Mononegavirales contains non-segmented negative sense RNA viruses (nsNSV). These viruses transcribe positive sense, capped and polyadenylated mRNA that are indistinguishable from host transcripts. Due to this, it is assumed that these viruses use canonical translation machinery. However, the mRNA of these viruses possesses characteristics, such as extremely short 5’UTRs and strong stem-loop structures, that would preclude canonical translation initiation and scanning methods. Using a series of auxin-inducible degron (AID) systems, we have systematically probed the requirements of individual translation factors for protein synthesis. Vesicular stomatitis virus (VSV) is a member of the Mononegavirales order. Its translation has been the most studied of the nsNSVs. We have demonstrated that VSV mRNAs translate independently of factors necessary for canonical translation, leading us to believe that viral translation occurs through an alternative mechanism. This proposal aims to characterize the mechanism of VSV translation, a first step to expanding the knowledge of nsNSV translation. Long-term, this work will contribute to increasing the basic understanding of viral replication as well as identifying targets for the development of antivirals. Training Plan: I will receive guidance and feedback from my sponsor, Dr. Shawn Lyons, and co-sponsor, Dr. John Connor. In the lab, I will develop and refine my skills in biochemistry, translational research methods, and virology. Participation in regular lab meetings and journal clubs will hone my scientific and critical thinking skills, while attendance at departmental seminars will broaden my understanding of biochemistry and cell biology. Furthermore, I will gain expertise in RNA biology through monthly RNA club meetings, providing a specialized area of focus. I will regularly exercise my presentation skills, presenting in various fostering effective scientific communication skills. This comprehensive training will equip me with a strong foundation in biochemistry, virology, and RNA biology, positioning me for success in my current research endeavor. Further, this will provide me with the expertise necessary to obtain a postdoctoral training fellowship, which will guide me toward my ultimate goal of becoming a principal investigator in an academic setting. Environment: The Lyons lab is well-equipped with ample bench space, with various machines at our disposal. These include a Chemidoc and TurboBlot Transfer system, for western blotting, and a BioComp, for polysome analysis. We have access to shared spaces that accomadate cold storage and tissue culture. Within the building, we have access to several microscopes and a BioRAD NGC chromatography system, for protein purification. Additional equipment is available through various core facilities on Boston University’s Medical School and Charles River campuses.

NIBIB - National Institute of Biomedical Imaging and Bioengineering

PROJECT ABSTRACT Mesenchymal stem/stromal cells (MSCs), the most abundant adult precursor cells in the human body, have been widely explored for various experimental and clinical applications and were recently approved for clinical use by the FDA. Nevertheless, a daunting challenge remains: the poor survival and reduced regenerative capability of MSCs in hostile microenvironments in the recipient tissue markedly undermine their efficacy and treatment outcome. Our proposal, “Reinvent Mesenchymal Stem Cells - A Synthetic Biology Approach to Engineer Programmable Adult Stem Cell Theranostics,” aims to overcome these limitations by engineering a programmable cellular theranostic platform for MSCs. We previously developed synthetic genetic circuits (SGCs) having upstream genetic sensors to detect intracellular signaling and downstream secretory effector molecules to program cellular signaling and desirable cellular functions under conditions of stress or disease. Here, we propose to integrate SGCs into MSCs to engineer Autonomous Impairment-inducible MSCs (aiMSCs). aiMSCs would spontaneously detect stress- or disease-induced intracellular signals via genetic sensors and initiate transgene expression to enhance cell survival and treat targeted pathologies. To ensure the safety and translational potential of aiMSCs, we will embed two types of autonomously programmable control mechanisms: 1) dual intracellular signaling feedback controls at the sensor and effector levels, and 2) a safety switch based on endogenous microRNA binding, to respond to the microenvironment in real time and increase effector output levels when the tissue damage intensifies or turn off the SGC when the tissue heals. As proof-of-concept, we propose two specific aims to develop the aiMSC technology and explore its potential as a next-generation MSC therapy. We will use synthetic biology, genetic engineering, and computational tools to engineer: 1) murine bone marrow (BM)-derived MSCs that automatically detect and respond to inflammatory signals, augment MSC survival, and promote a destructive-to-constructive transition in tissue inflammation (aiMSC-I); and 2) human BM-MSCs (hMSCs) that detect and respond to metabolic distress- induced signals and promote hMSC survival, anti-oxidation, and mitochondrial protection (HaiMSC-M). We will use cellular, organoid, and animal disease models to validate aiMSC-I and HaiMSC-M and to demonstrate enhanced MSC survival and functioning, as well as the self-contained and self-regulated modulation of disease conditions. Large-scale genetic sensor screening and machine learning will be used to identify unique MSC- specific pathology sensors. aiMSCs represent an adaptive, self-programmed theranostic approach that augments MSCs on demand in a safe and controlled manner. aiMSCs would significantly advance patient treatment and offer new perspectives for precision medicine, designer therapeutics, and stem cell therapies.

NIA - National Institute on Aging

Abstract Hematopoietic stem cell (HSC) transplantation (HSCT) and HSC based gene and cell therapies hold curative potential for diverse hematologic and immunologic disorders. However, donor age remains a critical determinant of transplant success. Aging drives profound HSC dysfunction, manifested by diminished regenerative potential, lineage skewing toward myelopoiesis, and an increased burden of clonal hematopoiesis (CH) associated mutations. These defects heighten the risk of graft failure, donor-derived leukemia, and poor survival after HSCT. Aging-associated HSC decline is driven in large by mitochondrial dysfunction. Aged HSCs exhibit impaired mitophagy, aberrant oxidative phosphorylation, and disrupted bioenergetics, changes that are further amplified by chronic inflammation and remodeling of the bone marrow (BM) niche. The fate and function of HSCs are shaped not only by their intrinsic metabolic state but also by their communication with niche partners, particularly mesenchymal stromal cells (MSCs). Our recent work demonstrated that HSPC-BM niche interactions are metabolically coupled via Connexin-43 dependent mitochondrial transfer, preserving HSC survival and niche function. Moreover, targeted mitochondrial supplementation into HSC preserves mitochondrial integrity, enhances metabolic adaptability, and maintains self-renewal during stress hematopoiesis, highlighting the importance of both mitochondrial quality and intercellular mitochondrial communication in hematopoietic regeneration. Our preliminary data show that mitochondrial transfer from HSPCs to MSCs markedly declines with age, compromising MSC bioenergetics and weakening their ability to sustain balanced hematopoiesis. We further identified that supplementation of aged HSCs with young mitochondria rescues mitochondrial membrane potential, restores AcH4K16 polarity, and rejuvenates transcriptome of aged HSC. Together, these findings highlight mitochondrial quality and transfer as central drivers of hematopoietic aging and compelling therapeutic targets. This proposal seeks to define the mechanistic basis and therapeutic potential of mitochondrial engineering to rejuvenate aging hematopoiesis. In Aim 1, we will test whether heterochronic mitochondrial supplementation and augmentation of mitochondrial function restore the youthful potential of aged HSCs by rewiring metabolic flux, enhancing autophagy, and resetting epigenetic programs. In Aim 2, we will dissect how HSPC-MSC mitochondrial transfer governs niche metabolism, trophic function, and the competitive fitness of aged versus CH-mutant HSPCs. By integrating metabolic, epigenetic, and intercellular communication pathways, this work addresses fundamental drivers of hematopoietic aging. The anticipated outcomes will provide mechanistic insight into how restoring mitochondrial quality and transfer can normalize aged HSC function and niche support. Ultimately, this study lay the foundation for innovative, clinically translatable strategies to improve HSCT outcomes in older patients and donors, while reducing risks of clonal dominance and age associated hematologic disease.

NIH

For decades, orthopaedic endoprostheses have been manufactured using traditional machining techniques. Specifically, the stem of the endoprostheses would be fabricated using mills and/or lathes, then the osseointegrated (OI) region would be added onto the stem using small metal beads, then sintered for strength. Recently, additive manufacturing, also known as 3-dimensional (3D) printing, has been introduced to provide affordable devices for limited markets. Instead of the traditional multi-step machining process, both the endoprosthetic stem and the OI region are designed to be manufactured in one continuous process, saving valuable resources. While there are FDA-related issues to address before 3D-printed devices become commonplace in the US healthcare system, many short-term implanted medical devices like orthopaedic fixation plates, screws, pins and wires, and even some long-term dental devices like dental fillings, crowns, and dentures are now 3D-printed. However, 3D-printing of many devices, including percutaneous OI endoprosthesis, is not yet widely accepted by the FDA because of the lack of data verifying that the device designed meets the engineering requirements, and validating that the device produced meets the need for which it was designed. Because of this, 3D-printing manufacturers are apprehensive to put their devices directly into humans. Fortunately, our research team has a well-developed sheep forelimb amputation model which has been directly used for this application and has been accepted previously by the FDA as a valid, preclinical model. In this proposed study, we plan to replicate the existing human Percutaneous Osseointegrated Docking Systems (PODS) endoprostheses to develop a 3D-printed version for use in sheep, which we will call sPODS, an acronym for Sheep PODS. The sPODS will be manufactured not only using a 3D-printing process, but also using a traditional machining process to act as a baseline for direct comparison. Both the 3D-printed and the traditionally machined sPODS will have the same external geometry (length, diameters, tapers, etc.), with the only difference being the method used to create the device. Once manufactured, the 3D-printed and the traditionally machined sPODS will be verified through benchtop testing, measuring the amount of bone loss during implantation, the contact area between the bone and the endoprostheses, and the fixation strength post-implantation. This will verify that the device manufactured meets the specified engineering requirements. Next, production quality 3D- printed and traditionally machined sPODS will be surgically implanted into our amputated sheep metacarpal model and validated against our published historical sheep data, confirming that the device produced meets the need for which it was designed. This research project with the following Specific Aims: Specific Aim 1: To quantify the surface, material, and mechanical properties of the 3D-printed sPODS and the traditionally machined sPODS, then to measure and compare the initial tensile and torsional stabilities of devices implanted into sheep carcass metatarsals. Specific Aim 2: To validate that the bone morphology and the tensile and torsional stability of the 3D-printed sPODS are not inferior to traditionally machined sPODS following 6-months in situ in a sheep amputated metacarpal model. Prior to implementing PODS clinically, this study is essential to confirm that device design aligns with engineering and material requirements. Ultimately, these efforts will immediately contribute to enhancing functional independence and quality of life of the Veterans with transhumeral amputations but will also serve as guidance for all teams designing and testing 3D-printed percutaneous OI devices at any anatomic site.

NIH

Each year, millions of individuals receive repetitive head injuries (RHI) from playing contact sports or through military service. RHIs are a type of traumatic brain injury characterized by mild, mostly non-concussive injuries that, in the context of a sport like American football, can occur dozens of times a day for years. In addition to long-term disability and dysfunction, individuals who have a history of RHI are at an increased risk of developing neurodegenerative diseases, likely stemming from a neuroinflammatory environment that results from the constant low-level head trauma. To that end, our preliminary single nucleus RNA sequencing (snRNAseq) studies have demonstrated inflammatory SPP1+/Hif1a+ microglia are observed in cases with exposure to RHI but have not yet developed pathology, suggesting inflammation precedes protein deposition. Interestingly, it has become clear that neuropathologies like Alzheimer’s disease (AD) in the context of RHI are not identical to their non-RHI counter parts. In contrast to the normal confluent appearance of cortical hyperphosphorylated tau (ptau) distribution observed in AD, individuals with AD and an RHI history (AD+RHI) were observed to have a sulcal predominance of ptau. Additionally, preliminary bulk sequencing studies suggest AD+RHI cases have an altered neuroinflammatory environment. These observations raise the question if other “classical AD” features are altered during RHI. The implications for differences are significant, as imaging biomarkers for AD diagnosis rely on understanding the known progression pattern of neuropathology but altered pathology makes it harder to diagnose AD. Also, the altered neuropathologic burden and distribution may skew clinical symptoms, which complicates clinical assessment and results in improper treatment strategies. To better examine RHI-specific changes in AD, we will deeply characterize the neurodegeneration, pathologic protein regional progression, and clinical phenotypes observed in individuals with a history of RHI and a neuropathologic diagnosis of AD. We will use our unique resource—the NIA-funded P30 Boston University AD Research Center brain bank, the largest RHI brain bank in the world, to compare 7 groups: individuals either with Low, Intermediate, or High AD neuropathologic changes with or without exposure to RHI (n = 379), and a no pathology/no RHI control group. Overall, we hypothesize that the exposure to RHI will result in altered AD neuropathology, which will also have direct associations with clinical outcomes. Using digital pathology and artificial intelligence toolsets, we will perform disease progression modeling using a machine learning tool called subtype and stage inference algorithm (SuStaIn), to examine whole-slide digital images taken from 19 brain regions per case that are stained for ptau, Aβ, TDP43, and a-syn. SuStaIn uses spectrums of neuropathology data to predict progression patterns of diseases through the brain and can determine cases that fall outside the normal range identifying subtypes. We will compare progression patterns between AD and AD+RHI cases encompassing early, late, and end stage disease. We will also determine if specific SuStaIn subtypes correlate with distinct clinical symptom presentation. Next, we will perform snRNAseq to compare how cell population might be altered in our 7 groups using tissue taken from the dorsolateral frontal, temporal, and calcarine cortex representing early, late, and end stage pathology. In addition, we will use proximal frozen tissue to perform pTau and Aβ histology to measure pathologic accumulation directly related with the cells assayed by snRNAseq. Finally, we will perform a spatial histologic analysis across AD and AD+RHI cases to investigate how local cell populations are directly related to pathology. We will again utilize tissue from the dorsolateral frontal, temporal, and calcarine cortex to capture the full spectrum of disease related changes and investigate if previously observed RHI-induced neuroinflammatory cell populations are present in brain structures most susceptible to RHI damage. Overall, these findings will be critical in advancing our understanding of how RHI alters neuropathology and shapes clinical presentations. The direct impact of this work will be enhanced criteria and methods to better distinguish AD- and RHI-specific changes.

NIAMS - National Institute of Arthritis and Musculoskeletal and Skin Diseases

Project Summary Cutaneous capillary malformation (CM, a.k.a, Port Wine Birthmark, PWB) is a defect of primitive capillaries in the skin during development. It mainly appears on the face with an estimated prevalence of 0.3-0.9% in newborns and is highly associated with many complicated types of vascular malformations and outgrowth syndromes, such as Sturge-Weber syndrome (SWS), Parkes-Weber syndrome, Klippel-Trenaunay syndrome, arteriovenous malformations (AVM), and CLOVES syndrome. Photobiological-based modalities, such as pulsed dye laser (PDL) or photodynamic therapy (PDT), are the common treatment options for CM; unfortunately, complete removal occurs in less than 10% of patients treated. In addition, about 20% of lesions have no response to laser, e.g., laser-resistant (PDL- or PDT-resistant) CM. The inadequate outcomes are unmet clinical barriers. This study will tackle these challenging clinical barriers by repurposing an FDA-approved anti- diabetic medicine sitagliptin to target laser-resistant CMs. In this proposal, a series of clinically relevant in vitro and in vivo models including CM-derived inducible pluripotent stem cells (iPSCs), their induced endothelial cells (iECs), vascular organoids (VOs), and mouse models with xenograft of CM iECs will be used. We will determine the therapeutic window of sitagliptin on laser-resistant CM iECs in vitro. We will dissect sitagliptin-mediated inhibition of antioxidant pathways as a novel mechanistic action to sensitize CM lesions. We will characterize how sitagliptin-modulated GPX activity, GSH and ROS levels in response to PDT. We will test if sitagliptin improves the outcomes of laser therapy on VOs in vitro and determine if oral administration of sitagliptin at non-toxic doses enhances the efficacy of PDT in xenograft mouse models. This study is highly translational. First, sitagliptin is among the top list of compounds generated through our data-driven drug repurposing pipline using the multiome datasets of CM iPSCs, iECs and patients’ biopsies. Second, sitagliptin is an FDA-approved drug, thus repurposing sitagliptin would be easier, cheaper, and more feasible than other candidate compounds. Third, PK/PD, safety, and real-world data of sitagliptin are available for its’ repurposing. Third, sitagliptin shows efficacy in nanomolar ranges, displaying a wide therapeutic window for pediatric patients. The successful completion of this proof-of-concept study will serve as a milestone and basis for a Go/No-Go decision for the further repositioning sitagliptin for off-label trials in patients.

NIMH - National Institute of Mental Health

Recent advances in human genetics defined hundreds of causal variants for Autism Spectrum Disorder (ASD) and other neurodevelopmental disorders (NDDs). However, substantial effort is now required to identify downstream disease processes and guide development of interventions. One such new NOD gene is ZNF292: mutations were recently associated with ASD and other NDDs in humans, but ZNF292 requirements for brain development and consequences of pathogenic mutation have not been studied in any animal or human cellular model. Here, we propose a comprehensive mechanistic investigation of ZNF292, using both established cuttingedge workflows and innovative new approaches to study the consequences of both deficiency and pathogenic mutation at the molecular, cellular, structural, and functional and behavioral circuit levels. We use two complementary experimental systems, mouse models and human pluripotent stem cell (hPSC)-derived neurons, to define ZNF292 requirements for neurodevelopment. We focus initially on hPSC models carrying six pathogenic ZNF292 variants identified in patients with ASD, intellectual disability, and other NOD clinical phenotypes (e.g., microcephaly, epilepsy), and comparison with hPSC lines with constitutive or inducible ZNF292 deficiency. Our preliminary work has already demonstrated shared disruptions of neurodevelopment, transcriptional regulation, and neuronal network function stemming from either ZNF292 deficiency or pathogenic mutation in these models. We also developed conditional and non-conditional mouse knockout models of ZNF292 deficiency and demonstrated that these exhibit NOD-relevant circuit disruptions and, accordingly, altered behavior. Further, we developed cutting-edge tools for temporally controlled reversal of ZNF292 deficiency in our hPSC models, enabling us to investigate the effects of restoring ZNF292 gene function either during development or in mature neurons. Related landmark experiments profoundly changed our understanding of other NDDs by demonstrating that a substantial proportion of chronic NOD phenotypes were reversible, thus spurring the development of therapeutics based on either restoring gene expression or reversing its chronic consequences for neuronal function. In complementary efforts, we continue to model additional cases in this rapidly expanding patient population, linking NOD clinical phenotypes to shared, reversible endophenotypes related to altered neuronal network function. Based upon our preliminary data, we hypothesize that impaired circuit and neuronal network function stemming from chronic reduction of ZNF292 activity contributes substantially to NDDs in this patient population. These deficits may be tractable for molecular or pharmacological treatment to develop interventions. Therefore, together, the experiments performed here will elucidate requirements for and mechanisms by which ZNF292 normally controls brain development and function, will determine how these are disrupted by pathogenic ZNF292 mutation, and could also chart a course towards ZNF292-targeted therapies.

Dept of the Army -- Materiel Command

This solicitation invites applications (also referred to as proposals ) for basic research projects. The proposals must align with the research areas of interest to the DoW (which includes the USW(R&E) and the Agencies) and enhance the education of students in areas of STEM that align with the DoW research interests. Information about these areas of interest (including websites) is discussed below. The USW(R&E) Critical Technology Area descriptions are at https://www.cto.mil/wp-content/uploads/2025/11/CTA-One-Pager-Option-Nov2025.pdf. The critical technology priorities rely on innovation and workforce talent. The critical technology areas are: - Applied Artificial Intelligence (AAI) - Biomanufacturing (BIO) - Contested Logistics Technologies (LOG) - Quantum and Battlefield Information Dominance (Q-BID) - Scaled Directed Energy (SCADE) - Scaled Hypersonics (SHY) Basic research projects in research areas of interest to the Agencies are presented in their respective Broad Agency Announcements (BAAs), which are available as follows: Army Research Laboratory combined Broad Agency Announcement is available at: https://www.arl.army.mil/collaborate-with-us/opportunity/arl-baa/. This BAA may also be found on Grants.gov (https://www.grants.gov) by entering the BAA number, W911NF-23-S-0001, in the Search Grants keyword box. Office of Naval Research: https://www.onr.navy.mil/ Select Work With Us, then Funding Opportunities, and then BAAs, FOAs and Special Program Announcements to see the FY26 Long Range Broad Agency Announcement for Navy and Marine Corps Science and Technology, BAA N00014-23-S-B001. This BAA may also be found on Grants.gov (https://www.grants.gov) by entering the BAA number in the Search Grants keyword box. In addition to providing details about the Agencies research interests, the above documents include names and contact information of technical program managers. Principal Investigator and a Co-Principal Investigator (PI/Co-PI) are encouraged to peruse the research interests of each Agency and to contact the respective program managers to discuss mutual research interests. Applications with relevance to the interests of multiple Agencies may receive multiple reviews. Additional information and questions about the critical technology areas should be directed to Agency Contacts identified in Section II.G. of this NOFO. Other research areas that are not aligned with the (OUSW(R&E)/ASW(S&T) critical technology priorities listed in I.B.7 will be considered. The Agencies BAA listed above under I.B.6 provides other research areas of interest to the DoW. NOTE: Use the above-referenced Agency documents only to identify research areas of interest to the Agencies. Disregard instructions contained therein regarding application preparation, content, and submission requirements. Instead, follow the instructions in this NOFO. Projects proposed for funding under this NOFO must be for basic research. As defined by DoW, basic research is systematic study directed toward greater knowledge or understanding of the fundamental aspects of phenomena and of observable facts without specific applications toward processes or products in mind. It includes all scientific study and experimentation directed toward increasing fundamental knowledge and understanding in those fields of the physical, engineering, life sciences, and information sciences related to long-term national security needs. Principal Investigator and a Co-Principal Investigator (PI/Co-PI) are encouraged to consider innovative approaches for their research projects with a view toward enhancing the ability of their institution to develop stronger science and engineering programs that will enable the institution to participate more competitively in a variety of defense research programs, attract and retain good students by exposing them to state-of-the-art research, and encourage them to pursue careers in STEM disciplines. Methods through which these goals can be achieved are varied. Factors such as research capabilities, facilities, and equipment are unique to each institution. Therefore, DoW will not prescribe the approach for a research project; instead, it expects applications to reflect the unique needs and capabilities of the applicant institution.

U.S. National Science Foundation

The Research in Disabilities Education (RDE) program seeks to broaden the participation and achievement of people with disabilities in all fields of science, technology, engineering, and mathematics (STEM) education and associated professional careers. The RDE program has been funding this objective since 1994 under the prior name "Program for Persons with Disabilities." Particular emphasis is placed on contributing to the knowledge base by addressing disability related differences in secondary and post-secondary STEM learning and in the educational, social and pre-professional experiences that influence student interest, academic performance, retention in STEM degree programs, STEM degree completion, and career choices. Projects also investigate effective practices for transitioning students with disabilities across critical academic junctures, retaining students in undergraduate and graduate STEM degree programs, and graduating students with STEM associate, baccalaureate and graduate degrees. Research project results inform the delivery of innovative, transformative and successful practices employed by the Alliances for Students with Disabilities in STEM to increase the number of students with disabilities completing associate, undergraduate and graduate degrees in STEM and to increase the number of students with disabilities entering our nation's science and engineering workforce. RDE projects contribute to closing the gaps occurring for people with disabilities in STEM fields by successfully disseminating findings, project evaluation results, and proven good practices and products to the public.Innovation through Institutional Integration (I3) projects enable faculty, administrators and others in institutions to think and act strategically about the creative integration of NSF-funded awards, with particular emphasis on awards managed through programs in the Directorate for Education and Human Resources (EHR), but not limited to those awards. For Fiscal Year 2010 proposals are being solicited in nine EHR programs that advance I3 goals: CREST, GSE, HBCU-UP, ITEST, LSAMP, MSP, Noyce, RDE, and TCUP.

Naval Supply Systems Command

<p>This FOA is intended for proposals related to basic and applied research in the STEM categories, and not related to the development of a specific system or hardware procurement.</p><p><br></p><p>The proposal submission process has two stages:</p><p>I.&nbsp;Applicants&nbsp;<u>are encouraged&nbsp;</u>to submit a white paper first to Grants@NPS.edu, ; and</p><p>II. Applicants must submit a full proposal through Grants.gov (do not submit white papers through Grants.gov, only full proposals)</p><p>Applicants are encouraged to submit a White Paper in advance of a Full Proposal to minimize the labor and other costs associated with the production of detailed full proposals that have little chance of being selected for funding.&nbsp;Based on an assessment of the white papers, the responsible Research Program Officer will provide informal feedback notification to the prospective awardees to encourage or discourage submission proposals.&nbsp;The Research Program Officer may also, on occasion, provide feedback encouraging re-work to strengthen a proposal.&nbsp;</p><p><br></p><p>White Papers may be submitted at any time during the open period of this FOA. A separate White Paper is required for each research proposal.&nbsp;</p>

Naval Supply Systems Command

This FOA is intended for proposals related to basic and applied research in the STEM categories, and not related to the development of a specific system or hardware procurement.The proposal submission process has two stages:I. Applicants are encouraged to submit a white paper first to Grants@NPS.edu, ; andII. Applicants must submit a full proposal through Grants.gov (do not submit white papers through Grants.gov, only full proposals)Applicants are encouraged to submit a White Paper in advance of a Full Proposal to minimize the labor and other costs associated with the production of detailed full proposals that have little chance of being selected for funding. Based on an assessment of the white papers, the responsible Research Program Officer will provide informal feedback notification to the prospective awardees to encourage or discourage submission proposals. The Research Program Officer may also, on occasion, provide feedback encouraging re-work to strengthen a proposal. White Papers may be submitted at any time during the open period of this FOA. A separate White Paper is required for each research proposal.

NIMH - National Institute of Mental Health

PROJECT SUMMARY The brain is an extraordinarily complex organ containing many millions of neurons and non-neuronal cells that are organized into highly specialized yet intricately integrated circuits controlling various activities, such as sensory perception, motor control, and cognitive processes. The brainstem is a critical region responsible for regulating essential bodily functions, like heart rate, blood pressure, and digestion, and thus maintaining body homeostasis. The individual neurons in brainstem can be classified into types based on shared characteristics like gene expression. Binning individual cells into cell types is fundamental for advancing our understanding of complex biological systems, like the brain, from normal tissue function to disease processes. The characterization of cell types enables creation of tools to gain genetic access to groups of cells, it enables dissection of cellular heterogeneity, identify key players in various contexts like disease and aging, and lay the groundwork for targeted interventions and therapies. We recently built a comprehensive, high-resolution atlas of cell types across the entire adult mouse brain and the cell type diversity in brainstem exceeded our expectations. Brainstem is home to a highly heterogeneous group of neurons that does not share a specific gene module, yet these neurons are highly similar to one another. In addition, these cell types intermingle in various regions and their function is strongly determined by their input/output relationship. This suggests that a high-dimensional combinatorial gene expression code is needed to resolve the unique transcriptomic cell types in this region. Our goal is to create a refined atlas of cell types in brainstem using a combination of single cell transcriptomic profiling, spatial transcriptomic profiling, and mapping of projection patterns to transcriptomic cell types in brainstem. In addition, we will computationally align brain stem cell types from mouse, non-human primate, and human to define a cross-species consensus atlas of brain stem. Cell type homologies across species can be established based on conserved marker expression. This enables inference of cellular properties, such as long- range projection targets, that are difficult to measure in humans. The proposed efforts will lead to a significantly improved understanding of brainstem cell types and their function and lay the foundation for a better understanding of disease processes related to that region.

NICHD - Eunice Kennedy Shriver National Institute of Child Health and Human Development

Project Summary The mammalian female reproductive tract (FRT), consisting of the oviducts, uterus, cervix and vagina, is essential for pregnancy establishment and a frequent site of human disease, including infertility and cancer. The embryonic origin of FRT is the Müllerian ducts, a pair of epithelial tubes with a surrounding mesenchyme. Once formed, the Müllerian duct regionally divides into segments along the anterior- posterior axis with each segment developing into distinct structure (oviduct, uterus, cervix and upper vagina). Classical tissue recombination experiments have shown that the Müllerian duct epithelial cell fate determination along the anterior-posterior axis is mediated by signals from the underlying stroma and retinoic acid (RA) signaling has been proposed to be the stromal cue for uterine epithelial cell fate determination. Despite advances in the molecular understanding of MDE specification during FRT development, there remains a striking knowledge gap in our understanding of how adult uterine cell fate is maintained. Recently a group of uterine epithelial cells at the intersection of luminal and glandular epithelium has been proposed to be a uterine stem cell population capable of differentiating into either luminal or glandular cells. However, little is known how these stem/progenitor cells acquire and maintain uterine cell fate and whether stromal signals are required for their specification. Our preliminary studies provide strong genetic data supporting the idea that RA signaling is continually required to maintain uterine epithelial cell fate during adult uterine homeostasis. In addition, our data suggest a model in which an antagonistic relationship between RA and estrogen signaling regulates Müllerian duct epithelial cytodifferentiation. These hypotheses will be tested in two aims. Aim 1 will examine the cell-autonomous function of retinoic acid receptors in FRT development and in adult uterine cell fate determination. Aim 2 will test the hypothesis that an RA-estrogen antagonism drives FRT cell fate determination both in mouse and in human. Successful completion of these studies may provide novel insights into female infertility and uterine cancer as a result of signaling imbalance between RA and estrogen, which could have a long-lasting impact in multiple research fields including development, fertility and cancer research.

NINDS - National Institute of Neurological Disorders and Stroke

Project Summary Neural stem cells (NSCs) in the brain generate newborn neurons throughout life, providing an endogenous stem cell pool that can be harnessed to improve cognitive function during aging and neurodegenerative disease. Thus, understanding how adult neurogenesis is regulated may provide new targets and opportunities for therapeutic upregulation in these conditions. Intermediate filament (IF) proteins such as nestin and glial fibrillary acidic protein (GFAP) have been invaluable as markers for NSCs, increasing our understanding of the different cell states and cell types of the neurogenic niche. The IF protein vimentin is also expressed in NSCs, but due to variability in antibody quality and the lack of reporter mouse lines, very little is known about when and where it is expressed in the neurogenesis cascade. Recently, my lab has demonstrated many unique aspects of vimentin’s function and regulation in adult hippocampal NSCs in vitro. We found that vimentin mRNA is stabilized during quiescence, yet translationally repressed through an RNA-binding protein interaction with vimentin mRNA’s 3’UTR. As qNSCs activate, repression is removed, resulting in a rapid increase in vimentin protein. Additionally, as qNSCs activate, they traffic accumulated proteins that need to be degraded to the centrosome to form an aggresome. Vimentin collapses around the aggresome, forming a vimentin cage, bringing with it interacting proteins such as proteasomes. During cell division, the aggresome, vimentin cage, and associated proteins are asymmetrically segregated into one daughter cell. The daughter which inherits these cargoes has a decreased proliferation rate, whereas the non-inheriting daughter has a normal proliferation rate, resulting in a rejuvenative asymmetry between daughter cells. Vimentin is also required for efficient quiescence exit both in vitro and in vivo, further suggesting that vimentin’s role in NSCs is not only as a potential marker, but also as a key component to intrinsic mechanisms of quiescence exit. However, most of these findings were largely performed in vitro, thus we do not know if this process is conserved in the adult brain, nor how this asymmetric inheritance would affect the outcome of daughter cells in the neurogenic niche itself. To address these open questions, we created a novel transgenic mouse with endogenous vimentin fused to linker-mScarlet. We will characterize vimentin-mScarlet expression at the mRNA and protein level in cells of the hippocampus, and through prospective sorting followed by cell behavior analyses, we will reveal when and where vimentin mRNA and protein are expressed in the hippocampus. Importantly, we will also perform chronic in vivo imaging in cranial windows in these mice to visualize vimentin-mScarlet protein during quiescence exit and its asymmetric segregation during divisions, following the consequence of this inheritance in vivo. These studies will not only provide an important novel tool to the scientific community, but also reveal new knowledge on NSC subpopulation dynamics, answering critical questions about how NSCs rejuvenate their niche.

NIDCR - National Institute of Dental and Craniofacial Research

PROJECT SUMMARY/ABSTRACT Dental enamel is formed by ameloblasts that are derived from dental epithelium. How dental epithelial stem cells (DESCs) commit to ameloblast lineage remains elusive. A potential critical factor that drives the commitment of DESCs to the ameloblast lineage is retinoic acid (RA). The complex system that drives ameloblast lineage commitment and the abundance of molecules that determine the RA signaling system require us to examine the transcriptomics of developing teeth at single-cell and spatial levels, followed by biological validations. Our preliminary data showed the diversifications of DESCs and the continuous differentiation of ameloblasts in a mouse incisor scRNAseq dataset. We sorted the differentiating ameloblasts into novel clusters in both mouse and human incisor scRNAseq datasets and replicated these findings using RNAscope. Our findings also suggest that RA signaling is inhibited in pre-secretory stage ameloblasts but activated when ameloblasts transition into the secretory stage. We identified potential RA response elements (RARE) in genes that are critical for secretory stage enamel formation. Therefore, we hypothesize that the sequential ameloblast differentiation is specified by critical genes through the retinoic acid (RA) signaling. By integrating scRNA-seq data analyses with molecular validations in developing teeth, we can 1) elucidate the differentiation trajectory of ameloblasts and 2) reveal critical roles of RA signaling in ameloblast differentiation. Aim 1. Determine the ameloblast differentiation trajectory. We will integrate the scRNAseq data obtained from 14 studies in different tooth types from mice, rats, and humans. We will conduct cluster analysis within tooth types and species to identify each phase of the continuous differentiation paths predicted by trajectory inference. We will compare the ameloblast differentiation trajectory across tooth types and species, with an emphasis on molecules relevant to RA degradation and signaling activation. To validate the trajectory defined by bioinformatic analyses, we will perform RNAscope HiPlex assay on mouse developing teeth using identified genes. Aim 2. Determine the critical roles of RA signaling at the onset of secretory stage enamel formation. First, we will conduct spatial transcriptomics and consequent bioinformatic analyses to map spatial distributions of molecules involved in RA synthesis, signaling activation, and metabolism, together with potential target genes of the RA signaling, in mouse enamel organ epithelium and adjacent dental mesenchyme. Second, we will perform the CUT&Tag sequencing to identify RAREs in RA signaling targets across the genome in mouse secretory ameloblasts. We will validate these findings by analyzing spatial transcriptomic and existing scRNAseq data. The completion of this project will allow us to identify critical factors in ameloblast differentiation. These insights will shed light on the mechanisms of tooth morphogenesis and congenital tooth disorders. This project will provide essential information to the development of bioengineering strategies for tooth regeneration.