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NIDCR - National Institute of Dental and Craniofacial Research

Project Summary There are no viable long-term treatments for salivary gland (SG) dysfunction and degeneration as a result of disease or chronic injury, driving a need for new, translatable solutions. SG dysfunction severely compromises the oral health and quality of life of patients: saliva protects the oral mucosa, facilitates articulation and food digestion, and aids in the remineralization of dental hard tissues. Therapeutic ionizing radiation (IR) for head and neck cancer where SGs are inadvertently irradiated along with the tumor (~50,000 cases/year) is a prime source of dry mouth (xerostomia). To develop treatment strategies for this detrimental injury, it is essential to understand the mechanisms that control the generation and regeneration of the SG. Generation of SG from stem cells transplanted into the tissue (now in clinical trials) offers great benefit for patients with severe loss of glandular tissue and has often utilized developmental strategies. However, the ability to produce the specific cell lineages necessary for long-term function remains poorly understood. Although we and others have made great inroads into regenerating the existing salivary tissue after IR induced damage, an outcome we have achieved through the application of synthetic muscarinic agonist (cevimeline), much more is needed to restore the tissue to a healthy state. For this purpose, we propose to focus on a genome organizer protein, SATB1, that acts to establish three-dimensional chromatin architecture, recruiting transcription and epigenetic factors to specific gene loci, and regulate cell type-specific expression of a large cohort of genes. Our preliminary studies show critical roles of SATB1 in the establishment of acinar cells and cellular architecture during postnatal maturation of submandibular glands (SMGs), highlighting it as a potential regulator of lineage specification. Our preliminary data also support a role for SATB1 in DNA repair and induction of Satb1 expression post-IR. Based on these results taken together, we hypothesize that SATB1 plays a fundamental role in generating and regenerating SMG epithelial cell lineages after injury. We will address our central hypothesis via two specific aims: Aim 1, Determine how SATB1 regulates chromatin architecture and gene expression during SG postnatal development, and Aim 2, Investigate SATB1’s role in SG maturation and regeneration after injury. These aims will be achieved using a combination of developmental and regenerative mouse models in conjunction with transcriptomic, epigenetic, biochemical, and high-resolution imaging techniques. We envisage our findings will greatly contribute to our understanding of the critical factors promoting the generation/regeneration of SG that can then be targeted for development of effective long-term therapies.

NIAID - National Institute of Allergy and Infectious Diseases

Project Summary Tuberculosis (TB) remains a leading cause of mortality worldwide, with lung damage being a key driver of disease severity and poor outcomes. Alveolar epithelial cells are critical for maintaining lung homeostasis and promoting repair, processes that are tightly regulated by Wnt/β-catenin signaling. Our preliminary data indicate that Mycobacterium tuberculosis (Mtb)-induced inflammation disrupts alveolar epithelial integrity in TB-susceptible mice, leading to impaired surfactant production and defective lung regeneration. Strikingly, this is associated with a significant reduction in β-catenin levels. Notably, inhibition of type I interferon (IFN-I) signaling restores β-catenin expression, suggesting a previously unrecognized role of IFN-I in suppressing Wnt/β-catenin activity and alveolar repair. We aim to investigate how chronic IFN-I signaling impairs Wnt/β-catenin function, leading to defective epithelial repair and exacerbated lung pathology in TB. Specifically, in aim1, we will define the role of Wnt/β-catenin in alveolar epithelial repair following Mtb infection. We will assess how Wnt/β-catenin activation or inhibition influences alveolar type 2 (AT2) cell proliferation, differentiation, and stemness using murine and human primary alveolar cells. Additionally, we will evaluate lung histopathology, epithelial marker expression, and AT2 cell differentiation in TB-resistant and susceptible mice. In aim2, we will determine how IFN-I signaling suppresses Wnt/β-catenin activity during TB-induced lung damage. Using genetic and pharmacological approaches, we will investigate the molecular mechanisms by which IFN-I signaling modulates Wnt/β-catenin function and identify key mediators of IFN-I–Wnt/β-catenin crosstalk as potential therapeutic targets. Finally, in the aim3 we will evaluate the therapeutic potential of targeting Wnt/β-catenin and IFN-I pathways to enhance alveolar repair. We will test Wnt/β-catenin activators, such as GSK3β and Porcupine inhibitors, as well as IFN-I blockade using anti-IFNAR antibodies in murine TB models. Therapeutic efficacy will be assessed through histopathological analysis, epithelial barrier integrity, inflammatory responses, and bacterial burden. This study will provide novel insights into the interplay between IFN-I signaling and Wnt/β-catenin in TB pathogenesis, uncovering mechanisms that impair alveolar repair. By identifying host-directed therapeutic strategies, we aim to enhance lung recovery and improve outcomes for TB patients.

NCI - National Cancer Institute

The interaction between cancer cells and platelets plays important roles in regulating cancer cell function. Understanding how platelets communicate with cancer cells to modulate cancer cell colonization at distant organs may identify novel strategies to halt cancer spreading. We recently showed that recruitment of platelet to cancer cells is essential for the colonization of circulating tumor cells (CTCs) at the secondary organs. However, the molecular mechanism by which platelets modulate cancer cell function to promote cancer cell colonization remains to be determined. By analyzing RNA-seq data from CTCs and primary tumors, we found that platelet- specific mRNA was significantly enriched in CTCs. RNAscope and Translating Ribosome Affinity Purification (TRAP) analyses showed the delivery of platelet mRNA and translation of platelet-derived mRNA in cancer cells. In vivo functional screening identified multiple platelet-derived mRNAs contribute to colonization of breast cancer cell at distant organs. These results reveal the new role of platelet mRNA in mediating intercellular communication and in promoting cancer cell spreading. The overall objective of this proposal is to define the molecular mechanism by which platelet mRNA is delivered into breast cancer cells and determine roles of platelet mRNA as the signaling molecular in promoting cancer cell colonization at distant organs. We showed that CD9 expression in CTCs correlated with the accumulation of platelet-specific mRNA. Silencing CD9 in breast cancer cells significantly reduced platelet mRNA transferring and colonization of cancer cells. Platelet factor 4 (PF4) is a small cytokine belonging to the CXC chemokine family that is highly expressed in platelets. We showed that the transfer of PF4 mRNA from platelets to breast cancer cells enhanced stemness and colonization of cancer cells. Based on these results, the central hypothesis of this proposal is that the CD9-dependent mRNA transfer mediates the platelet-cancer cell communication and promotes cancer cell stemness. We propose the following two aims to test this hypothesis and achieve our objective. Aim 1. Elucidate the mechanism by which platelet mRNA is transferred into cancer cells. Aim 2. Determine how the transfer of platelet PF4 mRNA in cancer cells promotes cancer metastasis.

SAE Foundation

Supports STEM education programs in automotive, aerospace, and mobility engineering for K-12 students and educators.

Samsung Foundation

Funds STEM education, disability support, and youth development across Asia and globally.

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

PROJECT SUMMARY This grant application seeks funding for the 2026 Santa Cruz Developmental Biology Meeting, which will be held on the campus of University of California at Santa Cruz from August 24-28, 2026. This meeting is a biennial, grass-roots meeting organized by and for the scientific community working at the cutting edge of developmental biology. The Santa Cruz meeting, which has run continuously since 1992, occupies a unique niche by combining international reputation with a relatively small size (~150 attendees) and a wholly new line-up of invited speakers at each gathering. As detailed in our application, we have planned for considerable participation by graduate students and postdocs by including short talks, posters, two work- shops aimed at career issues, and a career-perspective talk from a prominent scientist whose storied career pathway epitomizes the multi-disciplinary nature of developmental biology. The meeting format is based around single-platform sessions and three non-overlapping poster sessions so that all participants are engaged with the same topic and activity for the entirety of the meeting. The 2026 SCDB meeting will occur from August 24-28 and is organized around the theme: “Biomedicine, Biomechanics, and the Biosphere.” Our central goal is to highlight the deep reach of developmental biology across distinct realms of science. To this end, we have invited a set of speakers who all explore developmental principles but are driven by distinct ends and thus apply distinct approaches to a wide range of organisms. As a group, these scientists use a wise repertoire of state-of-the-art approaches to probe critical aspects of development across a broad range of model organisms and organoid systems. The work discussed at this meeting will positively impact human health by generating knowledge that is critical to our understanding of congenital diseases and to the development of tissue engineering strategies and stem cell- based therapies, as well as bioengineering approaches to food production and famine prevention. A second major goal will be to provide a forum for a broad range of undergraduates, graduate students, and postdoctoral fellows to engage with and present their work to leaders in the field through talks, poster sessions, and informal discussions fostered by an isolated and relaxed campus setting.

NIAMS - National Institute of Arthritis and Musculoskeletal and Skin Diseases

PROJECT SUMMARY. Pediatric cancer affects thousands of children each year, and while advancements in treatment have markedly improved survival rates, the adverse effects of chemotherapy on skeletal muscle growth and function remain a significant and understudied clinical concern. The standard chemotherapy regimen used to treat many types of pediatric cancers, such as leukemia, lymphoma, and brain cancers, consists of cyclophosphamide, doxorubicin hydrochloride (hydroxydaunorubicin), vincristine sulfate (Oncovin), and prednisone (CHOP). Although this regimen is effective at killing cancer cells, CHOP leads to blunted muscle growth and compromised motor development, in addition to impairing muscle stem cell (i.e., satellite cell) function. Given the essential role of satellite cells in muscle growth during early development, interventions aimed at preserving their activity may mitigate these harmful effects. The proposed research hypothesizes that pharmacologic activation of satellite cells will prevent CHOP-induced defects on muscle growth and development in pediatric mice. Specific Aim 1 will assess whether enhancing satellite cell proliferation using a small molecule (CEP-701) or transient overexpression of MYC specifically in satellite cells (Pax7-MYC) can protect muscle growth and development during CHOP treatment. This aim will be completed using a myonuclear labeling model, microCT assessment of body composition, skeletal muscle histology and single muscle fiber quantification of myonuclei, and single nuclear and cell RNA sequencing. Specific Aim 2 will define the impact of CHOP on myonuclear gene transcription and chromatin accessibility in newly fused satellite cells through the use our myonuclear-labeling (HSA-GFP) mouse model, in addition to spatial and single cell RNA sequencing. This approach will allow us to identify and quantify resident and newly fused (satellite cell-derived) myonuclei to determine if the CHOP-mediated alterations in the satellite cell transcriptome is carried over to the muscle fiber upon satellite cell fusion. Specific Aim 3 quantifies the longitudinal impact of CHOP on skeletal muscle mass, physical function, glucose metabolism and insulin sensitivity, and rate of age-mediated muscle atrophy. Upon successful completion of Aim 3, we will have a more complete picture regarding the impact of pediatric chemotherapy on skeletal muscle homeostasis and aging. The project’s innovative approach will provide the first in vivo assessment of satellite cell-targeted therapies for chemotherapy-induced muscle damage in pediatric models and will demonstrate the enduring consequences of childhood chemotherapy on muscle development through the fusion of defective satellite cells. This study will have a significant impact by informing therapeutic strategies to preserve musculoskeletal health in childhood cancer survivors and by identifying new molecular targets to prevent or reverse long-term muscle dysfunction.

U.S. National Science Foundation

Through this solicitation, NSF seeks to foster a network of S-STEM stakeholders and further develop the infrastructure needed to generate and disseminate new knowledge, successful practices and effective design principles arising from NSF S-STEM projects nationwide. The ultimate vision of the legislation governing the S-STEM parent program[1] (and of the current S-STEM-Net solicitation) is that all Americans, regardless of economic status, should be able to contribute to the American innovation economy if they so desire. To support collaboration within the S-STEM network, NSF will fund several S-STEM Research Hubs (S-STEM-Hub). The S-STEM Network(S-STEM-Net) will collaborate to create synergies and sustain a robust national ecosystem consisting of multi-sector partners supporting domestic low-income STEM students in achieving their career goals, while also ensuring access, inclusion, and adaptability to changing learning needs. The Hubs will investigate evolving barriers to the success of this student population. It will also disseminate the context and circumstances by which interventions and practices that support graduation of domestic low-income students (both undergraduate and graduate) pursuing careers in STEM are successful. The target audience for this dissemination effort is the community of higher education institutions, faculty, scholars, researchers and evaluators, local and regional organizations, industry, and other nonprofit, federal, state, and local agencies concerned with the success of domestic low-income STEM students in the United States. [1] https://www.nsf.gov/pubs/2022/nsf22527/nsf22527.htm

U.S. National Science Foundation

The Science, Technology, and Society (STS) program supports research that uses historical, philosophical, and social scientific methods to investigate the intellectual, material, and social facets of the scientific, technological, engineering and mathematical (STEM) disciplines. It encompasses a broad spectrum of STS topics including interdisciplinary studies of ethics, equity, governance, and policy issues that are closely related to STEM disciplines, including medical science. The program s review process is approximately six months. It includes appraisal of proposals by ad hoc reviewers selected for their expertise and by an advisory panel that meets twice a year. The deadlines for the submission of proposals are February 2nd for proposals to be funded as early as July, and August 3rd for proposals to be funded in or after January. There is one exception: Doctoral Dissertation Improvement Grant proposals will have only one deadline per year, August 3rd. The Program encourages potential investigators with questions as to whether their proposal fits the goals of the program to contact one of the program officers.

Office of Naval Research

The ONR seeks proposals for developing innovative solutions that directly support the development and maintenance of a robust STEM workforce. The goal of any proposed effort should be to provide "game changing" solutions that will establish and maintain a diverse pipeline of U.S. citizens who are interested in uniformed or civilian DoN (or Navy and Marine Corps) STEM related workforce opportunities. While this announcement is relevant for any stage of the STEM pipeline, for FY15, funding efforts will be targeted primarily towards High School, Post-Secondary education, and outreach designed to enhance the DoN (or Naval) STEM workforce and its mission readiness. Emphasis will be given both to key engineering and scientific areas outlined in the Naval S&T Strategic Plan such as our National Naval Responsibilities (see ONR website), and to identified STEM related workforce gaps and new strategic goals on the uniformed and civilian side. The FULL ANNOUNCEMENT is available on the Grants.gov website.

U.S. National Science Foundation

The Directorate for STEM Education (EDU) STEM Education Postdoctoral Research Fellowships (STEM Ed PRF) Program funds postdoctoral fellowship projects designed to enhance the research knowledge, skills, and practices of STEM Education research by recent doctoral graduates in STEM, STEM Education, Education, and related disciplines. This solicitation supports individual postdoctoral fellowship awards; a companion solicitation (STEM Ed OPRF) supports organizational postdoctoral fellowship programs. The STEM Ed PRF Program as a whole seeks to broaden the pool of researchers who can advance knowledge regarding STEM learning and learning environments, broadening participation in STEM fields, and STEM workforce development. The Program is designed tosupport postdoctoral fellows engaged in experiences that will advance their career goals by developing their expertise, skills, and competencies to conduct fundamental STEM education research. Principal Investigators who are women, veterans, persons with disabilities, and from groups underrepresented in STEM, or who have attended community colleges and minority-serving institutions (e.g., Historically Black Colleges and Universities, Tribal Colleges and Universities, Hispanic Serving Institutions, Alaska Native Serving Institutions, and Hawaiian Native and Pacific Islander Serving Institutions) are especially encouraged to apply. STEM Ed IPRF awards provide direct support to Fellows to enable them to engage in ongoing research, to develop independent research, and to implement an independent professional development plan under the guidance of a sponsoring researcher. Fellows must affiliate with an appropriate host organization and are expected to devote themselves full time to the fellowship activities for the duration of the fellowship.

U.S. National Science Foundation

The Directorate for STEM Education (EDU) STEM Education Postdoctoral Research Fellowships (STEM Ed PRF) Program funds postdoctoral fellowship projects designed to enhance the research knowledge, skills, and practices of STEM Education research by recent doctoral graduates in STEM, STEM Education, Education, and related disciplines. This solicitation supports organizational postdoctoral fellowship projects; a companion solicitation (STEM Ed IPRF) supports individual postdoctoral fellowship awards. The Program is designed to broaden the pool of researchers who can advance knowledge regarding STEM learning and learning environments, broadening participation in STEM fields, and STEM workforce development. Principal Investigators who are women, veterans, persons with disabilities, and from groups underrepresented in STEM, or who have attended community colleges and minority-serving institutions (e.g. Historically Black Colleges and Universities, Tribal Colleges and Universities, Hispanic Serving Institutions, Alaska Native Serving Institutions, and Hawaiian Native and Pacific Islander Serving Institutions) are especially encouraged to apply. STEM Ed OPRF awards provide support to organizations as they develop a STEM education postdoctoral research fellowship project and support a cohort of fellows. The program should enable fellows to engage in ongoing research, to develop independent research, and to implement an independent professional development plan under the guidance of a sponsoring researcher. Fellows are expected to devote themselves full time to the fellowship activities for the duration of the fellowship.

U.S. National Science Foundation

The Science, Technology, Engineering, and Mathematics Talent Expansion Program (STEP) seeks to increase the number of students (U.S. citizens or permanent residents) receiving associate or baccalaureate degrees in established or emerging fields within science, technology, engineering, and mathematics (STEM). Type 1 proposals are solicited that provide for full implementation efforts at academic institutions. Type 2 proposals are solicited that support educational research projects on associate or baccalaureate degree attainment in STEM.

NCI - National Cancer Institute

PROJECT SUMMARY Malignant brain tumors such as glioblastomas are among the most lethal cancers. The five-year survival estimates for glioblastoma are a dismal 4 to 5%, additional treatment options are thus urgently needed. In our studies on how proliferation and differentiation are regulated during normal brain development, we identified a protein-protein interaction network comprising EphrinB, RGS3, KIF20A and SEPT7, which sequentially binds to one another (referred to as the ERKS axis). Genetic functional results demonstrated that the ERKS axis proteins are essential for maintaining a proliferative state of normal neural progenitor cells and loss-of-function of the axis leads to differentiation. Because tumors often originated from progenitor/stem cells that lost the control on proliferation vs. differentiation decisions, we reasoned that the ERKS axis may act similarly in brain tumor progenitor/stem cells to control proliferation. In proof-of-concept studies, we depleted the mitotic kinesin KIF20A in cancerous progenitor/stem cells in animal models of brain tumors. Depletion promoted daughter cells to undergo a differentiative path, which blocked cell proliferation leading to suppression of brain tumor growth. In addition, disruption of protein-protein interaction (PPI) within the ERKS axis by competitive inhibition with protein binding domains could block the growth of brain tumor stem cells. These results thus indicate that the ERKS axis proteins can serve as targets for developing novel differentiation therapy for brain tumor treatment. In this study, we propose to develop inhibitors targeting specific interactions within the ERKS axis. We will employ a PPI- based high throughput screening (HTS) assay to isolate small molecule inhibitors from compound libraries and further validate candidate hits using additional secondary and tertiary cell free and cell-based protein binding assays as well as cellular functional assays. We anticipate that the proposed studies will identify and validate candidate hit inhibitors of the ERKS axis, providing a foundation for further developing the lead molecules into potential therapeutics for clinic use in brain tumor treatment.

NCI - National Cancer Institute

Title: Second-generation new-chemical-entity nanomedicine to target treatment resistance in pancreatic cancer Project Summary Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers, with treatment resistance posing a major challenge to effective clinical management. Cells that survive therapy—such as pancreatic cancer stem- like cells (PCSCs) and drug-tolerant persister (DTP) cells—play a critical role in driving drug resistance, tumor recurrence, and metastasis. Notably, both cell populations depend heavily on elevated autophagy, a self- digestion process that enables survival under stress. Therefore, targeting autophagy pathways holds significant promise for improving treatment outcomes in PDAC. Autophagy inhibition with aminoquinoline drugs, such as chloroquine (CQ) or hydroxychloroquine (HCQ), have limited potency for autophagy inhibition, and the concentrations of CQ/HCQ required to inhibit autophagy are not consistently achievable in the clinic. The overall goal of this application is to develop a second-generation new-chemical-entity nanomedicine as an effective autophagy inhibitor to improve the treatment of PDAC in preclinical animal models, providing validation regarding the feasibility for clinical translation. Recently, we have developed an Autophagy inhibitor Self-delivered Nanodrug (AiSN) that offers superior potency for autophagy inhibition and specific drug delivery to improve PDAC treatment to HCQ. AiSN is a self-therapeutic nanoparticle that contains pure bisaminoquinoline (BAQ) derivative as the building block which has outstanding autophagy inhibiting- and lysosomal disrupting- capabilities. AiSN (BAQ13 nanoparticle, BAQ13 NP) is 20-30 times more effective than HCQ in a panel of PDAC cell lines. It preferentially accumulated at PDAC tumor sites with dense fibrotic stromal tissue. It was efficacious in various PDAC models and prevented cancer stem-like cell mediated tumorigenesis in mice. The FDA has recently approved our Investigation New Drug (IND) application (IND#165331) for moving the AiSN (BAQ13 NP) into clinical trials. The FDA has also granted Orphan Drug Designation for BAQ13 for the treatment of pancreatic cancer. Using BAQ13 as the lead compound, we have recently designed and synthesized 30 new compounds as the second-generation AiSNs, among which BAQ42 and BAQ152 have shown better potency than BAQ13, improving the IC50 value from micromolar to nanomolar levels. Furthermore, our study demonstrated that autophagy is significantly upregulated in DTP cells of PDAC. Although DTP cells exhibit resistance to gemcitabine, they can be effectively eliminated by BAQ42. These results have laid a strong foundation for this R01 application, where we plan to: 1) optimize the structure and formulation of second-generation AiSNs to enhance their anti-PDAC potency and nanoparticle-forming properties; 2) characterize their pharmacokinetics and spatiotemporal distribution; and 3) validate their pharmacology and toxicology in various PDAC models. Successful completion of this research will make this new generation AiSN ready for IND-enabling studies seeking IND approval. The novel design of AiSNs, with significantly improved potency and targeted delivery capabilities, is expected to greatly enhance efficacy while minimizing toxicity in PDAC treatment.

U.S. National Science Foundation

Our world is at a pivotal moment where the boundaries dividing the physical and social worlds from the cyber world have become blurred. Cyberspace has evolved from an interconnected digital environment into a complex and interdependent cyber ecosystem that involves hardware, software, networks, data, people, organizations, countries, and the physical world. Critical functions of everyday life are deeply intertwined with computing, including health, government, commerce, the public sphere, education, critical infrastructure, interpersonal communication, and transportation. The complexity and inter-dependencies in cyberspace can be misused and exploited by malicious actors. These in turn can trigger adverse outcomes such as disruption of critical infrastructure and systems; theft of intellectual property and sensitive data; amplification of inequalities; disclosure of private information of individuals, organizations, and governments; and threats to lives, livelihoods, and reputations. Furthermore, constant attacks on the data and assets of corporations, governments, and individuals undermine people s trust in decision-making and processes that depend critically on these cyber systems. The Security, Privacy, and Trust in Cyberspace (SaTC 2.0) program aims to build trust in global cyber ecosystems. Trust is the core tenet of this program and, for the purposes of this solicitation, is broadly defined to include our confidence in the security, privacy, and resilience of cyberspace, particularly in the face of malicious intent. Achieving this level of confidence in cyberspace requires not only understanding the vulnerabilities in a system that could be exploited and how they can be addressed, but also understanding the social and technical dimensions of trust in cyber systems, along with the educational efforts needed to increase public awareness of risks in cyberspace, and building a well-trained corps of privacy and security professionals. SaTC 2.0 spans the interests of NSF's Directorates for Computer and Information Science and Engineering (CISE), Mathematical and Physical Sciences (MPS), Social, Behavioral and Economic Sciences (SBE), and STEM Education (EDU). Proposals must be submitted pursuant to one of the following designations, each of which may have additional requirements: RES: The Research (RES) designation is the focus of the multidisciplinary SaTC 2.0 research program. RES projects are limited to $1,200,000 in total budget, with durations of up to four years. Proposals with a total budget of more than $600,000 have additional requirements including Broadening Participation in Computing and collaboration plans. RES proposals may include an optional Transition to Education (TTE) plan with a budget up to $50,000 (within the RES total budget request) to co-evolve novel educational initiatives in the context of the proposed research. EDU: The Education (EDU) designation is used to identify proposals focusing on education and workforce training in building trust in security, privacy, and resilience of cyberspace. EDU proposals are limited to $500,000 in total budget, with durations of up to three years. EDU proposals that primarily focus on education research with demonstrated collaboration, as reflected in the PI team between cybersecurity subject matter experts and education researcher(s), may request an additional $100,000 beyond the $500,000 limit. SEED: The Seedling (SEED) category is intended for special topics defined by accompanying Dear Colleague Letters. SEED projects are limited to $300,000 in total budget, with durations of up to two years.

Advanced Research Projects Agency Energy

The purpose of this modification is to clarify the meaning of the Program Policy Factors in Section V.C. To obtain a copy of the Notice of Funding Opportunity (NOFO) please go to the ARPA-E website at https://arpa-e-foa.energy.gov. To apply to this NOFO, Applicants must register with and submit application materials through ARPA-E eXCHANGE (https://arpa-e-foa.energy.gov/Registration.aspx). For detailed guidance on using ARPA-E eXCHANGE, please refer to the ARPA-E eXCHANGE User Guide (https://arpa-e-foa.energy.gov/Manuals.aspx). ARPA-E will not review or consider concept papers submitted through other means. For problems with ARPA-E eXCHANGE, email ExchangeHelp@hq.doe.gov (with NOFO name and number in the subject line). Questions about this NOFO? Check the Frequently Asked Questions available at http://arpa-e.energy.gov/faq. For questions that have not already been answered, email ARPA-E-CO@hq.doe.gov. AGENCY OVERVIEW The Advanced Research Projects Agency Energy (ARPA-E), an organization within the Department of Energy (DOE), is chartered by Congress in the America COMPETES Act of 2007 (P.L. 110-69), as amended by the America COMPETES Reauthorization Act of 2010 (P.L. 111-358), as further amended by the Energy Act of 2020 (P.L. 116-260): (A) to enhance the economic and energy security of the United States through the development of energy technologies that (i) reduce imports of energy from foreign sources; (ii) reduce energy-related emissions, including greenhouse gases; (iii) improve the energy efficiency of all economic sectors; (iv) provide transformative solutions to improve the management, clean-up, and disposal of radioactive waste and spent nuclear fuel; and (v) improve the resilience, reliability, and security of infrastructure to produce, deliver, and store energy; and (B) to ensure that the United States maintains a technological lead in developing and deploying advanced energy technologies. ARPA-E issues this Notice of Funding Opportunity (NOFO) under its authorizing statute codified at 42 U.S.C. 16538. The NOFO and any cooperative agreements or grants made under this NOFO are subject to 2 C.F.R. Part 200 as supplemented by 2 C.F.R. Part 910. ARPA-E funds research on, and the development of, transformative science and technology solutions to address the energy and environmental missions of the Department. The agency focuses on technologies that can be meaningfully advanced with a modest investment over a defined period of time in order to catalyze the translation from scientific discovery to early-stage technology. For the latest news and information about ARPA-E, its programs and the research projects currently supported, see: http://arpa-e.energy.gov/. ARPA-E funds transformational research. Existing energy technologies generally progress on established learning curves where refinements to a technology and the economies of scale that accrue as manufacturing and distribution develop drive improvements to the cost/performance metric in a gradual fashion. This continual improvement of a technology is important to its increased commercial deployment and is appropriately the focus of the private sector or the applied technology offices within DOE. In contrast, ARPA-E supports transformative research that has the potential to create fundamentally new learning curves. ARPA-E technology projects typically start with cost/performance estimates well above the level of an incumbent technology. Given the high risk inherent in these projects, many will fail to progress, but some may succeed in generating a new learning curve with a projected cost/performance metric that is significantly better than that of the incumbent technology. ARPA-E will provide support at the highest funding level only for submissions with significant technology risk, aggressive timetables, and careful management and mitigation of the associated risks. ARPA-E funds technology with the potential to be disruptive in the marketplace. The mere creation of a new learning curve does not ensure market penetration. Rather, the ultimate value of a technology is determined by the marketplace, and impactful technologies ultimately become disruptive that is, they are widely adopted and displace existing technologies from the marketplace or create entirely new markets. ARPA-E understands that definitive proof of market disruption takes time, particularly for energy technologies. Therefore, ARPA-E funds the development of technologies that, if technically successful, have clear disruptive potential, e.g., by demonstrating capability for manufacturing at competitive cost and deployment at scale. ARPA-E funds applied research and development (R&D). The Office of Management and Budget defines applied research as an original investigation undertaken in order to acquire new knowledge directed primarily towards a specific practical aim or objective and defines experimental development as creative and systematic work, drawing on knowledge gained from research and practical experience, which is directed at producing new products or processes or improving existing products or processes. 0F1 Applicants interested in receiving financial assistance for basic research (defined by the Office of Management and Budget as experimental or theoretical work undertaken primarily to acquire new knowledge of the underlying foundations of phenomena and observable facts )1 should contact the DOE s Office of Science (http://science.energy.gov/). Office of Science national scientific user facilities (http://science.energy.gov/user-facilities/) are open to all researchers, including ARPA-E Applicants and awardees. These facilities provide advanced tools of modern science including accelerators, colliders, supercomputers, light sources and neutron sources, as well as facilities for studying the nanoworld, the environment, and the atmosphere. Projects focused on early-stage R&D for the improvement of technology along defined roadmaps may be more appropriate for support through the DOE applied energy offices including: the Office of Energy Efficiency and Renewable Energy (http://www.eere.energy.gov/), the Office of Fossil Energy and Carbon Management (https://www.energy.gov/fecm/office-fossil-energy-and-carbon-management), the Office of Nuclear Energy (http://www.energy.gov/ne/office-nuclear-energy), and the Office of Electricity (https://www.energy.gov/oe/office-electricity). ARPA-E encourages submissions stemming from ideas that still require proof-of-concept R&D efforts as well as those for which some proof-of-concept demonstration already exists. Submissions can propose a project with the end deliverable being an extremely creative, but partial solution. PROGRAM OVERVIEW The Seeding Critical Advances for Leading Energy technologies with Untapped Potential (SCALEUP) Ready program provides a vital mechanism for the support of innovative energy R&D that complements ARPA-E s primary focus on early-stage transformational energy technologies that require proof of concept. Technologies that achieve substantial technical advancement under ARPA-E support may still face significant technical and commercial challenges upon completion of an award's funding period, and thus are at risk of being stranded in their development path once ARPA-E funding ends. Experience across ARPA-E s diverse energy portfolios, and input from a wide range of investors and industry stakeholders, indicate that pre-commercial scaling projects are critical to establish practical performance and cost parameters. These pre-commercial scaling projects aim to 1) translate the performance achieved at bench scale to commercially scalable versions of the technology, 2) integrate the technology with broader systems, 3) provide extended performance data, and 4) validate the manufacturability and reliability of new energy technologies. Successful scaling projects should enable industry stakeholders to justify the substantial commitments of financial resources, personnel, manufacturing facilities, and materials necessary to subsequently deploy the technologies at a commercial scale. SCALEUP Ready seeks to scale the most promising technologies previously funded by ARPA-E. The possibility of ARPA-E-funded technologies becoming stranded along their development pathways leaves substantial intellectual property developed with American taxpayer dollars vulnerable to adoption by foreign competitors, who capture it for continued development and economic benefit overseas. This harms national competitiveness, as U.S. industries often fall behind on the development, scaling, and manufacturing of technologies necessary to compete in rapidly evolving global energy markets. Thus, projects selected for SCALEUP Ready will meet ARPA-E s statutory goals by accelerating transformational technological advances in areas that industry by itself is not likely to undertake because of technical and financial uncertainty."

Advanced Research Projects Agency Energy

<p>The purpose of this modification is to clarify the meaning of the Program Policy Factors in Section V.C.</p> <p><br></p> <p>To obtain a copy of the Notice of Funding Opportunity (NOFO) please go to the ARPA-E website at https://arpa-e-foa.energy.gov.&nbsp;To apply to this NOFO, Applicants must register with and submit application materials through ARPA-E eXCHANGE (<a href="https://arpa-e-foa.energy.gov/Registration.aspx" target="_blank">https://arpa-e-foa.energy.gov/Registration.aspx</a>).&nbsp;For detailed guidance on using ARPA-E eXCHANGE, please refer to the ARPA-E eXCHANGE User Guide (https://arpa-e-foa.energy.gov/Manuals.aspx).&nbsp;ARPA-E will not review or consider concept papers submitted through other means. For problems with ARPA-E eXCHANGE, email ExchangeHelp@hq.doe.gov (with NOFO name and number in the subject line).</p> <p>Questions about this NOFO? Check the Frequently Asked Questions available at <a href="http://arpa-e.energy.gov/faq" target="_blank">http://arpa-e.energy.gov/faq</a>.&nbsp;For questions that have not already been answered, email ARPA-E-CO@hq.doe.gov.&nbsp;&nbsp;</p> <p><br></p> <p>AGENCY OVERVIEW</p> <p>The Advanced Research Projects Agency – Energy (ARPA-E), an organization within the Department of Energy (DOE), is chartered by Congress in the America COMPETES Act of 2007 (P.L. 110-69), as amended by the America COMPETES Reauthorization Act of 2010 (P.L. 111-358), as further amended by the Energy Act of 2020 (P.L. 116-260):</p> <p>“(A) to enhance the economic and energy security of the United States through the development of energy technologies that—</p> <p>(i) reduce imports of energy from foreign sources;</p> <p>(ii) reduce energy-related emissions, including greenhouse gases;</p> <p>(iii) improve the energy efficiency of all economic sectors;</p> <p>(iv) provide transformative solutions to improve the management, clean-up, and disposal of radioactive waste and spent nuclear fuel; and</p> <p>(v) improve the resilience, reliability, and security of infrastructure to produce, deliver, and store energy; and</p> <p>(B) to ensure that the United States maintains a technological lead in developing and deploying advanced energy technologies.”</p> <p>ARPA-E issues this Notice of Funding Opportunity (NOFO) under its authorizing statute codified at 42 U.S.C. § 16538. The NOFO and any cooperative agreements or grants made under this NOFO are subject to 2 C.F.R. Part 200 as supplemented by 2 C.F.R. Part 910.</p> <p>ARPA-E funds research on, and the development of, transformative science and technology solutions to address the energy and environmental missions of the Department. The agency focuses on technologies that can be meaningfully advanced with a modest investment over a defined period of time in order to catalyze the translation from scientific discovery to early-stage technology. For the latest news and information about ARPA-E, its programs and the research projects currently supported, see: http://arpa-e.energy.gov/.</p> <p>ARPA-E funds transformational research. Existing energy technologies generally progress on established “learning curves” where refinements to a technology and the economies of scale that accrue as manufacturing and distribution develop drive improvements to the cost/performance metric in a gradual fashion. This continual improvement of a technology is important to its increased commercial deployment and is appropriately the focus of the private sector or the applied technology offices within DOE. In contrast, ARPA-E supports transformative research that has the potential to create fundamentally new learning curves. ARPA-E technology projects typically start with cost/performance estimates well above the level of an incumbent technology. Given the high risk inherent in these projects, many will fail to progress, but some may succeed in generating a new learning curve with a projected cost/performance metric that is significantly better than that of the incumbent technology. ARPA-E will provide support at the highest funding level only for submissions with significant technology risk, aggressive timetables, and careful management and mitigation of the associated risks.</p> <p>ARPA-E funds technology with the potential to be disruptive in the marketplace. The mere creation of a new learning curve does not ensure market penetration. Rather, the ultimate value of a technology is determined by the marketplace, and impactful technologies ultimately become disruptive – that is, they are widely adopted and displace existing technologies from the marketplace or create entirely new markets. ARPA-E understands that definitive proof of market disruption takes time, particularly for energy technologies. Therefore, ARPA-E funds the development of technologies that, if technically successful, have clear disruptive potential, e.g., by demonstrating capability for manufacturing at competitive cost and deployment at scale.</p> <p>ARPA-E funds applied research and development (R&amp;D). The Office of Management and Budget defines “applied research” as an “original investigation undertaken in order to acquire new knowledge…directed primarily towards a specific practical aim or objective” and defines “experimental development” as “creative and systematic work, drawing on knowledge gained from research and practical experience, which is directed at producing new products or processes or improving existing products or processes.”0F1 Applicants interested in receiving financial assistance for basic research (defined by the Office of Management and Budget as “experimental or theoretical work undertaken primarily to acquire new knowledge of the underlying foundations of phenomena and observable facts”)1 should contact the DOE’s Office of Science (http://science.energy.gov/). Office of Science national scientific user facilities (http://science.energy.gov/user-facilities/) are open to all researchers, including ARPA-E Applicants and awardees. These facilities provide advanced tools of modern science including accelerators, colliders, supercomputers, light sources and neutron sources, as well as facilities for studying the nanoworld, the environment, and the atmosphere. Projects focused on early-stage R&amp;D for the improvement of technology along defined roadmaps may be more appropriate for support through the DOE applied energy offices including: the Office of Energy Efficiency and Renewable Energy (http://www.eere.energy.gov/), the Office of Fossil Energy and Carbon Management (https://www.energy.gov/fecm/office-fossil-energy-and-carbon-management), the Office of Nuclear Energy (http://www.energy.gov/ne/office-nuclear-energy), and the Office of Electricity (https://www.energy.gov/oe/office-electricity).</p> <p>ARPA-E encourages submissions stemming from ideas that still require proof-of-concept R&amp;D efforts as well as those for which some proof-of-concept demonstration already exists. Submissions can propose a project with the end deliverable being an extremely creative, but partial solution.</p> <p>PROGRAM OVERVIEW</p> <p>The Seeding Critical Advances for Leading Energy technologies with Untapped Potential (SCALEUP) Ready program provides a vital mechanism for the support of innovative energy R&amp;D that complements ARPA-E’s primary focus on early-stage transformational energy technologies that require proof of concept.</p> <p>Technologies that achieve substantial technical advancement under ARPA-E support may still face significant technical and commercial challenges upon completion of an award's funding period, and thus are at risk of being stranded in their development path once ARPA-E funding ends. Experience across ARPA-E’s diverse energy portfolios, and input from a wide range of investors and industry stakeholders, indicate that pre-commercial scaling projects are critical to establish practical performance and cost parameters. These pre-commercial scaling projects aim to 1) translate the performance achieved at bench scale to commercially scalable versions of the technology, 2) integrate the technology with broader systems, 3) provide extended performance data, and 4) validate the manufacturability and reliability of new energy technologies. Successful scaling projects should enable industry stakeholders to justify the substantial commitments of financial resources, personnel, manufacturing facilities, and materials necessary to subsequently deploy the technologies at a commercial scale.</p> <p>SCALEUP Ready seeks to scale the most promising technologies previously funded by ARPA-E. The possibility of ARPA-E-funded technologies becoming stranded along their development pathways leaves substantial intellectual property developed with American taxpayer dollars vulnerable to adoption by foreign competitors, who capture it for continued development and economic benefit overseas. This harms national competitiveness, as U.S. industries often fall behind on the development, scaling, and manufacturing of technologies necessary to compete in rapidly evolving global energy markets. Thus, projects selected for SCALEUP Ready will meet ARPA-E’s statutory goals by “accelerating transformational technological advances in areas that industry by itself is not likely to undertake because of technical and financial uncertainty."</p>

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

Project Summary: The goals of this project are to determine how sex chromosome dosage (SCD) influences allelic gene regulation in the context of placental development and how SCD imbalance leads to impaired trophoblast differentiation and placental health and function. One fundamental difference between males and females is the sex chromosome content (46,XY and 46,XX), which causes imbalances in X/Y expression. While X chromosome inactivation (XCI) specifically silences one X chromosome in females to restore balanced expression, some genes escape XCI and thus have female-biased expression. In addition, Y-linked genes are only expressed in males. Prior to the onset of sex hormones, the effects of SCD on sex differences in autosomal gene expression and phenotypes are largely mediated by the dosage of sex-linked genes, especially X- and Y- paralogs. Notably, there is a marked effect of fetal sex on pregnancy outcomes. For example, carrying a male fetus is associated with increased risk of gestational diabetes and placental abruption, while carrying a female fetus is associated with increased risk of fetal growth restriction and preeclampsia. Allelic gene expression in males and females contributes to fetal sex differences. However, whether SCD contributes to allele-biased gene expression in placental development remains unknown. We previously showed that manipulation of X-linked gene dosage in mouse results in dysregulation of allelic gene expression. To determine the overall impact of differential SCD on allelic gene regulation and identify sex- linked candidate genes in human placental development as well as during trophoblast differentiation, we will use complementary ex vivo and in vitro approaches to leverage integrated multi-omics and functional studies. First, we will determine the effects of X- and Y-chromosome gene dosage on allelic gene regulation by single- nuclei and single cell assays performed in human 1st trimester placental tissue with varied sex chromosome content (Aim 1) and in trophoblast cell models derived from a unique collection of isogenic human induced pluripotent stem cells (hiPSCs) with different numbers of sex chromosomes (Aim 2). Second, we will investigate mechanisms controlling allelic gene expression by modulating the expression of sex-linked candidate X/Y paralogs and using allelic transcriptomic and epigenomic analyses to identify critical pathways (Aim 3). Third, functional assays will be carried out to evaluate phenotypic effects of differential SCD on trophoblast and trophoblast organoid function (Aims 2 and 3). Overall, this work will provide a comprehensive view of the effects of differential SCD on allele-specific gene regulation and on placental health and function. Results from this project will address a gap in our knowledge of the mechanisms underlying sex differences in allelic gene regulation at the fetal-maternal interface.

NHLBI - National Heart Lung and Blood Institute

ABSTRACT Hematopoietic stem cell transplantation (HSCT) is an important treatment for blood diseases and immune disorders. Donor-recipient compatibility, particularly sex matching, is one of the determining factors for HSCT success. Sex dimorphism in hematopoiesis and immunocompetence has been documented in both mice and humans. However, the sex variations in the bone marrow (BM) niche, their impact on hematopoiesis and HSCT, and the underlying mechanisms remain largely known. Our preliminary work showed that male mice have more mesenchymal stromal cells (MSCs) than females. Through sex-mismatched co-culture and transplantation experiments, we found that the male BM niche provides better support for colony formation in vitro and hematopoietic engraftment in vivo. Single-cell RNA sequencing identified the sex-specific changes in cell composition and molecular differences between male and female niche. Mechanistically, we found that a sex chromosome-linked histone demethylase gene, Kdm5c, contributes to the differential expression of Cxcl12 between male and female stromal cells. Moreover, sex- and MSC-specific reduction in Kdm5c expression increases the hematopoietic engraftment in HSCT. We hypothesize that sex dimorphism in the BM niche regulates hematopoietic engraftment in HSCT via sex-specific Kdm5c-Cxcl12 signaling. Aim 1 is to determine the cellular mechanisms by which Kdm5c regulates sex dimorphism in the BM niche. Aim 2 is to determine the molecular mechanisms by which Kdm5c-Cxcl12 signaling contributes to sex differences in the BM niche and hematopoietic engraftment. Aim3 is to determine the therapeutic value of BM niche sex dimorphism in HSCT. The findings advance our understanding of sex dimorphism in the BM niche and the underlying regulatory mechanism and provide the therapeutic implication for improving HSCT in the clinic.

NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases

PROJECT SUMMARY Islet transplantation is a promising treatment for insulin-dependent forms of diabetes, including type 1 diabetes and surgical diabetes induced by total pancreatectomy. In the U.S., total pancreatectomy with islet autotransplantation (TPIAT)—which is performed to relieve pain in patients with chronic pancreatitis-- has been the most prevalent form of islet transplant to date. At the same time, islet allotransplantation for type 1 diabetes is growing, and will continue to grow with the success of stem-cell derived islets and future approaches to reduce immunosuppression risks via technological advancements, genetic editing, or newer immunomodulation. Islet autotransplant is a useful research model to study adjunctive therapies for glycemic control and islet graft survival because it is free of the confounding factors of alloimmune rejection and recurrent type 1 diabetes. In TPIAT, about 70% of patients require exogenous insulin despite having some endogenous islet function, and attrition of islet function over time occurs in both auto and allografts. This attrition appears to be at least in part driven by metabolic stress on the transplanted beta cells. This pilot clinical trial, submitted in response to PAS-25-102, is designed to gather preliminary data on the efficacy and safety of SGLT2 inhibitor therapy (SGLT2i) in islet autotransplant recipients who have partial islet function. Our rationale for studying SGLT2i in this population is: (1) SGLT2i reduces blood glucose levels through increased glucosuria and do not directly stimulate islets (avoiding extra metabolic stress), nor does the benefit depend on presence of insulin resistance, which is often absent in islet transplant; (2) in both T1D and total pancreatectomy, there is evidence of reduced prandial glucose excursions with SGLT2i, which in turn may reduce metabolic beta-cell stress on transplanted islets in TPIAT; (3) SGLT2i are acceptable to patients as a once-daily oral medication. However, safety of these agents is unknown in TPIAT, and in theory they may increase risk for diabetic ketoacidosis in this population of patients who have partial insulin deficiency. We will enroll 30 patients with partial islet function >1 year after TPIAT, randomized to a standard care control arm (n=10) or one of 2 doses of empagliflozin (n=10 on 10 mg; n=10 on 25 mg) for 3 months, followed by a 3 month extension during which all patients will receive empagliflozin (25 mg daily). Specific Aim 1 will determine if empagliflozin improves glycemic control and reduces beta-cell specific endoplasmic reticulum stress after islet autotransplant. Specific Aim 2 will assess safety and feasibility of empagliflozin in islet autotransplant recipients. If results from this pilot study are promising, we will conduct a larger randomized blinded study. PI Bellin has led two multicenter TPIAT studies and has relationships with other centers to build a larger randomized trial. Importantly, we expect that results from this study will also inform the field of islet allotransplant for type 1 diabetes.

NCI - National Cancer Institute

SHP2 (PTPN11) has attracted much attention, because unlike most protein-tyrosine phosphatases (PTPs), it functions as a “positive” component of receptor tyrosine kinase (RTK) signaling. Germline mutations in PTPN11 are the most frequent cause of the “RASopathies” Noonan Syndrome (NS) and NS with multiple lentigines, somatic mutations contribute to benign and malignant neoplasms, and global SHP2 deficiency in mice leads to trophoblast stem cell (TSC) death/peri-implantation lethality. SHP2 has two N-terminal SH2 domains, a central catalytic (PTP) domain, and two C-terminal tyrosine phosphorylation (pY) sites and acts as an elegant molecular switch, residing in a closed, inactive form in the absence of pY-peptide ligands for its N-SH2 domain. Binding by such ligands, found in receptors and scaffolding adapters (e.g., GAB1, 2), activates SHP2. This mechanism was exploited to develop allosteric inhibitors (SHP2i) now in clinical trials. We know that SHP2 acts upstream of the RAS guanine nucleotide exchange factors SOS1/2 to promote RAS/ERK pathway activation, yet despite much progress, key knowledge gaps persist. How SHP2 signals to SOS1/2 is unclear, as are the precise roles of PTP activity and tyrosine phosphorylation in vitro and in mice. Our new Preliminary Data show that SHP2 is required for the assembly of large SOS1 clusters in response to RTK stimulation. Moreover, the PTP domain and Cterminal pY sites play distinct roles downstream of different RTKs, and neither all PTP-inactive nor tyrosine phosphorylation site mutants phenocopy the effects of global SHP2 deficiency. Most surprisingly, we recently found that PTP activity is dispensable for RAS activation. Instead, a specific conformation of the PTP domain, involving movement of a b-sheet is required. This conformation is mimicked by certain catalytic cysteine (Cyscat) mutants and induced by in vitro oxidation of Cyscat. We propose to (1) use super-resolution microscopy to determine how RTKs and SHP2 regulate SOS1 and GRB2/SOS1 clusters, correlate clusters with RAS activation, and define the involvement and requirement of other early components in RTK signaling, (2) determine whether SHP2 pYs all signal via GRB2, use redox probes/proteomics and SHP2 monobodies (Mb) to define the RTKinduced PTP domain oxidation state, test our “conformational switch” model for RAS activation via a structureinformed genetic approach, use SHP2C459D, which is full capable of RAS activation, and the signaling inactive mutant SHP2C459S in affinity purification/proximity MS proteomics to identify SHP2-interacting proteins critical for RAS activation/inactivation and validate them using reverse genetics, and test the effects of SHP2 sub-domain mutants/Mb on SOS1 and GRB2/SOS1 clusters, and (3) use Ptpn11 mutant knock-in mice to test the effects of SHP2 sub-domains on FGF-induced signaling, transcription, proliferation, differentiation, and survival of TSCs, test whether SHP2C459D mediates “adaptive resistance” to RAS/ERK pathway inhibitors, and ask if it causes “RASopathy” and/or myeloproliferative neoplasm/leukemia. Mice are essential to model these complex defects seen in humans with germline and somatic PTPN11 mutations and to develop new treatments.

NIDA - National Institute on Drug Abuse

Neurogenomic studies by the SCORCH (Single Cell Opioid Response in the Context of HIV) consortium strongly suggest that brains of individuals living with HIV in the context of opioid or (polys)substance use disorder (OUD/SUD) comorbidity harbor a molecular environment permissive for HIV viral replication and risk for cytotoxic damage. This conclusion also applied to donors who showed systemic, antiretroviral drug- mediated suppression of the virus. There was a stepwise progression of transcriptomic dysregulation in OUD+HIV+ brain, culminating in widespread neuronal pathology and pronounced inflammatory signatures in microglia from individuals with poor viral suppression. The goals of the current project are two-fold. First, we aim for single molecule validation of SCORCH single cell results, by analyzing~12-20kb single molecule fiber- seq libraries from cingulate cortex of SCORCH brains carefully annotated for OUD/SUD and systemic (HIV) suppression status. We will embark on single fiber-level multiomic profiling with differential analyses to uncover effects of HIV infection on nucleosome phasing, positioning and offset at transcription start sites, together with endogenous m5CpG methylation and transcription factor footprints. Integrating single cell (RNA+ATAC-seq) data already generated from the same set of SCORCH brain cohort, with our new single molecule multiomic fiber-seq mappings is expected to provide unprecedented neurogenomic insights into the HIV and substance-exposed brain. Second, we aim for additional functional validation of SCORCH data, by employing HIV-induced lineage tracing (HILT) in human induced pluripotent stem cell (hiPSC)-derived Neuron-Astrocyte-Microglia (hiPSC N-A-Mg) tricultures, in conjunction with CRISPRi for multiplexed microglial promoter repression focused on genes that are both (i) dysregulated in SCORCH SUD+ postmortem brain and (ii) implicated in HIV expression or replication. We will assess viral integration frequency, numbers and proportions of infected microglia, and compare transcriptomes and chromatin of infected/integrated HIV+ microglia with those from exposed bystander cells. This project is a first step to validate SCORCH genomic discoveries on the single molecule level, followed by the design of novel therapeutic tools targeting opioid/substance-dysregulated genes that could foster HIV infection and spread in the brain.

OD - NIH Office of the Director

Down syndrome is the most common genetic disorder that is primarily caused by an additional copy of human chromosome 21, trisomy 21 (T21). DS occurs in 16 per 10,000 live births, and is characterized by distinct facial appearance, intellectual disability, and developmental delays. A spectrum of co-occurring conditions are present in subjects with DS, with about half born with congenital heart defects (CHDs). Common CHDs in DS include atrial septal defects, ventricular septal defects, and atrioventricular septal defects. Genetically engineered mouse models including Dp1Tyb (triplication of MMU16) and TcMAC21 (transchromosomic Hsa21) mouse lines have been created to recapitulate CHDs in DS, with high penetrance of cardiac structural defects in septum and valve abnormalities. In parallel, DS patient-specific induced pluripotent stem cells (iPSCs) are versatile in vitro models with complete genetic content of T21 of affected patients. Human iPSC-derived compartment-specific cardioids including atrioventricular canal (AVC)-like cardioids may precisely mimic cell lineage architecture of the human heart and recapitulate septal defects in DS. While progress has been towards understanding clinical features of CHD in DS, underlying mechanisms by which T21 contributes to early cardiac cell lineage differentiation and septal defects are still not fully revealed. In response to this FOA PAR-22-247, we aim to establish a single-cell and spatial atlas of T21 hearts using both DS mouse model and patient-specific iPSCs to understand how T21 disrupts cardiac cell lineage differentiation. By leveraging in vivo Dp1Tyb/TcMAC21 mouse models and in vitro patient-specific iPSCs as well as cutting-edge single-cell and spatial transcriptomics, the overarching goal of this R24 project is to elucidate cellular and tissue mechanisms of septal defects in DS by deep phenotyping of DS iPSC-derived AVC-like cardioids and T21 mouse embryonic hearts at single-cell and spatial resolution. In Aim 1, we will determine in vitro mechanisms by which T21 leads to abnormal cardiac cell lineage differentiation and septal defects by single-cell and spatial transcriptomic analysis of DS iPSC-derived AVC-like cardioids. In Aim 2, we will interrogate in vivo etiologies of abnormal early cardiac cell development and septal formation in DS by single-cell and spatial transcriptomic analysis of mouse T21 hearts. In Aim 3, we will construct and disseminate single-cell and spatial atlas of human and mouse T21 hearts for open access through the INCLUDE Experimental Models of Down Syndrome (EMODS) portal. This R24 project will create a single-cell and spatial atlas of human and mouse T21 hearts that will be valuable resource for understanding how T21 leads to CHDs in DS using both mouse model and human iPSC-derived cardioids.