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NIA - National Institute on Aging

Summary TDP-43 pathology occurs in the majority of individuals with high Alzheimer's disease neuropathologic change (ADNC). This accumulation of cytoplasmic hyperphosphorylated aggregates of TDP-43 (pTDP-43) in neurons has been termed limbic predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC). LATE-NC occurs in similar brain regions that are affected by ADNC, however the underlying mechanisms of polyproteinopathies in the context of AD, including how they develop, if and how they interact, and the involvement of the diverse cell types of the CNS, are not well understood. We recently described a family with a pathogenic variant in the AD-associated gene SORL1 where several variant carriers underwent autopsy at the University of Washington Alzheimer's Disease Research Center. This variant, SORL1 R953C, segregated with high ADNC and a TDP-43 pathology that was characteristic for LATE- NC, but occurred in cases with much younger ages of onset. SORL1 has defined roles in endosomal trafficking and regulation of amyloid precursor protein (APP) processing, but how SORL1 in particular, and endosomal dysfunction in general, may contribute to polyproteinopathy in neurodegeneration remains to be explored. In this study we will use human induced pluripotent stem cell (hiPSC)-derived neural cells generated from SORL1 variant carriers and controls to investigate how dysfunction in endosomal trafficking and cellular stress may contribute to the accumulation, mis-localization, and phosphorylation of TDP-43. We will also test whether cells that harbor pathogenic SORL1 variants are more susceptible to modulation of TDP-43 expression. Because pathologic TDP-43 has been described in both neurons and glia, we will generate cortical neurons and astrocytes from hiPSCs for these experiments. We will perform a comprehensive characterization of endosomal pathology in post-mortem brain tissue from donors with ADNC+LATE-NC vs. ADNC or LATE-NC only. We will also analyze endosomal pathology from post-mortem samples of SORL1 variant carriers. For these studies we will use our newly established pipeline for high-resolution imaging of endosomal morphology in post-mortem tissue. Our goal in this exploratory R21 proposal is to test the hypothesis that endosomal dysfunction is a driver of TDP-43 co- pathology in AD and to develop a model of LATE-NC in a tractable, human in vitro system. Our studies will elucidate the molecular mechanisms of how dysfunction in SORL1 and endosomal pathways may lead to TDP- 43 pathology and provide a comprehensive analysis of endosomal pathology in brains of subjects with LATE-NC which, if successful, could open novel therapeutic avenues.

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

PROJECT SUMMARY Haploinsufficiency of chromatin remodeler CHD2 causes a neurodevelopmental disorder (NDD) characterized by developmental delay, intellectual disability, and epilepsy. Adjacent and upstream of CHD2 is a conserved long non-coding RNA (lncRNA) CHASERR. Deletion of CHASERR causes CHD2 overexpression and a more severe, early onset developmental disorder with significant motor and language delay, intellectual disability, and structural brain defects in humans. RNA-seq and western blot analysis of patient-specific induced pluripotent stem cells (iPSCs) and CRISPR-generated HAP1 cells have shown that CHASERR deletion increases CHD2 expression and protein levels in cis. While there is growing evidence of the role of lncRNAs in gene regulation, the mechanism of how CHASERR regulates CHD2, and the downstream consequences of too much CHD2 on global chromatin dynamics and neurodevelopment, is not well understood. Prior studies suggest that CHASERR is concentrated within its locus and binds to SPEN, a protein known to recruit HDAC3 and other chromatin remodeling proteins to repress transcription. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) in HAP1s showed loss of HDAC3 occupancy at CHD2 locus in CHASERR knockout (KO) but not wildtype (WT), suggesting that the CHASERR-SPEN complex is essential to recruit HDAC3 and repress CHD2 expression. Taken together, I hypothesize that CHASERR deletion results in loss of recruitment of SPEN and other repressive proteins at the CHD2 locus, leading to a more open chromatin state permissive of increased CHD2 expression, resulting in CHD2 overproduction and global changes in chromatin dynamics. Using CRISPR-generated CHASERR KO and antisense oligonucleotide (ASO) to knockdown CHASERR in WT HAP1 cells, as well as patient-specific iPSCs and neural progenitor cells (NPCs), I will address my hypothesis with two aims. In Aim 1, I will conduct CUT&RUN on chromatin remodeling proteins (HDAC3, CHD2, EZH2) and histone modifications (H3K27ac, H3K27me3) to determine which proteins CHASERR and SPEN recruit to change local chromatin structure and repress CHD2 expression. In Aim 2, I will use a multi- omics approach with WT, ASO knockdown, and patient-derived CHASERR+/- NPCs, to understand how CHD2 overexpression affects global chromatin dynamics and transcription in a neural model. Because treatment for CHD2-related NDDs requires precise dosage control of functional CHD2, the proposed studies will help understand CHASERR’s regulation of CHD2 and its potential as a therapeutic target for CHD2 patients. Furthermore, this study will contribute to broader understandings of lncRNA biology and the biological underpinnings of childhood developmental disorders. The diverse team of mentors and the premier facilities and equipment at Northwestern will be available throughout the award period to support rigorous training to carve a successful physician-scientist career uncovering genetic mechanisms of pediatric neurological disorders.

NHLBI - National Heart Lung and Blood Institute

Project summary/Abstract Epigenetic regulation is crucial for directing the intricate processes of heart development, and the disruption of these precise mechanisms underlies various congenital heart defects. Epigenetic mechanisms, such as histone modifications, play key roles in coordinating gene expression programs that guide early lineage specification and differentiation. Lysine-specific histone demethylase 1 (LSD1) is a critical epigenetic regulator that removes mono- and di-methyl groups from histone H3 lysine 4 (H3K4me1/2), thereby influencing chromatin accessibility and transcriptional activity. Beyond its enzymatic function, LSD1 also acts as a scaffold that coordinates transcription factors and chromatin remodelers. However, how these distinct functions of LSD1 contribute to cardiac lineage specification remains poorly understood. Studies have shown that LSD1 is essential for embryonic survival, and recent mouse models have revealed specific developmental cardiac defects in the absence of LSD1. For example, LSD1 hypomorphic mice with impaired protein-protein interactions exhibit ventricular septal defects and perinatal lethality. Additionally, cardiomyocyte-specific LSD1 knockout embryos display reduced heart size, dilation, and embryonic lethality, indicating that LSD1 is necessary at multiple developmental stages in specific tissues. Our lab has further shown that LSD1 knockout embryonic stem cells (ESCs) fail to generate mesoderm and endoderm, instead favoring neuroectodermal fates. Importantly, while the loss of LSD1’s catalytic activity impairs cardiac differentiation, complete loss of LSD1 fully blocks it, emphasizing the significance of its non- catalytic functions in early cell fate decisions. In this proposal, I aim to unveil the precise role and molecular mechanism of LSD1 in regulating cardiac specification and heart development. I will use in vitro and in vivo models to dissect the role of LSD1 in cardiac development. State-of-the-art approaches such as CRISPR/Cas9 guided genome engineering, novel animal models, epigenomics, and single-cell RNA-seq will be used to address the central question. This project will clarify how LSD1 regulates early cell fate decisions in cardiac development, with long-term implications for understanding congenital heart defects and advancing epigenetic-targeted therapies.

NIAMS - National Institute of Arthritis and Musculoskeletal and Skin Diseases

Retrotransposons are interspersed genomic repeats that constitute almost half of the mammalian genome. Largely residing in the heterochromatin, retrotransposons are transiently induced during early development to regulate lineage differentiation, and kept silenced in adult terminally differentiated tissues. However, in human diseases such as cancer and aging, retrotransposons often exhibit aberrantly elevated activities, whose underlying molecular trigger and functional consequences are less understood. Murine skin represents an excellent model to study retrotransposon silencing mechanisms. As our largest organ, skin harbors highly abundant, well characterized, and genetically accessible adult stem cells. Hair follicle stem cells reside in an anatomically distinct niche known as the bulge, alternating between quiescence and activation in a synchronized fashion to fuel cyclic bouts of hair growth. Over repeated insults, hair follicle stem undergo functional exhaustion, the molecular driving events of which were often unclear. In the current proposal, I plan to examine chromatin regulators that couple adult stem cell activation with retrotransposon suppression during adult skin and hair follicle regenerations. Two central heterochromatin pathways are known to silence retrotransposons: tri-methylation on histone 3 lysine 9 (H3K9), catalyzed by histone lysine methyltransferases (KMTs), and DNA cytosine methylation, catalyzed by DNA methyltransferases (DNMTs). Moreover, lineage gene expression during stem cell differentiation depends on DNA demethylation, catalyzed by the DNA demethylase ten-eleven translocation (TET). While TETs are crucial for DNA methylome remodeling in early development, their regulations of retrotransposons in adult tissues remain underexplored. My preliminary analysis of genetic models in which the endogenous retroviruses (ERVs, a type of retrotransposons), are reactivated to drive skin stem cell exhaustion and hair loss, afforded me a unique tool to tackle these questions. Specifically, my prelim data indicated that a critical signal connecting TET to H3K9 KMT and DNMT function is the post-translational modification known as O-linked-β-N-acetylglucosamine (O-GlcNAc). I hypothesize that OGlcNAc catalyzed by the OGlcNAc transferase (OGT) is essential to suppress ERVs by interacting with H3K9 KMT and DNMT in the skin. I will examine OGT-deficient skin phenotypes and O-GlcNAc changes upon ERV reactivation, and dissect the mechanisms of OGlcNAc-orchestrated ERV suppressions. Study proposed here leverage my previous training in mouse genetics, development, epigenetics, and skin biology, and are designed to further train me with the state-of-art technologies such as CRISPR and classic methodologies in biochemistry and molecular biology. My training plan and my sponsor/co-sponsor support have been tailored to further foster my critical thinking, scientific communication, leadership and career development goals within MDACC and GSBS training environment. The proposed study, if successful, will provide important mechanistic insights into retrotransposon biology in adult skin, and mature me into an independent researcher.

NIGMS - National Institute of General Medical Sciences

Project Summary Tissue stem cells are the building blocks during development, and they play a critical role in tissue regeneration and homeostasis throughout life. However, aging results in a decline in proper regulation of stem cell activity, leading to loss of homeostasis over time. Previous work in the Jones Lab demonstrated an important role for mitochondrial biogenesis and turnover in the regulation of adult stem cell behavior in Drosophila melanogaster. However, the mechanisms by which these cells maintain healthy pools of mitochondria throughout life remain unknown. I recently found that male germline stem cells (GSCs) traffic mitochondria to adjacent, somatic niche cells. Since its discovery in 2006, intercellular mitochondrial transfer has been described as a means for stem cells to maintain homeostasis under a wide range of oxidative stressors; however, transfer in vivo under physiological conditions has not been demonstrated. GSCs possess microtubule-based nanotubes that protrude to adjacent somatic niche (hub) cells and are the correct size and shape to facilitate mitochondrial transfer. Preliminary data suggest that the transfer of mitochondria between GSCs and the soma is more pronounced under stressors such as age and a high fat diet. Germline-specific knock-down of genes known to regulate mitochondrial dynamics reduced the frequency of mitochondrial transfer. Therefore, I hypothesize that GSCs utilize intercellular mitochondrial transfer to maintain a healthy pool of mitochondria throughout the life. I will use Drosophila genetics and advanced imaging techniques to test this hypothesis and characterize the specific mechanisms regulating mitochondrial transfer. Upon completion, this project will provide a better understanding of how stem cells maintain high quality organelles throughout life. In addition, my work will have strong implications for organelle-based therapies for treating age-onset diseases.

NIAMS - National Institute of Arthritis and Musculoskeletal and Skin Diseases

PROJECT SUMMARY: Distal arthrogryposis (DA) is a genetic skeletal muscle disorder characterized by congenital joint contractures, muscle weakness, and reduced mobility, leading to significant morbidity. Currently, there are no FDA-approved drugs to treat DA, making physical therapy the only alternative, though often with disappointing outcomes. Despite its significant clinical impact, the precise mechanisms underlying DA's pathology remain elusive. The present grant proposal seeks to comprehensively investigate the involvement of slow myosin binding protein-C (sMyBP-C) in the pathogenesis of DA, aiming to uncover novel therapeutic targets. The overarching long-term goal of my research is to delineate the role of sMyBP- C in health and disease. sMyBP-C is a critical regulator of sarcomere structure and function in skeletal muscle. Recent studies have linked mutations in the MYBPC1 gene, which encodes sMyBP-C, with the development of DA. However, the specific molecular mechanisms by which these mutations lead to the characteristic joint contractures and muscle dysfunction observed in DA patients are not fully understood. Preliminary studies used two newly generated knock-in mouse models carrying homozygous P295L (Human P319L) and E335K (Human E359K) mutations in C2 domain of Mybpc1 gene. In these mouse models, I observed kyphosis and decreased exercise capacity at three months of age and showed increased ex vivo isometric force generation and decreased relaxation rate at low electrical stimulation. Interestingly, calcium transient and speed of relaxation were significantly reduced in the single flexor digitorum brevis fiber of both mutant mice, compared to wild-type controls. Based on these findings, my central hypothesis holds that mutations in the C2 domain of sMyBP-C disrupt the regulation of actin-myosin interaction in striated muscle in the context of force generation, calcium handling and muscle fiber type, leading to the limited movement and contractures characteristic of DA. To test this hypothesis, I will use mouse models and isogenic human induced pluripotent stem cells (hiPSC)-derived myocytes to examine how sMyBP-C mutations affect muscle function, sarcomere structure, and signaling pathways. Therefore, the primary objectives of the proposal are to (i) define the impact of MYBPC1 mutations on skeletal muscle regulation, function, and structure, (ii) determine the molecular interactions that result in hypercontraction, delayed relaxation and calcium handling, and (iii) investigate the disease progression and test two candidate drugs (myosin inhibitor and/or sarcoplasmic reticulum calcium ATPase activator) to treat the phenotypes. The outcome of this research could revolutionize our understanding of DA, establishing a direct link between sMyBP-C mutations and the molecular basis of muscle weakness and thereby provide a foundation for the development of targeted therapies aimed at restoring sarcomere function and ameliorating the clinical manifestations of DA.

NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases

PROJECT SUMMARY/ABSTRACT Reprogramming is crucial for cellular renewal in adult organs that lack dedicated stem cells to replace loss after injury and inflammation. Because such cell plasticity is likely to be executed by a conserved cellular program, we have begun to identify the conserved cellular-molecular features of the process of recruiting differentiated cells as progenitors. The term paligenosis has been recently coined to describe an evolutionary conserved process that a differentiated cell uses to downscale its organelle contents, activate a progenitor-like gene network, and reenter the cell cycle. The upstream triggers and molecular mechanisms initiating this regenerative program remain poorly understood. This project investigates upstream triggers of paligenosis. Using a high-dose tamoxifen injury model to induce paligenosis in zymogenic chief cells of murine stomach corpus, ultrastructural changes in the rough endoplasmic reticulum (rER) were observed during paligenosis initiation (e.g., swelling of the rER lamellae, liberation of ribosomes from rER, and overall loss of ER). This leads to the hypothesis that dynamic changes in ER are an upstream event in paligenosis. ER functioning is in part monitored by the integrated stress response with the paramount ER stress sensor being PERK, a kinase that inhibits translation of mRNA on the ribosome by phosphorylating the translation initiation protein elF2a. Phosphorylated elF2a halts global translation while upregulating a specific set of genes to restore homeostasis. Data show that high-dose tamoxifen activates the integrated stress response in paligenotic zymogenic chief cells, triggering global attenuation of protein synthesis. Preliminary data also indicate that disassembly of rER is an early paligenosis event, supporting the hypothesis that early events of paligenosis are driven by the PERK-integrated stress response pathway and the dynamic regulation and autophagy of rER. Aim 1 of this project thus seeks to detail activation of PERK over a lime course early in paligenosis in the high-dose tamoxifen injury model, and then test the PERK requirement using PERK and integrated stress response inhibitors, and Pefkllll mice crossed to chief cell-specific promoter mice. Sufficiency will be tested by inducing ER stress and by drug-induced activation of PERK. Aim 2 will detail paligenotic ER remodeling in a high-dose tamoxifen model. Using ER-phagy defective mice (Ccpgt+), the effect of ER-phagy deficiency on paligenosis will be examined. The necessity of ER-phagy receptor in initiating and regulating autophagy will also be examined in a clinically relevant context, using human gastric adenocarcinoma cell line AGS and patient-derived organoid models of normal gastric corpus and intestinal metaplasia. This fellowship project ultimately seeks to define critical upstream events that initiate cellular reprogramming during regeneration, providing new insights into ER stress signaling and ER-phagy in gastrointestinal tissue repair and disease. This fellowship also supports a mentored training plan focused on the development of skills related to project management, imaging and analytical techniques, teaching, communication, leadership, and outreach.

NINDS - National Institute of Neurological Disorders and Stroke

PROJECT SUMMARY CLN3 disease is a rare lysosomal disease affecting approximately 1 in 100,000 live born children. It is caused by recessive mutations in the CLN3 gene, which encodes a transmembrane protein that primarily localizes to the lysosome. Affected children suffer from progressive blindness, seizures, psychosis, and cognitive and motor failure, and the disease is invariably fatal. CLN3 is implicated in various cellular processes including endolysosomal trafficking and lipid metabolism, but the primary function remains incompletely resolved. Interestingly, immune system changes have been described in CLN3 patients and animal models including early neuroinflammation in brain regions that later see the first neuronal cell dropout, suggesting the neuroimmune system plays a role in the neurodegenerative disease process. In a proteomics study of CLN3- deficient microglia, we recently discovered a dramatic elevation in the levels of the Tweety homolog protein, TTYH3, which was over 10-fold elevated in microglia isolated from presymptomatic mice, and over 20-fold elevated in microglia from symptomatic mice, suggesting TTYH3 elevation is a relatively early disease event and that it progresses with disease severity. Indeed, we also identified TTYH3 elevation in a neuronal progenitor cell model of CLN3 disease, indicating TTYH3 levels increase in response to loss of CLN3 function in both neurons and microglia. In this proposal, which is responsive to the NOFO for research projects of understudied proteins linked to rare disease (NOFO PAR-25-122), we aim to develop important tools to study the TTYH3 protein in the context of CLN3 disease. We hypothesize that TTYH3 is a novel lysosomal lipid transporter, and we will test this hypothesis by studying TTYH3 subcellular localization and by establishing Ttyh3/TTYH3 knockout mouse and human induced pluripotent stem (iPS) cell-based models that will be phenotyped to evaluate lysosomal function. Finally, we will evaluate whether modulation of TTYH3 impacts CLN3 disease pathophysiology, setting the stage for future work to fully uncover TTYH3 function and whether targeting TTYH3 in CLN3 disease holds therapeutic promise.

NCI - National Cancer Institute

PROJECT SUMMARY Acute myeloid leukemia (AML) is a genetically and cellularly heterogenous disease characterized by the expansion of hematopoietic cells across a range of cell states from stem-like cells to differentiated myeloid cells. The most mutated genes in AML are DNMT3A, NPM1 and the receptor tyrosine kinase FLT3. Despite early clinical responses, most patients relapse, and FLT3-mutant clones are not always eradicated. Our lab has developed genetically engineered mouse models of acute myeloid leukemia that are capable of activating mutations in Flt3 with Dre-recombinase, and then genetically reverting them with Cre-recombinase. We have used these models to benchmark Flt3 oncogene-addiction against best-in-class small molecule kinase inhibitors of FLT3, observing difference in disease remission and relapse. These studies have refined our interest on identifying which cells along the hematopoietic hierarchy are capable of driving relapse and which molecular pathways underlie their survival following chemical/genetic inhibition of FLT3. The major goal of this proposal is to understand the cellular mechanisms that maintain FLT3-mutant clone persistence during targeted therapy. Our preliminary data indicate that Flt3-inhibtion results in a profound differentiation response and induction of Type I Interferon signaling. We will complete integrative studies with human specimen and our innovative multi- recombinase mouse models of leukemia to derive clinically meaningful insights from mechanistic observations in model systems. In aim 1 we will determine which cells are capable of propagating leukemic disease and resolve cellular reservoirs of leukemic stem cell activity. We will perform these studies using genetically engineered mouse models, serial transplantation of purified cell populations, and functional cell ablation studies. We hypothesize that FLT3-inhibtion induced differentiation generates mature cells that are capable of reacquiring stem-like properties and drive relapse. These studies will resolve which cells are necessary to eliminate to prevent leukemic recurrence and provide a focusing lens for improving targeted therapy and relapse detection. In aim 2 we will determine the role of Type I Interferon signaling in differentiation and relapse using gain/loss of function systems. We will evaluate the therapeutic potential of interferon treatment in conjunction with FLT3 kinase inhibition. Finally, we will assess the clonal diversity of leukemic cell states using lentiviral barcoding and single cell RNA sequencing to evaluate which cells can induce an Interferon response, and what their long-term fate is following treatment. We hypothesize that Interferon signaling is necessary to potentiate FLT3-inhibitor driven differentiation, and that combined treatment will extend survival. We anticipate that these studies will more broadly inform the intersection between inflammation and differentiation in AML therapy.

NIEHS - National Institute of Environmental Health Sciences

Project Summary Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition affecting 1 in 36 U.S. children annually. While genetic, epigenetic, and environmental factors contribute to ASD, the mechanisms by which environmental exposures disrupt neurodevelopment remain poorly understood. Emerging evidence highlights the role of epitranscriptomic modifications, such as N6-methyladenosine (m6A), in regulating brain development and synaptic plasticity. This study investigates how prenatal environmental exposures (e.g., cadmium, PFAS) and protective factors (e.g., folic acid) disrupt epitranscriptomic crosstalk, contributing to ASD pathogenesis. Using the MARBLES and EARLI cohorts, we will analyze maternal exposure data and biospecimens to identify exposure-specific epitranscriptomic signatures. Brain organoids derived from induced pluripotent stem cells (iPSCs) will model the effects of environmental toxicants and folic acid on neurodevelopment and m6A regulation. Multi-omics approaches, including RNA-Seq, DNA methylation assays, and MeRIP-Seq, will uncover molecular changes linked to ASD. Machine learning algorithms will integrate multi-omics data to develop predictive models for ASD risk and severity. We propose to investigate four aims: Investigate prenatal environmental exposures’ effects on RNA modifications and DNA methylation; Assess sex-specific epitranscriptomic modifications linked to ASD phenotypes; Evaluate exposure impacts on ASD-associated epitranscriptomic changes using brain organoids; Develop predictive models for ASD risk based on disrupted epitranscriptomic crosstalks. This study bridges human epidemiologic data with organoid modeling to explore the etiology of ASD. By focusing on environmental exposures and protective factors, it addresses critical knowledge gaps and provides a foundation for non-invasive screening tools and targeted interventions. The findings will advance understanding of how environmental factors interact with epitranscriptomic regulation to influence neurodevelopment, paving the way for precision medicine strategies to mitigate ASD risk.

NCI - National Cancer Institute

SUMMARY ABSTRACT: Cancer stem cells (CSCs) are a small population of cancer cells that are typically quiescent, but capable of self- renewal and tumor initiation. Non-CSCs, which make up the majority of the cancer cell population, are cells that are constantly dividing. Since CSCs are non-dividing, they are resistant to standard chemotherapy and radiation therapy, which only target actively dividing cells. Persistence of CSCs after therapy can thus result in disease relapse. Importantly, our recent work showed that programs of stemness are activated in tumor cells as they disseminate from primary tumors. Therefore, understanding what influences the formation of disseminating CSCs may provide new potential targets for therapeutic interventions of metastasis. Metastasis is a multi-step process and, in each step, disseminating tumor cells (DTCs) encounter different physical constrictions (e.g., physical confinement, solid stress, matrix stiffness, interstitial fluid pressure, and shear stress) that may affect their behavior. Recent reports in the literature indicate that one pathway for induction of programs of stemness is through the YAP/TAZ mechanotransduction signaling pathway, indicating that physical forces may, in part, be responsible for the induction of stemness in DTCs. This project will investigate the role physical constriction plays in stem cell induction by modelling the different physical constrictions that DTCs experience as they disseminate from primary tumors. This project will draw upon engineering and biological sciences to combine a unique, validated, fluorescent biosensor for stemness with advanced microfabricated microfluidic in vitro assays, and state-of-the-art intravital imaging of the live murine lung. We propose to use this combination to study the influence of physical forces on the selection, induction, and/or sustainment of metastasizing cancer stem cells, and evaluate their retention, survival, and extravasation efficiency in the in vivo lung.

NCI - National Cancer Institute

Summary Melanoma cells exhibit remarkable plasticity, transitioning between melanocytic/proliferative and mesenchymal/invasive states. This plasticity drives intra-tumoral heterogeneity, disease progression, and therapeutic resistance. While the Microphthalmia-associated Transcription Factor (MITF) is a well-established driver of the melanocytic/proliferative phenotype, the mesenchymal/invasive phenotype and the mechanisms governing state transitions remain poorly understood. Our published and preliminary data identify the MITF paralog TFE3 and the pioneer factor TFAP2B as critical regulators of the mesenchymal state in melanoma. We identify two TFE3 isoforms, a short length (TFE3sl) and a full-length (TFE3fl), with TFE3fl specifically stabilized in invasive melanoma. Pan-TFE3 knockout reduced invasion and distal lung seeding of MITF-low melanoma cell lines. Moreover, MITF directly suppresses the mesenchymal phenotype by activating FNIP2, a key component of the non-canonical mTORC1 signaling pathway. This pathway facilitates lysosomal degradation of TFE3fl, leading us to hypothesize that TFE3fl drives metastasis. These findings suggest a molecular mechanism in which the balance of transcriptional regulation by MITF and TFE3fl, in combination with TFAP2B, governs melanoma plasticity. We hypothesize that melanoma cell plasticity is regulated by a TFE3fl-TFAP2B axis that promotes mesenchymal phenotypes and metastatic progression. To test this hypothesis, we propose the following aims: (1) identify the TFE3 isoform critical for melanoma plasticity and progression and (2) determine how the TFAP2B/TFE3fl axis establishes mesenchymal states within primary tumors. To achieve these aims, we will use patient-derived melanoma cell lines and complementary in vivo models. Zebrafish are uniquely suited for this work because we have generated a primary melanoma model that enables direct visualization of vertical tumor cell invasion in real time, combined with histological validation across multiple animals, providing high-throughput assessment of invasive behavior in the correct anatomical context. In parallel, mouse models will be essential for assessing cancer stem cell (CSC) dynamics, including tumor cell survival and dissemination within the bloodstream, as well as long-term metastatic colonization and survival outcomes. Together, these approaches will allow us to define how TFE3 and TFAP2B regulate melanoma plasticity in both early invasive transitions and later metastatic progression. This study will advance our understanding of melanoma plasticity and identify mechanisms that facilitate the adaptive nature of melanoma cells. Use of mice and zebrafish in this proposal: The rationale for utilizing mouse and zebrafish models is that normal and pathological cells behave differently in vivo due to a complex microenvironment that cannot be replicated in other model systems. Zebrafish have the added benefit of real time imaging of melanoma onset and progression

NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases

Project Summary / Abstract Partial lipodystrophy (PLD) syndromes are characterized by regional loss of white adipose tissue (WAT), leading to insulin resistance, diabetes mellitus, and dyslipidemia. While genetic research has provided significant insights into PLD, over 50% of patients lack a clear genetic diagnosis. The Rare and Atypical Diabetes Network (RADIANT) has identified novel pathogenic variants in key adipose tissue genes among PLD patients. We have demonstrated that modeling PLD using induced pluripotent stem cells (iPSCs), specifically for Familial Partial Lipodystrophy Type 2 (FPLD2) and the LMNA variant p.R482W, can elucidate adipose tissue pathology. However, controversy remains regarding the optimal approach for modeling PLD. One possibility is to reprogram patient-derived peripheral blood mononuclear cells (PBMCs) to iPSCs, correcting genetic variants via CRISPR/Cas9 before differentiating into adipocytes. Another possibility is to introduce multiple variants into a wild-type iPSC line, allowing for consistency and high-throughput testing. This proposal will test and compare these approaches for 5 patients with PLD harboring potentially pathogenic variants. Successful completion will identify new genetic causes of PLD, elucidate PLD pathophysiology, resolve modeling strategy debates, and pave the way for personalized cellular therapies. Additionally, it will establish a platform for screening therapeutic compounds, laying the groundwork for future studies improving the lives of individuals with PLD. Therefore, this proposal directly advances the NIDDK's priorities in understanding the heterogeneity of rare and atypical forms of diabetes.

NEI - National Eye Institute

Abstract This proposal addresses the lack of human retina cell models for mechanistic and therapeutic studies. Retinal diseases are a significant cause of vision impairment in humans and account for > 54% of blindness in the USA. Despite this, there are limited or no treatment options available for several retinal diseases. Most studies on human retinal diseases have so far used animal models, including the commonly used transgenic mice that are genetically engineered to carry the disease- related gene. Although these mouse models have provided important insights into the plausible disease mechanisms of vision loss in specific retinal diseases, due to the lack of physiological human retina cell models, there has been limited translatability of molecular and therapeutic discoveries identified in the non-primate models of human eye diseases. Furthermore, from the perspective of cell-based therapies of retinal degenerative diseases that predominantly affect the photoreceptor-retinal pigment epithelium (RPE) complex in the retina, a “planar tissue comprising the photoreceptor-RPE layers” that can integrate into the existing retina is an urgent unmet translational need. To complement in vivo animal model studies and develop human retina tissue for molecular and therapeutic applications, in this project, we will utilize a combination of human induced pluripotent stem cells (hiPSCs), engineered extracellular matrix (eECM), microbubble arrays, and microfluidics technology. Aim 1 experiments will develop a microphysiological model of comprehensive hiPSC- retina that will emulate the physiological spherical geometry of the human retina in vivo and thus will be suitable for disease modeling, molecular, and drug testing applications. Aim 2 experiments will develop a planar hiPSC-photoreceptor-RPE tissue for use in cell-based therapy targeting photoreceptor and RPE loss in retinal degenerative diseases. Ultimately, hiPSC- derived comprehensive retina (Aim 1) and planar photoreceptor-RPE (Aim 2) will be a tissue engineering breakthrough for in vitro (e.g., molecular, therapeutic testing) and in vivo (cell-based therapy) applications targeting human retinal diseases.

NCATS - National Center for Advancing Translational Sciences

Abstract Support is requested for a Keystone Symposia conference entitled “iPSCs: Progress, Opportunities, and Challenges,” organized by Drs. Shinya Yamanaka, Yanhong Shi and Yasushi Kajii, with scientific programming input from Keystone Symposia. The meeting will take place January 26–29, 2026 at the International Conference Center (ICC) Kyoto in Kyoto, Japan. This conference is being held to mark the 20th anniversary of breakthrough discoveries in induced pluripotent stem cell (iPSC) technologies, which have matured into viable platforms for embryology and disease modeling, drug discovery, and cell-based therapy development for a variety of human diseases. Moreover, the combination of iPSC technology with three-dimensional organoids, organ-on-chip and the emerging technologies of AI and machine learning ensures that iPSC-based platforms will yield new applications in biomedical and translational science. These innovative technologies and their applications are the primary focus of this meeting. Therefore, this conference has been designed to gather the leading scientists from academia and industry to push forward basic knowledge and medical application of iPSCs, especially those being tested in clinical trials worldwide, toward new insights and potential drugs. Additionally, this Keystone Symposia conference will provide a unique opportunity for researchers, clinicians, industrial experts and investors to interact, creating unusual collaborative prospects. Moreover, this conference will provide a rare opportunity for attendees to hear from renowned stem cell researcher and Nobel Laureate, Dr. Shinya Yamanaka, who will be giving the Keynote Address and is one of the meeting organizers. The sharing of knowledge at this meeting is expected to be transformative for the field and lead to the development of new cellular platforms and therapeutic products, which will ultimately impact clinical practice favorably.

NHLBI - National Heart Lung and Blood Institute

The ISEH Annual Scientific Meeting serves as a premier international forum for presenting and discussing the latest research in experimental hematology, including the understanding of normal hematopoiesis, non-malignant hematopoietic diseases, as well as developmental and HSC biology. For example, topics discussed at the ISEH meeting include sickle cell disease, hematopoiesis, bone marrow niche, cell cycle, apoptosis, and signaling. The discoveries reported at the ISEH Annual Scientific Meeting are fundamental to understanding and treating blood disorders, including but not limited to anemias, bone marrow failure syndromes, and leukemia. These topics align closely with NHLBI’s mission to advance scientific understanding and develop therapies for blood diseases, including stem cell biology and gene/cell-based treatments to repair and regenerate tissues. The ISEH Annual Scientific Meeting is intentionally designed to foster scientific exchange through a variety of presentation formats, including invited lectures, short talks selected from abstracts, featured poster teasers, and traditional poster sessions. Beyond showcasing the latest research findings, the meeting cultivates an environment where researchers are encouraged to ask challenging questions and build future collaborations that drive scientific discovery forward. ISEH places a strong emphasis on fostering early-career scientists (students, postdoctoral fellows, and junior faculty), as evidenced in meeting attendance. Between 2022 and 2025, PhD students, postdoctoral fellows, and junior faculty made up an average of 61% of attendees at the ISEH Annual Scientific Meeting. Of this young investigator attendee population, an average of 48% of these PhD students, postdoctoral fellows, and junior faculty attending the ISEH Annual Scientific Meeting were based in the United States, demonstrating strong participation of US-based junior investigators. Dedicated programming includes pre-meeting workshops, career development sessions, junior faculty career forums, innovating technology presentations, networking mixers, and featured poster presentations. Additionally, our travel grant program helps defray costs for young investigators presenting abstracts, ensuring broad participation in scientific exchange. In 2026, we are adding a third track of concurrent presentations to provide additional opportunities for trainees and junior faculty to present their work. This R13 grant application requests funds in support of trainees and early career investigators as well as accessibility focused activities at the 2026 scientific meeting totaling $41,064. This includes support for travel grants, awards, closed captioning services, as well as supplies needed for trainee/early-career investigator focused activities such as abstract submission, and poster board rental.

NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases

PROJECT SUMMARY/ABSTRACT Because it is unsafe to access human pancreatic islets from living donors, surrogate experimental systems are needed to answer important questions about the mechanisms through which insulin-producing β cells are destroyed in individuals who develop type 1 diabetes (T1D). Protocols for differentiating induced pluripotent stem cells (iPSCs) into islet-like clusters (SC-islets) provide a replenishable source of beta cells and are a promising alternative means for modelling interactions between human islet endocrine cells and immune cells. However, currently available biomimetic systems are not able to maintain the long-term viability of SC-islets and are not isogenic and therefore, unable to accurately model autoimmune interactions. To meet this need, this project will develop a vascularized 3D biomimetic microphysiological system (MPS) that will allow fully isogenic modelling of interactions between islets and immune cells in prolonged culture. Our basis for this model system is a proven perfusion-capable microfluidic skin-on-chip platform. This plexiglass-based chamber system has an open well on the top, which is readily adaptable to create an ideal system for culturing SC-islets. A microchannel network within the chamber promotes the formation of a vascular network in a supporting matrix. The system has been designed with inlet and outlet ports for perfusing endothelial cells, medium, cytokines, or immune cells. Furthermore, the system is configured to allow live imaging and removal of SC-islets and immune cells from the system for downstream analysis. We predict that this approach will overcome some of the described limitations of existing SC-islet culture systems and will allow mechanistic interrogation of mechanisms that promote sustained autoimmunity and pathologic interactions between SC-islets and autoreactive T cells. We will fully implement this system and demonstrate its suitability for studying interactions between human SC-islets and autoreactive T lymphocytes and then utilize it to ask specific questions about the effects of inflammatory stress on SC-islet phenotype. Importantly, our experiments will utilize T cell lines and T cell receptor sequences obtained from pancreatic organ donors with T1D, as these represent the most relevant T cells for mechanistic studies. Specifically, we will investigate the effects of inflammatory stress on islet phenotype, function and interactions with autoreactive T cells, first using 3D cultures (suitable for modeling short-term inflammatory stress) and then in the islet-on-chip system (suitable for short and long-term inflammatory stress). This will enable us to test the hypothesis that inflammatory stress alters beta cell phenotype and drives increased immune perception during the development of T1D. In addition, we will utilize the islet-on-chip system to investigate the role that the membrane repair pathway plays in dictating the vulnerability of beta cells to immune attack. We anticipate that modeling interactions between SC-islets and cytotoxic T cells will reveal a crucial role of the membrane repair pathway in determining vulnerability to immune attack. These insights are likely to suggest novel pathways that can be leveraged to treat T1D.

U.S. National Science Foundation

Revolutionizing Engineering Departments (hereinafter referred to as RED) is designed to build upon previous efforts in engineering education research. Specifically, previous and ongoing evaluations of the NSF Engineering Education and Centers Division program and its predecessors, as well as those related programs in the Directorate for STEM Education, have shown that prior investments have significantly improved the first year of engineering students experiences, incorporating engineering material, active learning approaches, design instruction, and a broad introduction to professional skills and a sense of professional practice giving students an idea of what it means to become an engineer. Similarly, the senior year has seen notable change through capstone design experiences, which ask students to synthesize the technical knowledge, skills, and abilities they have gained with professional capacities, using reflective judgment to make decisions and communicate these effectively. However, this ideal of the senior year has not yet been fully realized, because many of the competencies required in capstone design, or required of professional engineers, are only partially introduced in the first year and not carried forward with significant emphasis through the sophomore and junior years. The Directorates for Engineering (ENG) and STEM Education (EDU) are funding projects as part of the RED program, in alignment with the Improving Undergraduate STEM Education (IUSE) framework and Professional Formation of Engineers (PFE) initiative. These projects are designing revolutionary new approaches to engineering education, ranging from changing the canon of engineering to fundamentally altering the way courses are structured to creating new departmental structures and educational collaborations with industry. A common thread across these projects is a focus on organizational and cultural change within the departments, involving students, faculty, staff, and industry in rethinking what it means to provide an engineering program. In order to continue to catalyze revolutionary approaches, while expanding the reach of those that have proved efficacious in particular contexts, the RED program supports four tracks: RED Planning (Track 1), RED Adaptation and Implementation (Track 2), RED Innovation (Track 3), and RED Innovation Partnerships (Track 4). Two- and four-year institutions are encouraged to submit to any track as appropriate for their goals and context. RED Planning (Track 1) projects will support capacity-building activities at institutions of special interest to NSF s mission, including two-year engineering-centered programs building transfer partnerships, two-year or four-year institutions in EPSCoR jurisdictions, Primarily Undergraduate Institutions (PUIs), and Institutions of Higher Education (IHEs) in order to create more opportunities in engineering for students in every part of the country. Planning projects should provide the support for such institutions to explore the development of a RED Projects in Tracks 2, 3, & 4. RED Adaptation and Implementation (Track 2) projects will adapt and implement evidence-based organizational change strategies and actions to the local context, which helps propagate this transformation of undergraduate engineering education. RED Innovation (Track 3) projects will develop new, revolutionary approaches and change strategies that enable the transformation of undergraduate engineering education. RED Innovation Partnerships (Track 4) projects will achieve the same goals as Track 3 projects across multiple institutions. Of particular interest to this track are projects partnering two-year institutions with other eligible institutions. Projects in tracks 2, 3, & 4 will include consideration of the cultural, organizational, structural, and pedagogical changes needed to transform one or more departments to ones in which students are engaged, develop their technical and professional skills, and establish identities as professional engineers or technologists. The focus of projects in these tracks should be on the department s disciplinary courses and program. RED project initiatives are expected to be institutionalized at the end of the funding period. Proposals are especially encouraged that address areas of increased national interest including but not limited to advanced manufacturing, advanced wireless, artificial intelligence, biotechnology, microelectronics and semiconductors, net zero technologies, sustainability, systems engineering, and quantum engineering.

NIAMS - National Institute of Arthritis and Musculoskeletal and Skin Diseases

Project Summary/Abstract Muscle stem cells (MuSCs) provide myofibers with a robust tool for regeneration after injury. The efficiency of this muscle regenerating capacity depends upon the ability of MuSCs to integrate signals emanating from complementary cell types within the damaged muscle. Unfortunately, integration of these signals is often disrupted in disease, which results in a functional depletion of the MuSC population. MuSCs are still present, but they are not able to respond to regenerative cues from the environment. Although substantial evidence supports a role for epigenetic enzymes in orchestrating the transcriptional programs necessary for MuSCs to respond to niche-derived cues, how these enzymes enable MuSCs to actively shape the regenerative environment— particularly under inflammatory conditions—remains poorly understood. Our preliminary studies indicate that the H3K27 demethylase JMJD3 is rapidly induced in MuSCs after injury and regulates key genes that facilitate communication with immune cells, allowing MuSCs to exit quiescence and support tissue repair. Loss of JMJD3 in MuSCs leads to aberrant cytokine expression and excessive accumulation of inflammatory macrophages, suggesting that JMJD3 enables MuSCs not only to respond to signals but also to broadcast critical cues that help calibrate the immune response. Despite this emerging evidence, the underlying mechanisms through which JMJD3 governs MuSC–immune cell communication remain unknown. The overall objective of this project is to define the JMJD3-dependent transcriptional and epigenetic programs that allow MuSCs to modulate the inflammatory niche and initiate regeneration. We hypothesize that JMJD3 integrates signals from the regenerative environment by removing repressive H3K27me3 marks at immunomodulatory genes, permitting their expression to shape immune cell behavior and ensure efficient repair. We will address this through two aims: Aim 1: Use TEA-seq, a trimodal single-cell approach, to uncover the signaling pathways by which MuSCs regulate the magnitude and duration of the immune response to muscle injury. Aim 2: Determine how JMJD3-mediated H3K27 demethylation integrates niche-derived signals to control inflammatory resolution, testing whether modulation of H3K27me3 levels governs expression of MuSC immunomodulatory genes. Successful completion of these studies will elucidate how JMJD3 enables MuSCs to coordinate the inflammatory landscape necessary for regeneration, fundamentally advancing our understanding of how stem cells navigate and shape complex tissue environments. By revealing the extent to which epigenetic control of MuSC–immune communication influences regeneration, this work will provide a critical foundation for future efforts to fine-tune inflammation in muscle-wasting diseases.

Deere Foundation

Invests in workforce development, STEM education, and community prosperity in agricultural and rural regions.

U.S. National Science Foundation

The Launching of Early-Career Academic Pathways in the Mathematical and Physical Sciences (LEAPS-MPS) supports the launch of the careers of pre-tenure faculty whose research is in Mathematical and Physical Sciences (MPS) fields at institutions that do not traditionally receive significant amounts of MPS funding, such as Carnegie Research 2 (R2) universities, minority-serving institutions (MSIs), predominantly undergraduate institutions (PUIs). The LEAPS awards enable PIs from these institutions to initiate productive research programs and generate results useful for preparing subsequent competitive proposals to traditional NSF funding opportunities, such as a core program or a CAREER solicitation. A critical goal of the LEAPS-MPS Program is to develop the 21st-century STEM workforce representative of society s full spectrum of talent by increasing the participation in STEM research of members of communities underrepresented and/or underserved in STEM and the number of members of these communities who can serve as role models. Awards are for 24 months with budgets of up to $250,000 total costs (direct plus indirect). Proposals in response to this solicitation must be submitted for consideration tothe appropriate program in one of the five MPS Divisions.

U.S. National Science Foundation

The Law &amp; Science Program considers proposals that address social scientific studies of law and law-like systems of rules, as wellas studies of how science and technology are applied in legal contexts.The Program is inherently interdisciplinary and multi-methodological.Successful proposals describe research that advances scientific theory and understanding of the connections between human behavior and law, legal institutions, or legal processes; or the interactions of law and basic sciences, including biology, computer and information sciences, STEM education, engineering, geosciences, and math and physical sciences.Scientific studies of law often approach law as dynamic, interacting with multiple arenas, and with the participation of multiple actors.Fields of study include many disciplines, and often address problems including, though not limited, to: <ul type="disc"> <li>Crime, Violence, and Policing</li> <li>Cyberspace</li> <li>Economic Issues</li> <li>Environmental Science</li> <li>Evidentiary Issues</li> <li>Forensic Science</li> <li>Governance and Courts</li> <li>Human Rights and Comparative Law</li> <li>Information Technology</li> <li>Legal and Ethical Issues related to Science</li> <li>Legal Decision Making</li> <li>Legal Mobilization and Conceptions of Justice</li> <li>Litigation and the Legal Profession</li> <li>Punishment and Corrections</li> <li>Regulation and Facilitation of Biotechnology (e.g., Gene Editing, Gene Testing, Synthetic Biology) and Other Emerging Sciences and Technologies</li> <li>Use of Science in the Legal Processes</li> </ul> LS supports the following types of proposals: <ul type="disc"> <li>Standard Research Grants and Grants for Collaborative Research</li> <li>Conference Awards</li> </ul> LS also participates in a number of specialized funding opportunities through NSF&rsquo;s cross-cutting and cross-directorate activities, including, for example: <ul type="disc"> <li>Faculty Early Career Development (CAREER) Program</li> <li>Research Experiences for Undergraduates (REU)</li> <li>Research at Undergraduate Institutions (RUI)</li> <li>Grants for Rapid Response Research (RAPID)</li> <li>Early-concept Grants for Exploratory Research (EAGER)</li> </ul> For information about these and other programs, please visit the <a href="http://www.nsf.gov/funding/pgm_list.jsp?type=xcut">Cross-cutting and NSF-wide Active Funding Opportunities</a> homepage.

U.S. National Science Foundation

The Law &amp; Science Program considers proposals that address social scientific studies of law and law-like systems of rules, as wellas studies of how science and technology are applied in legal contexts.The Program is inherently interdisciplinary and multi-methodological.Successful proposals describe research that advances scientific theory and understanding of the connections between human behavior and law, legal institutions, or legal processes; or the interactions of law and basic sciences, including biology, computer and information sciences, STEM education, engineering, geosciences, and math and physical sciences.Scientific studies of law often approach law as dynamic, interacting with multiple arenas, and with the participation of multiple actors.Fields of study include many disciplines, and often address problems including, though not limited, to: Crime, Violence, and Policing Cyberspace Economic Issues Environmental Science Evidentiary Issues Forensic Science Governance and Courts Human Rights and Comparative Law Information Technology Legal and Ethical Issues related to Science Legal Decision Making Legal Mobilization and Conceptions of Justice Litigation and the Legal Profession Punishment and Corrections Regulation and Facilitation of Biotechnology (e.g., Gene Editing, Gene Testing, Synthetic Biology) and Other Emerging Sciences and Technologies Use of Science in the Legal Processes LS supports the following types of proposals: Standard Research Grants and Grants for Collaborative Research Conference Awards LS also participates in a number of specialized funding opportunities through NSF s cross-cutting and cross-directorate activities, including, for example: Faculty Early Career Development (CAREER) Program Research Experiences for Undergraduates (REU) Research at Undergraduate Institutions (RUI) Grants for Rapid Response Research (RAPID) Early-concept Grants for Exploratory Research (EAGER) For information about these and other programs, please visit the Cross-cutting and NSF-wide Active Funding Opportunities homepage.

Lemelson Foundation

Supports invention-based education, STEM learning, and inventor support programs. Focus on inspiring young inventors and commercializing socially beneficial inventions.