Univ Of Massachusetts Med Sch Worcester

NIH Research Projects · FY 2026 · 2026-06

BRCA1-deficient cancers are acutely sensitive to a broad range of anti-cancer therapies, yet the underlying mechanisms driving this vulnerability remain incompletely defined. While 53BP1 has been traditionally implicated in drug sensitivity through its suppression of homologous recombination (HR), emerging evidence suggests an alternative pathway. Our preliminary findings reveal that 53BP1 disrupts lagging strand processing in BRCA1-deficient cells, leading to defective Okazaki fragment maturation and accumulation of post-replication single-stranded DNA (ssDNA) gaps—even in the absence of exogenous DNA damage. These gaps coincide with mislocalized FEN1, implicating a defect in flap processing, and are marked by aberrant enrichment of 53BP1 at replication forks. We further demonstrate that these gaps create a dependency on RAD51 for protection and repair, revealing a previously unrecognized therapeutic vulnerability. The central goal of this proposal is to define how BRCA1 regulates lagging strand DNA synthesis to suppress replication-associated gaps—and how this process is antagonized by 53BP1 and related factors to drive treatment sensitivity. We hypothesize that BRCA1 promotes lagging strand flap engagement by restricting 53BP1, thereby enabling proper Okazaki fragment processing and limiting gap formation that would otherwise require RAD51-mediated protection. To test this model, we propose three specific aims: (1) define the role of BRCA1 in lagging strand synthesis; (2) determine how lagging strand processing defects are bypassed in BRCA1-deficient cells; and (3) elucidate how RAD51 protects and resolves replication-associated gaps. These aims will be addressed using proximity ligation assays (PLA), iPOND, chromatin proteomics, and functional genetic models. Collectively, these studies will challenge prevailing models of BRCA1 and 53BP1 function and reframe the origins of therapeutic sensitivity in BRCA1-deficient tumors. By defining how lagging strand defects and RAD51 dependencies arise, this work will uncover new avenues for targeting BRCA1-deficient and PARP inhibitor–resistant cancers.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY While animal models can provide surrogates for the in vivo evaluation of many aspects of gene editing therapeutics, the efficacy and genotoxicity of editing reagents in the context of human genome cannot be readily modeled in vivo for many organ systems. Our proposal is focused on developing human muscle xenograft models for the in vivo optimization of efficacy and assessment of genotoxicity of genome editing therapeutics for muscular dystrophies. As a proof- of-concept target, we are developing a prime editing therapeutic strategy for the correction of the most common FKRP mutation [L276I (c.826C>A)] associated with Limb Girdle Muscular Dystrophy R9 (LGMD2i or LGMDR9). Mutations in FKRP disrupt skeletal and cardiac muscle function, leading to progressive disability and often premature death. As the FKRP L276I LGMDR9 mutation is autosomal recessive, precise correction of a single L276I allele in muscle and satellite cells will provide an enduring treatment for this disease for which there are no curative therapeutics. Overall project goals are to develop a humanized muscle xenograft model of LGMDR9 for the in vivo assessment of the efficacy and the genotoxicity of prime editing therapeutics that correct the L276I mutation. The project has two Specific Aims. In Aim 1, prime editing correction of the FKRP L276I LGMDR9 mutation will be optimized to therapeutic levels in iPSC derived LGMDR9 myotubes in vitro, and genome-wide off-target analysis will be performed to assess and improve the precision of editing. In Aim 2, prime editing reagents (prime editor mRNA and chemically modified guide RNAs) will be packaged in lipid nanoparticles for delivery to LGMDR9 xenograft muscle and resident regenerative satellite-like cells (iSCs) by direct intramuscular injection or systemic delivery. Dose regimens will be optimized to maximize prime editing correction of FKRP L276I in myotubes and iSCs and minimize off-target editing, as assessed by deep sequencing. Therapeutic efficacy will be assessed using RNA-seq disease biomarker expression and TUNEL apoptosis assays. Our expectation is that development of efficient prime editing systems in the context of a patient muscle xenograft model will have broad impact on the development of safer and more effective editing therapeutics, and that this experimental approach will establish a general pathway for the translation of gene editing therapies to the clinic to treat the diversity of musculoskeletal disorders.

NIH Research Projects · FY 2026 · 2026-06

Project Summary A central challenge in neurobiology is understanding how to protect the brain from Alzheimer’s disease. Increasing evidence points to a critical link between synaptic function and neurodegeneration. Yet, the molecular mechanisms underlying this relationship remain poorly defined, largely because neurodegenerative diseases are highly context dependent: factors such as genetic predisposition and age strongly influence the onset and progression of neurodegeneration and cell death. Uncovering context specific mechanisms of disease demands that we investigate novel models of neurodegeneration and cell death in multiple types of animals. Such models offer untapped insights into the molecular pathways that drive or prevent neuronal decline and hold promise for informing innovative candidate therapeutic directions for neurodegenerative disease. We have identified multiple suppressors of neurotoxicity in aged animals using two novel models of age-related neurotoxicity that induce axon degeneration and cell death: one is caused by overexpression of a pore-modified ionotropic acetylcholine receptor subunit that produces excess synaptic activation, and the other is caused by prolonged oxidative stress due to paraquat exposure. Our investigations are performed in C. elegans, which have a relatively simple nervous system, are highly genetically tractable, and have been successfully used to identify conserved mechanisms of neurodegeneration, oxidative stress and synapse function. We are leveraging these strengths to answer the critical question of how context specific molecular mechanisms protect against neurodegeneration. Specifically, we will 1) determine how TIR-1/SARM1, a key and conserved regulator of axon degeneration, instead protects against persistent excitotoxicity- and oxidative stress-induced axon degeneration and cell death, and 2) determine how 10 mutations identified from an unbiased forward genetic screen protect against neurotoxicity. By identifying and characterizing molecular pathways that preserve neuronal integrity, our findings will advance our understanding of context-specific neuroprotection and potentially inform strategies to combat the devastating neurodegeneration seen in Alzheimer’s disease.

NIH Research Projects · FY 2026 · 2026-06

Project Summary Human immunodeficiency virus type 1 (HIV-1) remains a major global health challenge. While viral maturation has long been a promising target for inhibitor development, the emergence of resistance to protease inhibitors continues to limit their effectiveness. As such, the Group-Specific Antigen (Gag) polyprotein presents an alternative avenue for therapeutic intervention, marked by the recent development of novel antiretrovirals such as bevirimat and lenacapavir, which target the immature Gag and mature capsid (CA). Gag encodes the core structural proteins that form the viral particle and undergoes cleavage by the viral protease during maturation. Among the domains in Gag, CA-SP1 cleavage is the key determinant for CA maturation, a process marked by CA undergoing drastic conformational changes. In Aim 1, I will elucidate how the stability of SP1 helices evolves during proteolysis. SP1 helices are arranged mostly in relatively stable six-helix bundles in the immature lattice but are bound to the protease extended and unfolded. It remains unclear how SP1 loses its secondary structure as it binds to the protease. I hypothesize that the initial cleavage of a single SP1 helix destabilizes the six-helix bundle, promoting the unfolding of neighboring helices and allowing for easier access to the protease. Using MD simulations, I will elucidate and compare the unfolding timescale and mechanisms of SP1 helices within fully intact and partially cleaved hexamers. I predict that SP1 helices in the cleaved hexamers will unfold more readily, whereas the intact hexamer will remain predominantly stable. These simulations will provide mechanistic insights into how SP1 proteolysis propagates structural changes through the hexamer and contributes to how the crucial last step of Gag proteolytic processing occurs. The expertise from the Schiffer lab provides me with the necessary training needed to perform robust structural modeling and molecular dynamics simulations. In Aim 2, I will investigate how SP1 cleavage mediates CA conformational changes that facilitate maturation. The destabilization of the six-helix bundle has been identified as the key structural switch for CA maturation. Using smFRET, I will visualize the conformational changes of single CA molecules within oligomeric assemblies. I predict that destabilization of the six-helix bundle following CA-SP1 cleavage induces conformational changes to the CA domain that are relevant for virion maturation. These findings will provide mechanistic insights into the allosteric communication between the CA-SP1 cleavage site and CA domains, revealing how initial cleavage events prime the hexamer for further structural transitions. The Munro lab has a proven track record and expertise in visualizing dynamic events in virions using single molecule fluorescence- based techniques. This study will significantly advance our understanding of the molecular mechanisms underlying HIV-1 maturation, potentially shedding light on the maturation processes of other retroviruses.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY Focal gene amplification is a hallmark of many types of cancer that drives tumorigenesis, such as MYCN-amplified neuroblastoma. Gene amplification affords an opportunity for therapeutic exploitation if DNA damage can be site-specifically targeted to amplified loci, since the damage will accumulate specifically in cancer cells. DNA nicks (single strand breaks, SSBs) can create single ended double strand breaks (seDSBs) within a proliferating cell if encountered by a DNA replication fork, where large numbers of seDSBs can lead to cell death. SpCas9 nickase can be employed to selectively create large numbers of SSBs within the genome of proliferating cancer cells by targeting highly amplified loci resulting in a toxic level of seDSBs. MYCN-amplified neuroblastoma provides an ideal cancer to test the efficacy of Cas9 nickase as a cancer-selective genotoxic agent when targeting focal gene amplification. MYCN-amplified neuroblastoma is observed in ~20% of diagnosed cases and has an overall survival rate of ~50%. Thus, it represents a target with important unmet medical need. Based on our preliminary data, Cas9 nickase shows promise as a selective therapeutic agent for MYCN-amplified neuroblastoma cells in vitro and in vivo. We propose to improve the properties of Cas9 nickase for selective killing of MYCN-amplified neuroblastoma cells and demonstrate its therapeutic potential in vivo in an orthotopic xenograft model of MYCN-amplified neuroblastoma. Evaluation of the efficacy and safety of new anti-cancer therapeutics delivered systemically by nanoparticles are most appropriately evaluated in an in vivo mouse model of neuroblastoma, where the impact of therapeutic treatment on tumor metastasis, which is a critical component in high risk MYCNamplified neuroblastoma, can be assessed, which is not possible in cell culture/organoid systems. Tumor plasticity and evolution in response to genotoxic damage is best approximated with in vivo orthotopic/disseminated tumors that recapitulate the aggressive, highly vascular and invasive character of high risk MYCN-amplified neuroblastoma. In Aim 1, we will optimize the efficiency of neuroblastoma cell killing by Cas9 nickase through improvements to the nickase, sgRNA and choice of target site. In Aim 2, we will optimize our lipid nanoparticle carrier formulation for delivery of Cas9 nickase mRNA to an orthotopic xenograft model of neuroblastoma and evaluate the efficacy of tumor reduction by Cas9 nickase. In Aim 3, we will evaluate small molecule inhibitors of DNA damage response pathways for their ability to enhance Cas9 nickase toxicity. We have already demonstrated that Cas9 nickase toxicity is enhanced by a CHK1 inhibitor, which blocks a DNA damage response pathway that responds to cellular replication stress. We will then evaluate the efficacy of tumor reduction in vivo by Cas9 nickase in conjunction with promising inhibitors of DNA damage response pathways. At the conclusion of this study, we will have a therapeutic lead for the treatment of refractory MYCN-amplified neuroblastoma that can undergo further optimization, and efficacy and safety assessments in vitro and in vivo in the context of assembling a pre-IND package for FDA interactions.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY This proposal aims to address the challenges associated with opioid-induced respiratory depression (OIRD) leading to overdoses death, which pose significant risks in the current frontline treatment of severe pain using opioids. Despite the dangers of OIRD, existing treatments have limited efficacy, leading to diminished therapeutic index and compromised patient safety. Emerging evidence suggests opioid activation of mu-opioid receptors (MOR) transactivates receptor tyrosine kinases (RTKs), specifically platelet-derived growth factor receptor beta (PDGFRβ) via the release of platelet-derived growth factor type B (PDGF-B). Our team recently identified a key role for PDGFRβ in opioid deleterious effects. In published work, we demonstrated that pharmacological inhibition of PDGFRβ blocks fentanyl tolerance without altering analgesia. More recently, we found that it also blocks reward behaviors. Thus, showing that PDGFRβ is a promising target to mitigate undesired opioid effects. Our preliminary anatomical evidence that PDGFRβ is highly expressed in brainstem and prior studies showing that PDGFRβ signaling can inhibit ventilation3-5, prompted us to investigate whether PDGFRβ could also be involved in OIRD. This led to the groundbreaking discovery that imatinib6, 7, an inhibitor of PDGFRβ, prevented opioid-induced lethality in rodents. Our new findings indicate that PDGFRβ inhibition may maintain survival from OIRD through modulation of respiration rate via action in the brainstem. We now hypothesize that MOR activation in the brainstem transactivates PDGFRβ in neurons that modulate respiration, causing OIRD. To test this overarching hypothesis, we propose to use a combination of behavioral pharmacology and neuroanatomical protein and mRNA expression mapping in the mouse brainstem to complete two aims that will: 1) test the hypothesis that PDGFRβ signaling is required for OIRD; and 2) test the hypothesis that fentanyl selectively activates PDGFRβ neurons in the brainstem to induce OIRD. In these aims, we will use a highly sensitive Piezo-electric system to detect respiratory rates with high resolution in freely moving rodents, which will allow us to assess the ability of PDGFRβ inhibitors to specifically prevent or reverse OIRD. In parallel, we will conduct a precise mapping of MOR, PDGF-B and PDGFRβ expression in the brainstem to examine expression and distribution of these factors in structures involved in respiration. We will also determine the impact of fentanyl OIRD on expression of these effectors. Finally, we will also assess immunoreactivity to the immediate early gene c-Fos to assess if specific neuronal circuits are engaged upon MOR-PDGFRβ transactivation to induce OIRD in the brainstem. Our proposal will shed light on the therapeutic potential of PDGFRβ in addressing OIRD. The utilization of FDA-approved treatments (e.g., imatinib) underscores the practical application of the research in combating the opioid epidemic. PDGFRβ, emerges as a promising and safe target for effective treatment of opioid addiction and prevention of fatalities due to opioid overdose.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY Rare cancers cumulatively account for about 20% of all cancer diagnoses, however, there are fewer available resources, models, and patient samples to enable their study as compared to common cancers. This has created in a significant gap in our understanding of their tumorigenesis. Many of rare cancers harbor specific and recurrent chromosomal translocations, resulting in unique fusion oncogenes which confer aberrant and/or neomorphic function of oncogenes, but the exact role of most fusions in the development of rare cancers remains uncharacterized. To enable high-throughput study of fusion oncogenes, we have constructed the Rare Cancer Fusion Oncogene Library (RCFOL), which is a collection of over 2.5k barcoded open reading frame (ORF) sequences which have been optimized for multiplexed functional genetics studies. In preliminary experiments with the library, I identified that fusions isolated from soft-tissue sarcomas caused fitness deficits in human mammary epithelial cells (HMECs), with EWSR1::CREB1 inducing autophagy-dependent cell death (ADCD) in response to oncogenic stress paired with upregulation of the innate immune response. However, fibroblasts were able to stably express EWSR1::CREB1 with no impact on cellular health, suggesting that certain cell types may be either “permissive”, or “non-permissive” to fusion oncogene expression. Thus, I hypothesize that the induction of autophagy-dependent cell death via innate immune signaling is a conserved response to fusion expression in non-permissive cell-types. In Aim 1, I will characterize the role of IL-6 and differential fusion binding patterns in the selective induction of ADCD in EWSR1::CREB1-expressing HMECs. I will modulate levels of IL-6 using short-hairpin RNAs and monitor autophagic flux, localization of autophagy regulators, and cell death through microscopy, immunocytochemistry, and flow cytometry. To identify if EWSR1::CREB1 directly influences the expression of autophagy and innate-immune response genes, I will conduct multi-CUT&Tag to map fusion binding patterns in both HMECs and BJ fibroblasts. These experiments will reveal how the underlying differences between fusion permissive and non-permissive cells result in disparate phenotypes in response to fusion expression. In Aim 2, I will profile if autophagy is a conserved tumor-suppressive response to oncogenic stress. I will conduct barcoded multiplexed proliferation assays of the fusion ORFs in the RCFOL paired with the GFP-LC3-RFP autophagic flux reporter. To validate which individual fusions induce ADCD and upregulate the innate immune response, I will analyze autophagic flux, cell death, and cytokine secretion. The experiments of Aim 2 will determine if the mechanisms by which fusion expression is restricted to certain cell-types are ubiquitous or highly specific to individual fusions. This proposal will characterize the mechanism of ADCD in EWSR1::CREB1-expressing HMECs, and profile the scope of ADCD as a response to fusion oncogene- mediated stress. While conducting this research, my mentorship team and I will work to improve my expertise in functional genomics and cell biology, while bolstering my mentorship and scientific communication skills.

NIH Research Projects · FY 2026 · 2026-06

5. ABSTRACT The Alkema lab investigates how internal states and environmental cues are integrated to regulate behavior. We are particularly interested in how animals prioritize competing drives and how these behavioral choices are shaped by signals from both the nervous system and the intestine. We use C. elegans as a model because it offers a uniquely powerful combination of a defined neural circuit, robust genetic tools, optical transparency, and a simple gut-brain axis. Our work examines how the nervous system sustains stable behavioral states like foraging, while preserving the flexibility to switch rapidly into high-arousal states like escape in response to threat. We have shown that tyramine, the invertebrate analog of adrenaline, coordinates the independent motor programs of the flight response. While tyramine drives escape and arousal responses, serotonin promotes feeding and the exploitation of food resources. We are testing the hypothesis that these two neuromodulators interact through mutual inhibition, forming a dynamic switch that prioritizes behavior based on internal state and environmental context. A second major question we address is how the nervous system regulates gut physiology. We find that tyramine and serotonin produce strikingly different patterns of intestinal calcium dynamics. We are using these differences to uncover molecular mechanisms of how the nervous system modulates gut function and internal states. We have developed tools to track behavior and intestinal calcium dynamics in real time, enabling us to investigate how neural, genetic, and microbial factors regulate gut activity. We have identified novel mutants that disrupt intestinal calcium rhythms, implicating metabolic signals as key regulators of gut-brain communication. Finally, we are working to define how physiological states, such as hunger, satiety and stress, are encoded in the gut and how gut-derived signals, in turn, influence brain function. Our findings support the view that the intestine acts as a neuroendocrine organ, integrating neural, metabolic, and microbial cues to regulate the release of gut-derived peptides, including insulin-like and neuropeptides. By combining behavioral assays, genetics, metabolomics, and in vivo imaging, our lab aims to uncover molecular mechanisms by which the gut and brain coordinate internal state and adaptive behavior. Understanding how internal and behavioral states are generated and modulated is essential for defining the general principles of gut-brain communication. This research will illuminate how neuromodulatory, metabolic, and intestinal signals are integrated to shape adaptive behavior. Given the evolutionary conservation of these pathways, discoveries in C. elegans may reveal novel and broadly relevant mechanisms of brain-gut signaling that are important for human mental and physiological health.

NIH Research Projects · FY 2026 · 2026-06

PROJECT SUMMARY/ABSTRACT Pancreatic ductal adenocarcinoma (PDAC) is the prototypical cancer associated with cachexia, a paraneoplastic syndrome that manifests as wasting of adipose tissue depots and muscle atrophy that reduces overall survival. PDAC patients exhibit the highest rates and most severe forms of cachexia across all cancer types, with ~80% of PDAC patients presenting with cachexia, and ~30% of patients succumbing to cachexia-associated complications. Currently, there are no therapeutic interventions to reverse or block cachexia, underscoring the need for meticulously investigating the novel molecular drivers of cachexia onset. Emerging clinical data shows that PDAC patients exhibit signs of cachexia up to ~18 months before PDAC diagnosis, at a stage when patients often present with chronic pancreatitis (CP). CP patients have an elevated risk of PDAC and experience significant weight loss prior to a cancer diagnosis. We will thus study cachexia onset in CP models to understand the molecular etiology of cachectic wasting. In addition to pancreatitis, obesity is associated with higher PDAC incidence, and obese PDAC patients have dysregulated adipose signaling that putatively alters cancer associated adipocyte-tumor cell crosstalk. Thus, the focus of this Early K99/R00 application is to investigate early stages of benign pancreatic disorders, such as CP and obesity in cachexia and PDAC, respectively. Our recent work shows that tumor-derived PTHrP is a master regulator of cachexia in PDAC, and PTHrP is upregulated during CP, but a causal role for PTHrP in initiating cachexia during pancreatitis has not yet been explored. In AIM 1 (K99 phase), we will characterize the functional role of PTHrP in causing pancreatitis- associated cachexia using PTHrP-centric mouse models we have developed. In AIM 2 (K99 phase), we will investigate novel mediators of cachexia during CP at the metabolic, transcriptomic, and proteomic levels to establish an integrated framework that informs their functional role in driving cachectic wasting. At the completion of these aims, we will have built a multi-organ timeline of CP-associated wasting that can signal an upcoming PDAC diagnosis and inform therapy regimens. In AIM 3 (R00 phase), we will interrogate how obesity and impaired adipose signaling networks promote PDAC initiation and progression. The bidirectional crosstalk between the host and tumor during premalignant and malignant transformation will greatly accelerate our understanding of this deadly malignancy and aid in designing robust therapeutic strategies. The K99 aims will be accomplished by training with Dr. Jason Pitarresi, an expert on pancreas cancer and cachexia mouse modeling, and under the co-mentorship of metabolism expert, Dr. David Guertin. I will obtain additional technical and career development from my K99/R00 advisory committee, consisting of Dr. Cholsoon Jang, Dr. Evan Rosen, Dr. Julie Xue, Dr. Anirban Maitra, and Dr. Jessica Spinelli. The successful completion of this study will lead to a panel of novel functional mediators of cachexia during early premalignant stages and elucidate the role of dysregulated adipose in PDAC development.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY/ABSTRACT Plasma membrane rupture (PMR) is the terminal step of pyroptosis, a form of programmed cell death that plays a critical role in host defense and inflammation. Pyroptotic cell death is especially important in macrophages, where PMR facilitates the release of pro-inflammatory cytokines and danger-associated molecular patterns (DAMPs) that initiate and propagate immune responses. However, dysregulated PMR contributes to the pathology of numerous chronic inflammatory diseases, including Crohn’s disease, systemic lupus erythematosus, and rheumatoid arthritis. Although gasdermin D (GSDMD) pores initiate membrane permeabilization, recent studies have identified ninjurin1 (NINJ1) as a key executor of PMR by oligomerizing into discs and cutting out sections of the cell membrane. Despite this discovery, the molecular mechanisms that regulate NINJ1 activity remain poorly understood. NINJ1 is subjected to glycosylation on asparagine 60 (N60) and can also be cleaved by matrix metalloproteinase 9 (MMP9). However, the functional outcomes of these modifications concerning PMR are unknown. This proposal aims to define how post-translational modifications regulate NINJ1-mediated PMR. I hypothesize that NINJ1 glycosylation and MMP9-mediated cleavage of NINJ1 regulate PMR. In Aim 1, I will investigate how interferon (IFN)-driven glycosylation of NINJ1 promotes its oligomerization. In Aim 2, I will determine how IFN signaling restricts MMP9- mediated NINJ1 cleavage to sustain PMR. These studies will employ a combination of biochemistry, mass spectrometry, microscopy, and genetic models to dissect NINJ1 regulation at a molecular level. This research will provide novel insights into the control of inflammatory cell death and may identify new targets for therapeutic intervention in inflammatory diseases. This proposed training will equip me with expertise in innate immunology, membrane biology, and translational inflammation research, supporting my long-term goal of being an independent investigator in immunology. In addition to the scientific advances made in this project, I will expand my technical skill set and scientific knowledge in the cell death and immunology fields, refine my career development plan and build my resume, and develop my translation research abilities. Together, the work I conduct during this fellowship will support my development to pursue a research career.

NIH Research Projects · FY 2026 · 2026-05

Project Summary/Abstract The goal of this proposal is to understand how the complement component C1q impacts multiple sclerosis (MS)-related neuroinflammatory disease, and to develop a novel strategy to target complement therapeutically. MS is a neurological disease with an increasing health burden in the US. Despite significant improvements in therapy to treat episodic inflammation in relapsing-remitting disease, many MS patients develop a progressive neurodegenerative disease characterized by significant synapse loss, axon degeneration and brain atrophy with no effective treatments available. This is largely because the mechanisms behind how neurodegeneration is initiated and propagated in progressive MS patients remain poorly understood. Our lab has shown in MS patient tissue, a marmoset model of MS, and a mouse model of MS, (Experimental Autoimmune Encephalitis, EAE) that synapse loss occurs in the visual thalamus via microglia which engulf synaptic proteins. In the thalamus, we also showed an increase in complement proteins C1q and C3, which are known to regulate synapse elimination in development and disease. Interestingly, only C3 localized to the synapses. This was particularly intriguing given that C1q is typically upstream of C3 and would also be expected to localize to the synapse. We have since shown that microglia surrounding chronic active lesions in MS patients are particularly high in C1q. We have also demonstrated that with microglia-specific C1q ablation in the mouse EAE model, microglia decrease expression of Clec7a, which is a marker of reactive microgliosis, and they adopt a more branched, homeostatic morphology. These findings suggest that C1q plays an important role in regulating the reactive state of microglia and beg a further understanding of its role in regulating microglial inflammatory signaling. I hypothesize that microglia-derived C1q triggers microglia to develop into a pro-inflammatory state, which is important for both propagating neuroinflammation and for inducing astrocytes to secrete C3 necessary for synapse loss. To answer these questions, I have acquired powerful in vivo molecular genetic tools to evaluate the role of C1q in regulating neuroinflammation and C3 production necessary for synapse loss (Aim 1). I will then assess whether knocking down C1q and C3 expression with antisense oligonucleotides (ASOs) will rescue synapses and attenuate both reactive gliosis and neuroinflammation (Aim 2). These aims will be accomplished under the guidance of my sponsor Dr. Schafer (expert in microglial complement biology and neuroinflammation) and co-sponsor Dr. Ram (clinician and expert in the complement system), where I will receive critical training in neuroinflammation, complement biology, microscopy, and transcriptomics. I will also receive training in the use of ASOs from my collaborator Dr. Watts. These studies will advance our understanding of how the complement system influences neuroinflammation and synapse loss with high therapeutic potential. In the process, I will also receive a strong foundation to support my future career as a physician scientist with a focus in neuroimmunology.

NIH Research Projects · FY 2026 · 2026-05

Mapping the m3C epitranscriptome in cancer Project Summary RNA modifications are critical regulators of gene expression, with over 170 types identified across RNA molecules. Among these, m6A, m5C, and m1A are quite extensively studied for their roles in mRNA transcription, stability, and translation. In contrast, 3-methylcytidine (m3C) has been predominantly associated with tRNA modification and function, and is required for normal mRNA translation. The potential role of m3C in mRNA remains poorly understood and controversial due to conflicting experimental evidence. Mass spectrometry has suggested the presence of m3C in poly(A)-enriched RNA, but transcriptome-wide studies using chemical cleavage and next-generation sequencing have yet to provide definitive confirmation. Current methods like HAC- seq, ARM-seq, and DM-tRNA-seq are effective for tRNA modifications but inadequate for low-abundance or sub- stoichiometric m3C in mRNA. To address these limitations, this proposal will establish a highly sensitive and precise method (HARP-seq) to map m3C modifications in mRNA at single-nucleotide resolution. By integrating advanced chemical labelling & enrichment strategie, high-throughput sequencing, and bioinformatics analysis, this research will comprehensively characterize the distribution of m3C in mRNA. We will apply the newly developed method to investigate m3C modifications in mRNA across various cancer cell lines, primary tumor samples, and matched normal tissues. These findings will not only resolve current controversies regarding m3C's presence in mRNA but may provide insights into cancer-associated m3C epitranscriptomic changes and advance our comprehension of epitranscriptomic contributions to oncogenesis.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY/ABSTRACT Angiogenin, an RNase A family protein, was discovered for its ability to stimulate angiogenesis, and is thus implicated in vasculature development and cardiovascular health. The RNase activity of angiogenin is required for angiogenesis, involving the proliferation and migration of endothelial cells. Within cells, angiogenin's RNase activity is held in check by RNase inhibitor (RI). When angiogenin levels exceed RI levels during hypoxia or stresses, angiogenin cleaves its key target—transfer RNA (tRNA)—within the anticodon, which contributes to translational repression. While the downstream roles of the tRNA fragments have been an active area of investigation in recent years, the molecular mechanism of cleavage and how angiogenin’s activity induces angiogenesis remained poorly understood. One key puzzle had been the low RNase activity of purified angiogenin (>10,000-fold lower than that of its family member RNase A), whereas angiogenin becomes highly active in cells or cell extracts, indicating a cellular activator. Our recent work showed that cytoplasmic ribosome is the long sought angiogenin’s activator. Angiogenin docks into the tRNA-binding A site of the ribosome, where it intercepts tRNAs and nicks their anticodons. In this proposal, we will test the hypothesis that the ribosome- angiogenin interaction reprograms the translatome to induce angiogenesis, and we will delineate the molecular mechanisms of this reprogramming. In Aim 1, we will use bulk and single-molecule biochemistry and single-particle cryo-EM techniques to kinetically and structurally identify if angiogenin has a preferred ribosomal functional state or mRNA codon activators, understand the mechanism of translational stalling and of the restart. These findings will reveal how ribosome binding by angiogenin changes the overall translational output. In Aim 2, we will use biochemical, sequencing and cryo-EM techniques to dissect how tRNA cleavage contributes to translational reprograming, which tRNAs are cleaved and whether they can be repaired, and we will visualize the active-site of angiogenin bound with substrates for the first time. In Aim 3, we will use separation of function mutants to de-convolve the consequences of cell-entry by angiogenin from its ribosome binding and nuclease activities in human endothelial cells using deep sequencing techniques, such as ribosome profiling and transcriptome sequencing, to answer whether angiogenin’s activation reprograms translation of a specific subset of mRNAs to induce angiogenesis. The long-term goals of our work are to understand how angiogenin’s interaction with the ribosome contributes to angiogenesis and cell proliferation.

NIH Research Projects · FY 2026 · 2026-05

PROJECT SUMMARY Gene therapies based on adeno-associated virus (AAV) vectors have been a revolutionary medical advancement in treating human genetic diseases. With a single dose, AAV-mediated gene therapies can confer long-term correction or abatement of disease for the lifetime of the patient. However, recent findings have found that vector DNA integration into the host-cell genome occurs at much higher frequencies than previously thought. Furthermore, integrated transgenes seem to substantially contribute to the long-term stable expression of the therapy. These reports have drastically shifted the safety status of AAVs. The only viral elements retained in AAV vectors used in gene therapy are the inverted terminal repeat (ITR) sequences found at both the ends of the vector genome. The ITRs are essential for the stability for the AAV vector genome after entry into the host cell. We recently revealed that vectors manufactured for gene therapy can harbor truncated or mutated (t/m)ITRs with fairly high frequencies. Interestingly, these types of imperfect ITRs match the truncated ITRs observed in integration sites. I, therefore, hypothesize that truncated/mutated ITRs in AAV viruses and in packaged vectors can influence the frequency of integration. This project proposal is divided into three main aims to define if and how truncated/mutated ITRs can alter the outcomes of AAV genomes, with paradigm-shifting implications for AAV-based gene therapy applications. • Aim 1: To examine ITR structures among wildtype AAVs. Examination of wildtype ITRs, which are proven to also integrate into the host cell infected with AAV, will help to inform on how ITR integrity in gene therapy vectors influences integration. We will perform advanced NGS-based identification of ITRs among natural proviral AAV genomes found in non-human primate tissues and test the ability of wtAAVs to spontaneously form t/mITRs. • Aim 2: To track the post-entry outcomes of vectors that bear a high percentage of t/mITRs. We will test vectors that harbor t/mITRs or wildtype (wt)ITRs for their ability to integrate into the host cell genome. We will develop novel cell culture and NGS-based workflows to interrogate t/mITR-mediated integration in cultured human hepatocytes and in humanized liver mouse models. • Aim 3: To find correlation between integration frequencies in treated non-human primate tissues with the prevalence of t/mITRs in test vectors. Examination of tissues from human patients receiving gene therapy is hard to justify. Non-human primate models are the best proxy to track the kinetics of integration. We will, therefore, examine tissues treated with AAV vectors sourced from previous studies to determine the rate of integration and the structure of ITRs in multiple treated tissues of NHPs.

NIH Research Projects · FY 2026 · 2026-04

PROJECT SUMMARY More than 20 million children in the US lack sufficient access to essential healthcare. School-based health centers (SBHCs) have been broadly implemented to address this unmet need, particularly for low-income and minoritized children, by providing primary healthcare at school. Despite proven feasibility with over 3000 SBHCs now in operation in the US, the effectiveness of SBHCs to improve health outcomes has yet to be established. It is critical to determine the effectiveness of SBHCs to inform future investment and policy focused on SBHC expansion or modification, as well as best practices. Our multidisciplinary team propose asthma as an ideal pediatric disease to examine SBHC effectiveness. Asthma is the most common chronic disease in childhood, affecting more than 6 million children in the US. It has detrimental consequences, particularly for low-income, Black and Latinx children who experience more missed schooldays, poor school performance, parental lost workdays, and urgent visits than their higher income and white counterparts from asthma. This disproportionate morbidity borne by marginalized children is largely due to poor access to guideline-based asthma care and adverse social determinants of health (SDOH). Many low-income, Black and Latinx children with asthma now receive care in SBHCs and have the potential to receive guideline-based asthma care at school. While prior cross-sectional and small cohort studies suggest that SBHCs improve pediatric asthma outcomes, there has yet to be a large-scale examination of the effectiveness of SBHCs to improve asthma care and outcomes for marginalized children. With traditional community health centers (CHCs) as a comparator condition, we propose to conduct an unprecedented, multi-state and longitudinal study examining the effectiveness of SBHCs to advance health equity in asthma care. We will examine electronic health record (EHR) data from 2015-2025 in the OCHIN, inc. data network, the largest data network of SBHCs and CHCs in the US serving >6 million low-income and vulnerable patients nationwide, including 395 SBHCs and 1280 CHCs in 16 states. Our data network includes longitudinal measures of asthma care and outcomes with novel linkages to geographically coded SDOH data on community-level economic, environmental, and structural factors. In Aim 1 we will determine whether SBHCs are more (or less) effective than CHCs at providing high quality asthma care and reducing asthma exacerbations among low-income children; and evaluate the potential synergy of these two settings for optimal asthma care. In Aim 2 we will examine whether SBHCs are more (or less) effective than CHCs at improving asthma outcomes given specific adverse SDOH. In Aim 3 we will conduct qualitative work with multi-level SBHC partners, including children/caregivers, SBHC staff and policymakers to explain quantitative findings in Aims 1 and 2. Leveraging this unique network of SBHCs, this study provides a landmark opportunity to examine the effectiveness of SBHCs to improve pediatric asthma care for marginalized children and will inform national SBHC policy.

NIH Research Projects · FY 2026 · 2026-04

Project Summary Understanding how genetic variation impacts gene regulation is essential for linking noncoding variants to disease risk and transcriptional dysregulation. While cis-regulatory elements (cCREs), such as enhancers and promoters, play a central role in transcriptional control, their activity is highly cell type-specific, and most allele specific regulatory studies have been conducted at the bulk tissue level, limiting resolution. Additionally, previous studies have largely focused on gene-level expression changes, overlooking how regulatory variation affects alternative isoform usage, which has important implications for human disease. This project will integrate large-scale regulatory annotations with allele-specific analyses at the single-cell level to improve our understanding of how noncoding variation shapes transcriptional regulation. Aim 1 will establish a cCRE workspace and analysis framework in AnVIL, integrating the ENCODE Registry of cCREs into a cloud-based platform to support scalable and reproducible analyses of transcriptional regulation. We will develop modular workflows for cCRE annotation, cell type-specific scoring, and transcription factor footprinting, along with the STELLA suite, a collection of computational tools for regulatory genomics. Aim 2 will investigate how allele-specific cCRE activity influences isoform usage in individual cell types using data from the Genomic Answers for Kids (GA4K) project. We will construct personalized diploid genomes to identify allele-specific cCREs (from single-cell ATAC-seq) and allele-specific isoform usage (from bulk long-read RNA-seq). Using a Dirichlet-Multinomial deconvolution model, we will infer cell type-specific isoform expression, validated with ENCODE Split-seq data. We will then use a hierarchical regression model to test whether allele-specific cCREs predict allele-specific isoform usage, incorporating cell type assignment probabilities. Finally, we will apply ChromBPNet deep learning models to assess the functional impact of noncoding variants on transcription factor binding. By integrating these analyses into AnVIL, this project will create generalizable computational frameworks for regulatory genomics, enhancing the usability of NHGRI-funded resources. The methods and resources developed will enable broad applications across diverse datasets and disease studies, ultimately improving our ability to interpret noncoding variation in gene regulation and human disease.

NIH Research Projects · FY 2026 · 2026-04

PROJECT SUMMARY/ABSTRACT Background: This K12 application is a required companion of the UMass CTSA (UM1) application. We build on the strengths of our KL2 program, which has trained 27 scholars since its inception in 2010. Collectively, they have published 978 peer-reviewed publications and garnered $339 million as PIs in extramural funding, with all remaining in research-intensive careers. Goal and rationale: The overall goal of our new K12 Program is to develop the careers of scientists who will drive the agenda of accelerating the translational process and changing paradigms in translational science (TS). Our program is designed to develop scholars with the 7 fundamental characteristics of a translational scientist, and they will also become skilled in the 8 Scientific and Operational TS Principles. We will recruit scholars and have faculty from all 5 campuses of the University of Massachusetts and its three clinical partners. Thus, we will equip our scholars with the tools to address major challenges facing the TS workforce, specifically, its currently siloed nature and its lack of sociodemographic and scientific diversity. Methods: There will be 4 NCATS-supported scholars at any given time, who will form the core of our umbrella K program, which will use institutional funds to support another 3 diversity scholars plus another 2 supported by our clinical partners, for a steady state of 9. All 9 scholars will follow the same career development approach, with the difference being only in the source (not the amount) of funding and support. Scholars will be junior faculty (typically assistant professors) with health-related scientific interests, though not necessarily clinicians. We will rely heavily on structured transdisciplinary team mentoring with mentoring contracts and individual development plans (IDPs). IDPs will provide the compass to tailor career development plans to the needs and scientific passion of each scholar. Scholars will participate in a combination of experiential and didactic experiences and be offered the choice of one of 6 scientific pathways. There will be a required core curriculum that includes, among others, data science, translational science, leadership, and entrepreneurship. Scholars will be supported by the K12 for 2 years and expected to submit an external NIH K individual career development or R-level award by the end of the 2nd year. The scholar's department chair will commit to a 3rd year of funding if the application is competitive but not funded on 1st submission. We have developed a metrics-driven evaluation for our K12 Program based on our logic model and built in feedback loops. We will collect short- intermediate-, and long-term (15 year) outcomes. Summary: Our K12 program is designed to:1) Include mentors and scholars across the translational spectrum; 2) Use a transdisciplinary team mentoring model; 3) Offer a flexible educational platform designed to achieve NCATS competency standards for TS; 4) Use IDPs that nurture the 7 fundamental characteristics of a translational scientist; and 5) Enhance institutional values of collective creativity and collaboration.

NIH Research Projects · FY 2026 · 2026-04

Inflammatory bowel diseases (IBD), including Crohn’s disease (CD), remain a significant clinical challenge with increasing prevalence, affecting millions worldwide despite recent therapeutic advances. Loss-of-function polymorphisms in the Nod2 gene are strongly associated with CD, which has long created a conundrum as NOD2 is a cytosolic innate immune receptor that senses small fragments of the bacterial cell wall (muropeptides) and triggers an inflammatory response. Several non-exclusive explanations for this conundrum have been proposed in the literature, including altered TLR signaling, reduced antimicrobial peptide production, or altered barrier function in the gut in the absence of Nod2. All of these reported changes may contribute to the microbial dysbiosis observed in mouse models and patients with alterations in Nod2. While it is clear that NOD2 protects against colitis through some or all of these reported pathways, the mechanisms by which muropeptides, like the NOD2 agonist MDP, transit from the gut lumen to cytosolic NOD2 are unclear. Emerging evidence from studies of skin and skin keratinocytes suggests that solute carrier (SLC) transport proteins, especially the SLC46 family, mediate the internalization of MDP and other muropeptides, although this hypothesis has not yet been examined in the gut epithelia or macrophages. Here, we propose to examine the role of the SLC46A3 transporter in facilitating MDP transport and subsequent NOD2 activation, with implications for IBD. Preliminary data from murine colitis models show that Slc46a3 knockout mice exhibit increased susceptibility to colitis, resembling the pathology seen in Nod2-deficient animals. This suggests a critical role for SLC46A3 in NOD2 signaling and gut homeostasis. In this exploratory R21 proposal, we will investigate the role of the SLC46A3/NOD2 axis in the context of MDP transport, sensing and mouse models of IBD.

NIH Research Projects · FY 2026 · 2026-04

PROJECT ABSTRACT The goal of the proposal is to understand the cellular and molecular mechanisms driving periventricular inflammation in demyelinating disease and define the role of ependymal cell (EPC) derived complement component 3 (C3) in mediating this process. Periventricular inflammation has been identified as an early event in many neurodegenerative diseases. This is evident in both animal models and human diseases. For example, periventricular white matter hyperintensities (PVWMHs) are commonly observed on MRI scans in conditions such as multiple sclerosis (MS), Alzheimer’s disease, and vascular dementias in humans. Additionally, cerebrospinal fluid (CSF), which is produced within the ventricles, often contains inflammatory mediators indicative of neuroinflammation early in disease, which is often preceding cognitive symptoms. Despite these findings, the cellular and molecular mechanisms driving periventricular inflammation remain poorly understood. Our preliminary data suggest that ependymal cells (EPCs) play a key role in this process by upregulating complement component 3 (C3). C3 is particularly interesting as we and others have shown that it can drive synapse removal in MS and other neurodegenerative diseases, and it is has been implicated in regulating inflammatory processes more generally in the periphery. While past work has suggested astrocytes are the source of C3 in the brain, our data provide EPCs as another novel source that could play key roles in the neuroinflammatory process, which are highly tractable for therapeutic delivery given that half their cell body sits within the CSF. I will now tackle these new questions: 1) How does EPC-derived C3 contribute to periventricular inflammation? 2) How do ventricle-associated cells, including EPCs, astrocytes, choroid plexus, and microglia, interact with each other and the CSF to regulate neuroinflammation? I hypothesize that EPC-derived signaling, including C3, is a key driver of neuroinflammatory processes and that selective ablation of EPC-derived factors will mitigate these pathologies. With powerful in vivo tools to manipulate and monitor EPCs combined with comprehensive -omic strategies, I will now use an EPC-specific C3 deletion model to determine how loss of C3 in EPCs affects EAE severity, gliosis, demyelination, BBB integrity, and peripheral immune cell infiltration (Aim 1). I will also employ single-cell RNA sequencing (scRNA- seq) and CSF proteomics to define intercellular signaling networks between periventricular cells driving neuroinflammation and disease progression (Aim 2). Through these studies, I will receive training in in vivo neuroimaging from Dr. Shazeeb and proteomics from Dr. Lehtinen. I will also receive training in neuroinflammation, molecular genetics, transcriptomics, and bioinformatics from my sponsor Dr. Schafer, with clinical insights from my co-sponsor Dr. McManus and collaborator Dr. Hemond. Together, this project will advance our understanding of periventricular inflammation in neurodegenerative diseases and provide a foundation for my career as a physician-scientist focused on neuroinflammatory disorders.

NIH Research Projects · FY 2026 · 2026-03

PROJECT SUMMARY Monocarboxylate transporters (MCTs) mediate the transport of key metabolic intermediates, such as lactate, urate, and pyruvate, across cellular membranes. Despite their importance in metabolic homeostasis and their implication in a range of diseases—including cancer, cardiovascular disease, and neurodegeneration—the MCT family remains poorly understood. Novel approaches are needed to study the role of MCTs in physiology and disease. MCTs are highly conserved in the nematode Caenorhabditis elegans. C. elegans is a highly tractable genetic model, and its defined anatomy, simple diet, and optical transparency offers several advantages for studying conserved molecular and physiological processes. Through a genetic screen for mutants with defecation defects, I found that a point mutation in slcf-1 causes a shortened defecation cycle. slcf-1 is expressed in the intestine and regulates intestinal calcium waves (ICWs) that drive the defecation motor program (DMP). These findings implicate a novel role for MCTs, metabolism and Ca²⁺ homeostasis. slcf-1 shares homology with MCT9, which has been implicated in hyperuricemia and can contribute to cardiovascular disease, gout, and renal cell carcinoma. The overarching goal of this project is to define the role of slcf-1 in intestinal Ca2+ dynamics and metabolism. In Aim 1, I will analyze how mutations in slcf-1 affect Ca²⁺ waves. I will quantify ICW properties, such as intervals and rise and fall times, perform tissue-specific rescue, and examine SLCF-1::GFP localization. In Aim 2, I will determine SLCF-1 substrates and how SLCF-1 is dynamically regulated using HEK293T transport assays and mutant slcf-1 promotor constructs. Finally, in Aim 3, I will investigate the metabolic consequences of slcf-1 loss, assessing mitochondrial morphology, activity, and stress, alongside broader metabolic pathway alterations. These studies will provide greater insight into how conserved monocarboxylate transporters connect metabolism, calcium signaling, and intestinal motility, and promote a broader understanding of MCTs’ role in human health and disease.

NIH Research Projects · FY 2026 · 2026-03

PROJECT ABSTRACT. Rates of anxiety disorders in childhood are increasing and anxiety in childhood often predates other diagnoses. Early identification of trait-based markers associated with anxiety disorder risk, and their neural correlates, is needed to develop childhood interventions that reduce later illness burden in adolescence and adulthood. High trait anxiety is one such behavioral marker that is present in children and is stable over the lifetime. High trait anxiety is characterized by misattribution of threat, such that nonthreatening stimuli are perceived as threatening. Given the developmental importance of social stimuli, faces are a particularly salient source of potential threat in those with high trait anxiety. Indeed, anxious adults tend to perceive threatening emotional expressions at a lower intensity, misattribute threat to neutral expressions, and perceive novel faces as threatening. While threat misattribution in anxiety disorders is often thought to involve reduced prefrontal regulation of limbic regions such as the amygdala, this model alone cannot account for differences in visual discrimination in anxiety, which are present at an early latency following stimulus onset and associated with differences in visual cortical networks. For example, in anxious adults, threat misattribution is associated with altered function of the ventral visual stream and limbic regions, particularly the fusiform gyrus and the amygdala. However, the function of this network and its relationship to anxiety has not been studied developmentally. Given the earlier development of visual cortices relative to prefrontal cortices, visual- limbic networks also likely play a role in high trait anxiety and anxiety disorder risk. Therefore, understanding the development of ventral visual stream regions associated with threat misattribution offers a potential novel target for early intervention. This longitudinal functional magnetic resonance imaging (fMRI) study seeks to characterize the development of the neurofunctional correlates of social threat perception in children ranging in trait anxiety. Children ages 8-12 (n=120) will be scanned, with a subset (n=60, ages 8 to 10 at baseline) scanned a second time two years later. We will collect measures of mood and anxiety symptoms at 3-month intervals following the baseline visit for all participants. The aims of this study are to assess the function of social threat perceptual networks in high trait anxiety. Specifically, we aim to understand the neural correlates of face identity discrimination (novel vs. familiar) and visual discrimination of subtle emotional expressions in children with high trait anxiety using a series of fMRI tasks. We also will explore the development of these circuits over time, and the predictive utility of the function of these regions for understanding the later development of anxiety symptoms and prefrontal regulation of the amygdala in anxiety.

NIH Research Projects · FY 2026 · 2026-03

Project summary/Abstract Cells are required to turn specific genes on, off, up or down in response to stimuli. Transcription factors (TFs) are largely responsible for tuning (regulating) gene expression by binding to specific sites on DNA to interact with (inhibit or enhance) the transcriptional machinery. While it is now possible to precisely measure the abundance of these molecules, where they interact and the resulting level of expression from a target gene, we are still unable to predict resulting levels of gene expression from the regulatory sequence of a given gene. This is largely due to the prevalence of complicating factors that simultaneously impact regulation; each natural gene tends to be regulated by one or more TF species acting on it simultaneously and each TF has tens to thousands of binding sites in the genome. The aim of this project is to systematically measure the function and occupancy of each TF in the model bacterium E. coli in order to parameterize a predictive model of gene regulation. This novel approach exploits a tight interplay between predictive theory and quantitative experimental measurements. We will achieve this goal by using a library of E. coli strains, created previously in my lab, where the concentration of any TF can be precisely induced and measured. This data will be interpreted through a biophysical model of gene expression to characterize the regulatory function of every transcription factor as it binds to the gene and its occupancy at binding sites throughout the genome. Importantly, based on this characterization process, our model predicts regulation of more complex scenarios such as promoters regulated by multiple TFs or expressed from different RNA Polymerase assemblies. Through this process we will reveal the basic features of gene regulation by single TFs in E. coli and test how this fundamental knowledge can be assembled into a more complete model of gene regulation. In the next 5 years, we will use these measurements the function and concentration-occupancy relationship for each TF in E. coli in order to build and refine our model. We will then use that model to test its predictions against organism-wide gene regulation patterns measured at different TF concentrations.

NIH Research Projects · FY 2026 · 2026-03

Project summary/Abstract Variants in the ubiquitin like modifier activating enzyme 5 (UBA5) result in an ultra-rare autosomal recessive disease with neurological presentations. UBA5 patients present with infantile spasms, failure to thrive, hypotonia, developmental delay, microcephaly, intellectual deficit, loss of motor skills and seizures. Most of the patients die in childhood. Current standard of care for UBA5 deficiency is focused on managing the clinical signs with standard anti-seizure medications or surgical procedures and physical therapies, but there is no treatment. Compound heterozygous mutations in UBA5 causes impairment in a ubiquitin-like post-translational modification pathway called Ubiquitin-fold modifier 1 (UFM1). UBA5 is an E1 activating enzyme on UFM1 pathway. The role of the UBA5 and UFM1 system in the central nervous system (CNS) has not been studied. This stems from lack of a viable mammalian model for UBA5 deficiency. Our team has identified the first viable Uba5 mouse model that carries patient mutation, exhibits an overt phenotype, and recapitulates presentations of UBA5 deficiency in patients including smaller body size, motor, cognitive and gait abnormalities. Our team has postmortem tissues of UAB5 patients, their clinical course, MRI and EEG records. The first neuropathological characterization of postmortem UBA5 patient brain indicates the shared features with Uba5 mice. To determine the top adeno associated virus (AAV) vector candidate for efficacy studies in Uba5 mouse, we developed four UBA5 expressing constructs and showed their 1) efficacy in restoration of expression and function of UBA5 in UBA5 Knockout HEK293T cells and 2) durability, safety, and cell type tropism in a one-year study in wild type mouse. The top candidate, AAV9-JeT-UBA5, restored motor, cognitive and most aspect of gait abnormalities in Uba5 mouse model treated by neonatal intracerebroventricular (ICV) treatment. However, weight of treated Uba5 mice did not get normalized. We hypothesize that gradual loss of transduced cells in liver prevented long term weight gain normalization. Since the overarching goal of this project is to develop a transformational AAV gene therapy to treat our symptomatic UBA5 patient cohort at UMass Chan, we need to address the therapeutic imperfections and develop biomarkers. We will perform CNS and periphery wide gene therapy of JeT-UBA5 in pre and post symptomatic Uba5 mouse to determine the therapeutic window and feasibility of gene therapy to rescue or modify disease course. We will use 1) AAV9 capsid for combined CSF and periphery wide gene delivery in Uba5 mouse and 2) a new blood-brain barrier penetrant capsid (BI-hTFR1; interact with human Transferrin Receptor (TFRC)) for very efficient gene delivery to CNS and periphery by systemic injection. We will perform an in-depth characterization of the Uba5 mouse model and its humanized version, expressing TFRC, with clinically relevant outcomes measure (MRI and EEG) and compare them with patient findings (Aim 1). Four gene therapy approaches will be performed in Aim 2. In Aim 3 metabolomic based biomarker discovery will be performed and the best gene therapy approach to normalize transcriptomic profile of Uba5 mouse of will be determined.

NIH Research Projects · FY 2026 · 2026-03

PROJECT SUMMARY/ABSTRACT The UMCCTS was funded in 2010 with the vision of building healthier communities together through translational innovation. Our mission is to advance learning and discovery to solve Translational Science challenges and improve well-being by: 1) catalyzing, rigorously testing, and disseminating evidence-driven approaches that remove Translational Science (TS) roadblocks to efficient, high quality, and impactful translational research (TR); and 2) building a workforce of skilled professional staff and investigators capable of changing paradigms in TS and TR. As Massachusetts’ only public university system (UMass) partnered with 3 large clinical systems (UMass Memorial Health; Baystate Health; Lahey Health), we share an enduring focus on public engagement and societal benefit. The UMCCTS engages a broad range of interest holders (communities, patient groups, foundations, industry, NCATS, and CTSA hubs) to ensure that the research we support and workforce we train address problems important to the communities we serve. With our partners, we identify important problems and needs, develop and validate enabling platforms, and provide resources that facilitate transdisciplinary team science. We use data and analytics to generate knowledge, apply that knowledge to improve performance, then use lessons learned to inform and refine the next improvement cycle. UMCCTS workforce development programs ensure the future sustainability of the TS enterprise. Our four Specific Aims correspond to NCATS strategic goals stated in the NCATS NOFO and build on our prior successes: Aim 1: Promote individual and community health by building community-centered systems and approaches that expand and sustain the engagement of participants, communities, and research teams; Aim 2: Develop a robust set of digital tools and informatics systems that engage a broad range of study participants, promote data sharing, enable actionable insights, and that extend our Learning Health System across partners and into home and community settings; Aim 3: Provide resources that overcome TS and operational barriers to continuously improve the quality, efficiency, and impact of TR across the spectrum; Aim 4: Advance the development of a skilled TS workforce through innovative educational curricula, transdisciplinary team-based training, and career development programs. By working with our partners on each of these aims we will accomplish our overarching goal of speeding the development of evidence-based, real-world approaches that promote health, treat disease, and respond to urgent public health needs locally, regionally, and nationally.

NIH Research Projects · FY 2026 · 2026-02

Title: Investigating the role of TNF signaling in CX3CR1hi macrophages in the regulation of Tertiary Lymphoid Structure Formation & their Immunological Consequences in Inflammatory Bowel Disease Tumor Necrosis Factor (TNF) is a cytokine crucial for inflammation, immune regulation, & development of secondary lymphoid organs. TNF signaling is detrimental in inflammatory bowel disease (IBD). High levels of soluble TNF receptor 2 (TNFR2) & the polymorphisms in the TNFR2 gene are associated with Crohn’s Disease (CD). Biologics that neutralize TNF considerably improved IBD treatment. However, nearly a third of patients do not respond initially & some patients become refractory, with the reasons for this variability remaining unclear. Tertiary lymphoid structures (TLS) are disorganized lymphoid aggregates found near intestinal inflammatory lesions in IBD patients. Our prior work in Salmonella colitis showed that TLS are initiated by a distinct subset of antigen-presenting macrophages. TLS reduce infection progression, however, the mechanisms that drive TLS formation in IBD & their role in IBD are largely unknown. Increased TNF production can lead to the development of IBD-like colitis & TLS formation. Our preliminary data in Salmonella colitis show that TNF is required for TLS development & mucosal IgA response to Salmonella through TNFR1 signaling in mucosal macrophages. Similarly, Tnfrsf1(TNFR1)–/–Il10–/– mice develop colitis at an earlier age than Il10–/– mice, suggesting a protective role of TNF in IBD that remains unexplored. On the other hand, recent single-cell RNA sequencing analysis of intestinal mucosa in IBD patients identified cellular modules (enriched in IgG plasma cells, inflammatory mononuclear phagocytes, & activated T & stromal cells) named GIMATS that were associated with resistance to anti-TNF therapy. If the GIMATS represent TLS, this suggests that the progression of TLS to the preferential IgG response is independent of TNF. Thus, I hypothesize that TNFR1 signaling in macrophages supports TLS development with a pathobiont-specific protective IgA response, while excessive inflammation promotes the evolution of TLS to pathogenic IgG production, which is TNF-independent. This proposal aims to link TNF signaling in mucosal macrophage subsets to TLS formation & function in IBD, addressing the gaps in understanding TNF’s role in IBD pathogenesis & resistance to TNF therapy. We will use mice deficient in TNF & a transgenic mouse model with TNF receptors selectively removed from mucosal macrophages to assess TNF’s influence on TLS composition & function in Salmonella & Il10–/– colitis. Aim 1 will establish the contribution of macrophage-intrinsic TNFR signaling to colitis progression. Aim 2 will determine the role of macrophage-intrinsic TNFR signaling in TLS formation & antibody responses. Aim 3 will determine how macrophage-intrinsic TNFR signaling regulates the cellular composition of TLS identified in the single-cell RNAseq dataset of TLS from Salmonella & Il10–/– mice we have generated.