Biology subjects

Poholek, A. C.

Publications and source records attributed to Poholek, A. C..

9 recordsLinked to original sources

bioRxiv2025

Characterizing spatial functional microniches with SpaceTravLR

The advent of spatial omics has revolutionized our understanding of tissue biology; however, these technologies remain largely descriptive and do not capture how changes in gene regulation propagate across spatial neighborhoods. While in-silico perturbation methods and foundation models aim to model the impact of genetic perturbations, these methods are limited to single-cell approaches that lack spatial resolution. Other studies can delineate morphological domains based on transcriptional similarity, but not spatial functional microniches. We address this major unmet need by developing SpaceTravLR (Spatially perturbing Transcription factors, Ligands and Receptors), a novel interpretable machine learning approach that generalizes across tissues and species, uncovering spatial features linked to functional outcomes, thereby capturing functional microniches with spatial resolution. SpaceTravLR infers how single or combinatorial genetic perturbations rewire signals across the tissue neighborhood, by propagating effects through underlying spatially resolved molecular networks, thereby modeling how perturbations can reshape both the targeted cell and its surrounding neighborhood. SpaceTravLR defines novel spatial microniches across a range of tissues at different scales of organization (niches, neighborhoods and tissues), disease and developmental contexts. SpaceTravLRs perturbation predictions are made solely from spatial omics data and closely align with experimental validation or known outcomes based on mechanistic studies. Critically, our approach enables the generation of mechanistic hypotheses underlying identified niches. We show SpaceTravLR discovered a novel mechanism for Ccr4 that drives the spatial location of a pathogenic population of allergen-specific T helper 2 (Th2) cells as they develop in the lymph node, which was experimentally validated in a murine model. Overall, SpaceTravLR provides a novel interpretable and experimentally validated framework for uncovering how genes act individually and combinatorially through cell-intrinsic and cell-extrinsic circuits to shape spatial tissue organization and function.

systems biology↗

bioRxiv2025

A unified network systems approach uncovers a core novel program underlying T follicular helper cell differentiation

T follicular helper (Tfh) cells are central to the adaptive immune response and exhibit remarkable functional diversity and plasticity. The complex nature of Tfh cell populations, inconsistent findings across experimental systems and potential differences across species have fueled ongoing debate regarding core regulatory pathways that govern Tfh differentiation. Many studies have experimentally investigated individual proteins and circuits involved in Tfh differentiation in limited contexts, each providing only a partial understanding of the process. To address this, we adopted a novel multi-scale network systems approach that incorporates both regulatory and protein-protein interactions. Our approach integrates diverse data types, captures regulation across multiple levels of immune system organization, and recapitulates known drivers. Further, we discover a core Tfh gene set that is conserved across tissue types and disease contexts, and is consistent across data modalities - bulk, single-cell and spatial. While components of this set have been individually reported, a novel aspect of our work lies in the discovery, characterization, and connectivity of this core signature using a single unbiased approach. Using this method, we also uncover a novel function of IL-12, a molecule with reported conflicting functions, in the regulation of Tfh differentiation. Notably, we find that, in both humans and mice, IL-12 is permissive for the differentiation of Tfh precursors, but blocks subsequent differentiation into GC Tfh cells. Overall, this work elucidates novel networks with unexplored roles in governing Tfh cell differentiation across species and tissues, paving the way for novel -therapeutic interventions.

immunology↗

bioRxiv2024

AMPK agonism optimizes the in vivo persistence and anti-leukemia efficacy of chimeric antigen receptor T cells

BACKGROUNDChimeric antigen receptor T cell (CART) therapy has seen great clinical success. However, up to 50% of leukemia patients relapse and long-term survivor data indicate that CART cell persistence is key to enforcing relapse-free survival. Unfortunately, ex vivo expansion protocols often drive metabolic and functional exhaustion, reducing in vivo efficacy. Preclinical models have demonstrated that redirecting metabolism ex vivo can improve in vivo T cell function and we hypothesized that exposure to an agonist targeting the metabolic regulator AMP-activated protein kinase (AMPK), would create CARTs capable of both efficient leukemia clearance and increased in vivo persistence. METHODSCART cells were generated from healthy human via lentiviral transduction. Following activation, cells were exposed to either Compound 991 or DMSO for 96 hours, followed by a 48-hour washout. During and after agonist treatment, T cells were harvested for metabolic and functional assessments. To test in vivo efficacy, immunodeficient mice were injected with luciferase+ NALM6 leukemia cells, followed one week later by either 991- or DMSO-expanded CARTs. Leukemia burden and anti-leukemia efficacy was assessed via radiance imaging and overall survival. RESULTSHuman T cells expanded in Compound 991 activated AMPK without limiting cellular expansion and gained both mitochondrial density and improved handling of reactive oxygen species (ROS). Importantly, receipt of 991-exposed CARTs significantly improved in vivo leukemia clearance, prolonged recipient survival, and increased CD4+ T cell yields at early times post-injection. Ex vivo, 991 agonist treatment mimicked nutrient starvation, increased autophagic flux, and promoted generation of mitochondrially-protective metabolites. DISCUSSIONEx vivo expansion processes are necessary to generate sufficient cell numbers, but often promote sustained activation and differentiation, negatively impacting in vivo persistence and function. Here, we demonstrate that promoting AMPK activity during CART expansion metabolically reprograms cells without limiting T cell yield, enhances in vivo anti-leukemia efficacy, and improves CD4+ in vivo persistence. Importantly, AMPK agonism achieves these results without further modifying the expansion media, changing the CART construct, or genetically altering the cells. Altogether, these data highlight AMPK agonism as a potent and readily translatable approach to improve the metabolic profile and overall efficacy of cancer-targeting T cells.

immunology↗

bioRxiv2024

Maternal Immunoglobulin A regulates the development of the neonatal microbiota and intestinal microbiota-specific CD4+ T cell responses

Breast milk is a complex mixture of nutrients and bioactives that promote infant development and decrease the incidence of chronic inflammatory disease. We investigated the role of one milk-derived bioactive, Immunoglobulin A (IgA) on the developing small intestinal microbiota and immune system. We demonstrate that early in life, milk-derived IgA suppressed colonization of the small intestine by Enterobacteriaceae and regulated the maturation of the small intestinal epithelium and the development of intestinal IL-17-producing CD4+ T cells. Enterobacteriaceae- specific CD4+ T cells, induced in the first weeks of life in the absence of milk-derived IgA, persisted in the intestine as memory T cells that can contribute to inflammatory disease later in life. Our study suggests that milk-derived IgA shapes mucosal immunity by regulating the neonatal microbiota thus preventing the development of long-lived intestinal microbiota-specific T cells.

immunology↗

bioRxiv2022

SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains

Modern multi-omic technologies can generate deep multi-scale profiles. However, differences in data modalities, multicollinearity of the data, and large numbers of irrelevant features make the analyses and integration of high-dimensional omic datasets challenging. Here, we present Significant Latent factor Interaction Discovery and Exploration (SLIDE), a first-in-class interpretable machine learning technique for identifying significant interacting latent factors underlying outcomes of interest from high-dimensional omic datasets. SLIDE makes no assumptions regarding data-generating mechanisms, comes with theoretical guarantees regarding identifiability of the latent factors/corresponding inference, outperforms/performs at least as well as state-of-the-art approaches in terms of prediction, and provides inference beyond prediction. Using SLIDE on scRNA-seq data from systemic sclerosis (SSc) patients, we first uncovered significant interacting latent factors underlying SSc pathogenesis. In addition to accurately predicting SSc severity and outperforming existing benchmarks, SLIDE uncovered significant factors that included well-elucidated altered transcriptomic states in myeloid cells and fibroblasts, an intriguing keratinocyte-centric signature validated by protein staining, and a novel mechanism involving altered HLA signaling in myeloid cells, that has support in genetic data. SLIDE also worked well on spatial transcriptomic data and was able to accurately identify significant interacting latent factors underlying immune cell partitioning by 3D location within lymph nodes. Finally, SLIDE leveraged paired scRNA-seq and TCR-seq data to elucidate latent factors underlying extents of clonal expansion of CD4 T cells in a nonobese diabetic model of T1D. The latent factors uncovered by SLIDE included well-known activation markers, inhibitory receptors and intracellular regulators of receptor signaling, but also honed in on several novel naive and memory states that standard analyses missed. Overall, SLIDE is a versatile engine for biological discovery from modern multi-omic datasets.

systems biology↗

bioRxiv2021

Excess dietary sugar impairs colonic epithelial regeneration in response to damage.

The colonic epithelium requires continuous renewal by intestinal stem cells (ISCs) to restore the barrier after damage and proliferation of epithelial cells is modulated by dietary metabolites. We demonstrate that mice fed a high sugar diet failed to repair colonic barrier damage, resulting in increased intestinal pathology. Culturing ISCs in excess sugar limited murine and human colonoid development, indicating that dietary sugar can directly affect colonic epithelial proliferation. Similarly, in vivo lineage tracing experiments and transcriptomic analysis indicated that dietary sugar impeded the proliferative potential of ISCs. ISCs and their immediate daughter cells predominantly rely on mitochondrial respiration for energy; however, metabolic analysis of colonic crypts revealed that a high sugar diet primed the epithelium for glycolysis without a commensurate increase in aerobic respiration. Colonoids cultured in high-glucose conditions accumulated glycolytic metabolites but not TCA cycle intermediates, indicating that the two metabolic pathways may not be coupled in proliferating intestinal epithelium. Accordingly, biochemically inducing pyruvate flux through the TCA cycle by inhibiting pyruvate dehydrogenase kinase rescued sugar-impaired colonoid development. Our results indicate that excess dietary sugar can directly inhibit epithelial proliferation in response to damage and may inform diets that better support the treatment of acute intestinal injury.

immunology↗

bioRxiv2021

Altered costimulatory signals and hypoxia support chromatin landscapes limiting the functional potential of exhausted T cells in cancer

Immunotherapy has changed cancer treatment with major clinical successes, but response rates remain low due in part to elevated prevalence of dysfunctional, terminally exhausted T cells. However, the mechanisms promoting progression to terminal exhaustion remain undefined. We profiled the histone modification landscape of tumor-infiltrating CD8 T cells throughout differentiation, finding terminally exhausted T cells possessed chromatin features limiting their transcriptional potential. Active enhancers enriched for bZIP/AP-1 transcription factor motifs lacked correlated gene expression, which were restored by immunotherapeutic costimulatory signaling. Epigenetic repression was also driven by an increase in histone bivalency, which we linked directly to hypoxia exposure. Our study is the first to profile the precise epigenetic changes during intratumoral differentiation to exhaustion, highlighting their altered function is driven by both improper costimulatory signals and environmental factors. These data suggest even terminally exhausted T cells remain poised for transcription in settings of increased costimulatory signaling and reduced hypoxia.

immunology↗

bioRxiv2019

Blimp-1 in adipose resident Tregs controls adipocyte beiging and obesity

Crosstalk between the immune system and adipocytes is critical for maintaining tissue homeostasis and regulating chronic systemic inflammation during diet-induced obesity (DIO). How visceral adipose tissue resident regulatory T cells (aTregs) signal to adipocytes in the visceral adipose tissue (VAT) is not understood. Here we show that Treg-specific ablation of the transcriptional regulator Blimp-1 resulted in increased insulin sensitivity, decreased body weight and increased Ucp-1 in adipocytes in high fat diet (HFD)-fed mice. Mechanistically, we demonstrate that Blimp-1 drives IL-10 production in Tregs, thus suppressing beiging and energy expenditure in adipocytes. Moreover, IL-10 mRNA expression positively correlated with increasing body weight in humans. These findings reveal a surprising relationship between aTregs and adipocytes in promoting insulin resistance during excessive caloric intake, placing Blimp-1-regulated IL-10 expression by aTregs at a critical juncture in the development of obesity and its associated comorbidities in mice and humans. SUMMARYHere we show that ablation of Blimp-1 in adipose tissue resident Tregs (aTregs) leads to decreased IL-10 production, resulting in increased Ucp-1 expression and beiging by adipocytes and protection from diet-induced obesity and insulin resistance.

immunology↗

bioRxiv2019

Allergen-induced airway inflammation and Th2 cell development requires Blimp-1

A Th2 immune response is central to allergic airway inflammation, which afflicts millions worldwide. However, the mechanisms that augment GATA3 expression in an antigen-primed developing Th2 cell are not well understood. Here, we describe an unexpected role for Blimp-1, a transcriptional repressor that constrains autoimmunity, as an upstream promoter of GATA3 expression that is critical for Th2 cell development in the lung, but dispensable for TFH function and IgE production. Mechanistically, Blimp-1 acts through Bcl6, which is necessary to drive GATA3 expression. Surprisingly, the anti-inflammatory cytokine IL-10, but not the pro-inflammatory cytokines IL-6 or IL-21, is required via STAT3 activation to upregulate Blimp-1 and promote Th2 cell development. These data reveal a hitherto unappreciated role for an IL-10-STAT3-Blimp-1 circuit as an initiator of an inflammatory Th2 response in the lung to allergens. Thus, Blimp-1 in a context-dependent fashion can drive inflammation by promoting rather than terminating effector T cell responses. SummaryThe transcriptional repressor Blimp-1 acts via a pro-inflammatory IL-10-STAT3 axis as a critical positive regulator of Th2 cells in the lung in response to allergens driving pathophysiology associated with asthma disease.

immunology↗