Biology subjects

Sumigray, K.

Publications and source records attributed to Sumigray, K..

12 recordsLinked to original sources

bioRxiv2026

Epigenetic regulators partition the genome by evolutionary and developmental constraint

Many epigenetic regulators play essential roles in animal development, but precisely how they function across different cell types without clear sequence preferences remains a foundational challenge. Here, we employed single-cell RNA sequencing to survey the mutant phenotypes of 30 essential regulatory pathways across over 450 gastrulation stage mouse embryo replicates, including essential factors associated with repressive chromatin states, RNA surveillance/processing, and other genomic roles. We then use this integrated manifold to partition mutant responses into a developmentally-resolved interaction network, revealing a hierarchy of heterochromatin-associated interactions that act orthogonally to Polycomb Repressive Complex-mediated control of embryo patterning. Compared to the embryo proper, we find that the developing placenta and yolk sac can accommodate broad swings in repetitive element expression, a resilience in keeping with the relative evolutionary recency and phenotypic plasticity of these tissues. Dense temporal sampling of Human Silencing Hub (HUSH) mutant embryogenesis further supports the notion that the gastrulating embryo is particularly constrained and depends on multiple layers of insulation, including the need to suppress evolutionarily young genetic elements to stably license highly conserved, phylotypic programs. In combination, our work highlights the power of single cell-resolved developmental genetics to contextualize the roles of epigenetic regulators, which restrict genomic action to support robust cellular identities and embryological forms.

developmental biology↗

bioRxiv2026

Folate deficiency disrupts key metabolic transitions within the developing neural ectoderm

Despite long-standing epidemiological associations, the mechanism linking folate availability to gestational neural tube defects remains unclear, partly because measuring and interpreting metabolic activity in dynamic biological systems remains challenging. Here, we apply a deep-learning-based graph-guided variational autoencoder (MeRN; Metabolic Representation Network) to infer single-cell metabolic activity and states from scRNA-seq data of mouse embryogenesis. By analyzing folate-deficient embryogenesis from E7.0 to E9.0, we identify a transient state within the nascent neural lineage that is acutely sensitive to folate availability, leading to an interconnected disruption between key bioenergetic pathways and de novo purine biosynthesis. Moreover, metabolically induced growth defects lead to permanent morphological disruptions along the dorsal-ventral axis, which we confirm by generating whole-embryo fate maps using a prime-editing-based lineage recorder (PEtracer). Collectively, our results establish a highly scalable framework for interpreting dynamic changes in embryonic metabolism and elucidating the mechanistic bases underlying environmentally linked congenital disorders.

genomics↗

bioRxiv2026

Tissue geometry encodes a surface tension gradient that drives epithelial renewal

The mammalian intestinal epithelium renews itself every few days through coordinated cell movement and extrusion along the crypt-villus axis, yet how these processes are physically organized across intact tissue remains unknown. Using long-term live imaging of intact intestinal tissue, nuclear strain mapping, and targeted perturbations of cell-cell adhesion, actomyosin contractility, and extracellular matrix adhesion, we find that epithelial cells experience a graded mechanical landscape encoded by villus geometry; tension is highest at the villus tip and decays toward the base. This tissue-scale tension gradient, generated by E-cadherin-mediated adhesion and actomyosin contractility, is the dominant predictor of collective cell velocity, outperforming force magnitude and cell density. Artificial re-establishment of a tension gradient is sufficient to reorient epithelial migration, whereas disruption of the gradient arrests both cell movement and extrusion. Epithelial renewal further requires a precise balance between this tension gradient and extracellular matrix-derived friction; excessive friction uncouples migration from extrusion, leading to pathological cell accumulation. Together, these findings reveal that intestinal epithelial homeostasis is organized by a geometry-encoded mechanical gradient that coordinates collective cell motion, extrusion, and tissue repair through a single tissue-scale framework.

cell biology↗

bioRxiv2025

Planar cell polarity aligns epithelial migration to coordinate tissue architecture and functional zonation

Epithelial tissues must coordinate collective migration with functional specialization to maintain organ integrity, but the mechanisms linking these processes remain unknown. Here, we define the planar cell polarity (PCP) pathway as a master coordinator that translates molecular asymmetry into tissue-scale organization during postnatal intestinal development. We show that PCP drives the developmental transition from random to linear epithelial migration by aligning actin-based basal protrusions and polarizing basement membrane integrins. This creates coherent cellular streams that form characteristic villus ribbons. Strikingly, we discover that disrupting this migration coherence directly perturbs functional zonation, as loss of PCP causes disordered migration that expands specialized metabolic domains beyond their spatial boundaries. These findings reveal a previously unrecognized principle of epithelial organization: directional collective migration actively maintains functional compartmentalization, establishing migration pattern as a fundamental determinant of how tissues preserve specialized function during continuous turnover.

developmental biology↗

bioRxiv2025

ATR promotes genome instability via CENP-A eviction from centromeres under replication stress

Replication stress leads to genome instability in part by promoting missegregation of chromosomes lacking centromeres. Yet the molecular mechanism linking replication stress to centromere dysfunction has remained elusive. Here, we show that sustained replication stress induces eviction of the histone H3 variant CENP-A. Displaced CENP-A relocalizes to nucleoli. This process is dependent on the DNA damage response kinase, ATR, and occurs in both human and mouse cells. We show that ATR promotes CENP-A eviction by recruiting the AAA+ ATPase VCP to centromeres, destabilizing CENP-A-containing nucleosomes. The canonical CENP-A chaperone, HJURP, but not H3 histone chaperones DAXX or ATRX, is necessary for nucleolar CENP-A localization. Importantly, ATR-dependent CENP-A eviction endures after cell-cycle re-entry and correlates with the emergence of acentric chromosomes, linking replication stress directly to segregation defects. Our findings reveal an undiscovered role for ATR in regulating centromere identity under stress and uncover a mechanistic pathway that drives genome instability.

cell biology↗

bioRxiv2025

Fibroblast depletion reveals mammalian epithelial resilience across neonatal and adult stages

Regenerative organs, like the skin, depend on niche-stem cell interactions that sustain continuous cellular turnover. In cell culture, skin fibroblasts promote epidermal stem cell proliferation and differentiation. Yet, it remains elusive how fibroblasts regulate epidermal stem cell behaviors and differentiation in skin in vivo. Here, we asked how fibroblast depletion may impact epidermal stem cell proliferation in the context of adult homeostasis. Surprisingly, we find that significant depletion of fibroblast density does not affect epidermal stem cell proliferative capacity during adult stages in vivo. We next probed earlier neonatal stages when skin is actively remodeling but found no change in epidermal stem cell proliferative capacity following fibroblast depletion. These results demonstrate that across different ages, epidermal stem cell proliferative capacity can persist in the face of a largely reduced fibroblast population. Interestingly, neonatal fibroblast depletion does not significantly reduce their secreted collagen I density but affects basement membrane mechanics and epidermal stem cell delamination. Despite these changes, the skin continues to maintain its protective barrier function. Thus, our work demonstrates the skin regenerative program employs robust compensatory mechanisms in the face of fibroblast depletion to maintain functional capacity.

cell biology↗

bioRxiv2025

Epidermal Stem Cells Control Periderm Injury Repair via Matrix-Driven Specialization of Intercellular Junctions

Epidermal stem cells interact with the extracellular matrix (ECM) to regulate their differentiation and maintain skin architecture. Here, we demonstrate a novel role for basal epidermal stem cells (BECs)-ECM interaction in regulating adhesion molecules expressed by the periderm--the superficial epidermal cells (SECs) of the embryonic bilayered skin. Using the developing zebrafish fin fold, we identify BECs form distinct regions of collagen-versus laminin-enriched basement membranes through integrin-mediated adhesions. Mechanistically, collagen-associated BECs form desmosomes and adherens junctions (AJs) with SECs while laminin-associated BECs display reduced desmosomes but sustain AJs and actomyosin expression with SECs. Notably, we show both in vivo and in a bilayered human keratinocyte model, that laminin, compared to collagen, is sufficient to repress desmosome formation while sustaining AJs specifically at the interlayer cell contacts. In vivo, laminin deficiency enhances desmosome expression across layers and impairs the wound-healing capacity of SECs. This defect was partially rescued by genetic reduction of the desmosome protein Desmoplakin-1a, highlighting the role of ECM-dependent junctional specialization in mediating differences in SEC injury response. Overall, our findings identify that stem cells, through their matrix, establish specialized junctions in the overlying stratified epithelium, which contribute to skin healing properties.

developmental biology↗

bioRxiv2025

CFTR High Expresser BEST4+ cells are pH-sensing neuropod cells: new implications for intestinal physiology and Cystic Fibrosis disease

Single-cell RNA sequencing (scRNA-seq) studies identified a novel subpopulation of epithelial cells along the rostrocaudal axis of human intestine specifically marked by bestrophin 4 (BEST4) that are enriched for genes regulating pH, GPCR acid-sensing receptors, satiety, cGMP signaling, HCO3- secretion, ion transport, neuropeptides, and paracrine hormones. Interestingly, BEST4+ cells in the proximal small intestine express CFTR but have not been linked to the previously described CFTR High Expresser Cell (CHE) subpopulation in rat and human intestine. ScRNA-seq studies in rat jejunum identified CHEs and a gene expression profile consistent with human small intestinal BEST4+ and neuropod cells. Protein immunolocalization confirmed that CHEs express CFTR, BEST4, neuropod proteins, high levels of intracellular uroguanylin (UGN), guanylyl cyclase-C (GC-C), and the proton channel otopetrin 2 (OTOP2), and display long basal processes connecting to neurons. OTOP2, GC-C, and CFTR traffic robustly into the apical domain of CHEs in response to acidic luminal conditions, indicating their roles in luminal pH regulation. In the {Delta}F508 cystic fibrosis (CF) rat jejunum, the loss of apical CFTR did not affect BEST4 protein expression in CHEs. However, there was an increased abundance of CHE cells in the {Delta}F508 rat jejunum compared to wild-type animals. Furthermore, {Delta}F508 rat CHEs expressed higher levels of GC-C at the apical domain compared to wild-type. These data implicate CHEs in intestinal CF disease pathogenesis. NEW & NOTEWORTHYThis is the first study to identify CFTR High Expresser cells in the rat small intestine as neuropod cells capable of sensing and responding to luminal pH. This study also provides the first characterization of CFTR and relevant mRNA and proteins in CHEs in CF rat models that provide insights into the significance of CHEs to CF intestinal disease.

physiology↗

bioRxiv2025

Fibroblast contractility drives network reorganization and epithelial proliferation in intestinal polyposis

Fibroblasts are critical regulators of epithelial homeostasis through mechanics and signaling. However, the regulatory principles governing fibroblast behaviors are largely unknown. Fibroblast dysregulation has emerged as a pathological contributor in epithelial diseases such as intestinal polyposis. Here, using an inducible Bmp-loss-of-function polyposis model, we define stepwise mechanisms unraveling how dysregulated signaling perturbs fibroblast behaviors, which in turn, disrupt their function to regulate epithelial homeostasis. Intriguingly, the first initiating event leading to epithelial polyps was architectural and impacted the fibroblasts, not the epithelium. Bmp signaling inhibition caused fibroblasts to become hypercontractile, leading to their reorganization from an elaborate network into collapsed clusters beneath crypts. Disrupted fibroblast mechanics and compartmentalization preceded epithelial hyperproliferation in polyps. Using in vitro models, we show that fibroblast hypercontractility not only disrupted fibroblast organization, but also enhanced the ability of fibroblasts to support epithelial growth, leading to epithelial dysregulation. Overall, our studies reveal stepwise regulatory mechanisms underlying fibroblast signaling, mechanics and organization critical for their function to regulate epithelial homeostasis.

cell biology↗

bioRxiv2024

A second wave of Notch signaling diversifies the intestinal secretory lineage

The small intestine is well known for the function of its nutrient-absorbing enterocytes; yet equally critical for the maintenance of homeostasis is a diverse set of secretory cells, all of which are presumed to differentiate from the same intestinal stem cell. Despite major roles in intestinal function and health, understanding how the full spectrum of secretory cell types arises remains a longstanding challenge, largely due to their comparative rarity. Here, we investigate the fate specification of a rare and distinct population of small intestinal epithelial cells found in rats and humans but not mice: CFTR High Expressers (CHEs). We use pseudotime trajectory analysis of single-cell RNA-seq data from rat intestinal jejunum to provide evidence that CHEs are specified along the secretory lineage and appear to employ a second wave of Notch-based signal transduction to distinguish these cells from other secretory cell types. We further validate the general order of transcription factors that direct these cells from unspecified progenitors within the crypt and experimentally demonstrate that Notch signaling is necessary to induce CHE fate both in vivo and in vitro. Our results suggest a model in which Notch is reactivated along the secretory lineage to specify the CHE population: a rare secretory cell type with putative functions in localized coordination of luminal pH and direct relevance to cystic fibrosis pathophysiology.

cell biology↗

bioRxiv2022

Maf Family Transcription Factors are Required for Nutrient Uptake in the Neonatal Gut

There are fundamental differences in the way that neonatal and adult intestines absorb nutrients. In adults, macromolecules are efficiently broken down into simpler molecular components in the lumen of the small intestine, then absorbed. In contrast, neonates are thought to rely more on bulk intake of nutrients and subsequent degradation in the lysosome. Here, we identify the Maf family transcription factors, MafB and cMaf, as markers of terminally-differentiated intestinal enterocytes throughout life. The expression of these factors is regulated by HNF4/{gamma}, master regulators of the enterocyte cell fate. Loss of Maf factors results in a neonatal-specific failure to thrive and loss of bulk uptake of nutrients. RNA-Seq and CUT&RUN analyses defined an endo-lysosomal program as being downstream of these transcription factors. We demonstrate major transcriptional changes in metabolic pathways, including fatty acid oxidation and increases in peroxisome number in response to loss of Mafs. Finally, we show that deletion of Blimp1, which represses adult enterocyte genes in the neonatal gut, shows highly overlapping changes in gene expression and similar defects in nutrient uptake. This work defines transcriptional regulators that are necessary for bulk uptake in neonatal enterocytes.

physiology↗

bioRxiv2017

Rap1 acts via multiple mechanisms to position Canoe/Afadin and adherens junctions and mediate apical-basal polarity establishment

Epithelial apical-basal polarity drives assembly and function of most animal tissues. Polarity initiation requires cell-cell adherens junction assembly at the apical-basolateral boundary. The mechanisms underlying this remain key issues. Drosophila embryos provide a superb model, as 6000 polarized cells assemble simultaneously. Current data place the actin-junctional linker Canoe (mammalian Afadins homolog) at the top of the polarity hierarchy, where it directs Bazooka/Par3 and adherens junctions positioning. Here we define mechanisms regulating Canoe localization/function. Spatial organization of Canoe is multifaceted, involving membrane-localization, recruitment to nascent junctions and macromolecular assembly into cables at tricellular junctions. Our data suggest apical activation of the small GTPase Rap1 regulates all three events, but support multiple modes of regulation. The Rap1GEF Dizzy/PDZ-GEF is critical for Canoe tricellular junction enrichment but not apical retention. Canoes Rap1-interacting RA-domains mediate adherens junction and tricellular junction recruitment but are dispensable for membrane-localization. Our data also support a role for Canoe-multimerization. These multifactorial inputs all shape Canoe localization, correct Bazooka/Par3 and adherens junction positioning, and thus apical-basal polarity. We integrate existing data into a new polarity establishment model.\n\nAbbreviations used-cat, alpha-catenin; {beta}-cat, beta-catenin; AJ, adherens junction; Arm, Armadillo; Baz, Bazooka; CA, constitutively active; Cno, Canoe; DE-cad, Drosophila E-cadherin; Dzy, Dizzy; GAP, GTPase activating protein; GDP, guanosine diphosphate; GEF, guanine nucleotide exchange factor; GFP, green fluorescent protein; GTP, guanosine triphosphate; IF, immunofluorescence; MIP, maximum intensity projection; RA, Ras-associated; RFP, red fluorescent protein; SAJ, spot adherens junction; shRNA, short hairpin RNA; TCJ, tricellular junction; WT, wildtype

developmental biology↗