Biology subjects

Sherman, M. E.

Publications and source records attributed to Sherman, M. E..

8 recordsLinked to original sources

bioRxiv2026

Human caspase-4 and caspase-5 assemble into non-canonical inflammasomes in response to overlapping and distinct LPS structures

Innate immune sensing of bacterial lipopolysaccharide (LPS) is critical to host defense, but a dysregulated response can lead to sepsis, a life-threatening condition associated with multiple organ failure and shock. LPS is sensed at the cell surface by Toll-Like Receptor 4 (TLR4) and in the cytosol by mouse caspase-11 (Casp11) or its human orthologs, caspase-4 and 5 (CASP4/5). In response to cytosolic LPS, Casp11 oligomerizes in a catalytically dependent manner into supramolecular organizing centers (SMOCs). We demonstrate that CASP4 and CASP5 also form catalytically dependent SMOCs in response to bacterial LPS in macrophages. Furthermore, we find that CASP4 and CASP5 differentially respond to distinct LPS structural variants that fail to activate CASP11 and that only activating LPS structures induce SMOC formation by the corresponding caspase. Notably, transgenic mice expressing CASP4 in lieu of Casp11 exert more effective control of Francisella novicida, a rodent pathogen whose LPS evades TLR4 and Casp11 detection. Conversely, CASP4-expressing mice are more susceptible to sepsis when exposed to E. coli expressing a lipid A variant that fails to activate TLR4 and Casp11. Together, these findings reveal human CASP4 and CASP5 have evolved to assemble into SMOCs in response to a broader range of LPS structures than mouse Casp11 and highlight the potential tradeoff between systemic inflammation and control of bacterial infection that may underline these differences. Our findings may inform the development of targeted therapeutic strategies for gram-negative bacterial infection and sepsis that are effective in humans.

immunology↗

bioRxiv2026

The polysaccharide portion of LPS is critical for caspase-11 inflammasome activation

Caspase-11 (Casp11) is a murine zymogen that becomes active upon sensing cytosolic lipopolysaccharide (LPS), enabling it to form the non-canonical inflammasome and execute an inflammatory cell death known as pyroptosis. The lipid A acylation state of LPS is thought to be the primary regulator of Casp11 activation. However, our data demonstrate that the polysaccharide moiety of LPS, and particularly the polysaccharide phosphates, are critical for eliciting maximal Casp11 activation. Accordingly, the polysaccharide was required for Rhodobacter sphaeroides LPS to act as an inflammasome antagonist. Furthermore, isolated polysaccharide was sufficient to antagonize Casp11 activation. Mechanistically, our findings support a two-step model of non-canonical inflammasome activation where the polysaccharide recruits Casp11 to LPS and the lipid A acylation state governs oligomerization efficiency. These findings provide new insight into the molecular basis of LPS-driven Casp11 activation, with implications for the design of future therapies that target the non-canonical inflammasome.

microbiology↗

bioRxiv2026

The Human Male Mammary Gland has Similar Epithelial Populations to Female but Distinct Composition and Transcriptional Properties

The normal adult male breast has not been characterized at single-cell resolution, leaving the cellular basis of male breast cancer (MBC) biology undefined. Here we present an integrated single-cell RNA sequencing atlas of the adult human breast comprising 174,471 cells from 17 donors (3 male, 14 female), including 18,117 male-derived cells. This revealed that the male breast retains all three epithelial populations, basal (BC), luminal progenitor (LP), and luminal committed cells (LC), but with an increase in LC at the expense of BC and LP across all three male donors. Male LC were distinguished from female by elevated ESR1 and PGR mRNA, enrichment of RNA processing and ribosome biogenesis programs, reduced inflammatory cytokine and growth factor signaling, elevated estradiol gene set enrichment scores, and higher inferred activity of developmental patterning transcription factors. This pattern was observed across differential expression, gene ontology, ligand profiling, and regulon-based analyses, and was not restricted to sex chromosome-linked gene expression. This is consistent with the near-universal estrogen receptor (ER) positivity that characterizes MBC clinically. This atlas provides the first cellular and transcriptional reference for the normal male breast and a resource for investigating sex differences in mammary biology, germline susceptibility variant interpretation, and modeling breast malignancies.

cancer biology↗

bioRxiv2025

A Rare Multipotent Peg-like Epithelial Cell is a Candidate Cell-of-Origin for High-Grade Serous Ovarian Cancer

To illuminate the origins of high-grade serous ovarian cancer (HGSOC), the most lethal and common form of ovarian cancer, we have created a comprehensive living organoid biobank of human fallopian tube tissue, which is thought to be the origin of this cancer. Through optimized culture protocols and integrated multi-omic profiling--including single-cell RNA sequencing, chromatin accessibility (ATAC) analysis, proteomics, and secretomics--we assembled the largest molecular atlas of the fallopian tube epithelium to date. This resource revealed diverse epithelial lineages and regulatory networks, including a rare, multipotent epithelial subpopulation with hybrid epithelial-mesenchymal features. Spatially localized to the basal epithelium and resembling mesonephric developmental precursors, these cells exhibit transcriptomic and proteomic similarities to the mesenchyme-like subtype of HGSOC, implicating them as potential cells-of-origin. Their molecular identity is preserved in organoid models, enabling future mechanistic and translational studies. This resource, which advances fundamental understanding of epithelial hierarchy and cancer susceptibility, provides a platform to inform early detection and prevention strategies for aggressive forms of ovarian cancer. HighlightsO_LIEstablishment of a clinically annotated fallopian tube organoid biobank enables delineation of epithelial lineage hierarchies and differentiation capacity. C_LIO_LIMulti-omics integration defines robust, lineage-specific transcriptional and regulatory networks in the fallopian tube epithelium. C_LIO_LIA rare basal epithelial subpopulation with mesenchymal features aligns with a mesenchyme-like subtype of high-grade serous ovarian cancer. C_LIO_LIRare basal peg cells exhibit fetal mesonephric developmental transcriptional programs and are maintained ex-vivo in fallopian tube organoids. C_LI

cancer biology↗

bioRxiv2025

Receptor Tyrosine Kinase Profiling Identifies Chronic Constitutive Floodgate Oxidative Signaling in Glutathione-Independent Human Mammary Luminal Progenitor Cells

The human mammary epithelium contains a subset of luminal progenitor (LP) cells that are distinct from basal cells in both lineage potential and redox biology. LPs are uniquely equipped to tolerate oxidative stress through glutathione-independent mechanisms and have been implicated as candidate cells of origin in basal-like breast cancers. In this study, we identify the receptor tyrosine kinase (RTK) cKIT (CD117), as a defining feature of LPs and a key mediator of their expansion. cKIT is developmentally restricted to the LP compartment via Polycomb-mediated epigenetic repression in basal and luminal-committed cells. It is expressed in scattered epithelial cells within both ductal and alveolar regions of resting human mammary glands. Using RTK-engineered MCF10A models, we demonstrate that cKIT ligand/stem cell factor (SCF)-activated wildtype cKIT signaling is sufficient to drive proliferation in the absence of epidermal growth factor (EGF) and that cKIT is responsive not only to canonical ligands but also to hydrogen peroxide (H2O2). In primary human LPs, cKIT is rapidly phosphorylated upon exposure to SCF and H2O2, with concomitant AKT activation. These responses are enhanced when cKIT and EGFR signaling are co-engaged, suggesting a cooperative mitogenic program. In mammary gland, phosphorylation of the antioxidant enzyme PRDX1 is selectively detected in LPs, consistent with a floodgate model of redox signaling in which transient oxidative inactivation of peroxiredoxins (PRDXs) facilitates RTK signaling under elevated intracellular reactive oxygen species conditions. Clinically, elevated cKIT expression is associated with shorter progression-free survival in certain basal-like breast cancer, supporting a link between LP-like redox signaling states and aggressive tumor behavior. Together, these findings define a redox-integrated RTK signaling axis centered on cKIT that drives LP expansion and is associated with poor outcomes in a subset of basal breast cancers. This work establishes a mechanistic framework for targeting redox-responsive progenitor populations in both regenerative and oncologic context.

cancer biology↗

bioRxiv2025

TNF signaling maintains local restriction of bacterial founder populations in intestinal and systemic sites during oral Yersinia infection

Enteroinvasive bacterial pathogens are responsible for an enormous worldwide disease burden that critically affects the young and immunocompromised. Yersinia pseudotuberculosis is a Gram-negative enteric pathogen, closely related to the plague agent Y. pestis, that colonizes intestinal tissues, induces the formation of pyogranulomas along the intestinal tract, and disseminates to systemic organs following oral infection of experimental rodents. Prior studies proposed that systemic tissues were colonized by a pool of intestinal replicating bacteria distinct from populations within Peyers patches and mesenteric lymph nodes. Whether bacteria within intestinal pyogranulomas serve as the source for systemic dissemination, and the relationship between bacterial populations within different tissue sites is poorly defined. Moreover, the factors that regulate Yersinia colonization and dissemination are not well understood. Here, we demonstrate, using Sequence Tag-based Analysis of Microbial Populations in R (STAMPR), that remarkably small founder populations independently colonize intestinal and systemic tissues. Notably, intestinal pyogranulomas contain clonal populations of bacteria that are restricted and do not spread to other tissues. However, populations of Yersinia are shared among systemic organs and the blood, suggesting that systemic dissemination occurs via hematogenous spread. Finally, we demonstrate that TNF signaling is a key contributor to the bottlenecks limiting both tissue colonization and lymphatic dissemination of intestinal bacterial populations. Altogether, this study reveals previously undescribed aspects of infection dynamics of enteric bacterial pathogens. ImportanceBacterial escape from the intestine can lead to severe disease, including sepsis, organ damage, and death. However, the intestinal bacterial population dynamics governing the colonization of mucosal and systemic tissues and the intestinal sites that seed systemic spread are not clear. Yersinia pseudotuberculosis is a rodent and human intestinal pathogen closely related to the plague agent and provides a natural rodent-adapted model to study systemic bacterial dissemination. Our findings define the infection dynamics of enteric Yersinia and the impact of the innate immune system on Yersinia colonization of the intestine and systemic organs.

microbiology↗

bioRxiv2023

Targeted lipid A modification of Shigella vaccine strains reduced endotoxicity without compromising immunogenicity or invasiveness

Shigella infection contributes significantly to the global disease burden, especially affecting young children in developing countries. Currently, a vaccine against Shigella is unavailable and the prevalence of antibiotic resistance amongst Shigella species is continually rising. Live-attenuated Shigella vaccine candidates developed at Walter Reed Army Institute of Research have shown remarkable immunogenicity but exhibit adverse reactogenicity, most likely due to the highly toxic lipid A moiety present on the bacterial membrane. Previous attempts at reducing the endotoxicity have focused on deletion of intrinsic lipid A biosynthesis enzymes. In this study, we instead introduce exogenous lipid A modifying enzymes, generating targeted modifications in the lipid A structure, leading to a dampened TLR4 response within the host. In doing so, we generated vaccine candidates with detoxified lipid A and unaltered O-antigen structure thereby preserving the serotype-specific immunity while reducing endotoxicity.

microbiology↗

bioRxiv2021

Barcoded Competitive Clone-Initiating Cell (BC-CIC) Analysis Reveals Differences in Ovarian Cancer Cell Genotype and Niche Specific Clonal Fitness During Growth and Metastasis In Vivo

During oncogenesis, pathogenic clones develop which contain cells capable of spreading throughout the body, ultimately compromising vital organ functions and physiology. Understanding how metastatic clones develop and spread is critical for improving cancer treatments. However, our understanding of these processes has been hampered by a paucity of quantitative methodologies to comprehensively map, track and characterize such clones. To address this shortcoming, we have developed a DNA barcoding and next-generation sequencing based system-wide clonal tracking technology integrated with a computational data analysis pipeline called Clone-Initiating Cell (CIC) Calculator. The CIC Calculator interfaces with the CIC Morbus Mandala (CIC-MM) plot, a novel tool to visually comprehend and detect four distinct categories that explains their complex relationships with various tissues/organ sites. Further, we describe machine learning approaches to study CIC number, frequency, and estimate clone size and distribution demonstrating distinct growth patterns, and their inter-relationships and their routes of metastatic spread at clonal resolution. We demonstrate these methodologies, using our novel multifunctional lentiviral barcode libraries, and specifically barcoded tubal-ovarian metastatic OVCAR5 cell lines (engineered to express varying levels of metastasis promoting LRRC15 gene) and co-injected cells in a competitive CIC assay into tubal or ovarian sites in highly immunodeficient NSG mice. DNA was isolated from primary tumors, omental/bowel metastasis and system-wide anatomical site/organs. Amplicon sequencing libraries were constructed with spike-in-control barcodes (serving as internal calibration controls) to estimate absolute clone sizes. The computational pipeline CIC Calculator was then used to deconvolute and filter the data, set stringent thresholds, and generate high-quality information on CIC numbers and frequencies, clone sizes, linkages across sites and classify clones based on their extent of metastatic activity. Using of CIC-MM plot, statistical models and machine learning approaches, we generated high-resolution clonal maps of metastasis for each animal. The information generated included clone types and system-wide metastasis, similar and dissimilar clonal patterns of dominance at heterotopic sites and their routes of metastases. The data revealed previously unknown influences of cellular genotype and their implanted sites on selecting certain clones with specific system-wide clonal patterns, and identified rare LRRC15 expressor clones (classified as CIC.Toti) predisposed to exploit all sites, albeit at varying degrees of dominance. The genomic technology and computational methodology described here are tissue-agnostic. They enable rapid adoption for an investigation into various stages of system-wide metastasis and growth of transplantable malignant cells at the highest clonal resolution.

cancer biology↗