Biology subjects

May, M.

Publications and source records attributed to May, M..

14 recordsLinked to original sources

bioRxiv2026

Neoantigen-reactive CD8+ T cell engagement marks exceptional survivors of pancreatic cancer

Pancreatic cancer (PC) is largely refractory to immune checkpoint blockade (ICB), although homologous recombination-deficient (HRD) tumors may derive benefit. In the POLAR trial of maintenance pembrolizumab plus olaparib after platinum-based chemotherapy for metastatic PC, responses remained heterogeneous. To define determinants of productive antitumor immunity, we integrated longitudinal blood TCR sequencing with tumor single-cell and spatial profiling. Durable benefit was associated with rare tumor-infiltrating, peripherally expanding (TIE) CD8+ T cell clonotypes, a subset of which were functionally neoantigen-reactive. TIE patients showed markedly prolonged survival beyond established genomic and immune biomarkers. Conversely, resistance was associated with spatial T cell exclusion, myCAF-rich stromal remodeling, basal-like/KRAS-associated malignant-cell programs, and expansion of CTLA4 regulatory T cells linked to local immunosuppressive remodeling. These findings define a clonotype-resolved framework for immune monitoring and identify complementary stromal, tumor-intrinsic, and regulatory immune barriers that may guide rational combination immunotherapy in PC.

cancer biology↗

bioRxiv2026

DESI-MS-Based Analysis of Drug Distribution in Human Renal Cystic Tissue Using the Chorioallantoic Membrane (CAM) as a 3D In Vivo Model

The chorioallantoic membrane (CAM) model represents a promising three-dimensional in vivo platform for preclinical drug testing in human tissues. In this study, we investigated whether the tissue penetration and distribution of benzbromarone, a known inhibitor of the Ca2+ activated chloride channel TMEM16A and potential therapeutic agent for autosomal dominant polycystic kidney disease (ADPKD), can be successfully visualized in human renal cyst tissue cultured on the CAM. To this end, desorption electrospray ionization mass spectrometry imaging (DESI-MSI) combined with an ultrahigh-resolution time-of-flight mass spectrometer was employed. We achieved spatially resolved molecular mapping of endogenous metabolites and lipids as well as the applied compound. MSI enabled clear differentiation between CAM and cystic tissue based on their distinct lipid profiles. Benzbromarone was reproducibly detected in the cyst specimens and exhibited selective accumulation along the cyst epithelium, which is considered the principal site of action. These observations were complemented by multivariate analyses including Uniform Manifold Approximation and Projection (UMAP), and sparse multinomial logistic zero-sum classification. The data-driven approach confirmed molecular differences between tissue types and allowed accurate classification of drug-treated and untreated regions. This study demonstrates that topically applied benzbromarone penetrates human renal cyst tissue in the CAM model and localizes to pharmacologically relevant tissue regions, notably the location of the Ca2+ activated chloride channel TMEM16A in the epithelial lining. The integration of high-resolution DESI-MSI with advanced statistical analysis provides a robust and label-free method to study drug distribution in human tissue grafts. Our findings contribute to the advancement of translational research in analytical chemistry and pharmacology.

biochemistry↗

bioRxiv2026

An Altered Glycome Shapes IgA B-Cell Responses and Gut Immunity During Intestinal Inflammation

A healthy gut immune system balances pathogen defense and tolerance to beneficial microbes. This equilibrium is sustained by coordinated mechanisms where B cells (BCs) play a central role, and secretory immunoglobulin A (SIgA) regulates microbiome composition. In ulcerative colitis (UC), impaired tolerogenic pathways result in exaggerated immune activation, epithelial dysfunction, and tissue damage; however, the contribution of BCs to disease pathogenesis remains unclear. Notably, sialylation is crucial to B-cell function, but its relevance in the intestinal IgA B-cell response has been scarcely explored. Here, we show that SIgA from active UC patients displays an inflammation-dependent reduction in (2,6)-sialylation. This desiaylation is recapitulated in dextran sodium sulfate-induced colitis, where IgA plasma cells (IgA+ PCs) and BCs exhibit a similar glycophenotype. Functional analyses reveal that BCs lacking (2,6)-sialylation on N-glycans exhibit defective differentiation into IgA PCs and diminished capacity to suppress intestinal inflammation in vivo, with increased neutrophil infiltration. Moreover, transcriptomic analyses of UC patient samples suggest a synergistic contribution of neuraminidase activity and reduced bioavailability of sialic acid precursors, leading to SIgA desialylation. Collectively, these findings uncover a glycosylation-dependent pathological circuit in which altered sialylation of SIgA and BCs disrupts their function, compromising mucosal homeostasis in intestinal inflammation.

immunology↗

bioRxiv2025

Superior batch alignment and hyper-dimensional cytometry representations allow ultra-sensitive classification of disease phenotypes

Analysis of cytometry data predominantly relies on clustering and dimensionality reduction approaches for computational tractability. This is particularly relevant for modern spectral flow cytometers, which can simultaneously measure an increasingly large number of antibody marker channels. While dimensionality reduction provides for more efficient data processing, this comes at the expense of data loss that may miss subtle patterns among rare cell types that may be critical for disease detection. Maintaining analysis at full dimensions presents opportunities to preserve resolution and provides complete downstream data interpretability. However, a significant obstacle to analysis of cytometry data without dimensionality reduction is the significant batch effects observed in this data between experiment days, operators and equipment types. Here we show a new strategy to denoise batch variation from both flow- and mass-cytometry datasets using an autoencoder neural network architecture. We generated a benchmark flow cytometry dataset in mice to compare this approach to current toolsets and find our approach shows superior preservation of biological signals, whilst also performing batch correction equal to current best methodology. Our batch alignment approach works to such an extent that it becomes practically possible to project batch aligned data into multidimensional space to generate a novel representation of cellular phenotype for downstream model building. This hyperdimensional approach maintains original data resolution without requiring dimensionality reduction, and thus any resultant cell populations that differentiate phenotypes remain fully interpretable. We show with two large clinical datasets that our batch-alignment approach coupled with the multi-dimensional representation successfully detects meaningful patterns in cases where the original analysis methods struggled. This new framework removes some of the inherent technical limitations encountered in the integration of large, multi-batch cytometry datasets and provides a framework for machine learning model building from this modality. An implementation of this framework and an associated web application accompanies this manuscript at http://voxelcoder.cloud. Significance StatementThis work addresses a critical bottleneck in cytometry analysis by introducing a neural network-based approach that effectively removes technical batch variation while preserving biological signals. The novel hyperdimensional representation maintains full data resolution without dimensionality reduction, enabling more sensitive detection of disease-associated cellular signatures than current methods. Importantly, this framework enables reliable batch normalization of fresh samples processed at different times and locations, overcoming the practical constraints of clinical sample collection where simultaneous processing is often impossible. The enhanced sensitivity for identifying pathogenic cellular patterns has immediate implications for biomarker discovery and personalized medicine applications.

systems biology↗

bioRxiv2025

Benchmark of Wide Range of Pairwise Distance Metrics for Automated Classification of Mouse Mutant Phenotypes from Flow Cytometry Data

Precision medicine requires a comprehensive mapping of genotype to phenotype to provide patients with individually tailored treatment. However, when using flow cytometry to identify phenotypes, such as the quantity of various immune cell populations in tissue and blood used to identify autoimmune disorders, it is often unclear which cellular phenotypes are from healthy and disease individuals, especially when including the effects of population diversity, due to the high-dimensional nature of the data. To identify and segregate healthy phenotype from various disease phenotypes, we use pairwise distance metrics between each samples cell populations. By comparing distance metrics between C57BL/6 clone mice with mutations of known phenotype, we find that cosine similarity is best suited for segregating wildtype from mutant samples while respecting minute differences in already small cell populations, and that standardised Euclidean distance is best suited for machine-learning input due to its sensitivity. Both metrics outperform other tested metrics (including Aitchison, Euclidean, Manhattan, Earth-Movers Distance, and squared Euclidean). We demonstrate the utility of these different pairwise metrics through their application to a classification task of known mutant phenotypes: using an existing FACS phenotype dataset derived from X000 inbred C57BL/6 mice that harbour potentially phenotypic genetic variation introduced through ENU mutagenesis of individual pedigree-founding G0 male mice.

bioinformatics↗

bioRxiv2024

Functionally constrained human proteins are less prone to disruption of stability caused by single amino acid substitutions

It is well understood that missense mutations that disrupt protein structural stability are a common pathogenic mechanism in human genetic disease. At a proteome-wide scale, we have quantitated potential disruption of protein stability due to amino acid substitution and show that the most functionally constrained proteins are typically less susceptible to large mutational changes in stability. Mechanistically, this relates to greater intrinsic disorder among constrained proteins, but also to increased B-factors in the ordered regions of constrained proteins. This phenomenon means that constrained proteins exhibit smaller stability effects due missense mutations, and partly explains why overtransmission of pathogenic missense variation is less prevalent in genetic disorders characterised with protein truncating variation. From analysis of the predicted protein stability effects of missense genetic variation across all human proteins, we show that the most functionally constrained proteins are depleted of both destabilising ({Delta}{Delta}G > 0.5 kcal/mol) and overly-stabilising ({Delta}{Delta}G < -0.5 kcal/mol) amino acid variation in disease-free populations. Despite this, amino acid substitutions with large stability effects in functionally constrained proteins are still highly prevalent among pathogenic human genetic variation. Importantly, we observe that there are approximately five times more missense variants with large stability effects than there are unambiguous loss-of-function mutations. Missense variants with disruption of stability effects recapitulate the per-gene patterns of functional constraint observed with protein truncating loss-of-function variation, yet their relative abundance abrogates difficulties encountered when estimating functional constraint for the shortest human genes.

genomics↗

bioRxiv2023

Cytotoxic chemotherapy potentiates the immune response and efficacy of combination CXCR4/PD-1 inhibition in models of pancreatic ductal adenocarcinoma

PurposeThe CXCL12-CXCR4 chemokine axis plays a significant role in modulating T-cell infiltration into the pancreatic tumor microenvironment. Despite promising preclinical findings, clinical trials combining inhibitors of CXCR4 (AMD3100/BL-8040) and anti-programmed death 1/ligand1 (anti-PD1/PD-L1) have failed to improve outcomes. Experimental DesignWe utilized a novel ex vivo autologous patient-derived immune/organoid (PDIO) co-culture system using human peripheral blood mononuclear cells and patient derived tumor organoids, and in vivo the autochthonous LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx-1-Cre (KPC) pancreatic cancer mouse model to interrogate the effects of either monotherapy or all combinations of gemcitabine, AMD3100, and anit-PD1 on CD8+ T cell activation and survival. ResultsWe demonstrate that disruption of the CXCL12-CXCR4 axis using AMD3100 leads to increased migration and activation of CD8+ T-cells. In addition, when combined with the cytotoxic chemotherapy gemcitabine, CXCR4 inhibition further potentiated CD8+ T-cell activation. We next tested the combination of gemcitabine, CXCR4 inhibition, and anti-PD1 in the KPC pancreatic cancer mouse model and demonstrate that this combination markedly impacted the tumor immune microenvironment by increasing infiltration of natural killer cells, the ratio of CD8+ to regulatory T-cells, and tumor cell death while decreasing tumor cell proliferation. Moreover, this combination extended survival in KPC mice. ConclusionsThese findings suggest that combining gemcitabine with CXCR4 inhibiting agents and anti-PD1 therapy controls tumor growth by reducing immunosuppression and potentiating immune cell activation and therefore may represent a novel approach to treating pancreatic cancer.

cancer biology↗

bioRxiv2023

IL-38 regulates intestinal stem cell homeostasis by inducing WNT signaling and beneficial IL-1beta secretion

The IL-1 Family member IL-38 has been characterized primarily as an anti-inflammatory cytokine in human and mouse models of systemic diseases. Here, we examined the role of IL-38 in the murine small intestine (SI). Immunostaining of SI revealed that IL-38 expression partially confines to intestinal stem cells. Cultures of intestinal organoids reveal IL-38 functions as a growth factor by increasing organoid size via inducing WNT3a. In contrast, organoids from IL-38 deficient mice develop more slowly. This reduction in size is likely due to downregulation of intestinal stemness markers (i.e., Fzd5, Ephb2, Olfm4) expression compared with wild type organoids. IL-38 binding to IL-1R6 is postulated to recruit the co-receptor IL-1R9. Therefore, to analyze the molecular mechanisms of IL-38 signaling, we also examined organoids from IL-1R9 deficient mice. Unexpectedly, these organoids, although significantly smaller than wild type, respond to IL-38, suggesting that IL-1R9 is not involved in IL-38 signaling in the stem cell crypt. Nevertheless, silencing of IL-1R6 disabled the organoid response to the growth property of IL-38, thus suggesting IL-1R6 as the main receptor used by IL-38 in the crypt compartment. In organoids from wild type mice, IL-38 stimulation induced low concentrations of IL-1{beta} which contribute to organoid growth. However, high concentrations of IL-1{beta} have detrimental effects on the cultures that were prevented by treatment with recombinant IL-38. Overall, our data demonstrate an important regulatory function of IL-38 as a growth factor, and as an anti-inflammatory molecule in the SI, maintaining homeostasis. SignificanceThe IL-1 family member IL-38 has been characterized primarily as an anti-inflammatory cytokine for systemic diseases. Here we describe a fundamental role of IL-38 in driving intestinal stem cell differentiation through the upregulation of WNT3a and IL-1{beta}. Our findings reveal a dual role of IL-38 in regulating intestinal functions; (a) in resting conditions IL-38 maintains intestinal homeostasis, driving WNT3a production and organoid budding, whereas (b) in highly inflamed conditions, IL-38 contributes to proper recovery, by exerting anti-inflammatory activities. Thus, we demonstrate a pivotal role of IL-38 in driving tissue turnover and maintenance of homeostasis in intestinal health.

cell biology↗

bioRxiv2020

The genomic impact of mycoheterotrophy: targeted gene losses but extensive expression reprogramming.

ABSTRACTMycoheterotrophic plants have lost the ability to photosynthesize and they parasitize their associated fungus to get the mineral and organic nutrients they need. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy to mycoheterotrophy occurred independently in almost all major lineages of land plants, but most often in Orchidaceae. Yet the molecular mechanisms underlying this shift are still poorly understood. The comparison of the transcriptomes of Epipogium aphyllum and Neottia nidus-avis, two mycoheterotrophic orchids, to other autotrophic and mycoheterotrophic orchids showed massive molecular function losses restricted to photosynthetic activities. In addition to these targeted losses, the analysis of their expression profiles showed that many orthologs had inverted root/shoot ratios compared to autotrophic species. Fatty acid and amino acid biosynthesis as well as primary cell wall metabolism were among the pathways most impacted by this expression reprogramming. Our study suggests that, while associated with function losses rather than metabolic innovations, the shift in nutritional mode from autotrophy to mycoheterotrophy remodeled the architecture of the plant metabolism.View Full Text

plant biology↗

bioRxiv2020

Selectomic and Evolvability Analyses of the Highly Pathogenic Betacoronaviruses SARS-CoV-2, SARS-CoV, and MERS-CoV

SARS-CoV-2, the causative agent of COVID-19, is widespread in several countries around the world following its late-2019 emergence in the human population. Rapid development of molecular diagnostic tests and subunit vaccines have been prioritized, and as such evaluating the SARS-CoV-2 genomic plasticity and evolutionary dynamics is an urgent need. We determined the SARS-CoV-2 selectome by calculating rates of pervasive and episodic diversifying selection for every amino acid coding position in the SARS-CoV-2 genome. To provide context for evolutionary dynamics of a highly pathogenic betacoronavirus following a zoonotic spillover into human hosts, we also determined the selectomes of SARS-CoV and MERS-CoV, and performed evolvability calculations for SARS-CoV-2 based on SARS-CoV. These analyses identify the amino acid sites within each coding sequence that have been subjected to pervasive diversifying selection or episodic diversifying selection, and report significantly evolvable sites in the ORF1a polyprotein, the spike protein, and the membrane protein of SARS-CoV-2. These findings provide a comprehensive view of zoonotic, highly pathogenic betacoronavirus evolutionary dynamics that can be directly applied to diagnostic assay and vaccine design for SARS-CoV-2.

microbiology↗

bioRxiv2020

Three-dimensional mapping identifies distinct vascular niches for myelopoiesis

In contrast to virtually all other tissues in the body the anatomy of differentiation in the bone marrow remains unknown. This is due to the lack of strategies to examine blood cell production in situ, which are required to better understand differentiation, lineage commitment decisions, and to define how spatial organizing cues inform tissue function. Here we developed imaging approaches to map all myeloid cells in whole bones and generated 3D atlases of granulocyte and monocyte/dendritic cell differentiation during homeostasis. We found that myeloid progenitors leave the hematopoietic stem cell niche during differentiation. Granulocyte and monocyte dendritic cell progenitors (MDP) do not interact, instead they localize to different sinusoids where they give rise to clusters of immature cells. MDP cluster with Ly6Clo monocytes and conventional dendritic cells; these localize to a unique subset of colony stimulating factor 1 (CSF1, the major regulator of monopoiesis1) -expressing sinusoids. Csf1 deletion in the vasculature disrupted the MDP clusters and their interaction with sinusoids, leading to reduced MDP numbers and differentiation ability, with subsequent loss of peripheral Ly6Clo monocytes and dendritic cells. These data indicate that there is a specific spatial organization of definitive hematopoiesis and that local cues produced by distinct blood vessels are responsible for this organization. These maps provide a blueprint for in situ analyses of hematopoiesis in blood disorders.

immunology↗

bioRxiv2018

Mechanism of Microbicidal Action of E-101 Solution, a Myeloperoxidase-Mediated Antimicrobial, and its Oxidative Products

E-101 Solution is a first in class myeloperoxidase-mediated antimicrobial developed for topical application. It is composed of porcine myeloperoxidase (pMPO), glucose oxidase (GO), glucose, sodium chloride, and specific amino acids in an aqueous vehicle. Once activated, the reactive species hydrogen peroxide (H2O2), hypochlorous acid and singlet oxygen are generated. We evaluated the treatment effects of E-101 solution and its oxidative products on ultrastucture changes and microbicidal activity against methicillin-resistant Staphylococcus aureus (MRSA) and Escherichia coli. Time kill and transmission electron microscopy studies were performed using formulations with pMPO or GO omitted. The glutathione membrane protection assay was used to study the neutralization of reactive oxygen species. The potency of E-101 solution was also measured in the presence of serum and whole blood by MIC and MBC determinations. E-101 solution demonstrated rapid bactericidal activity and ultracellular changes in MRSA and E. coli cells. When pMPO was omitted, high levels of H2O2 generated from GO and glucose demonstrated slow microbicidal activity with minimal cellular damage. When GO was omitted from the formulation no antimicrobial activity or cellular damage was observed. Protection from exposure to E-101 solution reactive oxygen species in the glutathione protection assay was competitive and temporary. E-101 solution maintained its antimicrobial activity in the presence of inhibitory substances such as serum and whole blood. E-101 solution is a potent myeloperoxidase enzyme system with multiple oxidative mechanisms of action. Our findings suggest the primary site that E-101solution exerts microbicidal action is the cell membrane by inactivation of essential cell membrane components.

microbiology↗

bioRxiv2018

Mechanisms of Host Cell Binding and Neurotropism of Zika Virus

Zika virus (ZIKV) recently emerged in the Western Hemisphere with previously unrecognized or unreported clinical presentations. Here, we identify two distinct binding mechanisms of ancestral and emergent ZIKV strains featuring the envelope (E) protein residue ASN154 and viral phosphatidylserine (PS). Short (20-mer) peptides representing the region containing ASN154 from strains PRVABC59 (Puerto Rico 2015) and MR_766 (Uganda 1947) were exposed to neuronal cells and fibroblasts, expecting interactions to be representative of ZIKV E protein/cell interactions, and bound MDCK or Vero cells and primary neurons significantly above a scrambled PRVABC59 control peptide. Peptides also significantly inhibited Vero cell adsorption by ZIKV strains MR_766 and PRVABC59, indicating that we have identified a binding mechanism of ancestral African ZIKV strains and emergent Western Hemisphere strains.\n\nPretreatment of ZIKV MR_766 and PRVABC59 with the PS-binding protein annexin V significantly inhibited replication of PRVABC59, but not MR_766, suggesting that Western hemisphere strains are additionally utilizing PS-mediated entry to infect host cells. Taken together, these data indicate that we have identified an ancestral binding mechanism of ZIKV, and a secondary binding mechanism utilized by Western Hemisphere strains.

microbiology↗

bioRxiv2016

The complex sequence landscape of maize revealed by single molecule technologies

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate elucidation of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here, we report the assembly and annotation of maize, a genetic and agricultural model species, using Single Molecule Real-Time (SMRT) sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and significant improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed over 130,000 intact transposable elements (TEs), allowing us to identify TE lineage expansions unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by SMRT sequencing. In addition, comparative optical mapping of two other inbreds revealed a prevalence of deletions in the low gene density region and maize lineage-specific genes.

genomics↗