Biology subjects

Zhou, H.

Publications and source records attributed to Zhou, H..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

cellSTAAR: Incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of non-coding regions

Whole genome sequencing (WGS) studies have identified hundreds of millions of rare variants (RVs) and have enabled RV association tests (RVATs) of these variants with complex traits and diseases. Analysis of non-coding variants is challenged by the considerable variability in regulatory function which candidate Cis-Regulatory Elements (cCREs) exhibit across cell types. We propose cellSTAAR, which integrates WGS data with single-cell ATAC-seq data to capture variability in chromatin accessibility across cell types via the construction of cell-type-specific functional annotations and variant sets. To reflect the uncertainty in cCRE-gene linking, cellSTAAR also links cCREs to their target genes using an omnibus framework which aggregates results from a variety of popular linking approaches. We applied cellSTAAR on Freeze 8 (N = 60,000) of the NHLBI Trans-Omics for Precision Medicine (TOPMed) consortium data to four lipids phenotypes: LDL cholesterol, a binary variable corresponding to high LDL cholesterol, HDL cholesterol, and triglycerides. We also provide replication results for all four phenotypes using UK Biobank (N = 190,000). Evidence from simulation studies and our real data analysis demonstrates that cellSTAAR boosts power and improves interpretation of RVATs of cCREs.

genetics↗

bioRxiv2025

Exploring non-invasive sexing of early chick embryos in intact eggs using Laser Speckle Contrast Imaging (LSCI) and Deep Neural Network (DNN)

The ability to image blood flow in early-stage avian embryos has significant applications in developmental biology, drug and vaccine testing, as well as determining sex differentiation. In this project, we used our recently developed laser speckle contrast imaging (LSCI) system to non-invasively image extraembryonic blood vessels and used these images to attempt early sex identification of chick embryos. Specifically, we captured images of blood vessels from 1,251 living chicken embryos between day three and day four of incubation. We then applied deep neural network (DNN) models to evaluate whether it is possible to differentiate sex based on vascular patterns. Using ResNetBiT and YOLOv5 models, our results indicate that sex differentiation from extraembryonic blood vessel images was not achievable with sufficiently high accuracy or statistical significance for practical use. Specifically, ResNetBiT had a five-fold cross-validated average accuracy of 59%{+/-}5% (fold-wise p-value, p [≤] 0.3) at day 3 and 61%{+/-}3% (fold-wise, p [≤] 0.04) at day 4. YOLOv5 had a five-fold cross-validated average accuracy of 55%{+/-}3% (fold-wise, p [≤] 0.3) at day 3 and 53%{+/-}3% (fold-wise, p [≤] 0.5) at day 4. Our findings suggest that using vascular pattern imaging alone is inconclusive for reliable early sex identification in chicken embryos.

bioengineering↗

bioRxiv2025

Targeting protein glycosylation and cholesterol metabolism in chemoresistant pancreatic cancer

Chemotherapy remains the cornerstone of pancreatic ductal adenocarcinoma (PDAC) treatment. However, most cases of PDAC finally progress to advanced chemoresistant disease. This highlights an urgent need to develop new pharmacological strategies to overcome chemotherapy resistance using clinical grade inhibitors. Here, we established a biobank comprising 260 organoid lines derived from 322 pancreatic cancer patients. These organoids underwent extensive multi-omics profiling and drug sensitivity testing for both chemotherapy and targeted therapy. Increased protein glycosylation and cholesterol metabolism signaling pathways were especially enriched in chemoresistant organoid lines. Importantly, chemoresistant PDAC organoids were effectively targeted with statins, inhibitors of cholesterol synthesis. Statins treatment attenuated protein glycosylation, cholesterol levels, and the epithelial-to-mesenchymal transition (EMT) signature in PDAC organoids. We further conducted a phase 2 clinical trial (NCT06241352) combining atorvastatin with chemotherapy in patients with advanced chemoresistant pancreatic cancer. Among 29 patients, 21 (72.4%) demonstrated a response, with tumor markers decreasing by more than 20%, suggesting durable responses and potential clinical benefits in this challenging patient population. ClinicalTrials.gov identifier: NCT06241352.

cancer biology↗

bioRxiv2025

Disturbing immune homeostasis by neutrophil loss of Uba1 induces VEXAS-like autoinflammatory disease in mice

ObjectiveVEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) syndrome is an identified haemato-rheumatoid disease caused by somatic UBA1 mutations in hematopoietic stem cells. We report Uba1 loss in various mouse hematopoietic cell types leads to diverse effects, with approximately 70% Uba1 depletion in neutrophils inducing non-lethal VEXAS-like symptoms. MethodsUsing nine different Cre/flox-mediated conditional-knockout (CKO) models, we interrogated the phenotypes caused by hematopoietic loss of Uba1. Neutrophil-specific depletion of Uba1 were validated and VEXAS-like phenotypes were examined. ResultsUba1 loss in HSCs induces extensive hematopoietic cell death while in B or T cells, or megakaryocytes induces corresponsive cell death but these mutants appear normal. Uba1 loss in monocytes and neutrophils failed to induce cell death and the mutants are viable. Among the models, only Uba1 loss in neutrophils manifests autoinflammatory symptoms including increased counts and percentage of neutrophils, increased proinflammatory cytokines, vacuoles in myeloid cells and dermatitis. Residual Uba1 is about 30% in the mutant neutrophils, which manifest disturbed cellular hemostasis. Genetic loss of Morrbid partially mitigated the VEXAS-like symptoms. ConclusionOur study reveals diverse effects of Uba1 loss in hematopoietic cells and establishes a VEXAS-like murine model, facilitating understanding and potential treatments for this syndrome prevalent in aged men. HIGHLIGHTSO_ST_ABSWHAT IS ALREADY KNOWN ON THIS TOPICC_ST_ABSVEXAS syndrome is a recently identified hematological and immunological disease prevalent in adult man but rarely in adult woman. Somatic mutations in the E1-enzyme encoding gene UBA1 in hematopoietic stem cells is the driver on the top of the genetic etiology of the disease. However, the major pathogenic cell type(s) for VEXAS syndrome has not been experimentally examined and mouse models recapitulating the disease are lacking. WHAT THIS STUDY ADDSO_LIUsing nine different conditional-knockout (CKO) murine models, we interrogated the pleiotropic phenotypes caused by loss of the ubiquitin activation enzyme Uba1 in different hematopoietic cell types; C_LIO_LIOur results demonstrated that among the nine tested CKO mutants, only neutrophil loss of Uba1 results in VEXAS-like autoinflammatory disease; C_LIO_LIThe VEXAS-like symptoms in the S100a8Cre-CKO mutant mice include: increased counts of white blood cells and neutrophils, increased percentage of neutrophils, increased serum level of proinflammatory cytokines (IL-1{beta}, IL-6 and TNF), observation of vacuoles, increased survival, and increased phagocytosis in mutant neutrophils; C_LIO_LIPharmacological treatments with IL-1 inflammatory pathway inhibitors Anakinra or Canakinumab or genetic loss of the myeloid pro-survival regulator Morrbid partially mitigated the VEXAS-like symptoms in the S100a8Cre-CKO mutants; C_LI HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYThe study reports a technical strategy of developing the murine models for VEXAS syndrome. In addition, the study dissects cellular and molecular mechanisms, especially the cell-type-dependent tolerance and pathogenicity of loss of function of Uba1, for the occurrence of the autoinflammation diseases in mice. The study provides translational implications in etiology and potential treatment choices for the newly-identified haemato-rheumatoid syndrome in clinical management.

immunology↗

bioRxiv2025

MENDELSEEK: An algorithm that predicts Mendelian Genes and elucidates what makes them special

Although individual Mendelian diseases--those caused by a single gene--are rare, their collective disease burden is substantial. Identifying the causal gene for each condition is essential for accurate diagnosis and effective treatment. Yet, despite decades of research, the genetic basis of more than half of all known Mendelian diseases remains unresolved. To address this gap, we introduce MENDELSEEK, a machine learning framework that predicts Mendelian genes by integrating residue variation scores with pathway participation, Gene Ontology processes, and protein language model features. In benchmarking across 16,946 human genes with 10-fold cross-validation, MENDELSEEK achieved an AUC of 0.869 and an AUPR of 0.737--substantially outperforming the next best methods, ENTPRISE+ENTPRISE-X (AUC 0.781; AUPR 0.626), and REVEL (AUC 0.585; AUPR 0.401). When applied to the full set of 17,858 human genes, MENDELSEEK predicted 1,277 novel Mendelian gene candidates with precision greater than 0.7. Analysis further revealed that Mendelian genes engage in significantly more protein-protein interactions than non-Mendelian genes and are evolutionarily ancient. Together, these results highlight MENDELSEEK as a major advance over existing methods, offering new insights into the biochemical features that distinguish Mendelian from non-Mendelian genes.

genomics↗

bioRxiv2025

Two telomere-to-telomere, gap-free genome assemblies and comparisons revealed the conserved key genes associated with sugar accumulation in Rubus genus

For the first time, we assembled two highly continuous, completely gap-free reference genomes of the Rubus subgenus: Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP), which are widely distributed in southern China with similar phenotypic traits (Figures 1A, 1B, and Figure S1), yet ripe fruits display distinct sugar accumulation levels (Table S1), making them ideal candidates for investigating the mechanisms underlying sugar accumulation in the Rubus genus. The XMM (213.53 Mb, 28,204 genes) and DHP (218.26 Mb, 28,569 genes) genomes exhibit close evolutionary relationships, diverging approximately 3.21 Mya. Comparative genomics identified extensive synteny, interspecific structural variations (translocations, inversions, segmental duplications), and presence/absence variation (PAV). Using Hi-C interaction heatmaps and Sanger sequencing, we validated interspecific structural inversions. Additionally, we identified a sugar transporter gene (MFS1), which is present in XMM but absent in DHP. Combined analysis of the gene family expansion/contraction and transcriptome identified two conserved key genes (RhSTP13 and RhSTP7) associated with sugar accumulation in Rubus genus and displayed distinct roles through transient expression assay. To facilitate functional genomics study, we also established a comprehensive Rubus database, RubusDB, a freely accessible repository consolidating all genomic, transcriptomic and phenotypic data of Rubus genus. These findings provide a foundational framework for elucidating the genetic basis of sugar accumulation, genome diversification, and trait improvement in Rubus species. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/646780v2_fig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@1baca20org.highwire.dtl.DTLVardef@2c01eaorg.highwire.dtl.DTLVardef@131dc00org.highwire.dtl.DTLVardef@62a04f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFIGURE 1.C_FLOATNO Phenotypic characterization, de novo genome assemblies, variation, and evolution of Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP). (A) Illustration of XMM whole plants, stem, flower bud and flower, respectively. (B) Illustration of DHP whole plants, stem, flower bud and flower, respectively. (C) The chromosome karyotype analysis of XMM. Bar = 10 {micro}m. (D) Circular diagram of XMM and DHP reference genomes. (a) Chromosomes are represented by centromeres (dark red) and telomeres (blue); (b) CEN18 density; (c) CEN17 density; (d) Gene density; (e) TE density; (f) PAV density; (g) SNP density; (h) Collinear lines at the center of diagram highlight homoeologous chromosomes relationships and non-homoeologous regions. (E) Genomic alignments between XMM and DHP. Inversions, duplications and translocations are marked with orange, blue and green ribbons, respectively. (F) Identification of large inversions in chromosome 7 between XMM and DHP. The three heatmaps show the chromatin interaction matrix, including mapping Hi-C data of DHP against DHP genome (left), mapping Hi-C data of DHP against XMM genome (middle) and mapping Hi-C data of XMM against XMM genome (right). The lower panel illustrates gene alignments between XMM and DHP. (G) Synteny, structural rearrangements, monomer, and identity distribution in the 16-20 Mbp region of chromosome 6 between XMM and DHP. (H) Local genome synteny of chromosome 5, with a structural variation that is present only in XMM. The PAV region includes a gene related to sugar transporter (MFS1, XMM05G025540). (I) Gene-level matchings of MFS genes in the PAVs region between XMM and DHP. (J) Phylogenetic relationships and divergence times between raspberries and other Rosaceae species. The black numbers close to the divergence nodes indicate the divergence times and the red bars represent the 95% confidence intervals. The red and black numbers indicate expanded and contracted ortholog groups at the corresponding node. Scale bar corresponds to 10 Mya. C_FIG

genomics↗

bioRxiv2025

Targeted Protein Degradation by KLHDC2 Ligands Identified by High Throughput Screening

Proteolysis targeting chimeras (PROTACs) enable the selective and sub-stoichiometric elimination of pathological proteins, yet only two E3 ligases are routinely used for this purpose. Here, we expand the repertoire of PROTAC compatible E3 ligases by identifying a novel small molecule scaffold targeting the ubiquitin E3 ligase KLHDC2 using a fluorescence polarization-based high throughput screen. We highlight the utility of this ligand with the synthesis of PROTACs capable of potently degrading BRD4 in cells. This work affords additional chemical matter for targeting KLHDC2 and suggests a practical approach for identifying novel E3 binders by high throughput screening.

biochemistry↗

bioRxiv2025

High-throughput Monoclonal Antibody Screening from Immunized Rabbits via Droplet Microfluidics

The discovery of monoclonal antibodies (mAbs) is critical to advancing therapeutics, diagnostics, and biomedical research. While mouse-derived mAbs dominate current applications, their limitations--short serum half-life, human immunogenicity, and restricted recognition of human-specific antigens--underscore the need for alternative sources. Rabbit-derived mAbs have been gaining significant traction with their superior antigen-binding affinity, broader epitope diversity, and higher yield potential. However, the absence of well-defined surface markers on rabbit B cells has hindered efficient enrichment strategies, limiting the exploration of this valuable antibody repertoire. In this study, we present an integrated workflow that combines magnetic negative selection with high-throughput droplet microfluidics to overcome these barriers. By optimizing a pan B cell enrichment protocol using a tailored antibody cocktail, we achieved a notable boost in IgG secretion and B cell enrichment. Through two complementary droplet-encapsulated assays using particle aggregation for soluble antigens and reporter cells for membrane-bound antigens, we identified target cells capable of secreting high-affinity IgGs. Subsequent sequencing, in vitro antibody production and characterization confirmed the high affinity rate of the discovered antibodies, outperforming rates previously reported. The use of droplet microfluidics streamlines the analysis of rabbit IgG repertoires, providing a robust platform for rabbit single B cell antibody discovery with promising applications in precision medicines and diagnostics.

molecular biology↗

bioRxiv2025

Cortactin regulates metastatic dormancy of circulating tumor cells by suppressing mTOR-dependent senescence

Metastatic dormancy often refers to the stable cell cycle arrest of disseminated tumor cells (DTCs) at distant sites. However, whether circulating tumor cells (CTCs) in the blood microenvironment can enter a dormant state prior to extravasation and becoming DTCs remains unclear. Using patient-derived melanoma CTC lines and animal explant models (CDX), we identified a previously unrecognized role of the cytoskeletal regulator cortactin (encoded by CTTN) in controlling mTOR/p53-dependent senescence and metastatic dormancy. Cortactin was localized to Rab7-postive endosomes and engaged in late endosomal tethering and homeostasis. The depletion of cortactin resulted in the accumulation of aberrantly enlarged late endosomal aggregates that were positive for Rab7 and mTOR. The mTOR protein complex was accumulated and activated within these abnormal vesicular structures, leading to robust p53 activation through phosphorylation at serine (S) 15 and S33 sites. Consequently, melanoma CTCs underwent G0/G1 cell cycle arrest and entered cellular senescence. This unusual oncogene-induced senescence (OIS) mechanism was characterized by SASP upregulation, {beta}-galactosidase activity, depletion of Ki-67 and Lamin B1, and elevated mitochondrial ROS (mtROS) levels. Notably, a positive feedback loop between p53 and mtROS was essential for maintaining stable senescence in CTCs. In preclinical CDX mouse models, we developed a sequential therapeutic strategy combining cortactin depletion with anti-Bcl-xL senolytic drugs. Such "One-two punch" treatment strategy effectively eliminated viable CTCs and suppressed metastatic tumor growth in vivo. Thus, targeting cortactin to induce CTC senescence, followed by senolytic therapy, may represent a promising strategy to block CTC-mediated metastatic progression.

cancer biology↗

bioRxiv2025

BioBatchNet: A Dual-Encoder Framework for Robust Batch Effect Correction in Imaging Mass Cytometry

MotivationImaging Mass Cytometry (IMC) is a cutting-edge technology for analysing spatially resolved protein expression at the single-cell level. However, its downstream analyses are often hindered by batch effects, which introduce systematic biases and obscure true biological variations. Existing correction methods, largely developed for scRNA-seq data, struggle to achieve precise control, leading to either over-correction by removing critical biological information, or under-correction by leaving residual batch effects. Moreover, these methods face challenges in adapting to IMC data due to differences in data characteristics. Furthermore, IMC data often feature imbalanced and overlapping cell populations, complicating clustering and downstream analysis. These challenges underscore the need for a robust and controllable batch effect correction approach tailored to IMC data. ResultsWe present BioBatchNet, a dual-encoder framework utilising adversarial training to explicitly disentangle batch-specific and biological signals. BioBatchNet enables controllable batch effect correction, effectively balancing correction with the preservation of biological variation. We evaluated BioBatchNet on three IMC datasets, where it outperformed seven benchmarking methods with robustness in both correction and biological signal conservation. Additionally, we developed a Constrained Pairwise Clustering (CPC) method, which employs constrained pairs to improve clustering performance, even in datasets with imbalanced and overlapping cell populations. To validate its generalisability, BioBatchNet was also applied to four scRNA-seq datasets, where it delivered competitive performance compared to eight typical methods. These results demonstrate BioBatchNets generalisability and robustness in correcting batch effects across diverse single-cell datasets and underscore its potential for large-scale biological analyses.

bioinformatics↗

bioRxiv2025

Proteomic Analysis of PTEN-Deficient Cells Reveals Src-Mediated Upregulation of EphA2 and Therapeutic Potential of Dual Inhibition

Loss of the tumor suppressor PTEN is frequently observed in various cancers and promotes tumorigenesis by activating the PI3K-AKT pathway. However, the effectiveness of therapies targeting this pathway is limited by complex signaling crosstalk and compensatory mechanisms. Here, we employed quantitative proteomic and phosphoproteomic analyses using MCF10A PTEN knockout models to comprehensively map the signaling alterations induced by PTEN loss. Our analyses revealed that PTEN deficiency not only activates canonical PI3K-AKT signaling but also induces widespread changes in cytoskeleton organization, cell cycle regulation, and central carbon metabolism. PTEN loss also substantially elevates the activity of a variety of tyrosine kinases, including Src kinase and EphA2, a receptor tyrosine kinase (RTK) implicated in cancer progression. Mechanistic studies demonstrated that Src activation, rather than the canonical AKT signaling pathway, drives the upregulation of the receptor tyrosine kinase EphA2. The activation of the noncanonical tyrosine kinase signaling renders AKT inhibition alone insufficient in PTEN-deficient cancers. Importantly, combined treatment with the FDA-approved AKT inhibitor capivasertib and the Src inhibitor dasatinib synergistically induced apoptosis and suppressed the tumor cell growth in various PTEN-deficient cell lines as well as in three-dimensional cultures of endometrial cancer patient-derived xenograft models. Our study reveals that PTEN loss drives oncogenic signaling via dual activation of PI3K-AKT and tyrosine kinase pathways. Specifically, Src-mediated upregulation of EphA2 in PTEN-deficient cells highlights a therapeutic vulnerability that can be exploited by combined AKT and Src inhibition. This approach addresses the resistance associated with AKT inhibition alone and enhances therapeutic efficacy in PTEN-deficient cancers, supporting its potential application in targeted combination therapies.

cancer biology↗

bioRxiv2025

AI-Guided Precision in Antibody Humanization: Structural Modeling to Minimize Immunogenicity and Preserve Efficacy

Antibody humanization is an essential part of converting animal-derived antibodies into clinical candidates however conventional CDR grafting techniques often faces challenges, especially when essential antigen-binding sites extend beyond CDR regions. Additionally, the CDR grafting process tends to retain undesired non-human elements within the CDR regions. In this study, we overcame these challenges by using our proprietary AI-predicted antigen-antibody complex algorithm to effectively humanize a murine antibody. During our AI-powered humanization process, in contrast to traditional CDR grafting techniques, only the crucial paratopes identified through our AI-predicted complex structure were precision grafted onto a select human germline. This paratope grafting technique significantly reduced the antibodies immunogenicity risk while maintaining bioactivity. Moreover, all AI-guided deep humanized antibody variants demonstrated favorable developability, including thermal stability, poly-reactivity, and hydrophobicity. These results not only advance antibody humanization techniques but also demonstrate the power of AI in expediting antibody engineering and derisking clinical research.

bioengineering↗

bioRxiv2025

Harnessing Uniform Design to Enhance AI-Driven Predictions of Physicochemical Properties of Short Peptides

Short peptides hold significant promise in drug discovery and materials science due to their biocompatibility, multifunctionality, and ease of synthesis. However, accurately predicting their physicochemical properties, a prerequisite for application development, remains a challenge. This study presents an innovative approach integrating uniform design (UD) with artificial intelligence (AI) to enhance prediction of key physicochemical properties, including aggregation propensity (AP), hydrophilicity (logP), and isoelectric point (pI). Using UD, we generate 31 distinct peptide datasets, with a consistent amino acid occupation fraction of 5% at each position, thereby creating unbiased training data for AI models. The performance of each AI model is rigorously evaluated using various testing schemes, and optimal sample sizes are determined for accurate prediction of each property. Additionally, Shapley Additive Explanations (SHAP) analysis identifies aromaticity, logP, net charge, and pI as the primary factors affecting peptide aggregation. This work provides comprehensive datasets on the physicochemical properties of all tetrapeptides, develops robust AI-based predictive models, and elucidates the relationships between key physicochemical characteristics and self-assembly behavior. By integrating experimental design, AI modeling, and peptide domain knowledge, our approach facilitates the discovery and optimization of functional peptides, offering new opportunities for peptide-based therapeutic applications.

bioinformatics↗

bioRxiv2025

NLRP10 Cleaves Oxidized DNA inhibited by OGG1 inhibitors: A Newly Identified Role in DNA Damage Processing and Senescence Regulation.

Mitochondrial DNA (mtDNA) release into the cytosol is a critical event in innate immune activation, often acting as a damage-associated molecular pattern (DAMP) that triggers inflammasome assembly. Here, we demonstrate that NLRP3 plays a direct role in cleaving and facilitating the release of D-loop mtDNA into the cytosol. We further show that NLRP3 interacts with NLRP10. NLRP10-mediated ox-DNA cleavage involves a Schiff base intermediate and is inhibited by small molecules known to inhibit glycosylases. These findings support a model where NLRP10 interaction with oxidized DNA may contribute to long-term senescence secretory phenotype and modulate inflammasome activation. Our study highlights a novel mechanism by which NLRP10 can respond to mitochondrial stress signals to influence innate immunity and suggests therapeutic potential for targeting these interactions in inflammatory diseases.

immunology↗

bioRxiv2025

The TONSL-MMS22L complex and FANCM form an interdependent complex on chromatin to counter replication stress

FANCM is branchpoint DNA translocase essential for cellular response to replication stress. Here, we show that replication stress stimulates FANCM and the TONSL-MMS22L heterodimer bound to histones H3-H4 to form an interdependent complex on chromatin. TONSL-MMS22L recruits FANCM and Fanconi anemia (FA) core complex to stalled and collapsed forks, maintains FANCM on replication-stressed chromatin, promotes FANCD2 monoubiquitination, facilitates both repair and replication traverse of DNA interstrand crosslinks (ICLs), and suppresses sister chromatid exchanges, through its interactions with FANCM and H3-H4. Reciprocally, both DNA translocase activity and phosphorylation of FANCM facilitate recruitment of TONSL-MMS22L and RAD51 to perturbed forks. Moreover, TONSL-MMS22L and FANCM function together to promote activation of the FA pathway, ICL repair, homologous recombination and replication traverse. Cancer patients with tumors with wildtype FANCM and low expression of TONSL-MMS22L have a more favorable prognosis than those with high expression. Thus, FANCM-TONSL-MMS22L acts coordinately as a complex on chromatin that resolves replication stress, and this complex may present a therapeutic target for wildtype FANCM-linked cancer.

cell biology↗

bioRxiv2025

Bacterial Vaginosis Toxins Impair Sperm Capacitation and Fertilization

Study questionWhat effect do toxins produced by bacterial vaginosis (BV) bacteria have on sperm function? Summary answerBacterial vaginosis toxins dysregulate sperm capacitation and intracellular calcium homeostasis and impair the ability of sperm to fertilize oocytes. What is known alreadyIn bacterial vaginosis, which is linked to infertility, overgrowth of Prevotella and Gardnerella in the vagina is accompanied by elevated concentrations of the toxins lipopolysaccharide (LPS) and vaginolysin (VLY). Study design, size, durationThis was a laboratory study in which human semen samples were collected from consenting healthy donors with normal semen parameters. Mouse sperm samples were obtained from the caudal epididymis. Participants/materials, setting, methodsMotile mouse and human sperm were isolated via swim-up and treated under non-capacitating or capacitating conditions. LPS from Escherichia coli was commercially available. VLY was produced by cloning the Gardnerella VLY protein in the ClearColi expression system. Mouse sperm were pre-incubated in in vitro fertilization medium with LPS or VLY and then co-cultured with ovulated cumulus-oocyte complexes. The effects of LPS and VLY on sperm motility and hyperactivation were assessed with computer-assisted sperm analysis. Effects on viability were assessed by Hoechst staining. Acrosomal exocytosis was assessed in sperm from transgenic Acr-eGFP mice and in human sperm stained with Pisum sativum agglutinin FITC. Intracellular calcium dynamics were assessed by staining sperm with the calcium-sensitive dye Fluo-4 AM and fluorescent imaging several sperm at the single-cell level. The effects of LPS on sperm from CatSper knock-out mice were assessed. Additionally, sperm were treated with a toll-like receptor 4 antagonist and further exposed to LPS. Main results and the role of chanceExposure of mouse sperm to LPS or VLY significantly decreased in vitro fertilization (P < 0.05). Under capacitating conditions, both toxins initially increased mouse and human sperm hyperactivation, then significantly decreased sperm motility (P < 0.05), hyperactivation (P < 0.05), and acrosomal exocytosis (P < 0.01). These changes were accompanied by a rapid and irreversible increase in intracellular calcium concentration. Effects of LPS, but not VLY, were prevented by polymyxin-B, which aggregates LPS. The LPS-induced intracellular calcium increase required external calcium but not the calcium channel CatSper and was inhibited by the Toll-like receptor 4 antagonist. Limitations, reasons for cautionFirst, the commercially available LPS we used was isolated from Escherichia coli, rather than from the BV-associated bacteria Prevotella bivia. Second, we did not quantify the absolute sperm intracellular calcium concentration before or after LPS or VLY treatment. Third, all of our experiments were in vitro. Wider implications of the findingsThese studies suggest that BV-associated toxins contribute to infertility by, in part, impairing sperm capacitation and reducing their fertilizing ability. Study funding/competing interest(s)This work was supported by the National Institutes of Health (grant #R01 HD069631). The authors declare that they have no conflict of interest.

physiology↗

bioRxiv2025

Harnessing the Evolution of Proteostasis Networks to Reverse Cognitive Dysfunction

The integrated stress response (ISR) is a highly conserved network essential for maintaining cellular homeostasis and cognitive function. Here, we investigated how persistent ISR activation impacts cognitive performance, primarily focusing on a PPP1R15BR658C genetic variant associated with intellectual disability. By generating a novel mouse model that mimics this human condition, we revealed that this variant destabilizes the PPP1R15B*PP1 phosphatase complex, resulting in chronic ISR activation, impaired protein synthesis, and deficits in long-term memory. Importantly, we found that the cognitive and synaptic deficits in Ppp1r15bR658C mice are directly due to ISR activation. Leveraging insights from evolutionary biology, we characterized DP71L, a viral orthologue of PPP1R15B, through detailed molecular and structural analyses, uncovering its mechanism of action as a potent pan-ISR inhibitor. Remarkably, we found that DP71L not only buffers cognitive decline associated with a wide array of conditions--including Down syndrome, Alzheimers disease and aging--but also enhances long-term synaptic plasticity and memory in healthy mice. These findings highlight the promise of utilizing evolutionary insight to inform innovative therapeutic strategies.

neuroscience↗

bioRxiv2025

Cigarette Smoke and Decreased DNA Repair by Xeroderma Pigmentosum Group C Use a Double Hit Mechanism for Epithelial Cell Lung Carcinogenesis

Emerging evidence suggests a complex interplay of environmental and genetic factors in non-small cell lung cancer (NSCLC) development. Among these factors, compromised DNA repair plays a critical but incompletely understood role in lung tumorigenesis and concurrent lung diseases, such as chronic obstructive lung disease (COPD). In this study, we investigated the interplay between cigarette smoke, DNA damage and repair, focusing on the Nucleotide Excision Repair (NER) protein Xeroderma Pigmentosum Group C (XPC). We found decreased XPC mRNA expression in most NSCLCs compared to subject-matched, non-cancerous lung. In non-cancerous bronchial epithelial cells, cigarette smoke decreased NER, increased total DNA damage and resultant apoptosis, each exacerbated by XPC deficiency. In contrast, lung cancer cells exhibit greater resilience to cigarette smoke, requiring higher doses to induce comparable DNA damage and apoptosis, and are less reliant on XPC expression for survival. Importantly, XPC protects against chromosomal instability in benign bronchial epithelial cells, but not in lung cancer cells. Our findings support a "double hit" mechanism wherein early decreased XPC expression and resultant aberrant DNA repair, when combined with cigarette smoke exposure, may lead to loss of non-malignant epithelial cells (as observed in COPD), and contributes to early NSCLC transition through altered DNA damage response.

cancer biology↗