Biology subjects

Hou, R.

Publications and source records attributed to Hou, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatial transcriptomics reveals tumour cell-intrinsic and microenvironmental features associated with survival in high-grade serous ovarian carcinoma

High-grade serous ovarian carcinoma (HGSOC) is the most common form of ovarian carcinoma and accounts for the majority of deaths from the disease, with fewer than half of patients surviving five years after diagnosis. Bulk transcriptomic profiling has identified molecular subtypes and gene-expression signatures associated with shorter or longer survival. However, because bulk profiling measures a composite of tumour and microenvironmental gene expression, the cellular origins of these signatures and their relationship to the tumour microenvironment remain unresolved. To address this, we applied Xenium spatial transcriptomics to treatment-naive HGSOC tumours from 122 patients using a custom 480-gene panel designed to measure tumour-intrinsic gene expression and distinguish immune and stromal cell populations in the surrounding microenvironment. Analysis of tumour-intrinsic gene expression identified 61 genes nominally associated with overall survival, from which Elastic-Net modelling prioritised five genes associated with longer survival and nine associated with shorter survival. Notably, 46 of the 61 associations did not reach the nominal significance threshold when expression was instead aggregated across all cells from the same patients, highlighting how whole-tissue expression can obscure tumour-cell-specific survival associations. Complementary analysis of tumour-proximal cell populations revealed that multiple immune populations were associated with longer survival, whereas two fibroblast populations were associated with shorter survival. Integrating these analyses revealed that survival-associated tumour-intrinsic gene expression was correlated with the abundance of neighbouring immune and stromal populations that were themselves associated with survival. Pairwise Cox regression demonstrated substantial overlap in the prognostic information captured by these features, while analysis of individual gene-cell combinations showed that survival associations differed according to the abundance of neighbouring populations. Consensus clustering further identified four patient groups with distinct combinations of tumour-intrinsic expression and microenvironmental composition, broadly separating patients with longer and shorter survival. Together, this cohort-scale spatial analysis identifies tumour-intrinsic and microenvironmental features associated with HGSOC survival and reveals how their correlated patterns and combined associations relate to patient outcome.

cancer biology↗

bioRxiv2026

Beyond Generic Signal Peptides: ApexSP Enables Cargo-Specific Secretion Design

Recombinant proteins are widely used in biopharmaceuticals, industrial manufacturing, and molecular diagnostics; however, efficient secretion remains a major bottleneck limiting their large scale production. As core elements controlling protein entry into secretion pathways, signal peptides do not function solely based on their own sequences, but rather depend on coordinated compatibility among cargo protein properties, secretion pathways, and host backgrounds. Current signal peptide engineering mainly relies on a limited number of commonly used signal peptides, empirical selection, and individual experimental screening, making it difficult to design efficient secretion elements tailored to specific expression systems. Here, we present ApexSP, a signal peptide design framework for secretion engineering tailored to individual cargo proteins. ApexSP is built upon a large scale, high quality signal peptide knowledge base and integrates a discrete diffusion generative model constrained by evolutionary information, a multitask biological filter incorporating topology information, and a signal peptide and mature protein compatibility ranking model to enable integrated design of signal peptides for specific expression systems. ApexSP achieved high accuracy in multiple attribute prediction tasks, including pathway classification and cleavage site prediction, reaching or exceeding the performance of existing signal peptide prediction tools. Moreover, the cargo protein aware ranking module improved the enrichment of candidates with high secretion performance. Experimental validation across multiple eukaryotic and prokaryotic expression systems demonstrated that screening only 10 candidate sequences generated by ApexSP yielded multiple designed signal peptides outperforming reference signal peptides, with the best performing design in the ApGA expressed Pichia pastoris system achieving a 1.71 fold increase in secretion performance compared with the factor signal peptide. Overall, ApexSP advances signal peptide research from sequence prediction toward secretion element design, demonstrating that a single round of designed signal peptides can achieve high secretion performance suitable for further engineering optimization.

synthetic biology↗

bioRxiv2026

ANCHOR: haplotype-aware allelic and isoform inference from single-cell long-read RNA sequencing with de novo variant calling

Long-read RNA sequencing enables haplotype- and isoform-resolved allelic analysis of transcriptomes, yet extending this capability to single cells and distinct cell types remains computationally challenging due to sparse coverage, sequencing errors, incomplete variant information, and reference-biased transcript assignment. Here we present ANCHOR, a haplotype-aware framework for single-cell long-read RNA sequencing that performs de novo expressed-variant discovery, molecule-level haplotype assignment and isoform-resolved allelic quantification. ANCHOR combines a signed-graph variant caller, pair hidden Markov modelling and beta-binomial UMI aggregation to infer parental allele counts for genes and splice-resolved isoforms, without requiring a pre-existing phased genotype or deep learning. In human single-cell long-read RNA benchmarks, ANCHOR improved variant-calling performance over tested long-read RNA callers at single-cell and low-to-moderate coverage, and its beta-binomial model reduced depth-driven false positives in allele-specific expression testing. Applied to newly generated single-cell long-read RNA-seq data from reciprocal mouse crosses during gastrulation, ANCHOR resolved cell-type- and isoform-specific parent-of-origin imprinting and identified an antagonistic maternally biased Sgce isoform. ANCHOR provides a general framework for allele-and isoform-resolved analysis of diploid single-cell long-read transcriptomes.

bioinformatics↗

bioRxiv2026

Probiotic phage steering of disease suppressive rhizosphere microbiome

Current phage therapy approaches predominantly focus on targeting pathogenic bacteria, overlooking the vast potential of phages that interact with beneficial, plant growth-promoting (probiotic) bacteria. Here we tested if a single phage targeting a probiotic Stenotrophomonas maltophilia bacterium can steer the rhizosphere microbiome disease suppressiveness against Ralstonia solanacearum phytopathogen. We find that S. maltophilia quickly evolves resistance to its phage via mutations in ssb and TonB genes and by upregulating anti-phage defense systems. Crucially, evolution of phage resistance reprograms the bacterial transcriptome and metabolome, leading to unexpectedly enhanced antimicrobial activity against the R. solanacearum. Furthermore, exposing S. maltophilia to phage in the tomato rhizosphere increases the microbiota-wide disease suppressiveness by stabilizing bacterial diversity and facilitating pathogen suppression by other resident species. Our findings suggest that probiotic-specific phages could be used as ecological and evolutionary engineers to steer the rhizosphere microbiome disease suppressiveness through activation of antagonistic bacterial interactions.

evolutionary biology↗

bioRxiv2025

Torsins Organize CLCC1 Assembly to Safeguard ER Bilayer and Lipid Homeostasis

The TMEM41B scramblase and its regulatory partner CLCC1 initiate lipid flux by equilibrating newly-synthesized phospholipids across the endoplasmic reticulum (ER) bilayer, a fundamental process required for diverse events ranging from membrane biogenesis to bulk lipid supply. Loss of CLCC1/TMEM41B causes ER bilayer imbalance, inducing giant ER-enclosed lipid droplets (geLDs) and driving rapid progression into severe MASH. Here we identify CLCC1 as the long-missing client of the lumenal Torsin ATPases, which selectively engage oligomerized CLCC1 at sites of ER bilayer imbalance. Hepatic TorsinA inactivation triggers geLD formation amid disrupted lipoprotein biogenesis and severe MASH, closely phenocopying CLCC1/TMEM41B deficiency. Mechanistically, Torsins act as foldases that drive CLCC1 oligomerization for its recruitment to imbalanced bilayers. Remarkably, ectopic CLCC1 expression reverses cellular and systemic lipid disorders arising from hepatic TorsinA deficiency. Hence, Torsin ATPases emerge as fundamental regulators that organizes CLCC1 and the downstream TMEM41B scramblase to govern lipid partitioning and membrane homeostasis.

cell biology↗

bioRxiv2025

Multi-scale simulations of membrane adhesion mediated by CD47-SIRPα complexes

Adhesion of biological cells is essential for various processes, including tissue formation, immune responses, and signaling. It involves multiple length scales, ranging from nanometers to micrometers, which are characteristic of (a) the intercellular receptor-ligand binding that mediates the cell adhesion, (b) the spatial distribution of the receptor and lignad proteins in the membranes of adhering cells, (c) adhesion-induced deformations and thermal undulations of the membranes, (d) the overall size of the interface between adhering cells. Therefore, computer simulations of cell membrane adhesion require multi-scale modeling and suitable approximations that capture the essential physics of the system under study. Here, we introduce such a multi-scale approach to study membrane adhesion mediated by the CD47-SIRP binding, which is an immunologically relevant process. The synergetic use of coarse-grained molecular dynamics simulations and mesoscale kinetic Monte Carlo simulations allows us to explore both equilibrium properties and dynamical behavior of adhering membranes on the relevant length scales between 1 nm and 1 {micro}m on time scales ranging from 0.1 ns all the way up to about 20 s. The multi-scale simulations not only reproduce available experimental data but also give quantitative predictions on binding-induced conformational changes of SIRP and membrane-mediated cooperativity of the CD47-SIRP binding as well as fluctuation-induced interactions between the CD47-SIRP complexes. Our approach is applicable to various membrane proteins and provides invaluable data for comparison with experimental findings.

biophysics↗

bioRxiv2024

scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data

Three-prime single-cell RNA-seq (scRNA-seq) has been widely employed to dissect the variability of cellular transcriptomes, while only the cDNAs on reads 2 are routinely used, including to analyze polyadenylation sites (PAS). However, despite of high sequencing noise, we found the cDNAs on reads 1 are highly informative in precisely detecting PAS. Here, we further develop a computational method, scTail, to identify PAS using reads 1 and quantify its expression leveraging reads 2, which enables effective detection of alternative PAS usage (PAU). When compared with other methods, scTail detects PAS more sensitively and precisely. With various experimental data sets, we demonstrated that the combination usage of scTail and BRIE2 can discover differential alternative PAS usage in various biological processes including cell types in human intestinal, disease status of esophageal squamous cell carcinoma, and time point of mouse forelimb histogenesis, revealing critical insights in PAS regulations.

bioinformatics↗

bioRxiv2024

HIV-1 infection is associated with depletion of germinal center B cells and a decrease in IgA+ plasma cells in the GI tract

Gastrointestinal (GI) B cells and plasma cells (PCs) are critical to mucosal homeostasis and the host response to HIV-1 infection. Here, high resolution mapping of human B cells and PCs sampled from the colon and ileum during both viremic and suppressed HIV-1 infection identified a reduction in germinal center (GC) B cells and follicular dendritic cells (FDCs) during HIV-1 viremia. IgA+ PCs are the major cellular output of intestinal GCs and were significantly reduced during viremic HIV-1 infection. PC-associated transcriptional perturbations, including type I interferon signaling, persisted in antiretroviral therapy (ART)-treated individuals, suggesting ongoing disruption of the intestinal immune milieu during ART. GI humoral immune perturbations were associated with changes in the intestinal microbiome composition and systemic inflammation. These findings highlight a key immune defect in the GI mucosa due to HIV-1 viremia. One Sentence SummaryIntestinal germinal center B cell reduction in HIV-1 infection linked to reduced IgA+ plasma cells and systemic inflammation.

immunology↗

bioRxiv2024

Regulation of Interstitial Lung Diseases by Pulmonary Endothelial Cells via PLVAP

Withdrawal statementThe authors have withdrawn this manuscript because the preliminary results require further experimental validation and more comprehensive data collection to ensure scientific rigor. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

cell biology↗

bioRxiv2024

Antimicrobial resistance, virulence genes profiles and molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae strains from captive giant pandas (Ailuropoda melanoleuca)

This study aimed to investigate the antibiotic susceptibility, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence genes, and molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae (CRKP) strains isolated from giant pandas. The screening of 178 nonduplicated Klebsiella pneumoniae strains identified eight CRKP strains, with the most abundant ARGs observed in ampC/blaDHA, blaSHV-01, blaSHV-02, tetB-01, tetB-02, tetC-01, and tetC-02. MGE analysis revealed the presence of intI1 in all strains, while other MGEs exhibited varying detection rates. Strain 24 exhibited the highest diversity in terms of MGE species. Seven virulence genes including wabG, uge, ycf, entB, kpn, alls, and wcaG, showed positive results with different proportions across the strains. Molecular epidemiology analysis using pulsed-field gel electrophoresis (PFGE) patterns indicated a high level of genetic diversity among the CRKP strains. Multi-locus sequence typing (MLST) analysis classified the strains into different sequence types (STs). In conclusion, this study highlighted the diverse nature of CRKP strains found in giant pandas, which exhibited varying levels of antibiotic resistance along with multiple ARGs and virulence genes present. These findings emphasized the importance of monitoring and researching antibiotic resistance within wildlife populations to safeguard the health status of these endangered animals.

zoology↗

bioRxiv2023

Modulation of Salmonella virulence by a novel SPI-2 injectisome effector that interacts with the dystrophin-associated protein complex.

The injectisome encoded by Salmonella pathogenicity island 2 (SPI-2) had been thought to translocate 28 effectors. Here, we used a proteomic approach to characterise the secretome of a clinical strain of invasive non-typhoidal Salmonella enterica serovar Enteritidis, that had been mutated to cause hyper-secretion of the SPI-2 injectisome effectors. Along with many known effectors, we discovered the novel SseM protein. sseM is widely distributed between the five subspecies of Salmonella enterica, is found in many clinically-relevant serovars, and is co-transcribed with pipB2, a SPI-2 effector gene. Translocation of SseM required a functional SPI-2 injectisome. Following expression in human cells, SseM interacted with five components of the dystrophin-associated protein complex (DAPC), namely {beta}-2-syntrophin, utrophin/ dystrophin, -catulin, -dystrobrevin and {beta}-dystrobrevin. The interaction between SseM and {beta}-2-syntrophin and -dystrobrevin was verified in S. Typhimurium-infected cells and relied on the PDZ domain of {beta}-2-syntrophin and a sequence corresponding to a PDZ-binding motif (PBM) in SseM. A {Delta}sseM mutant strain had a small competitive advantage over the wild-type strain in the S. Typhimurium/mouse model of systemic disease. This phenotype was complemented by a plasmid expressing wild type SseM from S. Typhimurium or S. Enteritidis and was dependent on the PBM of SseM. Therefore, a PBM within a Salmonella effector mediates interactions with the DAPC and modulates systemic growth of bacteria in mice. ImportanceIn Salmonella enterica, the injectisome machinery encoded by Salmonella pathogenicity island 2 (SPI-2) is conserved among the five subspecies and delivers proteins (effectors) into host cells that are required for Salmonella virulence. The identification and functional characterisation of SPI-2 injectisome effectors advances our understanding of the interplay between Salmonella and its host(s). Using an optimised method for preparing secreted proteins and a clinical isolate of the invasive non-typhoidal (iNTS) Salmonella enterica serovar Enteritidis strain D24359, we identified 22 known SPI-2 injectisome effectors and one new effector - SseM. SseM modulates bacterial growth during murine infection and has a sequence corresponding to a PDZ-binding motif that is essential for interaction with the PDZ-containing host protein {beta}-2-syntrophin and other components of the dystrophin-associated protein complex (DAPC). To our knowledge, SseM is unique among Salmonella effectors in containing a functional PDZ-binding motif and is the first bacterial protein to target the DAPC.

microbiology↗

bioRxiv2023

CSTA: A Biomarker Regulating Esophageal Stricture Epithelial Barrier, Potential Medication Target

Esophageal strictures resulting from ESD/EMR in the esophagus are distressing, with uncertain causes and treatments due to epithelial barrier dysfunction. We explored cystatin A (CSTA) as a novel biomarker for the esophageal epithelial barrier. CSTA regulates the barrier and is influenced by tacrolimus (FK506). Analyzing biopsy samples by proteomics, we identified CSTA as an esophageal epithelial biomarker. Knocking down CSTA reduced responsiveness to triamcinolone acetonide (TA) and lowered expression of proteins related to cell-cell junctions and barrier function during inflammation. These findings suggest that down-regulate CSTA weakens tight junctions and the esophageal barrier, leading to strictures. Notably, FK506 showed promise in rescuing CSTA-knockdown cells by increasing the expression of proteins related to cell-cell junctions and barrier function. This highlights FK506 as a potential therapy for esophageal strictures in patients with CSTA mutations.

cell biology↗

bioRxiv2023

Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein driving the genesis of Omicron variants

Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralising public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidences to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.

biochemistry↗

bioRxiv2023

Timing-dependent modulation of working memory by VTA dopamine release in medial prefrontal cortex

Dopamine significantly modulates working memory (WM)1-8, a fundamental cognitive function that maintains information during a brief delay period9-11. The temporal precision of dopaminergic modulation in WM and related neural mechanisms remain elusive. Here we unveiled the pivotal role of dopamine timing in WM performance with head-fixed mice engaged in learning an olfactory WM task. Through electrophysiology and optogenetics, we found that dopaminergic neurons in the ventral tegmental area (VTA) could encode WM information during the delay period, and manipulating dopaminergic neuronal activity bidirectionally modulated WM performance in an inverted U-shaped manner. Optogenetic manipulation of VTA activity also induced bidirectional changes in WM-related neural activity in the medial prefrontal cortex (mPFC). Imaging with a dopamine-sensitive GPCR-activation-based sensor (GRABDA)12,13 revealed transient dopamine peaks in the mPFC specifically during the early-delay period. Optogenetic stimulation of VTA-to-mPFC dopaminergic projections during the early- and late-delay period enhanced and impaired WM performance, respectively. Manipulations outside these periods or involving the nucleus accumbens had no effect. Single-unit recordings demonstrated that optogenetic excitation of VTA-to-mPFC projections could modulate mPFC neuronal activity in a manner consistent with behavioral modulation. Thus, the timing of dopamine release is critical in modulation of neuronal activity and behavior.

neuroscience↗

bioRxiv2023

Myeloid cell influx into the colonic epithelium is associated with disease severity and non-response to anti-Tumor Necrosis Factor Therapy in patients with Ulcerative Colitis.

Ulcerative colitis (UC) is an idiopathic chronic inflammatory disease of the colon with sharply rising global prevalence. Dysfunctional epithelial compartment (EC) dynamics are implicated in UC pathogenesis although EC-specific studies are sparse. Applying orthogonal high-dimensional EC profiling to a Primary Cohort (PC; n=222), we detail major epithelial and immune cell perturbations in active UC. Prominently, reduced frequencies of mature BEST4+OTOP2+ absorptive and BEST2+WFDC2+ secretory epithelial enterocytes were associated with the replacement of homeostatic, resident TRDC+KLRD1+HOPX+ {gamma}{delta}+ T cells with RORA+CCL20+S100A4+ TH17 cells and the influx of inflammatory myeloid cells. The EC transcriptome (exemplified by S100A8, HIF1A, TREM1, CXCR1) correlated with clinical, endoscopic, and histological severity of UC in an independent validation cohort (n=649). Furthermore, therapeutic relevance of the observed cellular and transcriptomic changes was investigated in 3 additional published UC cohorts (n=23, 48 and 204 respectively) to reveal that non-response to anti-Tumor Necrosis Factor (anti-TNF) therapy was associated with EC related myeloid cell perturbations. Altogether, these data provide high resolution mapping of the EC to facilitate therapeutic decision-making and personalization of therapy in patients with UC.

immunology↗

bioRxiv2023

Prefrontal projections modulate recurrent circuitry in insular cortex to support short-term memory

Short-term memory (STM) maintains information during a short delay period. How long-range and local connections interact to support STM encoding remains elusive. Here we tackled the problem focusing on long-range projections from medial prefrontal cortex (mPFC) to anterior agranular insular cortex (aAIC) in head-fixed mice performing an olfactory delayed-response task. Optogenetic and electrophysiological experiments revealed behavioral importance of the two regions in encoding STM information. Spike-correlogram analysis revealed strong local and cross-region functional coupling (FC) between memory neurons encoding the same information. Optogenetic suppression of mPFC-aAIC projections during the delay period reduced behavioral performance, the proportion of memory neurons and memory-specific FC within aAIC, whereas optogenetic excitation enhanced all of them. MPFC-to-aAIC projections also bidirectionally modulated efficacy of STM-information transfer, measured by contribution of FC spiking pairs to coding ability of following neurons. Thus, prefrontal projections modulate functional connectivity and coding ability of insular neurons to support short-term memory.

neuroscience↗

bioRxiv2023

CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data

Five-prime single-cell RNA-seq (scRNA-seq) has been widely employed to profile cellular transcriptomes, however, its power of analysing transcription start sites (TSS) has not been fully utilised. Here, we present a computational method suite, CamoTSS, to precisely identify TSS and quantify its expression by leveraging the cDNA on read 1, which enables effective detection of alternative TSS usage. With various experimental data sets, we have demonstrated that CamoTSS can accurately identify TSS and the detected alternative TSS usages showed strong specificity in different biological processes, including cell types across human organs, the development of human thymus, and cancer conditions. As evidenced in nasopharyngeal cancer, alternative TSS usage can also reveal regulatory patterns including systematic TSS dysregulations.

bioinformatics↗

bioRxiv2023

Angiopoietin-like 4 promotes the proliferation and migration of epidermal stem cells and contributes to the re-epithelialization of cutaneous wounds

Proliferation and migration of epidermal stem cells (EpSCs) are essential for epithelialization during skin wound healing. Angiopoietin-like 4 (ANGPTL4) has been reported to play an important role in wound healing, but the mechanisms involved are not fully understood. Here we investigate the contribution of ANGPTL4 to full-thickness wound re-epithelialization and the underlying mechanisms using Angptl4 knockout mice. Immunohistochemical staining reveals that ANGPTL4 is significantly upregulated in the basal layer cells of the epidermis around the wound during cutaneous wound healing. ANGPTL4 deficiency impairs wound healing. H & E staining shows that ANGPTL4 deficiency significantly reduces the thickness, length and area of regenerated epidermis postwounding. Immunohistochemical staining for markers of EpSCs (6 integrin and {beta}1 integrin) and cell proliferation (PCNA) shows that the number and proliferation of EpSCs in the basal layer of the epidermis are reduced in ANGPTL4-deficient mice. In vitro studies show that ANGPTL4 deficiency impedes EpSC proliferation, causes cell cycle arrest at the G1 phase and reduced the expression of cyclins D1 and A2, which can be reversed by ANGPTL4 overexpression. ANGPTL4 deletion suppresses EpSC migration, which is also rescued by ANGPTL4 overexpression. Overexpression of ANGPTL4 in EpSCs accelerates cell proliferation and migration. Collectively, our results indicate that ANGPTL4 promotes EpSCs proliferation by upregulating cyclins D1 and A2 expression and accelerating cell cycle transition from G1 to S phase, and ANGPTL4 promotes skin wound re-epithelialization by stimulating EpSC proliferation and migration. Our study reveals a novel mechanism underlying EpSC activation and re-epithelialization during cutaneous wound healing.

cell biology↗