Biology subjects

Sharma, P.

Publications and source records attributed to Sharma, P..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Precision survival estimation in acute myeloid leukemia using evolutionary learning-derived microRNA signature

BackgroundAcute myeloid leukemia (AML) remains the most lethal acute leukemia in adults, with 5-year overall survival below 32% despite recent advances including venetoclax-, FLT3-, IDH1/2-, and Menin-targeted therapies. Clinical outcomes remain highly heterogeneous across patients, highlighting the need for robust molecular biomarkers capable of improving prognostic precision. MicroRNAs (miRNAs) are critical regulators of hematopoietic differentiation, apoptosis, and therapeutic resistance and are differentially expressed across AML subtypes. However, their clinical translation has been limited by high dimensionality, feature redundancy, and relatively small cohort sizes. MethodsWe developed and evaluated the AML Survival Estimator (AMLS), an inheritable bi-objective combinatorial genetic algorithm integrated with support vector regression (SVR), using TCGA-LAML miRNA expression profiles (n = 156). AMLS was benchmarked against ten widely used machine-learning approaches, including penalized regression, tree-based ensembles, support-vector regression, k-nearest neighbors, and multilayer perceptron models. Performance was assessed using stratified cross-validation with Pearson correlation (R), Harrells concordance index (C-index), and mean absolute error (MAE). Functional characterization of the derived miRNA signature was performed through consensus target integration followed by pathway enrichment, gene ontology analysis, network reconstruction, and Kaplan-Meier risk stratification. ResultsAMLS achieved superior prognostic performance with pooled out-of-fold metrics of Pearson R = 0.86, C-index = 0.788, and MAE = 7.49 months, substantially outperforming all comparator models. Restricting analyses to the AMLS-derived 28-miRNA signature improved all baseline learners by approximately 2-4-fold, with the multilayer perceptron achieving R = 0.674; however, none matched the native AMLS framework, indicating that the evolutionary optimization strategy contributes predictive information beyond feature selection alone. The prognostic signature included biologically established AML-associated miRNAs, including hsa-miR-191, hsa-miR-29c, hsa-miR-125b, hsa-miR-148a, hsa-miR-15b, hsa-miR-10b, and hsa-miR-30c, linked to DNA methylation, apoptosis, cell-cycle regulation, and oncogenic Wnt/MAPK signaling pathways. Functional analyses demonstrated significant enrichment of canonical AML-associated pathways, including p53, PI3K-AKT, TGF-{beta}, JAK-STAT, FoxO, and hematopoietic lineage signaling. ConclusionsOur findings demonstrate that evolutionary learning integrated with SVR can recover a compact and biologically interpretable miRNA prognostic signature that substantially outperforms conventional machine-learning approaches for AML survival prediction. The identified miRNA network converged on key leukemogenic pathways involved in apoptosis, cell-cycle regulation, and oncogenic signaling, supporting both the biological relevance and prognostic utility of the framework. Given the minimally invasive and quantitatively scalable nature of miRNA profiling, this approach may provide a practical molecular adjunct for improving prognostic assessment and precision medicine strategies in AML. Abstract FigureSchematic overview of the AMLS framework. Left: acute myeloid leukemia, a clonal hematological malignancy with persistent prognostic heterogeneity. Middle: AMLS couples an evolutionary learning-based feature selection algorithms to support vector regression for miRNA-based survival modeling. Right: AMLS recovers a 28-miRNA prognostic signature that predicts overall survival with Pearson R = 0.86 and MAE = 7.5 months. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/727196v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@11ead1org.highwire.dtl.DTLVardef@4f5c19org.highwire.dtl.DTLVardef@277de1org.highwire.dtl.DTLVardef@b95c9a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Sound Advice: A calibration framework for defining detection space in Passive Acoustic Monitoring

Passive Acoustic Monitoring (PAM) has emerged as a transformative tool for biodiversity assessment in recent years. Despite widespread acceptance and application for conservation-related outcomes, the synergistic effects of hardware limitations, signal propagation, and environmental conditions on how far a signal can be reliably detected remain critically understudied. We quantified changes in signal detectability using Autonomous Recording Units (ARUs) in a tropical agroecosystem using playback experiments of standardised pure-tone (1-8 kHz) in fallow rice paddy fields. We deployed a four-ARU array and broadcast signals over a 50- 300 m distance gradient, and modelled operative detectability of signals using a binomial Generalised Linear Mixed-effects Model (GLMM). Our findings show that the detection space of an ARU is highly frequency-dependent and environmentally modulated. Detection probability for low-frequency signals (1 kHz) decreased rapidly (50% threshold at [~]100 m), whereas mid-range frequencies (4-6 kHz) occupied an acoustic window that remained reliably detectable up to 250 m. Higher relative humidity significantly enhanced overall detection, while increasing temperatures disproportionately reduced low-frequency detectability. The orientation of the ARU to the signal source was important as the detection probability declined from 81% for recorders facing the source (0{degrees}) to 14% for rear-facing units (180{degrees}). Our findings underscore the importance of determining the detection space before undertaking PAM. We propose a Decision Support Framework that provides a pathway for researchers to integrate focal taxa traits with technical constraints to determine detection space and optimise study designs when using PAM for monitoring biodiversity and assessing conservation action.

ecology↗

bioRxiv2026

Helminth coinfection facilitates gammaherpesvirus infection in the wood mouse Apodemus sylvaticus

Helminths are widespread parasites that can modulate host immunity, potentially increasing susceptibility to viral infections. However, evidence for these effects varies across systems and environments, and links between laboratory and wild populations remain unclear. We developed a tractable system using wood mice, Heligmosomoides spp. nematodes, and wood mouse herpes virus (WMHV) to bridge this gap. Combining laboratory and field experiments with population modelling, we examined how helminth infection, anthelmintic treatment and diet affect viral dynamics. Across lab and field data, helminth infection consistently increased WMHV risk, with stronger effects at higher worm burdens. Field results showed that anthelmintic treatment reduced viral infection, and laboratory experiments showed that improved nutrition mitigates helminth-induced increases in viral susceptibility. Our population-level modelling suggested that helminth burden-dependent facilitation can generate nonlinear effects on viral spread, dependent on helminth virulence. Our findings highlight the potential importance of helminths as facilitators of viral infections, and suggest that anthelmintic treatment may provide indirect benefits for viral control. We also show the value of integrating lab and field approaches on the same (or closely related) species, in particular the potential offered by the wood mouse - Heligmosomoides - WMHV system, to understand the drivers and consequences of host-helminth-viral interactions.

ecology↗

bioRxiv2026

A generative reference grammar of healthy TCR repertoires reveals cancer-associated immune remodeling

T-cell receptor (TCR) repertoires record how adaptive immunity is organized and how cancer and therapy reshape it, but this signal is hard to read: treatment-associated change is entangled with the V(D)J recombination constraints that shape every repertoire. We present CRAFT (Cancer Repertoire Anomaly Finding Transformer), a conditional sequence-to-sequence transformer that learns a nucleotide-level generative grammar of productive TCR-beta CDR3 sequences from healthy donors, conditioned on germline V(D)J assignments. A dual-head decoder mirrors the independence of V-D and D-J recombination, and curriculum training produces embeddings that define a healthy-reference coordinate system in which cancer-associated change appears as structured, measurable deviation. In proof-of-concept applications to a neoadjuvant checkpoint-blockade cohort sampled longitudinally across blood, and to serial single-cell profiling of T-cell subsets during oncolytic immunotherapy, CRAFT geometric metrics capture response-associated remodeling, including shifts in repertoire organization over time. On antigen-labeled benchmarks, CRAFT organizes specificity classes coherently, recovering structure that reflects shared antigen recognition.

cancer biology↗

bioRxiv2026

Autoimmune-like CD8⁺ T Cell Responses Drive Atherosclerotic Plaque Instability and Predict Cardiovascular Events

Background and aimsAtherosclerotic plaque rupture is a major cause of myocardial infarction and stroke. However, the precise drivers of plaque destabilisation remain elusive. We hypothesised that antigen-driven, autoimmune-like T cell responses are central to the destabilisation and rupture of atherosclerotic plaques. MethodsTo dissect T cell responses specifically in unstable compared to stable plaques, we leveraged near-infrared autofluorescence (NIRAF) imaging-guided dissection of human carotid plaques. We also used our tandem stenosis model reflecting plaque instability as seen in patients to differentiate between unstable and stable plaques in mice. To explore T cell involvement, we studied T cell differentiation states and T cell receptor (TCR) repertoires by single-cell multi-omics. Then, testing if antigen-driven CD8+ T cell responses drive plaque instability in mice, we applied a combination of AAV8-PCSK9-induced atherosclerosis, tandem stenosis and TCR transgenic mice. Finally, we leveraged data from the AtheroExpress Biobank Study to link T cell immunity to histology-defined instability and cardiovascular outcomes. ResultsT cell responses in unstable versus stable atherosclerosis were distinct. Unstable human plaques contained highly expanded, autoimmune-like CD8 T cells with markedly increased cytotoxic signatures, reduced exhaustion and distinct clonal repertoires compared to stable regions. Most plaque CD8 T cells exhibited a pronounced tissue-resident transcriptional program. Moreover, the transcriptional signature of these plaque resident T cells was distinct from multiple other human tissues. Autoimmune-like cytotoxic and tissue-resident CD8+ T cell responses were also evident in murine atherosclerosis, where restricting the activation of antigen-driven CD8+ T cells prevented plaque destabilisation. Importantly, analysis of carotid endarterectomy samples from >1000 patients identified that intraplaque cytotoxic CD8 T cell gene signatures strongly correlated with histological instability and predicted future strokes. ConclusionsIntegrated human, murine and clinical analyses demonstrate that autoimmune-like, cytotoxic CD8 T cell responses are central drivers of plaque instability and major cardiovascular events. Targeting pathogenic CD8 T cell responses may thus offer a compelling immunomodulatory strategy to stabilise plaques and reduce the risks of stroke and myocardial infarction. Graphical AbstractO_ST_ABSKey QuestionC_ST_ABSRupture of unstable atherosclerotic plaques is a typical cause of myocardial infarction and stroke. To understand the underlying cause and to prevent plaque rupture, we addressed the central hypothesis that autoimmune-like T cell responses drive plaque destabilisation and rupture. Key FindingsCD8+ T cells are clonally expanded with increased cytotoxic signatures in unstable versus stable plaques (mice and humans) and require antigen recognition to drive plaque instability. Cytotoxic CD8+ T cell signatures in excised plaques correlate with increased future cardiovascular events. Take Home MessageAutoimmune-like adaptive immune reactions, dominated by CD8+ T cells, are a major driver of plaque instability/rupture. Therefore, targeting pathogenic CD8 T cell responses offers a compelling immunomodulatory strategy to stabilise plaques and reduce the risk of myocardial infarction and stroke. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/720043v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@bd83dcorg.highwire.dtl.DTLVardef@1bee3borg.highwire.dtl.DTLVardef@1b56bc0org.highwire.dtl.DTLVardef@1b5176f_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

Intrinsically disordered N-terminal and structured DNA-binding domains jointly regulate progesterone receptor transcriptional condensates

Transcriptional condensates (TCs) are dynamic, membrane-less assemblies of proteins and nucleic acids that form at specific genomic loci to control gene expression. The primary drivers of TC formation and function are long stretches of polypeptide chains that lack well-defined tertiary structure, known as the intrinsically disordered regions (IDRs) of Transcription Factors (TFs). However, the role of well-structured domains such as the DNA-binding domain (DBD) in condensate formation and downstream regulation remains poorly understood. Here, we investigated whether the DBD of the Progesterone Receptor (PR), a model TF regulated by hormone binding, contributes to the formation of PR TCs. By combining Single Particle Tracking (SPT) with deep-learning-based single-trajectory analysis, we demonstrated that both the IDR and the DBD are required for the formation of PR condensates. Furthermore, transcriptomic analysis showed that mutations of either of the two domains result in the expression of a distinct set of genes, with functional assays corroborating these findings and linking domain-specific transcription to differential effects on cell proliferation and migration. Together, our results show that domains beyond IDRs also play a role in TC formation and function and uncover domain-specific regulation of transcriptional and oncogenic programs.

biophysics↗

bioRxiv2026

Plasmodium Protein Kinase 2 is required for ookinete to oocyst transition, and parasite transmission by the mosquito.

Plasmodium spp., the parasites that are the causative agents of malaria, encode a repertoire of divergent protein kinases that coordinate essential processes including cell division and host cell invasion, yet the functions of many kinases are poorly defined. Plasmodium Protein Kinase 2 (PK2) is essential for asexual blood-stage proliferation and has been implicated in P. falciparum merozoite invasion of red blood cells. However, its role in the sexual stages of the Plasmodium life cycle responsible for transmission is unknown. Here, using live cell imaging, functional analyses, ultrastructure microscopy and phosphoproteomics, we demonstrate that PK2 has a significant role in the Plasmodium berghei life cycle in the mosquito. We show that PK2 is expressed in merozoites, ookinetes and sporozoites - the invasive stages of the parasite life cycle. A conditional knockdown approach revealed that PK2 is required for the ookinete to oocyst transition in the mosquito midgut, potentially associated with altered microneme positioning. Using haemocoel injection to bypass the midgut barrier revealed that PK2 is also required for sporozoite development after midgut invasion. Following PK2 knockdown, global proteome abundance was largely unaffected at 24 h post activation, whereas phosphoproteomics identified changes in phosphorylation of proteins linked to midgut traversal, parasite architecture, and gene regulation. These studies provide insight into the importance of PK2 function in Plasmodium sexual stages and parasite transmission through the mosquito, highlighting its essential function during the three invasive stages of the parasites life cycle.

microbiology↗

bioRxiv2026

CD8+ T cells are primed by cDC1 and exacerbate tau-mediated neurodegeneration

There are changes in adaptive immunity in Alzheimers disease (AD) and increases in activated CD8+ T cells in brain correlate with tau pathology1-3. However, which cells mediate T cell priming in tau-mediated neurodegeneration remains unclear. In different conditions such as cancer, viral infections, and autoimmune diseases outside the CNS, conventional type-1 dendritic cells (cDC1) perform antigen cross-presentation to prime CD8+ T cells4,5. We demonstrate that tauopathy mice deficient in cDC1 are markedly protected against tau-mediated neurodegeneration and display a selective decrease in brain CD8+ T cell infiltration and glial reactivity. The remaining CD8+ T cells showed an antigen inexperienced status with less clonal expansion, indicating suboptimal T cell priming. We confirm that brain derived antigens are presented in secondary lymphoid tissues to prime CD8+ T cells. Our study identifies cDC1 cells as critical for CD8+ T cell priming outside the CNS. This priming is required for a large increase of activated CD8+ T cells in the brain which promotes tau-mediated neurodegeneration.

neuroscience↗

bioRxiv2026

Regions of genome plasticity are systematically organized into recurrent integration spots that shape accessory-genome functional architecture: insights from a complete genome of strain F1C1 and pangenomic analysis of the Ralstonia solanacearum species complex

1The Ralstonia solanacearum species complex (RSSC) is a highly diverse plant pathogen whose evolution is shaped by horizontal gene transfer. We generated a complete, gap-free hybrid genome assembly of F1C1, a South Asian Phylotype I strain classified as R. pseudosolanacearum. The closed assembly resolves a bipartite genome (3.73 Mb chromosome; 2.03 Mb megaplasmid), enabling precise localization of mobile genetic elements. Using F1C1 together with 142 complete RSSC genomes, we implemented a lineage-stratified pangenome framework that reveals a hierarchically structured gene repertoire and shows that accessory gene content can discriminate host-associated lineages beyond core-genome. Pangenome-informed mapping of genome plasticity identified 651 conserved integration spots that concentrate accessory turnover and are enriched for adaptive functions, including type III secretion system effectors and antiviral defense systems (e.g., Wadjet and CRISPR-Cas). Genes within these spots display elevated Ka/Ks relative to housekeeping functions, consistent with conflict-driven diversification and/or relaxed constraint. Together, these results link RSSC genome architecture to adaptive potential and provide a spot-based framework for genomic surveillance and resistance breeding in bacterial wilt pathosystems.

genomics↗

bioRxiv2026

A citywide metagenomic analysis reveals surface-specific microbiome and resistome patterns in outdoor urban environments across Liverpool, UK.

Urbanisation is rapidly increasing worldwide, with increasing attention focused on its consequences for human populations and the environment. Despite the importance of outdoor urban environments for biodiversity and human wellbeing, their microbial ecology remains poorly characterised, particularly in relation to emerging microbial threats including antimicrobial resistance (AMR). Here, we present a citywide metagenomic study of outdoor public surfaces across Liverpool, United Kingdom, examining microbial community composition, diversity, and antimicrobial resistance gene (ARG) distribution across five distinct surface types. We show that patterns of human activity and surface use strongly influence both microbial community structure and AMR signatures in outdoor urban environments. Touchpoints were enriched for human-associated taxa and exhibited the highest overall resistome burdens, whereas Pathway and Waterside niches showed no strong taxonomic enrichment and exhibited low ARG prevalence. Refuse surfaces showed mixed patterns, characterised by sporadic but occasionally high-abundance ARG detections. Soil harboured the most distinct microbial communities but showed minimal ARG prevalence, which may partly reflect the limited representation of environmental taxa in current ARG databases. This study provides a baseline for understanding how urban infrastructure and behaviour shape microbial and resistance landscapes, and highlights the value of outdoor metagenomic surveillance for future environmental and public health research.

microbiology↗

bioRxiv2026

Lysosomal abundance in young and aged mouse hearts assessed by In Vivo Imaging Systems (IVIS) Lysotracker imaging and autophagy-related gene expression

Lysosomal function is essential for cardiac proteostasis and cellular health, yet its regulation during ageing remains poorly defined. We hypothesised that ageing alters both the abundance of acidic organelles and the machinery supporting their acidification. Using fluorescence-based In Vivo Imaging Systems (IVIS) with Lysotracker Red in young (2-4 months) and aged (18 months) mouse hearts, we quantified whole-heart acidic-vesicle signals and assessed expression of lysosomal and autophagy-related genes (Lamp2, Atp6v1a, Sqstm1, Cd63, Atg12, Nfe2l2, M6pr) by RT-qPCR. Whole-heart labelled Lysotracker fluorescence did not differ significantly between age groups, indicating preservation of the total acidic-vesicle pool. No changes in Atp6v1a and Lamp2 expression suggest acidification capacity and structural stability are maintained, whereas the minor, upregulation of Sqstm1 might indicate increased autophagic demand and altered vesicle trafficking, which warrants further investigation. No statistical significant changes in M6pr, Atg12, or Nfe2l2 were detected, suggesting transcriptional stability in enzyme trafficking, core autophagy, and oxidative stress pathways. Regionally, atria showed higher Lysotracker signal than ventricles, consistent with known enrichment of acidic vesicular stores in atrial physiology. These findings highlight the utility of IVIS imaging of Lysotracker-labelled hearts, providing rapid whole-organ assessment of acidic vesicle distribution, albeit with limited depth resolution. Complementary techniques such as RT-qPCR analysis is essential to interpret IVIS findings, enabling insight into underlying molecular changes in lysosomal and autophagy pathways during cardiac ageing.

physiology↗

bioRxiv2026

Skiver: Alignment-free Estimation of Sequencing Error Rates and Spectra using (k, v)-mer Sketches

BackgroundQuality control of sequencing datasets is an important first step in numerous bioinformatics pipelines such as mapping, variant calling, and assembly. Existing methods typically rely on alignment results or quality scores. However, the reference genome is not always available for mapping, and uncalibrated quality scores may yield biased estimates of error rates. ResultsWe present skiver, a reference-free and alignment-free algorithm that estimates sequencing error rates and calibrates Phred quality scores using (k, v)-mer sketches. By identifying the consensus from the sketched (k, v)-mers, skiver estimates survival and hazard rates that capture positional information of sequencing errors. Across simulated and real datasets from various sequencing platforms, skiver accurately recovers sequencing error rates and the proportion of different error types. We further demonstrate its ability to calibrate Phred scores. It also reliably handles complex datasets containing multiple strains, alleles, and repetitive regions through an iterative outlier filtering strategy. Skiver is computationally efficient and supports tools that need accurate sequencing error rate estimates or quality scores as prior knowledge. Availability and ImplementationAn implementation of skiver is available at https://github.com/GZHoffie/skiver, and dataset and scripts for reproducibility are available at https://github.com/GZHoffie/skiver-test.

bioinformatics↗

bioRxiv2026

Heterologous betacoronavirus spike immunization in nonhuman primates elicits cross-reactive antibodies that neutralize both sarbeco- and merbecoviruses

In anticipation of future coronavirus (CoV) pandemics, developing vaccines that elicit broadly neutralizing antibodies (bnAbs) against diverse CoVs is critical. Here, we vaccinated rhesus macaques with SARS-CoV-2 spike (S)-protein, then boosted with heterologous {beta}-CoV S-proteins to focus responses to common conserved S2 bnAb epitopes. Initial SARS-CoV-2 priming elicited receptor-binding domain (RBD)-focused responses, while MERS-CoV boosting redirected responses toward the S2 region, including the stem-helix bnAb site. Although S2-directed serum cross-neutralization was undetectable and most isolated cross-reactive monoclonal antibodies (mAbs) targeted non-neutralizing epitopes, two S2 stem-helix mAbs were identified from memory B cells. These bnAbs neutralized diverse sarbeco- and merbecoviruses, including MERS-CoV, and conferred robust in vivo protection against SARS-CoV-2 challenge. Structural studies revealed that these macaque bnAbs closely mimic human S2-stem bnAbs induced by infection. These findings provide proof-of-principle for vaccination strategies that elicit broadly protective {beta}-coronavirus responses and highlight non-human primates as a translational model for evaluating S2-targeted immunogens.

immunology↗

bioRxiv2026

Identification of small-molecule adjuvants that enhance the sensitivity of Escherichia coli to nitrofurantoin: Roles of Lon and MarA

The increasing cases of resistance among UTI pathogens pose a significant threat to the continued clinical use of nitrofurantoin. In this study, we explored the molecular mechanisms underlying nitrofurantoin resistance and investigated the potential of synergistic activity of salicylates in enhancing the antibacterial activity of nitrofurantoin. In our initial observation, deletion of lon ({Delta}lon) conferred enhanced susceptibility to nitrofurantoin. We identified the critical role of Lon protease in regulating the sensitivity to nitrofurantoin. Investigation into the mechanisms revealed that the lon deletion strains show a higher level of marA and nfsA, which is likely to facilitate the conversion of nitrofurantoin from its pro form to its active form. The {Delta}lon strains displayed an elevated level of ROS, membrane alteration and filamentation upon treatment with nitrofurantoin. Higher ROS levels and membrane alteration were reversed upon treatment with glutathione, further confirming the role of oxidative stress in mediating the sensitivity to nitrofurantoin. Building on these mechanistic insights, we tested salicylates to synergistically enhance the efficacy of nitrofurantoin by indirectly inducing marA through the repression of the mar operon, thereby enhancing nfsA transcription. Both sodium salicylate and acetyl salicylate enhanced the efficacy of nitrofurantoin and lowered the dose of nitrofurantoin required to inhibit the growth of the WT strain. Importantly, this synergistic effect with acetyl salicylate was also observed in nitrofurantoin-resistant clinical isolates, where the combination reduced the effective nitrofurantoin concentration required for growth inhibition. This work provides novel insights into the roles of transcriptional regulators and proteolysis in antibiotic susceptibility, advancing the notion that antibiotic adjuvants are a reliable means of reviving the efficacy of antibiotics. ImportanceThis study unravels the uncharacterised role of Lon protease in nitrofurantoin susceptibility and illustrates the enhanced efficacy of nitrofurantoin-salicylate combinations as a promising therapeutic strategy to overcome emerging resistance in UTI pathogens. This study highlights the importance of investigating the repurposing of other FDA-approved molecules to combat resistance.

microbiology↗

bioRxiv2026

Chemical genomics screening reveals novel functions for unannotated genes in Vibrio cholerae C6706

Vibrio cholerae, the causative agent of cholera, remains a major global health burden despite ongoing initiatives for vaccination and improved sanitation. Much of the V. cholerae life cycle occurs in aquatic environments, requiring gene functions that enable survival under diverse stresses associated with this niche and during the transition to the human host. Although numerous V. cholerae genome sequences are available, functional annotation across its pan-genome remains incomplete, and many annotated genes lack experimental validation. In this study, we employed a chemical genomics approach to profile fitness phenotypes across 104 diverse stress conditions using a library of 3,026 single-gene mutants of V. cholerae C6706, a widely used research strain. In total, we identified significant growth phenotypes for 1,518 mutants, of which 88 correspond to unannotated (hypothetical or putative) genes. Together, these data provide a comprehensive resource for exploring gene function in V. cholerae, supported by detailed quality metrics and open-access tools to facilitate community-driven discovery. AUTHOR SUMMARYAlthough many bacterial pathogens have been extensively sequenced, we still know relatively little about what many of their genes actually do. In many cases, gene functions are solely predicted by computer algorithms but have not been confirmed in the laboratory, and we can assume that some of those predictions may be incorrect. Chemical genomics -- a method that tests thousands of single-gene mutants under different stresses -- can help reveal what these genes are responsible for. Using this approach, we screened a library of Vibrio cholerae C6706 mutants under 104 different conditions. We found that more than half of the mutants showed measurable effects on growth, including many genes that were previously uncharacterized. Here, we describe our experimental pipeline, present key quality checks, and share how other researchers can use this dataset as a resource to explore V. cholerae mutant phenotypes.

systems biology↗

bioRxiv2026

Nanobodies against the S2 region of the spike protein potently neutralize SARS-CoV-2 viruses and show resistance to virus escape

Entry of coronaviruses into cells is mediated by the viral spike (S) glycoproteins each consisting of S1 receptor binding and S2 membrane fusion subunits. The sequence of the S2 region is very highly conserved amongst variants of SARS-CoV-2 and compared to the S1 unit shares significant sequence identity amongst different beta-coronavirus lineages. By targeting the S2 of SARS-CoV-2 we have identified two selective and potent neutralizing nanobodies (BA.1-C2 and BA.1-D3) that bind to two different quaternary epitopes in the S2 formed by the Heptad Repeat 2 (HR2) trimer at the base of the spike protein. The HR2 sequence is identical in SARS-CoV and SARS-CoV-2 but differs in other beta-coronaviruses explaining the lack of binding to the spike proteins of MERS-CoV or HuCoV-OC43. No viral escape was observed following serial passaging of SARS-CoV-2 (JN.1) with a combination of BA.1-C2 and BA.1-D3 and the most potent of these nanobodies reduced viral load in the hamster model of COVID-19, following intranasal administration. Overall, the results show the value of nanobody technology for identifying novel neutralising epitopes in the S2 region of beta-coronaviruses with potential for the development of new selective anti-viral agents.

molecular biology↗

bioRxiv2026

Explaining how mutations affect AlphaFold predictions

Proteins can adopt many distinct conformations, yet the sequence determinants governing which structural states are accessible remain poorly understood. Using fold-switching proteins and AlphaFold as an analytical lens, we identify an organizational principle in which access to alternative structural states-and in some cases the folded state-is governed by surprisingly few amino acids, termed gating residues. Gating generalizes to single-fold proteins, indicating that conformational accessibility is often hierarchically organized around a small number of disproportionately influential residues. AlphaFold has implicitly learned this principle but amplifies and sometimes misapplies it, concentrating conformational control onto too few or incorrect residues. Guided by this principle, targeted MSA editing recovered a conformation AlphaFold confidently mispredicted, suggesting a path toward more accurate prediction of alternative conformations and mutational effects.

bioinformatics↗

bioRxiv2025

Macrophage-Dendritic Cell-T-Cell Tetrads Orchestrate Antitumor Immunity and Response to Checkpoint Blockade

Immune checkpoint inhibitors (ICIs) elicit durable responses in only a subset of patients with solid tumors, underscoring the need to define the cellular architectures that govern effective antitumor immunity. Here we identify a spatially organized multicellular immune unit comprising macrophages, cDC1s, CD4 T-cells, and CD8 T-cells that emerges in response to anti-CTLA-4 or dual checkpoint blockade. We term these structures tetrads. Using multiplexed imaging and spatial transcriptomics in mouse and human tumors, we show that tetrads assemble early during immune priming, depend on the ICOS-ICOSL pathway, and are enriched for ICOS Th1-like CD4 T cells and ICOSLhigh cDC1s. CD8 T-cells within tetrads exhibit an activated, non-terminally differentiated state, while tetrad-associated macrophages display an interferon-{gamma}-responsive program that sustains CD8 T-cell function and prevents dysfunction. Functionally, ICOSL cDC1s are required for tumor eradication in vivo. In patients with bladder cancer treated with neoadjuvant dual checkpoint blockade, tetrad, but not triad or dyad formation correlates with clinical response. These findings establish tetrads as a fundamental cellular unit coordinating antitumor immunity and responsiveness to ICIs.

immunology↗