Biology subjects

Zhang, T.

Publications and source records attributed to Zhang, T..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

Evolutionary dynamics of insect odorant receptors reveal ecological tuning shaping olfactory perception

Insect olfaction is facilitated by a heterotetrameric odorant receptor-odorant receptor co-receptor (OR-Orco) complex, which is distinct from that of vertebrate ORs. However, extreme sequence divergence among insect ORs has hindered a unified understanding of their evolutionary history and ecological importance. In this study, we present a multiscale analysis of OR genes across 115 insect species. We overcome the limitations of traditional phylogenetic approaches by applying a protein similarity network-based strategy and introduce a "trunk-branch" framework to systematically describe the evolutionary trajectories of insect ORs across sequence, structural, and predicted olfactory potential levels. Although they possess different sequences and structural communities, all sampled insect orders contained ORs assigned to all six docking-derived functional communities. Notably, extant insect lineages with order-level origins spanning the end-Permian mass extinction (EPME) differed in docking-derived functional OR repertoires, and early-and late-diverging lineages differed in OR sequence-community diversity. The emergence of Orco represents a key evolutionary transition point, marking the shift from a homomeric to a heteromeric complex accompanied by specialization of the extracellular domain and binding pocket. Furthermore, we established robust associations between potential olfactory recognition breadth and ecological variables, including diet, circadian rhythm, and habitat. Our findings provide a class-level framework for investigating insect OR evolution and generate testable hypotheses about how receptor repertoire diversification may relate to ecological adaptation.

evolutionary biology↗

bioRxiv2026

Antibody-Dependent Heterotypic Syncytia Drive COVID-19 Inflammation and Disease Progression

Severe COVID-19 is characterized by profound immune dysregulation and excessive inflammation. Aberrant myeloid responses drive hyperinflammation, yet the precise mechanisms remain elusive. Here, we demonstrate that certain spike antibodies promote the formation of heterotypic syncytia between monocytes/macrophages and virus-infected pneumocytes, leading to excessive inflammatory cytokine release. This antibody-dependent syncytium formation requires Fc{gamma}RI (CD64) and ADAM10, as well as the assembly of the six-helix bundle by the spike S2 subunit. Notably, these syncytia exhibit a stronger proinflammatory signature compared to virus-infected epithelial cells. In vivo, sub-neutralizing antibody concentrations amplified inflammation and exacerbated disease in SARS-CoV-2-infected mice without increasing viral burden. Furthermore, scRNA-seq of postmortem lung tissues from COVID-19 patients implicated the monocyte/macrophage-derived syncytia as a key cellular source of inflammatory cytokines. Together, these findings define a novel mechanism of antibody-dependent enhancement of inflammation that helps explain the hyperinflammatory responses in severe COVID-19 and suggest new therapeutic opportunities targeting this pathway.

immunology↗

bioRxiv2026

Identification and characterization of ethR and ethA genes impacting the sensitivity of Mycobacterium abscessus to ethionamide

Mycobacterium abscessus is a rapidly growing non-tuberculous mycobacterium with rising global incidence. This pathogen exhibits intrinsic resistance to most antibiotics, presenting a major public health threat. Ethionamide (ETH) requires bioactivation by monooxygenase EthA to form the active ETH-NAD adduct. We previously identified MAB_3513 (NudC) as a phosphohydrolase that confers intrinsic resistance to M. abscessus by hydrolyzing this adduct. However, deletion of nudC results in only partial susceptibility to ETH, indicating the existence of additional resistance mechanisms. This study identified MAB_0984 as the EthR regulator in M. abscessus. Deletion of ethR in a nudC knockout background ({Delta}{Delta}ethR) significantly enhanced ETH-NAD adduct accumulation, leading to hypersusceptibility to ETH. Notably, the {Delta}ethR mutant exhibited higher susceptibility than {Delta}nudC, demonstrating that EthR is a more dominant mediator of ETH resistance than NudC. Furthermore, MAB_0985 (EthA1) and MAB_0103 (EthA2) were identified as the primary EthAs in M. abscessus. Deletion of either gene alone or in combination in the {Delta}nudC reduced adduct formation and increased resistance, while the triple mutant {Delta}{Delta}ethA1{Delta}ethA2 restored wild-type resistance. Using an intergenic region-eGFP reporter system and quantitative reverse transcription-PCR, we demonstrated that EthR confers resistance by specifically suppressing ethA1 expression in M. abscessus. The Mycobacterium tuberculosis EthR inhibitor BDM31343 could boost the efficacy of ETH against M. abscessus by inhibiting EthR. Collectively, this study identified the ethR and ethA genes in M. abscessus for the first time and elucidated their role in mediating resistance to ETH. Therefore, EthR is a promising target for potentiating the efficacy of ETH against M. abscessus. Impact statementMycobacterium abscessus constitutes an escalating global health threat, primarily due to its intrinsic resistance to most antibiotics. This study identifies MAB_0984 (EthR) as a dominant resistance determinant that exerts a more profound impact on ETH susceptibility than the previously characterized NudC. We demonstrate that EthR mediates resistance by specifically repressing the expression of EthA1 (MAB_0985), one of the primary monooxygenases responsible for ETH bioactivation. The EthRMtb inhibitor BDM31343 potentiated the activity of ETH against M. abscessus through inhibition of the EthR. These findings elucidated the mechanism of ETH resistance in M. abscessus, identifying EthR as a promising target for boosting the efficacy of ETH against M. abscessus.

microbiology↗

bioRxiv2026

PRISM: Niche-informed Deciphering of Incomplete Spatial Multi-Omics Data

Spatial multi-omics data, characterizing the knowledge of diverse molecular layers, have become indispensable for the in situ analysis of tissue architecture and complex biological processes. Nevertheless, current spatial multi-omics sequencing protocols are often hindered by incompatible protocols, resulting in incomplete spatial multi-omics pairing due to inconsistent field-of-view or spatial resolution. To address this, we present PRISM, a novel computational method tailored for this scenario. PRISM leverages a niche-informed graph to propagate information from paired to unpaired regions, jointly achieving the spatial domain identification and spatial omics imputation. Extensive benchmarking on five diverse simulated and real experimental datasets demonstrated that PRISM outperformed existing methods in spatial multi-omics analysis tasks. Application to the human Parkinsons disease data revealed that PRISM accurately recovered dopamine-associated spatial domains and metabolite distributions masked by incomplete data gaps. PRISM offers a robust solution for bridging the integration gap inherent in incompatible sequencing protocols, thereby facilitating more accurate downstream biological interpretation.

bioinformatics↗

bioRxiv2026

Endothelin 2-Mediated Neuroinflammation Drives Hypertension-Associated Retinal Dysfunction

Systemic hypertension is a significant risk factor for glaucoma, a leading cause of irreversible blindness, yet the mechanistic basis connecting the two conditions remains elusive. Here, we demonstrate that hypertensive rats develop accelerated retinal degeneration characterized by retinal thinning, functional impairment, reduced perfusion, and progressive neuroinflammation. Critically, these changes occur despite persistently lower intraocular pressure (IOP), indicating an IOP-independent mechanism of pathology. Transcriptomic and biochemical analyses identified a robust activation of the retinal endothelin system, with endothelin-2 (EDN2) being the earliest and most significantly upregulated component. AAV-delivered retinal Edn2 knockdown completely restored retinal function, ameliorated neuroinflammation, and enhanced retinal blood flow in hypertensive rats. Pharmacological blockade of endothelin receptor type A (EDNRA), but not type B, replicated these protective effects without altering IOP. Our findings establish EDN2 as a central, IOP-independent driver of hypertension-associated retinal neurodegeneration and identify the endothelin-EDNRA axis as a potential therapeutic target to prevent vision loss in hypertensive patients.

neuroscience↗

bioRxiv2026

A small molecule PTER-selective inhibitor reduces food intake and body weight

PTER (phosphotriesterase-related) is an amidohydrolase that mediates catabolism of the anorexigenic taurine metabolite N-acetyltaurine. However, the structural basis of PTER ligand binding and catalysis remain unknown, limiting our ability to harness this pathway therapeutically. Here we solve crystal structures of a eukaryotic PTER in apo and product-bound forms. These structures uncover an unexpected pocket homology between PTER and histone deacetylase (HDAC) enzymes. We exploit this similarity to engineer a first-in-class substrate-competitive PTER inhibitor called PTERi with nanomolar potency and >100-fold selectivity for PTER over HDACs in vitro. Administration of PTERi to diet-induced obese mice reduces feeding, enhances GLP1-RA (glucagon like peptide 1 receptor agonist)-induced weight loss, and prevents weight regain after GLP1-RA discontinuation. The structure of PTER connects histone and metabolite deacetylation into a parallel conceptual framework and enables proof-of-concept data for pharmacological inhibition of PTER in obesity.

biochemistry↗

bioRxiv2026

Cysteine Glutathionylation as a Global Dynamic Regulator of Protein Active Site Accessibility and Protein Complex Formation

Protein-glutathionylation is traditionally viewed as a protective mechanism that shields cysteine-residues from irreversible oxidative damage. Its broader functional roles remain poorly understood, in part due to technical limitations in detecting this modification at scale. Here, we develop and leverage a new mass-spectrometry approach that preserves protein-glutathionylation, thereby revealing its widespread distribution across the proteome in cell models, worms, mice and human cardiac tissues. In all cases, we find that glutathionylation sites are enriched at both protein-protein interfaces and protein-active sites, and are highly conserved across species. We find that glutathionylation is dynamically redistributed in response to environmental challenges, thereby driving remodelling of cellular protein-protein interaction (PPI) networks, and access to protein active sites, with functional and phenotypic consequences. Finally, we show that glutathionylation accumulates on key cardiac-sarcomeric proteins in aged-mice and human cardiomyopathy biopsies, revealing its role in cardiovascular dysfunction. These findings reposition glutathionylation as a crucial regulatory PTM, akin to phosphorylation, that orchestrates adaptive cellular responses. This work redefines the role of glutathionylation, with broad implications for cell biology and disease.

molecular biology↗

bioRxiv2026

The novel variant IBDV induces inflammatory responses via VP3-mediated pyroptosis by directly targeting Caspase-9

The novel variant infectious bursal disease virus (nVarIBDV), which has been widely prevalent since 2017, threatens the poultry industry by inducing severe bursal atrophy and intense inflammatory responses. Understanding the inflammatory mechanism underlying nVarIBDV infection is critical for preventing virus-induced damage. Pyroptosis, an inflammatory type of programmed cell death, may contribute to the inflammation and bursa of Fabricius damage induced by nVarIBDV. Here, we found that the nVarIBDV infection induced severe inflammatory responses both in vivo and in vitro, which were associated with pyroptosis. Further research revealed that the viral protein VP3 drove pyroptosis induced by nVarIBDV infection by indirectly activating the Caspase-3-GSDME pathway, leading to GSDME cleavage. Mechanistically, VP3 directly interacted with and activated Caspase-9, thereby initiating Caspase-9-Caspase-3-GSDME pathway. More importantly, the Serine 33 of VP3 was identified as the key amino acid for interacting with and activating Caspase-9. Mutation of this residue significantly weakened the ability of VP3 to interact with Caspase-9 and activate the Caspase-9-mediated pyroptosis pathway, altered the binding mode of the Caspase-9-VP3 protein complex, and ultimately reduced the ability of VP3 to induce pyroptosis. In conclusion, our results elucidated a novel mechanism by which nVarIBDV infection induced inflammatory responses whereby viral protein VP3 triggered pyroptosis by targeting the Caspase-9-Caspase-3-GSDME pathway. IMPORTANCEnVarIBDV is globally prevalent and poses a significant threat to the poultry industry by causing inflammation and damage to the bursa of Fabricius. This study revealed that nVarIBDV infection induced inflammatory responses and bursa of Fabricius damage, primarily mediated by the viral protein VP3 targeting Caspase-9 to induce pyroptosis. To our knowledge, this is the first report on the interaction between inflammatory responses induced by IBDV infection and pyroptosis. In addition, serine 33 was identified as the critical amino acid required for maintaining the stability of the interaction between VP3 and Caspase-9 and activation of the Caspase-9-Caspase-3-GSDME cascade pyroptosis pathway and further inflammatory responses. Collectively, our findings not only elucidate a novel mechanism by which nVarIBDV induces pyroptosis and further leads to inflammation but also suggest that the identification of this serine site may represent a potential therapeutic target to block nVarIBDV-induced inflammation and bursa of Fabricius damage.

microbiology↗

bioRxiv2026

Ac-FAPI-04 Promotes Anti-tumor Immunity via IL-27 Activation and Tnfaip3 Inhibition

BackgroundAccumulating evidence substantiates the capacity of targeted radionuclide therapy (TRT) to potentiate tumor immunotherapy responses. However, combining TRT and immunotherapies exhibits substantial varying efficacy, underscoring the importance of investigating mechanisms through which TRT remodels the tumor microenvironment (TME). Despite recent advancements, the specific signaling molecules mediated by TRT that regulate the functions of cytotoxic T lymphocytes (CTLs) remain unclear. MethodsGiven the demonstrated potential of -radionuclides targeting the fibroblast activation protein (FAP) in TRT, this study employed [225Ac]Ac-FAPI-04 to investigate the mechanisms of TRT-induced TME remodeling. The cytotoxic effects were first evaluated in the B16F10 cell line, followed by an assessment of its in vivo therapeutic efficacy in tumor-bearing mice. RNA-sequencing analysis was utilized to elucidate underlying signaling pathways involving immune responses. Results[225Ac]Ac-FAPI-04 significantly induced DNA double-strand breaks, further elevated ROS levels, and apoptosis in tumor cells. Transcriptomic profiling revealed that [225Ac]Ac-FAPI-04 activates the IL-27/JAK-STAT pathway to amplify interferon-mediated responses, indicating IL-27 serves as a critical regulatory signal for CTLs during TRT. A concomitant observation was the downregulation of Tnfaip3 following [225Ac]Ac-FAPI-04 treatment. Tnfaip3 is implicated in modulating CTLs behavior and intratumoral infiltration, while its downregulation was associated with the upregulation of cytotoxic effector molecules, as confirmed in this study. ConclusionThis study identifies a TRT-induced pattern of synergistic signaling mediated by IL-27 and Tnfaip3, which collectively enhances CTL recruitment and potentiates their cytotoxic function. These findings provide a detailed mechanistic rationale for strategies aimed at augmenting the therapeutic efficacy of TRT and immunotherapy combinations.

molecular biology↗

bioRxiv2026

The Red Rice Bran Extract (RRBE) Mitigates Photoaging by Targeting Mitochondrial Oxidative Stress and Regulating Thermal Damage Responses

The photoprotective efficacy of natural skin-active complexes is well recognized, yet their ap-plication is often hindered by the challenge of deciphering their complex, multi-component, and multi-target mechanisms. To bridge the gap between established phenotypes and molecular mechanisms, we developed an AI-driven integrated platform that combines phytochemical profiling, network pharmacology, and deep learning-based target prediction with rigorous biophysical validation. We applied this platform to investigate RRBE, a bioactive complex refined from red rice bran extract. In vivo clinical studies confirmed that RRBE significantly accelerates the resolution of UV-induced erythema, while cellular and 3D tissue models demonstrated robust suppression of oxidative stress and DNA damage responses. To decode its material basis, the platform deconstructed RRBE into 10 distinct chemical modules. Leveraging our SCOPE-DTI deep learning model for global target prediction, we identified flavonoids (Module 1) and phenolic acids (Module 10) as the primary bioactive drivers relevant to photoprotection. These computational predictions were structurally supported by molecular docking and definitively validated in a physiological environment via Cellular Thermal Shift Assay-Mass Spectrometry (CETSA-MS). Mechanistically, RRBE functions through a synergistic polypharmacology: (1) Module 1 components, represented by procyanidin B2, target NDUFA7 to stabilize mitochondrial function and mitigate ROS; (2) Module 10 components, exemplified by caffeic acid, ferulic acid, and p-coumaric acid, engage FKBP11 and HSP90AA1 to regulate protein homeostasis and stress responses. This work not only deciphers the polypharmacological basis of RRBEs photoprotective action but also validates a scalable "AI-guided, cell-validated" discovery pipeline, offering a rational paradigm for uncovering the protective benefits of complex natural extracts.

systems biology↗

bioRxiv2026

Functional characterization of a multi-cancer risk locus on chromosome band 2q33.1 near CASP8

Genome-wide association studies (GWAS) of melanoma have identified numerous susceptibility loci. However, causal genes and variants underlying risk have yet to be established for most. It is becoming apparent that many functional variants underlying complex traits act via cis-regulation that may be context-specific, dependent on availability of specific transcription factors/complexes in specific cell types and cell-states. To characterize a risk locus on chromosome band 2q33.1 associated with melanoma, breast cancer, and keratinocyte cancers, we integrated fine-mapping, cell-type specific expression quantitative trait locus (eQTL) analysis, a massively parallel reporter assay, individual luciferase assays, and SNP-based proteomics. Integrated analysis implicates the presence of multiple functional variants lying primarily within a promoter for CASP8. A haplotype containing rs3769823 appeared have the largest effect on expression. Strikingly, both tumor/normal context and this risk-associated haplotype play critical roles in mediating allelic cis-regulatory activity. Quantitative mass spectrometry for rs3769823 identified both E4F1, a transcriptional repressor, and IRF2, a transcriptional activator, as binding preferentially to risk-associated rs3969823-A. The binding of these transcription factors was validated via EMSA, supershift, and chromatin immunoprecipitation (ChIP) assays. The relative levels of E4F1 and IRF2 differ by cell-type and play a role in mediating transcriptional activity in a cell-type specific manner. Our results indicate that the top credible causal set variant rs3769823 likely influences expression of CASP8 and FLACC1 in a cell-type specific manner and may be a relevant functional variant for multiple cancers associated with this locus.

genetics↗

bioRxiv2025

Homology-independent targeted integration in vivo restores Cldn11 deficiency in mouse Sertoli cells and spermatogenesis

Defective testicular Sertoli cell (SC) function may be an underlying cause of male infertility/subfertility; however, in vivo gene therapy for nonobstructive azoospermia (NOA) caused by SCs has never been attempted. In this study, a CRISPR/Cas9-based homology-independent targeted integration (HITI) gene editing strategy was used to integrate an [~]3.7 kb DNA fragment containing a SC-specific enhancer/promoter and a region comprising three Cldn11 exons into the SCs of Cldn11-deficient mice. After the viral plasmids carried by recombinant adeno-associated virus serotype 1 (rAAV1) were delivered to SCs via testicular tubular injection, the phenotypes of blood-testis barrier loss, spermatogenesis blockage, and infertility in the mice were successfully rescued for 6 months, and first-generation offspring were produced using the sperm of the rescued mice. Our results suggest that despite the lack of proliferation and low division capacity of adult testicular SCs, the introduction of targeted strategies such as HITI could enable in vivo gene editing as a possible treatment for infertility caused by Sertoli cell defects.

genomics↗

bioRxiv2025

Revealing the Drivers Underlying Distinct Evolutionary Trajectories in Lung Adenocarcinoma

Elucidating the evolution of cancers allows us to understand their key events, and the order in which they occur. To chart and interpret these evolutionary trajectories, we leverage whole-genome sequencing of lung tumours, including those from the largest cohort to date of lung cancers in subjects who have never smoked. Through ordering frequent genomic alterations, we discover three distinct evolutionary paths taken by lung adenocarcinomas; two dominated by tumours from people who have never smoked (NS-LUAD), and one followed by the vast majority of those who have smoked (S-LUAD). However, one in six NS-LUAD follow the smoking-dominant trajectory. These tumours, surprisingly, have fewer somatic alterations than the other NS-LUAD, and have shorter latency. They are strongly enriched for KRAS mutations. Our results suggest that gaining KRAS mutations allows these tumours to evolve more rapidly, acquiring a set of smoking-associated key alterations, with less need for genomic instability to progress. These tumours are three times more frequent in subjects of European vs. East Asian ancestry. These findings could shape clinical management strategies for lung adenocarcinoma patients, particularly for tumours driven by smoking-like evolutionary trajectories.

cancer biology↗

bioRxiv2025

53BP1 condensates function as bioreactors for NHEJ directed DNA repair and insulators to determine pathway choice

Genomic integrity requires efficient resolution of DNA damage. Non-homologous end joining (NHEJ) is the primary mechanism of DNA double strand break (DSB) repair in mammalian cells and is mediated by 53BP1, a tumor suppressor involved in preventing DSB end-resection and homologous recombination. NHEJ repair foci form following DSB formation, however how mesoscale assembly occurs and whether 53BP1 is the driver of this process are unknown. Also, despite knowledge of the identify of key pathway molecules, the specific functions of mesoscale repair condensates in DNA repair and pathway selectivity are unknown. To address these gaps, we determined the minimal domain of 53BP1 sufficient for phase separation in vitro and identified the key residues that governing its condensation. Utilizing a separation-of-function mutant, we demonstrate that 53BP1and its protein condensation is the core driver of NHEJ foci formation. 53BP1 condensates function as bioreactor compartments, increasing the effective concentration of substrates near double strand breaks and are essential for efficient DNA damage resolution. Additionally, we show that 53BP1 condensates function as insulators around DSB sites to prevent end-resection and direct repair pathway selectivity. Collectively our work reveals a specialized compartment for DNA repair through the spatial clustering of 53BP1 molecules into repair foci essential to maintain genome integrity.

cell biology↗

bioRxiv2025

Identifying High-Dimensional Genomic Factors Modulating Biological Networks Across Multi-Omics Data

Biological traits such as genes, metabolites, and microbial taxa interact within complex networks, yet how genomic factors shape these interactions remains poorly understood. Here, we introduce GFBioNet, a computationally efficient method for identifying factors that modulate direct associations between biological traits within network models. Our two-stage strategy first estimates a baseline network using Gaussian graphical models and then tests whether genomic factors modulate specific network edges (trait-trait relationships), enabling scalable analysis of high-dimensional multi-omics data while explicitly controlling the false discovery rate (FDR). Simulations demonstrate reliable FDR control and high statistical power across a broad range of settings. Applied to multiple datasets, GFBioNet reveals host genetic variants influencing oral microbiome relationships, gut microbial taxa modulating metabolite networks in colorectal cancer, and somatic mutations and copy-number alterations reshaping gene expression networks in lung adenocarcinoma. By expanding network analysis to evaluate modifiers of trait-trait relationships, GFBioNet offers a versatile tool for uncovering the genomic architecture of biological networks across multi-omics studies.

genomics↗

bioRxiv2025

A K27-linked Ubiquitin Checkpoint Controls NOTCH Homeostasis

Cell surface receptors such as NOTCH1 must be tightly regulated to ensure developmental fidelity and prevent pathological activation. Although the proteolytic steps culminating in nuclear NOTCH1 signaling are established, how cells prevent excessive or uncontrolled activation has remained unresolved. Here we identify the autophagy-related protein UVRAG as a negative regulator of NOTCH1. Upon receptor activation, UVRAG, acting independently of autophagy, recruits and activates the E3-ligase ITCH to catalyze K27-linked ubiquitination of membrane-tethered NOTCH1, thereby licensing ESCRT-dependent lysosomal degradation. Disruption of the UVRAG-ITCH-ESCRT axis stabilizes activated NOTCH1 intermediates and amplifies oncogenic signaling. In T-cell leukemia models driven by constitutive NOTCH1 activity, restoring UVRAG expression reinstates receptor turnover, suppresses disease progression, and improves therapeutic response. These findings define a ubiquitin-directed safeguard circuit that enforces NOTCH1 signaling homeostasis and reveals a tunable axis for intervention in NOTCH1-driven cancers.

molecular biology↗

bioRxiv2025

DOMINO: diffusion-optimised graph learning identifies domain structures with enhanced accuracy and scalability

Spatial transcriptomics enables in situ molecular profiling, allowing to measure the cellular transcriptional output within the tissue. As the tissue architecture is conserved, spatial domains with specific transcriptional patterns can be identified, facilitating the discovery and understanding of functional tissue compartments. Thus, several methods to uncover and identify these spatial domains have been developed. However, most of these existing methods do not scale to rapidly increasing data sizes and focus only on local structure while missing the global view of the tissue. Here, we present DOMINO, a diffusion-optimised contrastive learning framework for spatial domain detection. DOMINO utilises graph diffusion convolution to propagate information beyond immediate neighbours and jointly optimises local and, importantly, global graph structure via contrastive learning. This novel framework yields biologically interpretable domains with clearer boundaries and scales to large datasets, outperforming state-of-the-art methods across healthy and malignant benchmark datasets. We apply DOMINO to a newly generated spatial transcriptomic dataset of endometriosis-associated ovarian cancers, which could not be processed by existing domain detection methods owing to its size. We uncovered conserved proliferative and non-proliferative tumour states that recurred across these tumours and were independently validated in an external clear cell ovarian cancer spatial transcriptomic dataset. Proliferative domains were characterised by elevated expression of EIF4A1 and HSPA8, increased cell cycle activity, reduced mast cell abundance, and coordinated stromal remodelling, including altered fibroblast states and spatial organisation. In parallel, integrative analysis across tumours revealed subtype-specific multicellular ecosystems associated with either endometrioid or clear cell ovarian carcinomas, together with a tumour-excluded stromal domain that could only be resolved through the integration of spatial and transcriptional information. These findings demonstrate how well DOMINO scales up and that it uncovers biologically meaningful spatial programs spanning tumour intrinsic states, tumour microenvironment interactions, and subtype-specific tissue architecture that are not recovered by conventional expression-based clustering approaches.

bioinformatics↗

bioRxiv2025

A division-associated envelope protein, MAB_2363, drives intrinsic resistance and virulence in Mycobacterium abscessus

Mycobacterium abscessus exhibits intrinsic resistance to conventional antibiotics, significantly limiting treatment options. Our previous studies established that MAB_2362 (SteA) is a key regulator of cell division that contributes to intrinsic resistance and virulence. Considering that SteA-like proteins often act alongside SteB counterparts, we hypothesized that the adjacent gene MAB_2363 encodes the corresponding SteB-like division regulator. In this study, we found that deletion of MAB_2363 significantly increased susceptibility to multiple antibiotics and disrupted cell wall permeability. Microscopy revealed striking cell division defects in the mutant, including elongated cell morphology and multiple septa. Subcellular localization of a GFP-MAB_2363 fusion protein demonstrated its enrichment at division septa, confirming its direct involvement in cell division. Deletion of MAB_2363 resulted in attenuated virulence, as evidenced by reduced bacterial survival in macrophages and murine infection models. To assess its functional relation with MAB_2362, we compared the single-deletion mutant of MAB_2363 with the single-deletion mutant of MAB_2362 and the double-deletion mutant of MAB_2362-MAB_2363. Notably, the phenotypes of the MAB_2363 mutant, including cell division defects, antibiotic susceptibility, and virulence, were markedly milder than those of the other two mutants. Collectively, these findings indicate that MAB_2363 functions as a secondary but essential division-associated factor that operates during cell division, thereby influencing intrinsic resistance and virulence in M. abscessus.

microbiology↗