Biology subjects

Zhang, Z.

Publications and source records attributed to Zhang, Z..

At least 289 records · Page 16Linked to original sources

bioRxiv2026

An additional site mutation in MITA/STING gain-of-function mutants abolishes the autoimmune SAVI phenotypes and directs a therapeutic strategy.

STING-associated vasculopathy with onset in infancy (SAVI) is an autoimmune disease caused by gain-of-function mutations (GOFs) of MITA/STING and the most frequent GOFs for SAVI are MITAN154S and MITAV155M. However, how MITA GOFs are spontaneously activated remains incompletely understood. Here, we show that the activity of MITA hinge-region GOFs is compromised by an additional mutation at Lys150 and that the SAVI phenotypes of MITAN153S/WT mice are completely abolished in the MITAK150N/N153S (MITANS/NS) mice. Mechanistically, MITA GOFs constitutively associate with iRhom2 for the spontaneous ER-to-Golgi translocation, which is substantially inhibited by the introduction of a mutation at Lys150. Interestingly, cGAMP binds to MITANS, triggers the ER-to-Golgi translocation of MITANS as well as the MITANS-iRhom2 interaction, and induces the expression of downstream genes in MitaNS/NS cells similarly as in Mita+/+ cells. Consistently, structural studies demonstrate an inactive open conformation of apo-MITANS characterized by connector region crossover and a curved filament of cGAMP-bound MITANS characterized by parallel connector regions, similar to those observed in wild-type MITA. Furthermore, we design a SAVI-inhibitory peptide (SIP) that selectively inhibits the interaction between MITAN153S and iRhom2 and the activity of MITA GOFs and thereby abolishes the SAVI phenotypes of the MITAN153S/WT[->]WT chimeric mice. These findings reveal a previously uncharacterized mechanism for the spontaneous activation of MITA GOFs and highlight a potential therapeutic intervention for SAVI.

immunology↗

bioRxiv2026

Aging, matrix metalloproteinase imaging, and survival prospects in aortic aneurysm

Age is a risk factor for aortic aneurysm (AA), and different segments of the aorta exhibit varying susceptibilities to aneurysm. The specific factors that contribute to the higher incidence of AA and its complications with aging remain unclear. Matrix metalloproteinases (MMPs) are elevated in AA. However, the connection between aging, aortic MMP activity, and the increased prevalence of AA and its complications has not been systematically evaluated. This study leveraged MMP-targeted molecular imaging to investigate how aging affects aortic MMP expression and activity, as well as aneurysm development and survival. MethodsAA development and animal survival were monitored for 28 days after Angiotensin (Ang)-II infusion in 8-10-week-old (young) and >51-week-old (old) Apoe-/- mice. Aortic MMP activation was quantified by PET/CT using an MMP-targeted tracer, 64Cu-RYM2, at baseline and 1 week after Ang II infusion. MMP activity and expression were quantified by tissue zymography and quantitative reverse transcription polymerase chain reaction, and compared between different segments of the aorta in young and old animals, and before and after Ang II infusion. ResultsOld animals survival to 28 days was significantly lower than that of young Ang-II-infused Apoe-/- mice (P < 0.05). 64Cu-RYM2 PET/CT showed significantly higher aortic MMP activation before and 1 week after Ang-II infusion in old compared to young Apoe-/-mice. The 64Cu-RYM2 signal was significantly higher in animals that did not survive 28 days than those that did (P < 0.01). MMP activity significantly increased by 4 days after Ang-II infusion, when dissection was found in a subset of Apoe-/- mice; and was significantly higher in the dissected, compared to adjacent, apparently normal, segments of the aorta. MMP activity was also significantly higher in the ascending thoracic aorta of untreated young and old mice, as well as of Ang-II-treated Apoe-/-mice (which was associated with significantly higher Mmp2 gene expression), and of old wild-type mice. ConclusionAging is associated with increased MMP activity along the aorta and worse AA survival. MMP-targeted molecular imaging can inform the aneurysm survival prospects. Selective MMP inhibitors and tracers may help prevent and track aneurysm growth, dissection, and rupture.

bioengineering↗

bioRxiv2025

SNAP: Streamlined Nextflow Analysis Pipeline for Immunoprecipitation-Based Epigenomic Profiling of Circulating Chromatin

Epigenomic profiling of circulating chromatin is a powerful and minimally invasive approach for detecting and monitoring disease, but there are no bioinformatics pipelines tailored to the unique characteristics of cell-free chromatin. We present SNAP (Streamlined Nextflow Analysis Pipeline), a reproducible, scalable, and modular workflow specifically designed for immunoprecipitation-based methods for profiling cell-free chromatin. SNAP incorporates quality control metrics optimized for circulating chromatin, including enrichment score and fragment count thresholds, as well as direct estimation of circulating tumor DNA (ctDNA) content from fragment length distributions. It also includes SNP fingerprinting to enable sample identity verification. When applied to cfChIP-seq and cfMeDIP-seq data across multiple cancer types, SNAPs quality filters significantly improved classification performance while maintaining high data retention. Independent validation using plasma from patients with osteosarcoma confirmed the detection of tumor-associated epigenomic signatures that correlated with ctDNA levels and reflected disease biology. SNAPs modular architecture enables straightforward extension to additional cell-free immunoprecipitation-based assays, providing a robust framework to support studies of circulating chromatin broadly. SNAP is compatible with cloud and high-performance computing environments and is publicly available at https://github.com/prc992/SNAP/. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/694452v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@47c734org.highwire.dtl.DTLVardef@674af8org.highwire.dtl.DTLVardef@16ae938org.highwire.dtl.DTLVardef@1f57a01_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

SF3A2 deacetylation at lysin 10 mitigates myocardial pathological remodeling by reprogramming cardiomyocyte metabolism

BackgroundDysregulation of splicing factor-mediated pre-mRNA alternative splicing (AS) underlies the progression of complex diseases, but the specific involvement of AS in myocardial pathological remodeling remains unclear. This study aimed to elucidate the role of splicing factor 3A, subunit 2 (SF3A2) in the development of myocardial pathological remodeling by regulating AS and its effect on metabolic reprogramming. MethodsWe evaluated the function and mechanism of SF3A2 in myocardial pathological remodeling using murine models induced by myocardial infarction (MI) and isoproterenol. The gain- and loss-of-function models (AAV9-cTNT delivery-mediated knock-in and lentivirus-mediated knockdown) combined with acetylomics, metabolomics, lipidomics, 13C-glucose tracing and immunoprecipitation coupled with liquid chromatography-tandem mass spectrometry (IP-MS) analyses were used to demonstrate the mechanism of SIRT7-mediated SF3A2 deacetylation at lysin 10 (K10). Unbiased RNA sequencing and AS analysis were conducted to identify the downstream effector of SF3A2. ResultsSF3A2 acetylation at lysine 10 was upregulated in cardiomyocytes in response to myocardial pathological remodeling. Functionally, the knock-in of a deacetylation-mimetic SF3A2 (K10R) mutant attenuated myocardial hypertrophy, fibrosis, and improved heart function. These phenotypes were accompanied by a redirection of glucose flux from anaerobic glycolysis to the TCA cycle, along with a promotion of fatty acid {beta}-oxidation by inhibiting CD36 translocation and decreasing ACLY activity. Mechanistically, SF3A2 mitigated metabolic reprogramming and mitochondrial dysfunction by regulating Nnt AS, a process involving the SF3A2-interacting protein Ddx1. IP-MS further identified SIRT7 as the deacetylase for SF3A2, which was found to be activated by ginsenoside Rg1 in a high-throughput screen, leading to improved heart function. ConclusionsOverall, our findings establish the SIRT7-SF3A2-Nnt axis as a critical regulator in metabolic reprogramming to delay pathological myocardial remodeling. Promoting SF3A2 deacetylation, mediated by AAV9 delivery or pharmacological activation of SIRT7, improved heart function, suggesting its potential as a therapeutic target for pathological myocardial remodeling.

molecular biology↗

bioRxiv2025

Pan-cancer tumor classification by a holistic tumor microenvironment atlas

The tumor microenvironment (TME) heterogeneity presents a major bottleneck to effective cancer immunotherapies. We address this by establishing a pan-cancer tumor classification system based on the holistic TME cellular components. First, using single-cell transcriptomes from 1,271 patients across 26 cancer types, we compile a TME cellular atlas, leading to the identification of recurrent cell states and multicellular modules across cancer types. Among these, we highlight a type I interferon (IFN-I)-related multicellular module, including IFIT1+ tumor-associated macrophages, as a critical contributor to immune-activation TMEs. From a holistic perspective, pan-cancer TMEs exhibit trichotomous patterns predominantly driven by T, myeloid, and stromal compartments. Leveraging fine-grained TME cellular composition, we further stratify all tumors into 10 stable groups. These groups display varying responses to immune checkpoint blockade (ICB), and each rationally selected therapeutic strategy specifically perturbs the corresponding expression signature. Our pan-cancer tumor classification scheme reveals the underlying patterns of TME heterogeneity and provides a framework for stratifying patients, guiding treatment selection, and developing novel therapeutic options.

cancer biology↗

bioRxiv2025

STEAP4+ neutrophils: a promising circulating biomarker for lung metastasis

As the leading contributor to cancer-related mortality, metastasis often evades detection until advanced stages, underscoring the critical need for early predictive biomarkers. Neutrophils are naturally circulating sentinels that have been implicated in pioneering pre-metastatic niche formation in distant organs. Nevertheless, their heterogeneity within evolving metastatic microenvironments remains poorly characterized. Here, through dynamically delineating neutrophil subsets via single-cell transcriptomics, we identified a conserved feature of lung metastasis in breast cancer and other cancer models. Among the core genes, a cell surface marker, STEAP4, was selected and validated to indicate lung metastases at both RNA and protein levels. In both humans and mice, these STEAP4+ neutrophils were detectable not only in lung metastatases but also in the circulation. Clinically, the abundance of circulating STEAP4+ neutrophils robustly discriminates patients with lung metastasis from those with localized primary tumor. Our findings uncover STEAP4+ neutrophils as a promising biomarker and lay the groundwork for a non-invasive, blood-based diagnostic strategy for metastatic disease.

cancer biology↗

bioRxiv2025

The conserved NUS-1/DHDDS complex links N-glycosylation to lipid and lysosomal homeostasis in C. elegans

N-glycosylation, driven by the cis-prenyltransferase (cis-PT) complex, a NUS1 and DHDDS heterotetramer, is vital for proteome integrity. Despite being linked to severe congenital disorders of glycosylation (CDGs), the systemic role of NUS1/DHDDS remains elusive. Here, we characterize the conserved C. elegans cis-PT complex and uncover a critical crosstalk with global lipid metabolism. cis-PT deficiency induces catastrophic ER stress, global glycoprotein defects, and developmental failure. Mechanistically, NUS-1 physically interacts with the core oligosaccharyltransferase (OST) complex, directly coupling substrate synthesis to N-glycan transfer. Loss of NUS-1 or DHDDS causes systemic lipopenia, lysosomal dysfunction, and cholesterol sequestration, resulting from impaired N-glycosylation of key regulatory glycoproteins like SCAP. Utilizing CDG-associated CRISPR models, we resolve the molecular basis for cis-PT dysfunction, identifying interface disruption and catalytic impairment as distinct disease etiologies. These findings collectively reveal a critical and previously unappreciated crosstalk between protein glycosylation and global lipid metabolism, establishing a robust system to explore CDG pathology and therapeutic strategies.

cell biology↗

bioRxiv2025

Reciprocal Homoeologous Replacement of MYB Factors Drives the Evolutionary Trade-off between Yield and Fiber Quality in Cotton

The long-standing phenotypic trade-off between Upland cotton (Gossypium hirsutum, high yield) and Sea Island cotton (G. barbadense, high quality) represents a major bottleneck in cotton breeding and industrialization. Despite rapid advances in genomics, the genomic structural variations driving the divergence of these two domestication strategies, and their subsequent impact on downstream transcriptional networks, remain unclear. This study integrates multi-tissue transcriptomic atlases spanning the full growth period with pan-genomic analyses of both Upland and Sea Island cotton, proposing a "Reciprocal Selective Retention (RSR)" strategy adopted by the two species during evolution. Transcriptomic analysis revealed that while the transcriptional chassis of the two species is highly conserved, a drastic "phase inversion" occurs during fiber development. Sea Island cotton appears to trade off for quality by specifically activating a "delayed elongation" module (at 20 DPA), whereas Upland cotton initiates a "precocious filling" program to pursue yield. Further Weighted Gene Co-expression Network Analysis (WGCNA), combined with genomic Presence/Absence Variation (PAV) analysis, identified a set of key transcription factors exhibiting a "3-vs-3" reciprocal loss pattern. Upland cotton specifically retained CRF10, WIND1, and MYB93, constructing a genetic foundation of "robust root system and strong regeneration" to support high yield. Conversely, Sea Island cotton specifically retained MYB111 and ERF105/017 to maintain long-staple characteristics and environmental buffering. Whole-genome structural variation and microsynteny analyses confirmed that these differences stem from asymmetric physical deletions (e.g., a 5 kb deletion in MYB111) or fragment sequence collapse (e.g., a 15.9 kb sequence divergence in MYB93) on homologous chromosomes. The RSR model proposed in this study not only offers a novel insight into the genetic roots of the negative correlation between yield and quality but also provides clear genomic targets for precision improvement using gene-editing technologies such as CRISPR.

genomics↗

bioRxiv2025

COPS5 is Essential for Sertoli Cell Function and Male Fertility in Mice

The COP9 signalosome subunit 5 (COPS5) is a multifunctional protein that regulates ubiquitin-dependent processes. Global knockout of Cops5 is embryonically lethal, and while it is known to be vital in germ cells and testicular smooth muscle, its function in Sertoli cells, the key somatic supporters of spermatogenesis, remains entirely unknown. This study investigates the critical role of COPS5 within Sertoli cells. Using Sertoli cell-specific Cops5 knockout mouse models, we demonstrate that COPS5 is essential for maintaining male fertility. Sertoli-specific Cops5 ablation resulted in age-dependent male infertility, despite normal initial development. Mutants exhibited progressive testicular atrophy, oligoasthenospermia, and significantly reduced testis weight. Histology showed vacuolated, disorganized tubules devoid of germ cells and sperm. Crucially, COPS5 loss disrupted Sertoli cell polarity, evidenced by aberrant cytoplasmic mislocalization of the nuclear marker WT1 and detachment from the basement membrane. Integrity of the blood-testis barrier (BTB) was severely compromised, with discontinuous and punctate expression of the tight junction adaptor ZO-1. Intercellular communication was also impaired, shown by a stark reduction in Connexin 43 gap junction signals. Our findings establish that COPS5 is an indispensable intrinsic regulator of Sertoli cell function. Its loss disrupts cell polarity, BTB architecture, and gap junction communication, leading to failed support of spermatogenesis and consequently infertility. This work defines a novel and critical somatic function for COPS5 in male reproduction. We conclude that COPS5 is intrinsically required in Sertoli cells to maintain their polarity and BTB function, which are foundational for supporting germ cell development and ensuring male fertility. This identifies COPS5 as a novel, essential regulator within the testicular somatic compartment.

genetics↗

bioRxiv2025

Pulmonary mRNA-LNP Vaccines for Rapid and Durable Protection Against Bacterial Infection

Pulmonary bacterial infections remain a major clinical challenge. Although vaccination reduces infection rates and mortality, the vulnerable post-vaccination immunity gap can still result in infection and vaccine failure. In addition, effective vaccines are unavailable for many clinically important bacterial pathogens. Here, we report a pulmonary mRNA-lipid nanoparticle (mRNA-LNP) vaccine incorporating a novel ionizable lipid engineered for localized high-level expression, which elicits both rapid and durable protections against bacterial lung infections, effectively bridging this critical window of vulnerability. Intratracheal delivery of mRNA-LNP rapidly primes lung neutrophils and macrophages into a transcriptionally pre-activated state, enhancing their phagocytic activity and enabling rapid, antigen-independent bacterial clearance during the early post-vaccination period (approximately 1-7 days). Subsequently, vaccination induces potent antigen-specific adaptive responses, conferring sustained protection against both laboratory and clinical drug-resistant Pseudomonas aeruginosa strains. Single-cell transcriptomics and immune profiling reveal coordinated activation of innate and adaptive immune programs. This dual-phase immune response exemplifies a paradigm-shifting vaccine design that integrates innate and adaptive immunity to confer both immediate and long-term protection. Our findings establish a mechanistic basis for rapid antibacterial defense and highlight pulmonary mRNA-LNP vaccination as a promising strategy for combating respiratory infections.

bioengineering↗

bioRxiv2025

Post-weaning social isolation impairs the orbitofrontal cortical circuit subserving contagious pain and prosocial behaviors

Empathic behaviors are sensitive to environmental factors like post-weaning social isolation (SI), yet the mechanisms by which SI affects empathy remain unclear. Here, we show that mice subjected to SI exhibit marked impairments in contagious pain and prosocial behaviors, including allo-grooming and allo-licking toward cagemates experiencing inflammatory pain. Mechanistically, we identify the glutamatergic projection from the ventromedial thalamic nucleus (VM) to the orbitofrontal cortex (OFC) as critical for these empathy-like responses. SI induces hypoexcitability of OFC glutamatergic neurons and attenuates excitatory synaptic transmission within the VM[->]OFC pathway. Remarkably, chemogenetic activation of OFC neurons or the VM[->]OFC projection restores empathic behaviors in SI mice. Furthermore, we uncover a molecular basis for SI-induced OFC hypoexcitability: the downregulation of Grik3, encoding a kainate-type glutamate receptor subunit. These findings reveal a previously uncharacterized thalamocortical mechanism through which early-life social deprivation disrupts empathic behaviors, offering insights into the underpinnings of social-affective dysfunction.

neuroscience↗

bioRxiv2025

Genomic Structural Variation Underlies Cell-Type-Specific Betacyanin Variegation in Chenopodium quinoa

The allotetraploid crop quinoa (Chenopodium quinoa) accumulates red/violet betacyanins, which function as vital stress-mitigating antioxidants. We investigated the genetic basis of red/green variegation observed in the aerial organs of the P0429 accession. We demonstrated that this color mosaic is primarily localized to the epidermal bladder cells (EBCs), with red EBCs accumulating [~]50-fold higher betacyanin levels than colorless EBCs. Cell-type-specific RNA-sequencing of EBCs identified the cytochrome P450 gene Cqu0091301 (CYP76AD) as the dominant and rate-limiting factor, exhibiting strong upregulation in red EBCs. This high pigmentation requires a specific structural variation in the P0429 accession: a [~]4-kb genomic insertion that restores the full functionality of Cqu0091301, which is otherwise truncated and non-functional in common reference genomes. Genomic analysis reveals that Cqu0091301 is part of a CYP76AD-DODA gene cluster. Notably, expression analysis revealed functional divergence between the quinoa subgenomes, with B-subgenome CYP76AD genes highly dominant in EBCs, while A-subgenome homologs were preferentially expressed in other tissues. Our results establish a clear link between structural genomic variation and cell-type-specific betalain biosynthesis, providing molecular insight into pigment regulation and subgenome specialization in allotetraploid quinoa.

plant biology↗

bioRxiv2025

Landscape Expansion Microscopy Reveals Interactions between Membrane and Phase-Separated Organelles

Landscape Expansion Microscopy (land-ExM) is a light microscopy technique that visualizes both lipid and protein ultrastructural context of cells. Achieving this level of detail requires both superresolution and a high signal-to-noise ratio. Although expansion microscopy (ExM) provides superresolution, obtaining high signal-to-noise images of both proteins and lipids remains challenging. Land-ExM overcomes this limitation by using self-retention trifunctional anchors to significantly enhance protein and lipid signals in expanded samples. This improvement enables the accurate visualization of diverse membrane organelles and phase separations, as well as the three-dimensional visualization of their contact sites. As a demonstration, we revealed triple-organellar contact sites among the stress granule, the nuclear tunnel, and the nucleolus. Overall, land-ExM offers a high-contrast superresolution platform that advances our understanding of how cells spatially coordinate interactions between membrane organelles and phase separations. eTOC SummaryZhuang et al. introduce land-ExM, a super-resolution approach that simultaneously maps protein and lipid ultrastructure in cells with high contrast. This method visualizes 3D interactions between membrane-bound organelles and phase-separated condensates, uncovering organelle contact sites such as stress granules at nuclear tunnels adjacent to nucleoli.

cell biology↗

bioRxiv2025

Differential Alterations of Gut Microbiota in Girls with Isolated Obesity, Isolated Precocious Puberty, and Their Comorbidity

BackgroundChildhood obesity and precocious puberty (PP) are escalating public health concerns with a significant comorbidity. Emerging evidence implicates gut microbiota dysbiosis in both conditions, yet microbial associations with their co-occurrence remain unexplored. MethodsA total of 68 girls (18 normal, 25 PP-only, 18 obesity-only, and 7 obesity-PP comorbidity) were enrolled. 16S rRNA sequencing was applied to determine gut microbiota of girls. Microbial diversity, composition, and differential abundant taxa were analyzed. ResultsWhile overall microbial diversity and community structure were similar across groups, obesity-only subjects exhibited significantly increased microbial richness (Chao1 index, P<0.01 vs. all groups), characterized by a higher Firmicutes/Bacteroidota ratio (P<0.001 vs. normal/PP), increased Proteobacteria (P<0.001 vs. normal), and enrichment of genera including Blautia, Faecalibacterium, Roseburia, Anaerostipes, Haemophilus, and Lachnospiraceae_NK4A136_group (P<0.05 vs. other groups). PP-only subjects showed reduced Verrucomicrobiota (P<0.001 vs. normal/obesity) and elevated Escherichia_Shigella (P<0.05 vs. normal). Most strikingly, the obesity-PP comorbid group exhibited a unique gut microbiota profile characterized by a dramatic depletion of Firmicutes compared to the obesity-only group (P<0.001) and a remarkable nearly 100-fold increase in Verrucomicrobiota abundance (P<0.001 vs. other groups), suggesting a distinct microbial ecotype potentially contributing to the pathophysiology of this comorbidity. ConclusionThis study delineated unique gut microbiota alterations associated with isolated obesity, isolated PP, and their comorbidity in girls. The distinct dysbiotic pattern in comorbid obesity-PP suggested complex microbiota-host interactions, providing a new microbiological perspective for understanding the mechanism of comorbidity between obesity and precocious puberty.

microbiology↗

bioRxiv2025

Network-based analysis reveals microRNA regulation of oncogenic pathways in SOX10-depleted uveal melanoma

SOX10 is essential for melanocyte development and maintenance and plays a critical role in uveal melanoma (UM) initiation and progression. While SOX10s transcriptional regulation of protein-coding genes is well characterized, its role on microRNA (miRNA) regulatory landscape in UM remains unexplored. Here, we employed network-based modeling to systematically characterize miRNA regulatory functions following SOX10 depletion in UM. First, we profiled mRNA and miRNA expression levels in SOX10 wild-type and knockdown UM cells. Then, we integrated the transcriptomic data, a UM network, and a Bayesian model to quantify miRNAs regulatory activities and identify key miRNAs. Subsequently, we employed pathway enrichment analysis combined with literature mining to elucidate the functional roles of identified miRNAs through their target genes and associated signaling pathways in UM. We identified 17 miRNAs that show significant changes in regulatory activities following SOX10 knockdown in UM cells. These miRNAs regulate the expression of genes involved in cancer hallmark pathways, including cell cycle progression, mTORC1 signaling, and fatty acid metabolism. Notably, miR-34a, miR-25, miR-186, and miR-211 have tumor-suppressive potential by targeting genes involved in UM progression and metastasis. Our results suggested that SOX10 depletion in UM can activate tumor-suppressive mechanisms through regulating miRNAs.

cancer biology↗

bioRxiv2025

GatorSC: Multi-Scale Cell and Gene Graphs with Mixture-of-Experts Fusion for Single-Cell Transcriptomics

Single-cell RNA sequencing (scRNA-seq) enables high-resolution characterization of cellular heterogeneity, but its rich, complementary structure across cells and genes remains underexploited, especially in the presence of technical noise and sparsity. Effectively leveraging this multi-scale structure is essentially an information fusion problem that requires integrating heterogeneous graph-based views of cells and genes into robust low-dimensional representations. In this paper, we introduce GatorSC, a unified representation learning framework that models scRNA-seq data through multi-scale cell and gene graphs and fuses them with a Mixture-of-Experts architecture. GatorSC constructs a global cell-cell graph, a global gene-gene graph, and a local gene-gene graph derived from neighborhood-specific subgraphs, and learns graph neural network embeddings that are adaptively fused by a gating network. To learn noise-robust and structure-preserving embeddings without labels, we couple graph reconstruction and graph contrastive learning in a unified self-supervised objective applied to both cell- and gene-level graphs. We evaluate GatorSC on 19 publicly available scRNA-seq datasets covering diverse tissues, species, and sequencing platforms. Experiments showed that GatorSC consistently outperforms state-of-the-art deep generative, graph-based, and contrastive methods for cell clustering, gene expression imputation, and cell-type annotation. The learned embeddings are used for accurate trajectory inference, recovery of canonical marker gene programs, and cell-type-specific pathway signatures in an Alzheimers disease single-nucleus dataset. GatorSC provides a flexible foundation for comprehensive single-cell transcriptomic analysis and can be readily extended to multi-omic and spatial modalities.

bioinformatics↗

bioRxiv2025

A tailored in vivo CRISPR screen identifies BAP1 as a potent tumor suppressor of soft tissue sarcoma

Undifferentiated pleomorphic sarcoma (UPS) is one of the most common soft tissue sarcomas (STS) in adults. Despite decades of research, therapeutic advancements for STS, including UPS, have remained limited. The genetic complexity of UPS, characterized by the absence of recurrent driver oncogene mutations, has hindered the development of effective targeted therapies beyond conventional chemotherapy and immunotherapy. To address this challenge, we conducted a customized in vivo CRISPR/Cas9 screen in mice to systematically identify potential tumor suppressors involved in UPS development. Our screen revealed BRCA1-associated protein 1 (Bap1) as a potent tumor suppressor in STS. Using total RNA sequencing, multiplex immunohistochemistry, and flow cytometry, we found that Bap1-deficient mouse sarcomas exhibit significant immune suppression. Further analysis indicated that polo-like kinase 1 (Plk1) is essential for the survival of Bap1-deficient sarcomas. Treatment with volasertib, a Plk1 inhibitor, markedly inhibited tumor growth in both syngeneic and spontaneous mouse models of Bap1-loss sarcoma. In conclusion, our findings suggest that PLK1 inhibition, or combined with immunotherapy, may represent a promising targeted therapeutic strategy for tumors lacking BAP1.

cancer biology↗

bioRxiv2025

Protein-protein interactions drive differences in the spatiotemporal dynamics of transcription factors NANOG and SOX2 in naïve pluripotent cells

Maintenance of naive pluripotency requires core transcription factors (TFs) like SOX2 and auxiliary TFs like NANOG, yet molecular mechanisms governing their intra-nuclear dynamics and DNA binding interactions remain unclear. Here, using high-density 3D single-molecule light-field microscopy combined with novel spatiotemporal analysis pipelines, we track SOX2 and NANOG dynamics in live cells. Despite lower protein abundance, NANOG displays a similar chromatin-bound fraction to SOX2. This arises partially because, while both TFs undergo frequent transient non-specific binding interactions ([~]0.5-0.7s), NANOG exhibits more stable specific binding ([~]25s vs [~]16s). Both TFs also assemble into phase-separated domains of [~]400 nm containing both freely diffusing and chromatin-bound proteins, which further influences their dynamics. Strikingly, NANOGs protein-protein interaction domain markedly increases chromatin residence time (>5-fold) and the size of these phase-separated domains. Our work uncovers how NANOG and SOX2 stabilise gene regulatory networks that maintain naive pluripotency while providing quantitative pipelines for dissecting spatiotemporal TF dynamics.

cell biology↗