Biology subjects

Ni, J.

Publications and source records attributed to Ni, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

A vagal gut-brain axis for feeding induced gastric secretion

Feeding begins with food-seeking and ends with nutrient absorption and waste elimination. Although meal-related sensory cues are known to shape feeding behavior, how they engage neural circuits to control digestion remains unclear. We dissected vagal gut-brain-gut pathways that mediate meal-induced gastric secretion. Vagal afferent neurons innervating the stomach were necessary and sufficient for secretion. Among those, Glp1r and Sst neurons robustly drove acid, pepsin, and gastrin secretion, whereas Oxtr and Vip neurons had little effect. Piezo2 was expressed in Glp1r mechanosensory afferents, and conditional deletion of Piezo channels attenuated distension-evoked secretion. On the efferent limb, genetically defined vagal motor neuron subsets differentially recruited secretory outputs: Cck neurons broadly increased acid, pepsin, and gastrin, whereas Grp neurons preferentially drove acid secretion. Finally, enteric circuit dissection revealed modular output control: Calb2 enteric neurons potently drove secretion with minimal motility effects, Grp enteric neurons coupled secretion to motility, and Cysltr2 enteric neurons selectively modulated acid output. Together, these results define a cell-type resolved vagal-enteric architecture for gastric control and show that secretory and motor programs can be segregated across dedicated enteric neuron subtypes.

neuroscience↗

bioRxiv2026

Targeting FGFR signaling overcomes therapeutic resistance and immune evasion in oncogenic PIK3CA-driven serous-like endometrial cancer

Serous endometrial cancer (SEC) is an aggressive subtype of endometrial cancer (EC) with poor prognosis and limited treatment options. Here, we developed a clinically relevant, immunocompetent serous-like mouse model incorporating oncogenic PIK3CA mutation, Trp53 loss, and MYC overexpression. Using this model together with human EC cell lines, patient-derived organoids (PDOs), xenografts, and patient datasets, we investigated mechanisms underlying resistance to PI3K-targeted therapy. Single-cell profiling reveals that FGFR1/2 upregulation associates with intrinsic resistance, whereas FGFR3 characterizes acquired resistance. Dual FGFR and PI3K inhibition produced superior tumor control compared with either agent alone. Mechanistically, FGFR signaling promotes immune evasion by downregulating MHC-I/HLA-mediated antigen presentation and enriching M2-type tumor-associated macrophages. FGFR inhibition reversed these changes and synergized with anti-PD-1 therapy to enhance antitumor immune responses and establish durable immune memory. Collectively, these findings identify FGFR signaling as a key driver of therapeutic resistance and immune escape in SEC and support FGFR-targeted combination strategies.

cancer biology↗

bioRxiv2025

An Lrs14 family protein functions as a nucleoid-associated protein regulating cell cycle progression in Sulfolobales

Archaea of the order Sulfolobales possess eukaryotic-like cell cycle. The chromatin organization in these archaea is supposed to rely on nucleoid-associated proteins (NAPs). Genomes of Sulfolobales species encode multiple members of the Lrs14 protein family, which have been postulated to function as NAPs. Here, we show that one of the Lrs14 family protein, named Sul14a, is a potential key player in dynamic chromatin organization in Saccharolobus islandicus. Sul14a is transcribed in a cell cycle-dependent manner and appears to be essential for cell viability. The protein exhibits DNA-binding activity preferring AT-rich sequences and can bridge DNA in vitro. ChIP-seq analysis revealed that Sul14a is enriched at AT-rich regions of the chromatin. Overexpression of Sul14a leads to cell cycle arrest at G2 phase. High-throughput chromosome conformation capture (Hi-C) and transcriptomic analyses indicate that Sul14a overexpression results in chromatin contact reduction and global transcriptional changes. In addition, we observed that the chromatin contact pattern changes markedly between 1h and 5h after release from G2 synchronization, corresponding to the lowest and highest levels of sul14a transcription, respectively, during the cell cycle. Our results establish that Sul14a is an NAP intimately associated with chromatin dynamics and global transcriptional changes during the cell cycle in Sulfolobales.

microbiology↗

bioRxiv2025

Global shifts in vegetation compositional resilience over the past 8,000 years

Vegetation resilience is critical for sustaining biodiversity and ecosystem services, yet its long-term dynamics and underlying drivers remain poorly resolved. Here, we assess changes in continental-scale vegetation compositional resilience over the past 8,000 years by applying established leading indicators (including autocorrelation, standard deviation, skewness, and kurtosis) to 482 fossil pollen records from all major landmasses except Antarctica. Using a machine learning approach, we evaluate the relative contributions of anthropogenic land cover change (ALCC) and climatic parameters (annual mean temperature, temperature seasonality, annual precipitation, and precipitation seasonality) in driving resilience shifts across continents. We further employ structural equation modeling (SEM) to disentangle how abiotic factors (ALCC and climatic variables) and biotic factors (species richness, evenness, synchrony, and temporal {beta} diversity) jointly shape long-term trends in vegetation resilience at the continental scale. Our results reveal a persistent, millennia-scale decline in resilience during the past 1.6 to 4.4 thousand years before present, with intensified anthropogenic land-use change identified as the dominant global driver. This finding suggests that the global decline in vegetation resilience observed over recent decades likely represents a continuation of the long-term trend established during the preceding Holocene. Notably, North America exhibited a resurgence in resilience over the past 1,200 years, primarily attributed to enhanced resilience in tundra and savanna ecosystems. SEM analyses uncover complex pathways through which abiotic and biotic predictors interact to shape millennial-scale resilience changes across continents. Despite the complexity of these underlying mechanisms, the analyses demonstrate that biotic factors collectively exert substantial, and often predominant, influences on long-term resilience dynamics. This underscores the indispensable role of biotic attributes in modulating long-term vegetation resilience, highlighting their potential as critical targets for ecosystem conservation and restoration.

ecology↗

bioRxiv2025

Three transcription factors coordinate the archaeal cell cycle progression through a regulatory braking point mechanism

Archaea of the order Sulfolobales execute a well-structured cell cycle program similar to that of eukaryotic cells. However, unlike eukaryotes, archaea lack cyclins and cyclin-dependent kinases and thus the mechanism of cell cycle regulation remained enigmatic. Here, we show that three essential ribbon-helix-helix domain transcription factors, namely, aCcr1, aCcr2, and aCcr3, play pivotal roles in controlling the cell cycle progression in the thermoacidophilic archaeon Saccharolobus islandicus. Coordinated expression of aCcr1 during M-G1 phase, aCcr3 during G1-S phase, and aCcr2 throughout the cell cycle ensures the timely transcription of the key genes that define the cell cycle phases. These include genes involved in chromosome dimer resolution, chromosome segregation, cell division, chromatin organization, DNA replication and repair, protein phosphorylation and degradation and metabolisms of amino acids, tRNA and carbohydrates. The synergy between aCcr1, aCcr2, and aCcr3 is achieved through their differencial affinities for the promoters and the levels of protein expression. We propose that the global regulation of the Sulfolobales cell cycle may be achieved not through transcriptional activation, but rather by repression of the key genes during strategic moments of the cell cycle. We propose a braking point model for the cell cycle control in Sulfolobales, which may represent a simple evolutionary intermediate on the way to the more complex cell cycle regulation in eukaryotes.

microbiology↗

bioRxiv2025

IRG1/itaconate/NRF2/GSH axis in tumor-associated macrophages drives therapy resistance and immune evasion in BRCA1-deficient breast cancer

Tumor-associated macrophages (TAMs) are major contributors to immunosuppression and therapeutic resistance, including resistance to PARP inhibitors (PARPi) in BRCA1-deficient breast cancer. However, the mechanisms underlying TAM-mediated PARPi resistance remain unclear. Here, we demonstrate that TAM-derived glutathione (GSH) impairs the efficacy of PARPi by protecting tumor cells from DNA damage and ferroptosis while suppressing STING-mediated immune activation. Mechanistically, STAT5-driven upregulation of the IRG1/itaconate axis in TAMs rewires mitochondrial metabolism and activates NRF2-dependent GSH biosynthesis. GSH is subsequently released into the tumor microenvironment, where it is taken up by tumor cells, protecting them from PARPi-induced cytotoxicity and dampening immune responses. Pharmacological inhibition of IRG1 reverses these effects, restoring PARPi sensitivity and enhancing anti-tumor immunity in BRCA1-deficient tumor models. Collectively, these findings uncover a TAM-specific immunometabolic program that limits PARPi efficacy and highlight the IRG1/NRF2/GSH axis as a promising therapeutic target to improve treatment outcomes in BRCA1-associated breast cancer.

cancer biology↗

bioRxiv2025

Dual Modes of Gene Regulation by CDK12

The process of transcription is driven forward by the activity of kinases including CDK7, CDK9 and CDK12. Accordingly, acute inhibition of any of these kinases results in profound downregulation of gene expression. Here, we discover that loss or inhibition of CDK12 also significantly upregulates a set of coding and non-coding loci, whose activation could contribute to the anti-proliferative effects of CDK12 inhibitors. Mechanistically, CDK12 inhibition impairs transcription elongation, leading to increased RNA polymerase II termination or arrest in long genes. However, short genes such as MYC and enhancer RNAs are highly transcribed in the absence of CDK12 activity. Indeed, in HER2+ breast cancer, a malignancy where CDK12 is co-amplified with HER2 and its expression correlates with disease status, CDK12 inhibition markedly elevates MYC expression to induce lethality. The dual effects of CDK12 inhibition elucidated herein clarify its role in transcriptional control and have significant translational implications.

cancer biology↗

bioRxiv2025

wspA mutation mediated Pseudomonas aeruginosa rugose small colony variant and its hyper-biofilm

Pseudomonas aeruginosa is a major multidrug-resistant pathogen whose biofilm formation complicates treatment. P. aeruginosa rugose small colony variants (RSCVs), characterized by enhanced biofilm production and resistance, pose significant clinical challenges. However, the formation mechanisms remain unclear in clinical strains. Paired clinical P. aeruginosa isolates AR8023-1 (wild-type) and AR8023-2 (RSCV) were collected from urine samples of a neurosurgery inpatient chronologically. The genome comparison was performed using Breseq, and plasmid complementation was performed to construct complemented strain (AR8023-2RifR::wspAAR8023-1). Then, all the aforementioned strains were examined RSCV phenotype, biofilm formation, and motility, and gene expression differences induced by the wspA mutation were analyzed via transcriptome sequencing, followed by quantification of c-di-GMP. In addition, we assessed antimicrobial susceptibility of the strains under both planktonic and biofilm conditions. The results showed that both AR8023-1 and AR8023-2 were identified as ST3420. AR8023-1 exhibited typical smooth morphology, while AR8023-2 displayed a RSCV phenotype. A single SNP difference was identified between the two strains, characterized by a deletion of glutamine at position 289 (CAG triplet deletion) in the wspA gene of strain AR8023-2. The complement isolates restored wild-type morphology, motility, and biofilm formation. Transcriptomics revealed a significant upregulation of c-di-GMP metabolic genes in RSCVs (P < 0.001), indicating that the WspA{Delta}289Q mutation activates diguanylate cyclase (DGC) activity, thereby elevating c-di-GMP synthesis. Intracellular c-di-GMP levels were significantly higher in RSCVs than those in WT and complement isolates, respectively (P < 0.001). Consequently, biofilm susceptibility testing demonstrated the {beta}-lactams MBIC of RSCVs was [≥]8-512-fold higher than those of WT and complement isolates. This study identifies a clinical WspA{Delta}289Q mutation that elevates c-di-GMP, driving RSCV formation and biofilm-mediated resistance. IMPORTANCEP. aeruginosa is a leading multidrug-resistant pathogen whose biofilm formation capability greatly complicates treatment outcomes. This study identifies a novel clinical mutation in the wspA gene (WspA{Delta}289Q) that drives the emergence of rugose small colony variants (RSCVs), a phenotype linked to heightened biofilm production and antimicrobial resistance. We demonstrate that this mutation upregulates cyclic di-GMP synthesis, leading to increased biofilm formation and markedly reduced susceptibility to {beta}-lactam antibiotics under biofilm conditions. These results provide important insights into the genetic basis of RSCV development in clinical settings and highlight the role of c-di-GMP signaling in biofilm-associated resistance. Our findings underscore the need to target c-di-GMP pathways as a potential strategy for combating persistent P. aeruginosa infections.

microbiology↗

bioRxiv2025

Novel infection by Mucor hiemalis kills Caenorhabditis hosts through intestinal perforation

The nematode Caenorhabditis elegans has emerged as a popular model system to investigate cell biology and host-pathogen interactions. Presently, C. elegans is studied as a natural host of intracellular pathogens such as microsporidia and Orsay virus along with extracellular bacterial and fungal pathogens. The use of C. elegans as a model in host-pathogen research is limited by the number of naturally occurring pathogens to the organism. Through a sampling project to identify new pathogens of C. elegans, we identified the fungus Mucor hiemalis as a pathogen of Caenorhabditis species. We observed the fungus in the intestinal lumen of wild-caught Caenorhabditis briggsae, and co-culturing the wild-caught species with infection reporter C. elegans confirmed infection by M. hiemalis. This study characterizes the fungal infection by M. hiemalis in Caenorhabditis nematodes. Fluorescence microscopy with fungal staining revealed the life cycle of M. hiemalis within multiple Caenorhabditis species at varying growth stages. We observed the killing of nematodes by M. hiemalis via intestinal perforation and assessed its host range through a series of lifespan assays. We investigated the food preference of C. elegans and determined that nematodes show a preference towards food that contains M. hiemalis spores. Lastly, we evaluated common C. elegans transcriptional immune responses and found that M. hiemalis does not induce genes associated with the intracellular pathogen response or other responses seen with previously studied bacterial and fungal pathogens. Characterization of this fungal infection in Caenorhabditis nematodes will provide new insights into the biology of pathogenic fungi and host immune responses.

microbiology↗

bioRxiv2025

Global Landscape of Human Kinase Motifs in Viral Proteomes

Viruses are classically viewed as targets of host sensing, yet whether they also sense and respond to host cues remains largely unexplored. We propose that host-driven post-translational modification of viral proteins allows viruses to dynamically sense host cellular states. We annotated human kinase motifs in 1,505 viral proteomes and discovered an enrichment for stress, inflammation, and cell-cycle kinases. Mapping kinase motifs onto 21,606 viral protein structures and integrating with phosphoproteomics of infected cells revealed surface-accessible residues were preferentially phosphorylated, showed greater kinase specificity, and were under positive selection for stress and immune kinase motifs. Temporal phosphoproteomics of alphavirus-infected cells confirmed stress kinase activation and viral protein phosphorylation, and MAP kinase inhibition reduced alphavirus replication and phosphorylation of ERK and JNK motifs on viral proteins. Our findings suggest that viruses evolved as biosensors of the host signaling state, unveiling new antiviral opportunities aimed at disrupting virus decision-making.

microbiology↗

bioRxiv2025

Phosphorylation of the α subunit inhibits proteasome assembly and regulates cell division in archaea

Archaea of the order Sulfolobales possess a eukaryotic-like cell division machinery and display a eukaryotic-like cell cycle, however, the cell division and cell cycle control mechanisms remain enigmatic. Here, we demonstrate that phosphorylation of the subunit by a eukaryotic-like protein kinase ePK2 affects 26S proteasome assembly and controls cell division in Saccharolobus islandicus. ePK2 exhibits cell cycle-dependent expression at both transcriptional and translational levels. Deletion or overexpression of ePK2 results in impaired cytokinesis, with the deletion cells being unable to generate single chromosome cells after synchronization and the overexpression cells exhibiting growth retardation and cell enlargement. Interestingly, overexpression of ePK2 leads to a coherent reduction in cellular proteasome activity and degradation of cell division proteins. We identify S200 and T213 of the proteasome subunit as specific target sites for ePK2 phosphorylation. Functional and structural analyses of site-directed mutants at S200 and T213 suggest that S200 phosphorylation disrupts the assembly of 20S into 26S proteasome whereas T213 phosphorylation interferes the de novo ring assembly. Collectively, our study uncovers an ingenious and efficient mechanism of proteasome phosphorylation-mediated cell division regulation, a prototype of the eukaryotic cell cycle regulation system, in Sulfolobales archaea.

microbiology↗

bioRxiv2025

Elevated GLUT4 Levels in Human Skeletal Muscle Microtissues is Accompanied by Functional Insulin Dependence

Insulin resistance in skeletal muscle is a hallmark of type 2 diabetes mellitus (T2D). While two-dimensional myotube cultures offer a controlled environment for studying T2D-related metabolic dysfunction, insulin-dependent glucose transporter type 4 (GLUT4) levels are limited and insulin-independent glucose transporter type 1 (GLUT1) expression dominates; reducing physiological relevance. Three-dimensional skeletal muscle microtissue cultures offer a promising alternative, and unlike 2D myotubes, are amenable to repeated contractile stimulation. However, microtissue GLUT1 and GLUT4 glucose transporter profiles remain under-characterized, particularly under physiological glucose and insulin conditions, which is evaluated herein. We report that GLUT1 levels trended [~]3.0-fold lower in microtissues compared with myotubes in 2D culture, although not statistically significant (p = 0.072), while GLUT4 levels were [~]12-fold higher (p < 0.0001), leading to a [~]60-fold increase in the GLUT4:GLUT1 ratio (p = 0.023). Notably, the microtissue GLUT4:GLUT1 profile approached, but did not match that of native human muscle. Microtissues required supraphysiological insulin conditions for the development of maximal contractility, while physiological glucose levels were sufficient. Insulin withdrawal restored insulin responsiveness but impaired microtissue contractile strength (p < 0.0001) and fatigue resistance (p = 0.015). Our findings indicate that the glucose transporter profile of microtissues offers improved physiological relevance. However, their reliance on insulin to maintain contractile function limits their suitability for modeling T2D. The implementation of a robust, insulin-free differentiation protocol would facilitate the development of a microtissue-based T2D model which can be applied to study contraction-mediated increases in insulin sensitivity as a therapeutic approach.

cell biology↗

bioRxiv2025

In vivo mRNA delivery to the lung vascular endothelium by dicationic Charge-Altering Releasable Transporters

Endothelial cells (EC) comprise the pulmonary vascular bed and play a significant role in health and disease. Consequently, the EC niche represents an attractive therapeutic target for treating a wide range of pulmonary vascular diseases. We have identified a new class of dicationic Charge-Altering Releasable Transporters. These single-component transporters selectively deliver mRNA to the lung upon intravenous administration without the use of a targeting ligand. Significantly, the number and spatial array of cationic charges within the repeating units of the CART polymer are found to control both mRNA delivery efficacy and tissue tropism. High-resolution imaging revealed efficient mRNA delivery to endothelial cells in pulmonary arteries, veins and capillaries. The selective lung tropism of these new CARTs, coupled with the efficient and tunable synthesis of this new family of CART amphiphiles, represents an enabling platform for research and clinical applications.

bioengineering↗

bioRxiv2025

A selective inhibitor of oncogenic JNK signalling perturbs metastatic outgrowth of triple-negative breast cancer through metabolic blockade

Although c-Jun N-terminal Kinase (JNK) represents an attractive anti-cancer target, its pleiotropic functionality limits the use of direct JNK inhibitors. Here, we identify a distinct subcellular pattern of JNK activity as a therapeutic vulnerability in breast cancer, where cytoplasmic JNK activity predicts poor survival outcomes, is elevated in triple-negative breast cancers (TNBC) and is essential for metastatic outgrowth. Mechanistic analyses reveal cytoplasmic JNK acts through multiple mechanisms, with downstream targets involved in cellular metabolism and cytoskeletal regulation. On this basis, we leveraged actin-based phenotypic drug-screening and identified K12, an indirect but selective inhibitor of cytoplasmic JNK that blocks TNBC metastatic outgrowth in vivo. We reveal that K12 inhibits glutaminase-1 and the pyruvate dehydrogenase complex, and that this poly-pharmacology overcomes pyruvate anaplerosis, a known resistance mechanism of existing glutaminase inhibitors. These findings demonstrate the potential of selectively targeting the oncogenic function of JNK, offering new treatment options for early-stage metastatic TNBC.

cancer biology↗

bioRxiv2025

A new class of OLD family ATPases functions in cell cycle progression in thermoacidophilic archaea

Overcoming lysogenization defect (OLD) proteins are diverse ATPases-nucleases functioning in antiphage defense in bacteria. However, the role of these proteins in archaea is currently unknown. Here, we describe a new class of archaeal OLD family ATPases and show that they do not appear to be involved in antiviral defense but play an essential role in cell cycle progression. The gene in Saccharolobus islandicus REY15A, named as Cran1 (Cell cycle related ATPase and nickase 1), cannot be deleted and exhibits cyclic expression patterns, with a peak expression during the transition from M-G1 to S cell cycle phase. Cran1 overexpression leads to significant growth retardation, cell size enlargement, and increased cellular DNA content. Cran1 displays potent nickase and ATPase activities in vitro, with the nickase activity being dependent on the presence of the ATPase domain. Notably, Cran1 copurifies with chromatin-associated proteins, such as Cren7 and a histone deacetylase homolog, suggesting its involvement in chromatin-related activities. Collectively our results suggest that Cran1 plays an important role in cell cycle progression, revealing a novel function of OLD family proteins.

microbiology↗

bioRxiv2025

Roles and transcriptional regulation of the endogenous cellulases in association with substrate and cellular processes in a thermoacidophilic archaeon

Microbes of the order Sulfolobales are potentially next generation platforms for cellulose degradation and utilization. However, the mechanisms of cellulose degradation and utilization remain unclear. In this study, we analyzed the enzymatic activity, localization, transcriptional regulation, and interplay of three endogenous cellulases Cel1, Cel2A, and LacS, and the association of transcription with cellular processes in the model thermophilic archaeon Saccharolobus islandicus REY15A. Overexpression strains based on a vector developed in this study as well as single and double deletion mutants of the three cellulase genes were constructed and analyzed. We reveal that Cel1 and Cel2A are membrane-associated, and a higher proportion of Cel2A is secreted into the medium than Cel1. The expression of all the three cellulases is induced by carboxymethylcellulose sodium (CMC). Furthermore, we found that the transcriptional levels of cel1, cel2A, and lacS are interdependent and cel1 and cel2A levels apparently increased with lacS deletion and overexpression of an ABC transporter, suggesting of an intracellular oligosaccharide-dependent regulatory mechanism. We showed that a cell cycle transcription factor aCcr1 binds to the promoter of cel1 in vitro. Additionally, we accidentally found that the cellulase genes expression increases in the presence of uracil synthesis pathway and deletion of the cellulase genes facilitates cell growth in CMC-containing medium. This study reveals an ingenious and intricated mechanism for cellulose utilization to adapt to extreme environment in archaea and provide insights for engineering Sulfolobales archaea as biomass-degrading and utilization platforms.

microbiology↗

bioRxiv2025

Application and mechanism of anticancer peptides in organoid models of intrahepatic cholangiocarcinoma

BackgroundThe clinical manifestations of intrahepatic cholangiocarcinoma (ICC) are non-specific, and only a small number of patients are eligible for surgical resection at the time of diagnosis, limiting treatment options. Anticancer peptides (ACPs) exhibit strong inhibitory activity against tumour cell lines, exhibit minimal side effects, are easily modified and optimised, and have low production costs. These attributes make ACPs a prospect for clinical applications. Simultaneously, the development of patient-derived three-dimensional organoids as a novel disease model has enabled the replication of the structure and heterogeneity of solid tumours. These organoids provide valuable tools for understanding disease mechanisms, conducting drug sensitivity tests, and developing targeted therapies. However, the effect of ACPs at the organoid level in ICC remains unknown. Therefore, this study aims to explore the potential of ACPs in treating ICC using patient-derived organoids as a model system to evaluate their efficacy and optimize therapeutic strategies. MethodsWe designed and synthesised a novel ACP sequence and applied it to a patient-derived organoids (PDOs) model. Organoids were evaluated using histochemistry analysis and whole-exome sequencing. ACPs were compared with representative chemotherapeutic drugs, including sorafenib and gemcitabine, to assess treatment differences. Additionally, scanning electron microscopy and flow cytometry were performed for further mechanistic analyses. ResultsOrganoid models exhibited histological characteristics similar to those of maternal tumours, especially showing strong positivity for EpCAM and KRT19 expression. Furthermore, whole-exome sequencing of the primary tumour and derived organoids revealed that PDOs closely recapitulated the genomic similarities of the primary tumour across multiple levels. Drug response analyses revealed that ACPs exhibited highly efficient anti-tumour effects, with specific differences observed between patients. ACPs affected the growth of tumour cells and exerted anticancer effects through direct membrane disruption and indirect induction of apoptosis. ConclusionIn this study, organoids derived from patients with ICC were established. This in vitro model provides valuable tools for evaluating the therapeutic response of ACPs and offers novel insight for the study of ICC.

cancer biology↗

bioRxiv2025

SCGclust: Single Cell Graph clustering using graphautoencoders integrating SNVs and CNAs

Intra-tumor heterogeneity (ITH) is a compounding factor for cancer prognosis and treatment. Single-cell DNA sequencing (scDNA-seq) provides cellular resolution of the variations in a cell and has been widely used to study cancer progression and responses to drug and treatment. While the low coverage scDNA-seq technologies typically provides a large number of cells, accurate cell clustering is essential for effectively characterizing ITH. Existing cell clustering methods typically are based on either single nucleotide variations (SNV) or copy number alterations (CNA), without leveraging both signals together. Since both SNVs and CNAs are indicative of the cell subclonality, in this paper, we designed a robust cell clustering tool that integrates both signals using a graph autoencoder. Our model co-trains the graph autoencoder and a graph convolutional network (GCN) to guanrantee meaningful clustering results and to prevent all cells from collapsing into a single cluster. Given the low dimensional embedding generated by the autoencoder, we adopted a Gaussian Mixture Model to further cluster cells. We evaluated our method on eight simulated datasets and a real cancer sample. Our results demonstrate that our method consistently achieves higher V-measure scores compared to SBMClone, a SNV-based method, and a K-means method, which relies solely on CNA signals. These findings highlight the advantage of integrating both SNV and CNA signals within a graph autoencoder framework for accurate cell clustering. SCGclust is publicly available at https://github.com/compbio-mallory/cellClustering_GNN.

bioinformatics↗