Biology subjects

Sun, W.

Publications and source records attributed to Sun, W..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Genetic barcoding of individual cells links cancer evolutionary trajectories and prognostic outcomes

Intratumoural heterogeneity (ITH) reflects cancer progression, by integrating clonal dynamics, cell plasticity, and metastatic potential of malignant cells. Defining the origins and evolutionary trajectories of tumour cells is central to preventing tumour growth and dissemination, yet significant gaps in knowledge persist. Here, we used an original single cell resolution lineage tracing system to investigate how ITH underlies changes in tumour cell states, such as the acquisition of an epithelial-to-mesenchymal transition (EMT) phenotype and invasive capacity. By combining in vivo genetic barcoding with single-cell transcriptomics, we uncover two parallel evolutionary trajectories toward EMT: one associated with alveolar differentiation, and another characterized by gene regulatory programs activated during stress and tissue regeneration. Of interest, only the gene modules defining the regenerative trajectory were found to correlate with poor survival in breast cancer patients. Our results also provide a quantitative framework to measure cellular plasticity that enables the identification of highly plastic cells and their gene signatures, correlating with rapid changes in transcriptional state, EMT features and aggressive cancer. These findings deliver a comprehensive view of in vivo clonal evolution in breast cancer, uncovering the interplay between lineage plasticity and tumour progression with quantitative and robust statistical approaches.

cancer biology↗

bioRxiv2025

Evolutionary diversity and function of odorant receptors in birds

Abstract: Odorant receptors (ORs) form among the largest gene families in vertebrates; most mammals have hundreds of intact OR genes. Although birds display diverse behavior and ecology, they were long thought to rely minimally on olfaction. We reexamine this idea by using genomic data to uncover diverse and variable OR repertoires in birds, including the nocturnal kiwi (Apteryx mantelli), which possesses the largest number of ORs known (3,750). We reveal that widespread gene conversion is shaping the evolution of bird ORs, reflecting a novel mechanism for generating functional diversity. We show that ORs are expressed in avian olfactory sensory neurons and show responses to defined, ecologically relevant odorants. Our results demonstrate the importance and functional mechanisms underlying olfaction in birds.

evolutionary biology↗

bioRxiv2025

Characterization of Cancer-Reactive T Cells and Neoantigen-specific T Cell Receptors

Not all tumor-infiltrating T cells are cancer-reactive (CR). Several studies have reported gene expression signatures associated with CR-T cells. To integrate these findings, we developed a computational workflow, CAT (Cancer-Associated T cells), which harmonizes existing CR-T cell signatures and applies them to identify CR-T cells across an atlas of one million T cells. Our findings reveal that the abundance of CR-T cells varies across cancer types and that baseline levels of CR-T cells predict patients responses to immunotherapy. In parallel, we established a high-throughput computational platform, Neo-TCR, for systematic screening of neoantigen-specific TCRs and their cognate neoantigens. The efficacy of Neo-TCR is validated by cross-validation studies and replications in two independent datasets. Together, our findings suggest a new direction for developing biomarkers for cancer detection and monitoring: integrating CR gene expression signatures with neoantigen-specific TCRs.

cancer biology↗

bioRxiv2025

A human arteriovenous differentiation roadmap reveals vein developmental mechanisms and vascular effects of viruses

Extracellular signals and cell-fate trajectories during vein development remain elusive, despite trailblazing insights into artery development. Here we exploit human pluripotent stem cell differentiation and mouse embryology to present a model that answers longstanding questions: vein endothelial cell (EC) differentiation unfolds in two steps driven by opposing extracellular signals. First, VEGF differentiates mesoderm into "primed" ECs, newly-defined progenitors that co-express certain arterial (SOX17) and venous (APLNR) markers. Second, primed ECs execute vein differentiation upon VEGF/ERK inhibition; however, upon VEGF activation they can instead form artery ECs. The arteriovenous plasticity of primed ECs was supported by intersectional lineage tracing. Future venous genes including NR2F2 harbor poised chromatin in primed ECs, but are only transcribed upon VEGF/ERK inhibition. SOXF transcription factors, including SOX17, confer primed ECs with vein differentiation competence. Collectively, this two-step vein differentiation model--entailing primed EC intermediates and VEGF/ERK inhibition to trigger vein differentiation--has implications for VEGF-modulating therapies.

developmental biology↗

bioRxiv2025

PTH-Induced Behavioral and Metabolic Alterations in Mouse Models of Hyperparathyroidism

Parathyroid hormone (PTH) is a critical endocrine regulator of calcium homeostasis and bone remodeling and is widely employed in clinical settings through synthetic analogs for the treatment of osteoporosis. Although traditionally considered a peripheral regulator, emerging evidence indicates that PTH also exerts effects through the central nervous system (CNS). This study investigated the neuropsychiatric impact of elevated PTH and explored potential CNS involvement using multiple murine models of hyperparathyroidism (HPT). Distinct behavioral phenotypes were observed across models, indicating that psychiatric symptoms vary depending on disease etiology and progression. The effects of hPTH(1-34), a clinically approved PTH analog, were further assessed in male and female mice. Under pharmacological concentrations, hPTH(1-34) enhanced locomotor activity in males but induced mild anxiety-like behavior in females. These behavioral changes in females were independent of the estrus cycle and were amplified by ovariectomy. Metabolic analysis indicates PTH affects the basic metabolism by inhibiting the respiratory exchange ratio, promotes the energy expenditure and locomotion without affecting the food consumption in a 48hr range. To further investigate the molecular effect of PTH in the brain, a PTH1R-Cre mouse line was generated to map PTH receptor-1 (PTH1R) expression. Widespread expression of PTH1R was detected across the brain, including in both neuronal and non-neuronal cell populations. These findings suggest that PTH may influence behavior through interactions with PTH1R-expressing cells in brain vasculature and circumventricular regions. However, further studies are warranted to define the specific brain nuclei and cell types involved in PTH-driven modulation of neurobehavioral function.

neuroscience↗

bioRxiv2025

Engineered Promoter System Enables High-efficiency Transgenic CRISPR Editing in Malaria Transmitting Mosquito Anopheles sinensis

The CRISPR/Cas9 system deployed through crosses of transgenic lines expressing Cas9 and gRNA facilitates efficient mutagenesis. However, its application in non-model insects remains limited, primarily due to a lack of well-characterized promoters capable of driving robust and stable expression of Cas9 and gRNA. In the malaria mosquito Anopheles sinensis, we evaluated several ovary-biased promoters--Asvasa2, Aszpg, and Asnanos--for driving Cas9 expression. Notably, the Asvasa2 promoter mediated mutagenesis in nearly 60% of G0 individuals following microinjection of gRNAAswhite. Among four RNA polymerase III promoters derived from AsU6 genes, AsU6-1 yielded the highest gRNA transcriptional output, enabling 62% editing efficiency in G0 offspring. In addition, hybrid crosses between established transgenic lines demonstrated that the Asvasa2-Cas9 and AsU6-1-gRNA combination enabled complete germline editing penetrance, where all F2 progeny inherited the intended mutations. This work provides a essential genetic toolkit for synthetic biology applications in Anopheles mosquitoes and a scalable framework for engineering other non-model insects.

genetics↗

bioRxiv2025

Oligodendrocyte progenitor cell responses to inflammatory demyelination with aging

Oligodendrocyte progenitor cells (OPCs) have the capacity to self-renew, differentiate, and remyelinate the CNS. Aging is associated with a reduction in the functional capacity of OPCs even in the absence of an autoimmune insult. To determine how aging affects the response of oligodendroglia to a strong inflammatory insult comparable to an immune-mediated demyelinating event in multiple sclerosis (MS), we performed adoptive transfer of young myelin-reactive Th17 T cells into young and aged OPC lineage tracing mice. After adoptive transfer, OPCs were enriched within spinal cord lesions of both young and aged mice. However differentiated oligodendrocytes (OLs) were significantly reduced after adoptive transfer. Both young and aged OPCs differentiated into mature OLs during adoptive transfer. Transmission electron microscopy revealed thinly myelinated axons without degenerative features that likely represent remyelinated axons in lesions of both age groups. Young and aged OPCs rise to the challenge after a strong auto-immune attack, suggesting that compensatory strategies permit both young and aged oligodendroglia to survive despite an inflammatory environment. Identifying pathways that promote resilience of oligodendroglia in the face of an inflammatory challenge will facilitate the development of remyelinating therapies for people with MS.

neuroscience↗

bioRxiv2025

An unbiased screening approach for identifying proteins with a mechanosensitive nuclear localization

Mechanical forces profoundly influence a wide range of cellular behaviors. However, the mechanisms by which these forces are sensed and transduced into specific biological signals remain incompletely understood. One established principle of mechanotransduction is the mechanical regulation of subcellular protein localization, which enables control over the activity of key regulators such as transcription and splicing factors. In this protocol, we present a screening approach to identify proteins that exhibit mechanosensitive nuclear localization. We describe the engineering of cell lines with tuneable actomyosin contractility and the application of a spatially restricted in situ biotinylation strategy. This method, combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS), enables the identification of proteins whose nuclear localization changes in response to mechanical cues. For a detailed application of this protocol, please refer to Tseng et al. (2025) [1]

cell biology↗

bioRxiv2025

Common origin for effector and regulatory Follicular and Tissue-Adapted CD4+ T cells in Non-Small Cell Lung Cancer

Tumor-invaded lymph nodes (LNs) serve as critical hubs for anti-tumor immunity, yet their role in orchestrating immune responses remains poorly understood. Using integrated single-cell RNA sequencing, T cell receptor sequencing, and chromatin accessibility profiling, we analyzed CD4+ T cells from matched blood, tumor-invaded LNs, and tumors of treatment-naive non-small cell lung cancer patients. We identified distinct immunological landscapes across these compartments. Compared to blood, tumor-invaded LNs and tumors were enriched for follicular regulatory T cells (Treg-Tfr), conventional T cell subsets with Tfh-like characteristics (Tconv-Tfh and Tconv-CXCL13), and tissue-resident memory Tregs (Treg-Trm). These populations share a BATF-dependent transcriptional program that governs T-cell activation and tissue adaptation, while simultaneously engaging distinct, subset-specific regulatory networks. Integrative TCR-RNA analysis revealed that tumor-reactive, neoantigen-specific T cell clones were enriched within these subsets and demonstrated extensive LN-tumor clonal sharing, indicating active recirculation between compartments. Through clonal coupling analysis and trajectory inference, we uncovered that Treg-Tfr cells function as multipotent progenitors that bifurcate into tissue-resident Treg-Trm or into ex-Tregs adopting a Tfh-like CXCL13+ ewector phenotype. Remarkably, follicular CD4+ T subsets from LNs and tumor were transcriptionally and epigenetically similar and localized to analogous germinal center niches. These findings establish tumor-invaded LNs as functional extensions of the tumor microenvironment that generate and maintain tumor-reactive CD4+ lineages. The identification of tissue-resident Treg-Tfr plasticity reveals a critical developmental checkpoint that could be therapeutically targeted to redirect immunosuppressive programs toward anti-tumor ewector responses.

immunology↗

bioRxiv2025

NudC moonlights in ribosome biogenesis and homeostasis in Drosophila melanogaster polyploid cells

Ribosomes, the cellular machinery responsible for protein synthesis, are fundamental across all kingdoms of life. Disruption in ribosome biogenesis (RiBi) can cause severe ribosomopathies, underscoring the critical need for precise regulatory mechanisms governing RiBi. In this study, we identified the gene NudC (nuclear distribution C, dynein complex regulator), a previously unrecognized regulator of RiBi in polyploid cells of Drosophila melanogaster larvae. RNAi-mediated depletion of NudC in polyploid salivary gland cells led to a significant reduction in ribosome abundance, accompanied by the loss of ribosome-binding sites on rough endoplasmic reticulum and impaired translation. These defects are linked to decreased levels of nucleolar ribosomal RNA. Notably, NudC knockdown also triggered a homeostatic response, characterized by increased transcription and translation of both ribosome biogenesis factors (RBFs) and ribosomal proteins. This response parallels that seen in RBF-deficient cells, suggesting that NudC and RBFs cooperate to maintain RiBi homeostasis. Meanwhile, NudC-deficient cells exhibited chromosome abnormalities, activated JNK signaling, and underwent autophagy, closely resembling the defects observed upon loss of RBFs. Finally, our findings suggest that the role of NudC in RiBi is independent of its established function in dynein regulation, indicating the moonlighting role in RiBi played by this gene. Together, these results uncover a new, fundamental function for NudC in maintaining RiBi and homeostasis in polyploid cells, with broader implications for understanding conserved mechanisms of NudC function and RiBi across species.

cell biology↗

bioRxiv2025

PU.1 Shapes Host Epigenetic Responses to Mycobacterium tuberculosis and Represents a Target for Host Directed Therapy

Mycobacterium tuberculosis (Mtb) infection induces widespread epigenetic changes in monocytes and macrophages. To characterize the critical factor responsible for Mtb-induced epigenetic responses, we performed an integrative analyses of chromatin modification (H3K27ac), transcription factor binding, and gene expression in human monocytes and macrophages. Our data identified PU.1 (SPI1) as a key transcriptional regulator to be upregulated and bound to gene promoters in response to Mtb. PU.1 enrichment was associated with enhanced proinflammatory and anti-apoptotic gene programs. PU.1 expression was also elevated in the lung tissues from Mtb-infected macaques and tuberculosis patients. PU.1 knockdown enhanced human macrophage apoptosis, dampened inflammation and reduced bacterial survival, suggesting its functional role in supporting Mtb infection. Pharmacological inhibition of PU.1 replicated the effects of knockdown, restricting Mtb growth without cytotoxicity. These findings identify PU.1 as a central node in the host epigenetic response to Mtb and a candidate for host-directed therapeutic targeting in tuberculosis.

immunology↗

bioRxiv2025

HIF2-driven PTHrP Causes Cachexia and Hypercalcemia in Kidney Cancer: Treatment with HIF2 Inhibitors

Kidney cancer frequently causes paraneoplastic syndromes, including hypercalcemia and cachexia, but the underlying mechanisms are incompletely understood. The most common form of kidney cancer, clear cell renal cell carcinoma, is frequently caused by loss of the pVHL tumor suppressor protein and the resulting upregulation of the HIF2 transcription factor. We show that PTHLH, which resides on a ccRCC amplicon on chromosome 12p, is a direct HIF2 transcriptional target in ccRCC. Further, we show that the increased PTHLH expression is both necessary and sufficient for the induction of hypercalcemia and cachexia in preclinical orthotopic cell line tumor models. Consistent with these observations, two different allosteric HIF2 inhibitors, belzutifan and NKT2152, rapidly ameliorated hypercalcemia and cachexia in ccRCC patients, including in some patients who did not exhibit objective tumor shrinkage.

cancer biology↗

bioRxiv2025

An interpretable molecular framework for predicting cancer driver missense mutations

Missense mutations play a critical role in human disease, contributing to both inherited disorders and cancer. However, accurately predicting their functional impact--particularly for cancer driver mutations--remains a major challenge due to limited validated labels and the complex molecular basis of oncogenesis. Here, we systematically characterized over 120,000 missense variants across pathogenic, benign, driver, passenger, recurrent somatic, and common population classes, using a comprehensive set of mechanistically grounded molecular features. By assessing the statistical burden of variations, we demonstrated that these features effectively discriminate among diverse variant classes and reveal a consistent enrichment of functional sites, structural integrity, and biophysical changes in pathogenic and driver mutations. Building on these insights, we developed MutaPheno, an interpretable framework for predicting the functional consequences of missense mutations. The model integrates 34 molecular-level features, encompassing structural, functional, physicochemical, and contextual descriptors, using a random forest algorithm. Trained exclusively on pathogenic and benign variants, MutaPheno achieved strong accuracy in predicting cancer driver mutations, outperforming both cancer-specific and general pathogenicity tools, while also demonstrating superior robustness when tested on unseen proteins. Our findings highlight the shared mechanisms between pathogenic and driver mutations and emphasize the role of molecular features in improving variant interpretation. MutaPheno provides a transparent and generalizable tool that can facilitate driver discovery and the development of targeted therapies.

bioinformatics↗

bioRxiv2025

The impact of a fatty acid synthase gene in regulating a complex multifunctional trait essential for survival and sexual communication

The genetic basis of multi-functional traits shaped by both natural and sexual selection remains poorly understood. In insects, cuticular hydrocarbons (CHCs) are an excellent example of such traits, providing protection against different micro-climatic conditions while simultaneously encoding cues predominantly used in sexual signaling. The fatty acid synthase (fas) gene family has been implied as an important cornerstone in initiating and maintaining CHC functionality, whereas their exact biosynthetic and regulatory mechanisms have remained poorly understood. Here, we characterize a single fatty acid synthase gene (fas3) impacting the main CHC functions in the parasitoid wasp model organism Nasonia vitripennis. Knockdown of fas3 significantly decreases wasp survival under desiccation stress while also completely depleting sexual attractiveness of female wasps, where this trait naturally functions as sex pheromone. Transcriptomic analyses revealed that fas3 regulates other fas and CHC-associated genes, as well as key biosynthetic pathway hubs. We also identified striking sex-specific expression differences in fas3 across individual developmental stages, suggesting divergent functional roles of this gene in males and females. These findings largely advance our knowledge on the multi-functionality of fas genes in governing survival and sexual signaling and underscore their relevance for future studies on metabolomics, ecological adaptation, and sexual communication. Author SummaryTraits that serve both adaptive and reproductive functions--such as those involved in survival and mating success--are often complex, and their genetic foundations remain poorly understood. In insects, chemical compounds on the outer cuticle represent a prime example: they help prevent desiccation and act as key sexual signals. In this study, we investigate the gene fas3, a member of the fatty acid synthase family, in the parasitoid wasp Nasonia vitripennis, whose knockdown drastically reduces these surface chemicals. Consequently, both of their natural functionalities, namely enhancement of survival in dry conditions and female sexual attractiveness, are severely impaired. Transcriptomic analysis further revealed that fas3 also regulates multiple other genes, including those in further major biosynthetic pathways. Our findings shed light on how a single gene can coordinate the expression of multifunctional traits, contributing to both ecological adaptation and sexual communication.

genetics↗

bioRxiv2025

Lysosome-Dependent Sphingolipid Regulation as a potential therapeutic Target for Cohen Syndrome

Cohen Syndrome (CS) is a rare autosomal recessive disorder caused by biallelic mutations in the VPS13B gene, affecting approximately 50,000 individuals worldwide. Clinical features include postnatal microcephaly, developmental delay, intellectual disability, neutropenia, and retinal dystrophy. VPS13B belongs to the bridge-like lipid transfer protein (BLTP) family, which also includes VPS13A, VPS13C, and VPS13D in mammals. Although its precise function remains unclear, VPS13B localizes to the Golgi complex, and its loss leads to Golgi fragmentation, a consistent cellular phenotype observed in VPS13B-deficient models. We used the rescue of this cell-autonomous phenotype as the basis for a microscopy-based high-throughput screening assay, through which we identified several small molecules capable of restoring Golgi morphology. Most of these compounds shared a common mechanism of action, relying on lipid accumulation in acidic organelles due to their cationic amphiphilic properties (CADs). Lipidomic profiling revealed a reduction in C18-N-acyl sphingolipids as a characteristic feature of VPS13B knockout (KO) cells, a defect that was reversed by the majority of the identified compounds. To evaluate the physiological relevance of these findings, we tested two compounds, azelastine and raloxifene, in cortical organoids (COs) derived from VPS13B KO human pluripotent stem cells. These organoids exhibited smaller size and reduced neurite outgrowth, reminiscent of the secondary microcephaly observed in CS patients. Treatment with either compound significantly recovered the neurite outgrowth phenotype, reinforcing physiological relevance of the compound effect. Taken together, our findings highlight a potential effect of the CAD on lysosome-dependent sphingolipid regulation, allowing the recovery of Golgi integrity and partial rescue in the cortical organoid CS model. Although additional studies are required to delineate the exact molecular targets, this work uncovers a potential mechanism that could be leveraged for the treatment of CS.

cell biology↗

bioRxiv2025

Lineage-Specific Epigenomic Mapping of Proximal and Distal Fallopian Tube Epithelium Reveals Mesenchymal/Wnt-Driven Tumor Phenotype Diversification

High-grade serous ovarian cancer (HGSC) typically originates from the distal fallopian tube epithelium (disFTE), while the proximal epithelium (proFTE) remains less explored. Here, Using isogenic murine organoid models with common oncogenic drivers (Tp53-/-; Krasmut; Pten-/-), we show that disFTE and proFTE generate distinct tumor subtypes driven by region-specific transcriptional programs. Unlike disFTE, proFTE demonstrates continuous activation of epithelial-mesenchymal transition (EMT) across wild-type, mutant organoids, and derived tumors. Additionally, mutated proFTE organoids and their tumors exhibit persistent WNT signaling activation and grow independently of WNT signals. Chromatin profiling shows that mutant proFTE maintains a distinctive epigenetic profile with promoters associated with EMT and WNT pathways. Human proFTE with BRCAmut also shows epigenetic activation of EMT- and WNT-related genes. Tumors near the uterotubal junction (UTJ)--anatomically akin to proFTE--exhibit a pronounced EMT signature, increased Vimentin+E-cadherin+ and nuclear {beta}-catenin expression. These findings suggest proFTE-derived tumors may occupy a unique niche in gynecological malignancies, with regional identity shaping tumor phenotypes.

cancer biology↗

bioRxiv2025

Dynamic Regulation of Cholesterol Metabolism Genes in Dopaminergic Neurons following Methamphetamine Treatment as Revealed by Single-Nucleus RNA Sequencing

Methamphetamine profoundly alters the function of midbrain dopaminergic neurons, yet the molecular mechanisms underlying these effects are not fully understood. Using single-nucleus RNA sequencing, we found that acute methamphetamine exposure leads to a marked up-regulation of cholesterol metabolism genes in dopaminergic neurons of the ventral tegmental area and substantia nigra--a response that was much less pronounced in astrocytes and largely absent in other cell types. Further analysis using a ribosome tagging strategy combined with RNA sequencing revealed that amphetamine, a structurally similar psychostimulant, induced similar gene expression changes, whereas methylphenidate, a structurally distinct psychostimulant, did not, highlighting drug-specific transcriptional responses. Notably, repeated methamphetamine exposure resulted in down-regulation of cholesterol metabolism genes in dopaminergic neurons. Interestingly, we also observed that, compared to neighboring cell types, dopaminergic neurons are highly enriched in genes encoding cholesterol biosynthesis enzymes, including the rate-limiting enzyme Hmgcr, and key regulators Srebf2 and Insig1, challenging the prevailing view that neurons rely mainly on astrocyte-derived cholesterol. In summary, our study highlights dynamic changes in cholesterol metabolism in dopaminergic neurons in response to amphetamines and uncovers the potential importance of cholesterol homeostasis for dopaminergic neuron function.

genomics↗

bioRxiv2025

Evaluating nongenetic maternal transmission and post-weaning persistence of gut microbiota in cross-fostering rabbits

Gut microbiota is widely recognized as an important source contributing to phenotypic variation of diverse host traits in livestock. In this regarding, it is promising to improve offspring production traits through direct selection on parental individuals with the desirable gut microbiota, and this is termed microbiome breeding. However, the extent of nongenetic maternal transmission of gut microbiota and its post-weaning persistence remains poorly understood. To fill this gap, we cross-fostered 120 newborn rabbits that are offspring of 20 does in this study, and compared gut microbiota of all kits at the weaning (35 days of age) and two weeks post-weaning, respectively. Based on variance component analysis, we found that the large proportions of phenotypic variation of four alpha diversity metrics for kits at weaning can be explained by the nursing does, ranging from 0.218 {+/-} 0.106 for Evenness index to 0.464 {+/-} 0.125 for the number of observed features. The significant effect of nursing does was supported further by comparing three beta diversity metrics among different relationships, using Kruskal-Wallis test and Dunns post-hoc comparisons. In contrast, the biological does showed no significant effect on gut microbiota composition of pre-weaning kits. In post-weaning kits, the influence of nursing does on gut microbiota was not obviously decreased, despite there was increasing contributions of additive genetic effects. In conclusion, this study provides direct evidence in rabbits that offspring gut microbiota is predominantly shaped by the nongenetic maternal transmission, with these maternal influences persisting post-weaning. These results indicate the possibility that the direct selection on parental gut microbiota will alter offspring gut microbiota.

microbiology↗