Biology subjects

Yang, F.

Publications and source records attributed to Yang, F..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

A novel dephosphorylation peptide inhibits 17β-HSD1 enzyme activity in ovarian granulosa cells and breast cancer cells

Estradiol (E2), a pivotal mammalian reproductive hormone, is closely associated with estrogen-dependent diseases. 17{beta}-hydroxysteroid dehydrogenase type 1 (17{beta}-HSD1), a critical E2 synthesis enzyme, has been understudied for its post-translational regulation-despite its potential as a therapeutic target, no clinically approved inhibitors are currently available. In our investigation of porcine follicular atresia mechanisms, we identified five differentially phosphorylated residues in 17{beta}-HSD1. Using in vitro site-directed mutagenesis and transgenic mouse models carrying point mutations, we established that Ser30 and Ser274 are critical phosphorylation sites that robustly modulate 17{beta}-HSD1 enzymatic activity. We further demonstrated that activin A and insulin-like growth factor 1 (IGF-1) enhance 17{beta}-HSD1 activity by promoting its phosphorylation at these two sites. To target these regulatory residues, we designed and synthesized cell-penetrating peptides (CPPs) that specifically suppress 17{beta}-HSD1 phosphorylation. Functional assays conclusively demonstrated that these CPPs significantly suppressed 17{beta}-HSD1 activity in vitro. Notably, they also inhibited the proliferation, migration and invasion of MCF-7 cells, as well as tumor growth in a mouse model of breast cancer. Our study provides novel mechanistic insights into the regulation of 17{beta}-HSD1 and E2 synthesis, addressing a critical gap in steroid hormone biology. The identification of Ser30/Ser274 as functional phosphorylation sites and the development of CPP-based inhibitors offer both theoretical advances and translational potential, opening new avenues for the treatment of estrogen-dependent breast cancer.

cell biology↗

bioRxiv2025

Chronic alcohol exposure drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells

Chronic alcohol use can cause pancytopenia and diminished immune responses against pathogens. However, its underlying molecular mechanisms remain unclear. Furthermore, whether chronic alcohol consumption directly induces inflammation in human hematopoietic stem progenitor cells (HSPCs) or whether it affects aging hematopoiesis differently is unknown. To examine how chronic alcohol use influences HSPCs, we performed single-cell RNA-seq in murine and human HSPCs and single-cell ATAC-seq in aged murine HSPCs following alcohol exposure. In the native murine bone marrow, chronic alcohol exposure primed HSPCs to differentiate into myeloid cells and to exhibit heightened inflammation, DNA damage, and epigenetic reactivation of transposable elements (TEs) in an age-dependent manner. Alcohol-exposed aged long-term hematopoietic stem cells (LT-HSCs) displayed increased chromatin accessibility at TE-containing loci correlated with aberrant TE transcription. This transposon derepression was associated with the accumulation of dsRNAs in aged bone marrow cells, and activation of innate immune pathways, perpetuating HSC inflammaging. Furthermore, we identified two epigenetically distinct LT-HSC clusters, LT-HSC1 and LT-HSC2, with the LT-HSC2 cluster expanding in response to chronic alcohol consumption, resembling activated HSCs. In xenotransplanted human HSPCs, chronic alcohol feeding resulted in a significant myeloid bias, heightened inflammation, upregulation of double-stranded RNA (dsRNA) sensors, activation of type I interferon responses, and increased expression of endogenous retroviruses. Despite these molecular alterations, we did not observe a decrease in long-term repopulation capacity in either human or murine HSCs. This suggests that HSC function may recover following alcohol cessation. However, previous chronic alcohol exposures imprint murine HSPCs to exhibit long-term myeloid bias and reduced cell cycle entry upon bacterial LPS challenge. Our data illuminate potential interactions between alcohol and aging that can reinforce inflammaging and epigenetic dysregulation in HSPCs. KeypointsO_LIAging perpetuates alcohol-induced myeloid bias, inflammation, DNA damage, and TE upregulation in murine HSPCs C_LIO_LIPrior chronic alcohol consumption does not affect long-term repopulation but causes persistent myeloid bias and inefficient stress responses after LPS challenge C_LIO_LIChronic alcohol consumption alters chromatin accessibility in TE-overlapping regions C_LIO_LIChronic alcohol consumption promotes myeloid bias, inflammation, and upregulation of endogenous retroviruses in xenotransplanted human HSPCs. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/696246v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@e0357aorg.highwire.dtl.DTLVardef@1d702fdorg.highwire.dtl.DTLVardef@10553ddorg.highwire.dtl.DTLVardef@c4e62e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Single-cell atlas reveals alveolar macrophage-specific Oncostatin-M drives pulmonary fibrosis via fibroblast activation in PCV2d infection

A hallmark of pulmonary fibrosis is the aberrant activation of lung fibroblasts into pathological fibroblasts that produce excessive extracellular matrix(1). Clarifying the cell-specific mechanisms by which viruses induce this process is crucial for developing effective strategies to intervene in disease progression. Here, we demonstrate that alveolar macrophage subsets specifically express tumor suppressor M (Osm) after infection by PCV2d infection and related intervention experiments in mice, combined with single-cell transcriptome sequencing (scRNA-seq). Through validation using histopathological analyses and an in vitro macrophage-fibroblast co-culture model, these alveolar macrophage-derived oncostatin M (Osm) were confirmed to specifically drive fibroblast activation. Vaccine intervention experiments further confirmed that targeted inhibition of oncostatin M (Osm) expression in alveolar macrophages significantly attenuated fibroblast activation and extracellular matrix deposition, thereby mitigating pulmonary fibrosis progression. Therefore, subgroup-specific secretion of oncostatin M (Osm) by alveolar macrophages represents a key driver mediating PCV2d infection-induced pulmonary fibrosis, and targeting this pathway offers a potential therapeutic strategy for viral-induced pulmonary fibrosis.

genomics↗

bioRxiv2025

Creating an energy efficient central metabolism for boosting biosynthesis without compromising cell growth of yeast

Long-term natural evolution selects glycolysis as the major metabolic mode for rapid cell growth, which however lacks sufficient NADPH supply to dive the biosynthesis of reduced chemicals such as free fatty acids (FFAs). Engineering energy economical pathway for chemical overproduction always compromises cellular fitness due to the rigidity of cellular metabolism. Here, we successfully replaced glycolysis metabolism with an optimized pentose phosphate pathway (PPP) in an industrial yeast Ogataea polymorpha, for the first time, which enabled a higher energy generation efficiency than glycolysis and a balanced supply of ATP and NADPH. More importantly, we discovered a global carbon metabolism regulator CMR that drives metabolic flux toward glycolysis for energy generation, and its disruption relieved the tight regulation of metabolic flux distribution and significantly enhanced the efficiency of cellular energy generation, which significantly boosted the FFA production by 63% in a FFA overproducing chassis. The final engineered yeast produced FFAs at a titer of 41.7 g/L, the highest titer reported by microbial fermentation. Our work provides valuable insights into the metabolic regulation mechanisms and a feasible approach for constructing energy efficient metabolism for chemical overproduction.

synthetic biology↗

bioRxiv2025

Circadian clock regulates epidermal endocrine system in homeostatic skin pigmentation

The circadian clock regulates various physiological processes in the skin, including local hormone synthesis and pigment production. However, the interplay between circadian regulation and epidermal endocrine signaling remains poorly understood. In this study, we investigated the functional roles of two core circadian transcriptional regulators, Basic helix-loop-helix ARNT-like protein 1 (BMAL1) and CLOCK circadian regulator (CLOCK), in human epidermal homeostasis. Primary normal human epidermal melanocytes were cultured and analyzed using quantitative real-time PCR, Western blotting, and immunofluorescence. Both BMAL1 and CLOCK were abundantly expressed in melanocytes. siRNA-mediated knockdown of either gene led to a significant reduction in melanin synthesis and altered the expression of hormone-related factors, notably decreasing the expression of vitamin D receptor (VDR) and its associated pathways. These molecular alterations were closely correlated with changes in melanogenic activity. Consistently, immunohistochemical analysis of vitiligo patient skin revealed reduced expression of the vitamin D-related enzyme CYP27A1 in melanocytes. Collectively, our findings demonstrate that circadian clock disruption impairs pigment production partly through modulation of vitamin D signaling, uncovering a previously unrecognized link between the cutaneous circadian system and endocrine regulation of melanogenesis.

pathology↗

bioRxiv2025

Large Language Models for Accessible Reporting of Bioinformatics Analyses in Interdisciplinary Contexts

Health and life scientists frequently rely on quantitative experts to perform complex data analyses, yet interpretation of these results often becomes a bottleneck due to communication barriers across disciplines. Large Language Models (LLMs) have the potential to act as intermediaries that translate analytical outputs into accessible scientific narratives, but their ability to reliably interpret outputs from real-world biomedical data analyses across disciplines remains unclear. In this study, we investigate how state-of-the-art LLMs behave when integrated into real bioinformatics analysis workflows as report-generation assistants for interdisciplinary teams. We evaluated LLM-generated summaries using both automated and human evaluation frameworks to ensure holistic evaluation. Automated assessment employed multiple choice questions designed using Bloom's taxonomy to assess multiple levels of understanding, while human evaluation tasked scientists to score summaries for factual consistency, lack of harmfulness, comprehensiveness, and coherence. All generally produced readable and largely safe summaries, confirming their value for first-pass translation of technical analyses, however frequently misinterpreted visualisations, produced verbose summaries and rarely offered novel insights beyond what was already contained in the analytics. Our findings suggest that LLMs are best suited for easing interdisciplinary communication rather than replacing domain expertise and human oversight remains essential to guarantee accuracy, interpretative depth, and the generation of genuinely novel scientific insights.

bioinformatics↗

bioRxiv2025

Combinatorial inhibition of LSD1 and Menin induces therapeutic differentiation in AML

Acute myeloid leukemia (AML) is characterized by differentiation arrest and uncontrolled proliferation. Differentiation therapy aims to treat AML by de-repressing latent myeloid maturation programs to induce cell cycle arrest and subsequent cell death. This approach is curative in the promyelocytic AML subtype, but has met with limited success in other subtypes. Genes such as LSD1 have emerged as intriguing non-APL AML differentiation therapy targets, but results as monoagents in clinical trials have been mixed. Here, we performed differentiation-specific CRISPR screens to identify targets whose inhibition synergizes with LSD1 inhibition to induce terminal differentiation of non-APL AML cells. Intriguingly, the MLL co-factor Menin scored as the top hit. Using cell lines, primary patient samples, and mouse AML models, we find that dual inhibition of LSD1 and Menin is a highly promising approach for differentiation therapy. Mechanistically, we determine that inhibition of Menin downregulates drivers of proliferation and stemness such as MEIS1, and inhibition of LSD1 induces inflammatory and interferon-related pro-myeloid differentiation expression programs. Surprisingly, we find that this combination is effective in selected AML models without mutations in MLL or NPM1, thus nominating dual inhibition of LSD1 and Menin as an attractive therapeutic approach for a mutationally diverse set of non-APL AMLs. HighlightsO_LIInhibition of LSD1 and Menin synergizes to induce differentiation of MLL-r and MLL-WT AMLs. C_LIO_LIInhibition of Menin downregulates drivers of proliferation and stemness. C_LIO_LIInhibition of LSD1 induces differentiation-associated inflammatory and interferon responses. C_LIO_LILSD1 and Menin occupy different areas of the genome. C_LI

cancer biology↗

bioRxiv2025

Emotional Responses to Naturalistic and AI-generated Affective Pictures: A Systematic Comparison

Pictures depicting naturalistic scenes are widely used in studies of human emotion. However, the practical use of affective pictures is limited by several factors, including the difficulty of obtaining content-diverse, high-quality, openly accessible, and standardized stimuli that are necessary for specific research questions. The use of artificially generated (AI) pictures could address this limitation, but it is unclear if AI-generated pictures evoke reliable emotional responses. The present study sought to address these challenges by comparing emotional responses to AI-generated pictures with responses to original, standardized, pictures. In two study iterations, standardized pictures containing pleasant, neutral, and unpleasant content were selected from the International Affective Picture System (IAPS) and other sources. Then, a matched AI-counterpart was created for each original picture using generative deep neural networks. A total of 109 participants viewed the picture sets while pupil diameter and electroencephalogram (EEG) were recorded. Evaluative ratings of hedonic valence and emotional arousal were also collected. For both AI and original exemplars, pictures depicting emotional content elicited stronger responses than neutral content for ratings and EEG-derived variables, with weaker effect sizes for the AI-generated pictures. Furthermore, picture-level analyses found that ratings and EEG measures were strongly correlated between matched AI and original pictures. Pupil data also showed the expected content effects in study iteration 2, but not in iteration 1. Together, this initial study suggests that AI-generated picture sets can effectively elicit well-established self-reported affect and physiological responses, presenting a promising avenue for future studies of human emotion.

neuroscience↗

bioRxiv2025

Disruption of ADAMTSL4 Causes Ectopia Pupillae in Zebrafish via COL8A1-Driven Cell Migration

Congenital ectopia lentis (EL) poses a significant threat to visual outcomes in children. Although emerging causative genes have been identified, their biological functions remain poorly understood. In this study, we investigated the contribution of ADAMTSL4 variants to congenital EL in a cohort of 702 pedigrees. Pathogenic variants in ADAMTSL4 were identified in 23 probands (3.28%), comprising 29 distinct variants, with 14 being novel, making ADAMTSL4 the second most frequently mutated gene in the cohort. All affected individuals exhibited EL, and 26.09% also presented with ectopia pupillae (EP), also referred to as ectopia lentis et pupillae. To explore the functional consequences of ADAMTSL4 deficiency, we generated a CRISPR/Cas9-mediated adamtsl4-knockout zebrafish model, that faithfully recapitulated cardinal human disease features with an incidence comparable to that observed in affected patients. Histological and ultrastructural analysis revealed disrupted zonular fiber anchorage at the lens capsule, even in mutated eyes without overt EL or EP. Transgenic overexpression of adamtsl4 successfully reversed the ocular phenotypes, confirming the genes essential role in ocular development. Single-cell RNA-sequencing and fluorescence in situ hybridization demonstrated enriched ADAMTSL4/adamtsl4 expression in the equatorial lens epithelium, retinal pigment epithelium (RPE), iris anterior pigmented epithelium, and choroid fibroblast. Functional assays using zebrafish and human RPEs revealed that ADAMTSL4 deficiency compromised cell adhesion and promoted cell migration. Transcriptomic profiling revealed significant enrichment of extracellular matrix organization and cell adhesion pathways, with cross-species validation identifying consistent upregulation of COL8A1/col8a1b. Notably, COL8A1 knockdown in ADAMTSL4-deficient RPEs partially reversed the aberrant migratory phenotype, suggesting a functional interaction. Together, these findings establish ADAMTSL4 as a major causative gene in ectopia lentis et pupillae, highlight its role in orchestrating ocular integrity via regulation of extracellular matrix and cell behavior.

genetics↗

bioRxiv2025

XPF mediates 3' flap processing for FEN1-independent Okazaki fragment maturation

Okazaki fragment maturation (OFM), the process that removes RNA-DNA primers, is a major source of DNA replication stress and mutations. It involves Pol{delta}-mediated DNA strand displacement synthesis that produces 5 flaps, FEN1-mediated 5 flap cleavage, and LIG1-catalyzed nick ligation. Recently, we discovered that under stress conditions, yeast cells convert 5 flaps into 3 flaps, which are degraded by 3 flap nucleases to produce ligatable DNA nicks. However, little is known about this stress-induced, 3 flap-based OFM in human cells. Here, we report that 3 flaps frequently form in various human cancer cells, and that FEN1 deficiency significantly enhances 3 flap levels. XPF1 is recruited to the replication forks in FEN1 mutant or FEN1-chemically inhibited cells. Notably, XPF deficiency or inhibition in those defective cells leads to accumulation of 3 flaps, replication-related DNA strand breaks, and unique mutation signatures. Furthermore, XPF and FEN1 inhibitors show synergistic effects in killing human cancer cells. In summary, we demonstrate that 3 flap-based OFM is an important alternative of 5 flap-based OFM in mammalian cells. XPF is a key nuclease to degrade 3 flaps and complete OFM for survival. Targeting this compensatory mechanism could provide new therapeutic strategies to selectively impair cancer cell survival under pre-existed replication stress. HighlightsO_LIXPF is recruited to DNA replication forks in mouse or human cells of functional deficiency of FEN1 due to genetic mutations or chemical inhibition. C_LIO_LIXPF gene deficiency or chemical inhibition results in accumulation of 3 flaps and replicative DNA single-stranded breaks. C_LIO_LIFunctional deficiency of XPF and FEN1 displays a synergy in inducing genome instability and cell death in human cancer cells. C_LI

cell biology↗

bioRxiv2025

AAV Kills Dividing Cells by Depleting PARP1 and Other DNA Damage Response Proteins

Recombinant adeno-associated virus (rAAV) is a replication-defective viral vector used in hundreds of human gene therapy trials, resulting in five FDA-approved therapies. Despite this success, rAAV-based gene therapies suffer from dose-limiting toxicities, resulting in several severe adverse reactions, including death. Previously, we discovered that rAAV rapidly kills mouse NPCs in vitro and in vivo. This vector contains a minimal genome comprised of 145-base pair inverted terminal repeats (ITRs) with a T-shaped hairpin structure that appears to be necessary and sufficient for this toxicity. However, the mechanism for AAV ITR toxicity is not known, and there have been few attempts to engineer ITRs to attenuate rAAV toxicity. In the current study, we explore the molecular mechanisms that drive dose-dependent rAAV toxicity in dividing human NPCs (hNPCs) and test whether disrupting these mechanisms mitigates this toxicity. Recombinant AAV infection induces aberrant cell cycle progression with activation of the ATM /CHK1/CHK2 pathway and expression of the DNA damage markers {gamma}H2AX and 53BP1. Affinity-based proteomics indicate that AAV ITRs bind to Poly-(ADP-Ribose)polymerase 1 (PARP1) and other DNA damage response (DDR) proteins involved in single-strand break repair (SSBR). Recombinant AAV infection attenuates poly-(ADP-ribose) (PAR) formation and mimics the antiproliferative effects of pharmacological PARP inhibitors used in cancer therapy. Moreover, treatment of hNPCs with PARP inhibitors is sufficient to reproduce many features of rAAV-induced toxicity. Finally, we demonstrate that eliminating the T-shaped hairpin within the AAV ITR reduces binding to SSBR proteins and the resulting rAAV toxicity. These findings suggest that rAAV infection induces replication stress and cell death in dividing hNPCs by functionally depleting PARP1 and other DDR proteins that are essential for DNA replication. This work fills substantial gaps in the understanding of the mechanisms of rAAV toxicity and has important implications for the development of safer rAAV-based human gene therapies. One Sentence SummaryThe rAAV genome binds to and depletes PARP1 and other SSBR proteins that are essential for DNA replication, resulting in DNA double stranded breaks, checkpoint activation, and cell death in dividing cells.

cell biology↗

bioRxiv2025

Joint analysis of expression and variation at single cell resolution by scVar

Tumor heterogeneity represents a critical determinant affecting both cancer diagnosis and therapeutic efficacy. Traditional bulk sequencing approaches are limited in their ability to resolve genomic alterations at the resolution of individual cells. In this study, we present scVar, an integrated analytical framework designed for mutation profiling using single-cell transcriptomic data. scVar enables sensitive and robust detection of single-nucleotide variants, particularly facilitating the identification of low-frequency variants. The framework incorporates customizable filtering parameters including variant allele frequency, and provides comprehensive functional and clinical annotations for identified mutations. Furthermore, scVar includes downstream analytical modules that facilitate the joint investigation of transcriptomic and mutational profiles within single cells. Benchmarking on simulated datasets and matched tumor samples demonstrates that scVar consistently outperforms existing methods, especially in detecting variants of low abundance, and shows strong concordance with whole-exome sequencing data. Application of scVar to non-small cell lung cancer samples effectively characterized ITH across spatially distinct tumor regions and diverse cellular populations. Collectively, scVar offers an integrated platform for concurrent analysis of somatic mutations and transcriptomic data derived from single-cell RNA sequencing, providing a powerful tool for elucidating tumor evolution and the complex interplay between genomic heterogeneity and the tumor microenvironment.

bioinformatics↗

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

Long-read sequencing-based atlas of tissue-specific expression of Drp1 transcript variants

Dynamin-related protein 1 (Drp1), encoded by DNM1L, is essential for mitochondrial fission, but its functional roles remain unclear due to isoform-specific effects from alternative splicing. Short-read RNA sequencing fails to resolve full-length isoforms involving distant exons, limiting our understanding. Here, we applied targeted long-read sequencing to profile full-length DNM1L transcripts in human left ventricle and iPSC-derived cardiomyocytes, recovering all annotated isoforms with conserved expression patterns and isoforms 1-4 being most abundant. Functional assays revealed that isoform abundance does not predict enzymatic activity. Extending this to six mouse tissues, we identified distinct, tissue-enriched expression profiles. Functional rescue in Drp1-knockout mouse embryonic fibroblasts showed isoform-dependent differences in mitochondrial fission. Isoforms lacking the A-insert (e.g., b and d) robustly rescued fission, while isoforms enriched in brain or muscle showed only partial rescue, suggesting exons 2 and 3 negatively regulate Drp1 activity. Our cross-species atlas integrates long-read transcriptomics with functional validation, revealing how isoform diversity underpins tissue-specific mitochondrial dynamics and physiological roles of Drp1. SummaryUsing long-read sequencing, we mapped full-length DNM1L/Dnm1l isoforms in human and mouse tissues, uncovering tissue-specific expression and isoform-dependent mitochondrial fission activity. This reveals how alternative splicing shapes Drp1 function, with implications for understanding its role in health and disease.

cell biology↗

bioRxiv2025

The fate of melanocytes and the disorganization of basement membrane in a guinea pig model of Rhododendrol-induced chemical vitiligo

BackgroundRhododendrol (RD) is a phenolic compound that was first developed as a skin-lightening agent that occasionally induces skin depigmentation. Although it has been shown that RD induces melanocyte death in vitro, it is still not fully understood why melanocytes are gone by RD in vivo. ObjectiveThis research aimed to investigate how melanocytes are eliminated in the animal model by RD. MethodsOn the backs of black guinea pigs (JY-4) with epidermal melanocytes in the basal layer, 30% RD was administered topically three times per day, five days per week. Skin tissues were collected sequentially and histologically analyzed. ResultsOn day 21, L* values in the RD-applied skin were significantly higher than in the vehicle-applied skin. From day 1 to day 7, the number of TRP1-positive melanocytes and melanin in the basal layer decreased, but no TUNEL-positive melanocytes were identified. On the other hand, an accumulation of melanin was newly found in the dermis. Immunohistochemical staining identified several melanocytes in the upper dermis or spinous layer, away from the basement membrane. An investigation of the epidermal-dermal interface showed a structural anomaly in a portion of the basement membrane with elevated MMP2 expression and increased dermal fibroblasts. The application of the MMP2 inhibitor Ilomastat abolished the basement membrane abnormality by RD. ConclusionThese findings suggest that RD-induced alterations in basement membrane structure may contribute to melanocyte detachment and loss, which is the cause of skin depigmentation not only in RD-induced vitiligo but also in vitiligo.

pathology↗

bioRxiv2025

Novel Calcin peptides from Scorpion Venom Exhibit Humidity-Dependent Expression and Ryanodine Receptor Activation

Scorpions are venomous animals of considerable pharmacological potential, traditionally used in East Asia to treat cardiovascular and autoimmune diseases. However, geographical variations in the expression of their venom components remain poorly understood. We performed transcriptome profiling on scorpion samples collected from eight distinct climatic and environmental regions in East Asia, we successfully identified two distinct scorpion species: Uroctonus mordax and Mesobuthus martensii. Furthermore, we identified two novel calcins from the venoms of these species, with their expression levels showing a significant correlation to environmental humidity. Functional assays revealed that these calcins differentially potentiate [3H]ryanodine binding to RyR isoforms and induce a persistent subconductance state, suggesting distinct mechanisms of action. Our findings suggest biogeographical variation in venom composition between species and suggest that environmental humidity as a key factor influencing calcin expression. These results expand the structural diversity of the calcin family and provide a mechanistic basis for the medicinal application and ecological adaptation of scorpion venom.

molecular biology↗

bioRxiv2025

Developmental Connectomics of the Mouse Cerebellum

To uncover the developmental processes that establish the precise patterns of synaptic connectivity in the CNS, we employed a connectomic approach in the mouse cerebellar cortex between birth and 2 weeks of age. There were dramatic quantitative and qualitative changes in the structure and connectivity of cerebellar cells. Parallel fiber synapses onto Purkinje cells increased [~]500-fold, with the most rapid growth taking place a week after birth. To support this profound synaptogenesis, Purkinje cells generated thousands of transient parallel fiber-oriented filopodia that received nascent synapses from parallel fibers. Importantly, we find that granule cells initiate synaptic output onto Purkinje cells only after receiving mossy fiber input, revealing a sequential, input-dependent logic for circuit assembly. In sharp contrast to the concurrent pruning of climbing fiber inputs, parallel fiber connectivity expanded and became highly individualized during development. Despite anatomical overlap, neighboring Purkinje cells share significantly fewer parallel fiber inputs than expected by chance. Moreover, parallel fibers themselves diverged spatially, further enforcing selective input allocation and resulting in highly specific parallel fiber cohorts for each Purkinje cell. Our findings uncover a mechanistic sequence in which early afferent activity and transient cellular structures guide the selective wiring and expansion of parallel fiber input to Purkinje cells, establishing developmental principles that ensure functional specificity in the mature brain.

neuroscience↗

bioRxiv2025

Uncovering directionally and temporally variable genes with STAVAG

Spatially variable genes (SVGs) are crucial for understanding spatial heterogeneity in spatial transcriptomics. Yet, SVGs are challenging to align with established biological axes and lack straightforward mechanistic interpretation, thereby limiting their ability to inform downstream experiments or clinical applications. Here, we introduce the concept of directionally variable genes (DVGs) and temporally variable genes (TVGs). Also, we propose a unified framework, STAVAG, that models spatial or temporal information to identify DVGs and TVGs. STAVAG effectively identifies biologically meaningful DVGs for uncovering prognostically relevant gene modules that align with the malignant-immune-stroma structure in the tumor microenvironment, identifying marker genes in three-dimensional brain data, and detecting 12 polarization genes regulating planarian regeneration. Furthermore, by tracking the progression of myocardial infarction and tissue development, STAVAG reveals critical TVGs that can serve as diagnostic biomarkers for the ultra-acute phase of myocardial infarction. STAVAG also identifies both global and local gene modules involved in mouse placentation, as well as tissue-specific and interactive TVG modules that dynamically evolve during mouse embryonic development.

bioinformatics↗