The pathophysiology of tension-type headache (TTH) remains poorly understood, and current treatments are largely symptomatic. Identifying genetically supported, causally relevant proteins may provide Show more
The pathophysiology of tension-type headache (TTH) remains poorly understood, and current treatments are largely symptomatic. Identifying genetically supported, causally relevant proteins may provide insights into disease mechanisms and enable precision therapeutics. We conducted a proteome-wide Mendelian randomization (MR) analysis integrating large-scale plasma proteomic quantitative trait loci with genome-wide association study data for TTH. Phenome-wide MR, enrichment, protein-protein interaction (PPI), and mediation analyses were performed to identify druggable targets and clarify potential biological pathways. Thirteen plasma proteins exhibited significant causal associations with TTH (Bonferroni correction This integrative genetic analysis identified multiple plasma proteins with causal and pharmacologically relevant roles in NRXN3, CCL22, CLEC1B, and LRIG1 emerged as promising and potentially safe therapeutic targets. The online version contains supplementary material available at 10.1186/s10194-025-02235-5. Show less
Colorectal cancer (CRC) is a prevalent digestive system malignancy accompanied by peritoneal metastasis occurring in 7% of cases. Methyltransferase-like 3 (METTL3) promoted the progression of CRC wher Show more
Colorectal cancer (CRC) is a prevalent digestive system malignancy accompanied by peritoneal metastasis occurring in 7% of cases. Methyltransferase-like 3 (METTL3) promoted the progression of CRC whereas its function in peritoneal metastasis was incompletely understood. Here, we found that METTL3 was upregulated in peritoneal metastasis tissues of CRC patients compared with CRC tissues. By sequencing the mRNA of above tissues, we discovered that METTL3-mediated N6-methyladenosine (m6A) modification regulated the downstream target Show less
Meningioma is a common primary central nervous system tumor that can cause a heavy burden on patients. Despite its well-established treatment modalities, pharmacological treatments are not sufficientl Show more
Meningioma is a common primary central nervous system tumor that can cause a heavy burden on patients. Despite its well-established treatment modalities, pharmacological treatments are not sufficiently abundant. Therefore, we explored potential therapeutic targets for meningiomas by integrating genomic and proteomic data. We integrated meningioma data from the UK Biobank and Finnish databases and subsequently explored potential therapeutic targets for meningiomas through multi-omics data using bioinformatics techniques and Mendelian randomization. These targets were finally evaluated using phenotype-wide association group analysis. We found that BET1L, COL17A1, CFAP43, SH3PXD2A, TTC28, ZNRF3, SLK, AKR1C3, NRXN3, and RSPO3 can be potential therapeutic targets for meningiomas. This study provides evidence and explores the biological significance of BET1L, COL17A1, CFAP43, SH3PXD2A, TTC28, ZNRF3, SLK, AKR1C3, NRXN3, and RSPO3 as potential therapeutic targets for meningiomas, providing new insights into the development of targeted therapy for meningiomas. Show less
Asthma severity assessment is essential for asthma management. Transcriptomics contributes substantially to asthma pathogenesis. Then, this study aimed to explore asthma severity-associated transcript Show more
Asthma severity assessment is essential for asthma management. Transcriptomics contributes substantially to asthma pathogenesis. Then, this study aimed to explore asthma severity-associated transcriptomics profile and promising biomarkers for asthma severity prediction. In discovery cohort, induced sputum cells from 3 non-severe and 3 severe asthma patients were collected and analyzed using RNA-seq. Multivariate analysis was performed to explore asthma severity-associated transcriptomics profile and differential expressed genes (DEGs). The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were used for pathway enrichment analysis. Subsequently, based on the previous study and clinical experience, the mRNA expressions of 6 overlapped asthma severity-associated DEGs and Distinct asthma severity-associated transcriptomics profile was identified in induced sputum cells in discovery cohort. Then, 345 DEGs were found, of which 38 terms and 32 pathways were enriched using GO and KEGG, respectively. In validation cohort, the mRNA expressions of Collectively, this study provides the first identification of the association between induced sputum cells transcriptomics profile and asthma severity, indicating the potential value of transcriptomics for asthma management. The study also reveals the promising value of serum C3 for predicting asthma severity in clinical practice. Show less
Sepsis arises from a dysregulated host response to infection, leading to multiorgan inflammatory injury. Early diagnosis and treatment necessitate the identification of reliable immune biomarkers. Thi Show more
Sepsis arises from a dysregulated host response to infection, leading to multiorgan inflammatory injury. Early diagnosis and treatment necessitate the identification of reliable immune biomarkers. This study investigated the relationship between aging, immunity, and sepsis by analyzing six human aging-related gene sets (656 genes). We identified 16 aging-related differentially expressed genes (DEGs) in sepsis. Among these, ATP11B, RBBP7, DOCK10, and NUP160 demonstrated the strongest connectivity with other genes and exhibited significant predictive power. Functional enrichment analysis (GO and KEGG) revealed distinct signaling pathway profiles between high-risk and low-risk sepsis groups (stratified based on risk scores). These dysregulated pathways, associated with multiple immune cells, were primarily linked to transcriptional dysregulation in cellular processes and cancer-related pathways. Experimental validation assays corroborated the roles of ATP11B and RBBP7. Collectively, our bioinformatic and experimental findings indicate that ATP11B, RBBP7, DOCK10, and NUP160 are implicated in the pathogenesis and progression of sepsis. But their potential for sepsis biomarkers still requires further verification. Show less
Lung adenocarcinoma (LUAD), the predominant histological subtype of non-small cell lung cancer, demonstrates critical regulatory involvement of RNA-binding proteins (RBPs) and circular RNAs (circRNAs) Show more
Lung adenocarcinoma (LUAD), the predominant histological subtype of non-small cell lung cancer, demonstrates critical regulatory involvement of RNA-binding proteins (RBPs) and circular RNAs (circRNAs) in tumorigenic processes. Emerging evidence highlights the circRNA-autophagy regulatory axis as a crucial modulator of cancer progression. This study systematically investigates the functional interplay within the RBP-circRNA-autophagy network in LUAD pathogenesis. Employing RNA pull down, mass spectrometry and RNA immunoprecipitation facilitated the exploration of the circRAPGEF5 binding protein. M6A methylation RNA immunoprecipitation-PCR was utilized for m6A analysis. Immunofluorescence (IF) and fluorescence in situ hybridization (FISH) assays were conducted to ascertain the subcellular localization of target genes. Employing mRFP-GFP-LC3 fluorescent lentivirus labelling facilitated the monitoring of autophagy flow levels. Xenografts in mice were instrumental in affirming the role of circRAPGEF5. Through comprehensive molecular profiling, we identified elevated circRAPGEF5 expression in LUAD cells, which significantly suppressed autophagic flux while promoting malignant phenotypes including enhanced proliferation, migration, and invasion. Mechanistic investigations revealed that circRAPGEF5 directly interacts with the KH3-4 functional domain of Insulin-like Growth Factor 2 mRNA-Binding Protein 2 (IGF2BP2), an m6A reader protein. This interaction facilitated IGF2BP2-mediated stabilization of NUP160 mRNA, a nuclear pore complex component. Genetic ablation of NUP160 through RNA interference effectively restored autophagic activity, thereby attenuating the aggressive biological behaviors of LUAD cells. In vivo validation using xenograft models demonstrated that the circRAPGEF5/IGF2BP2/NUP160 signaling axis promotes tumor growth and metastatic dissemination through autophagy suppression. Our findings reveal a novel epigenetic regulatory mechanism wherein m6A-modified circRAPGEF5 orchestrates autophagy inhibition via IGF2BP2-dependent stabilization of NUP160 transcripts, ultimately driving LUAD progression and metastasis. These results establish the circRAPGEF5/IGF2BP2/NUP160 axis as a potential therapeutic target for LUAD intervention. Show less
Steroid-resistant nephrotic syndrome (SRNS) is insensitive to steroid therapy and overwhelmingly progresses to kidney failure (KF), the known pathogenic genes of which include key subunits of the nucl Show more
Steroid-resistant nephrotic syndrome (SRNS) is insensitive to steroid therapy and overwhelmingly progresses to kidney failure (KF), the known pathogenic genes of which include key subunits of the nuclear pore complex (NPC), a less-recognized contributor to glomerular podocyte injury. After analyzing their clinical characterizations and obtaining parental consent, whole-exome sequencing (WES) was performed on patients with SRNS. Several nucleoporin (NUP) biallelic pathogenic variants were identified and further analyzed by cDNA-PCR sequencing from white cells of peripheral blood, minigene assay, immunohistochemical (IHC) staining, and electron microscopy (EM) ultrastructure observation of kidney biopsy, as well as multiple in silico prediction tools, including 3D protein modeling. Here, in six families with SRNS, we identified pathogenic mutations in NUP85/93/107/160 genes. Specifically, the patient with NUP93 mutation developed KF six months after diagnosis at 1 year 2 months. Two missense mutations, c.1655A > G and c.1604A > C, disrupted the protein stability of NUP93 by IHC staining of kidney biopsy. Ultrastructurally, the above mutations led to severe vacuolization and deformed nucleus in podocytes, torn and dissolved glomerular basement membrane, and diffuse foot process effacement. The patient with NUP85 mutation reached chronic kidney disease (CKD) stage 3 after 4 years follow-up, with exons 2-5 in-frame loss and a missense variant at c.511C > T, not affecting NUP85 expression but possibly weakened interaction with Seh1. Additionally, an extended endoplasmic reticulum (ER) tubule was readily observed under EM. Meanwhile, dilated ER was also found in two children with NUP160 mutations (c.3330 delA and c.2407 G > A; c.2241 + 1 (IVS17) G > T and c.3656 T > G), one of which has undergone kidney transplantation. Compound heterozygous variants in NUP107, c.1695 G > C and c.1360 C > T, were found in a 14-year-old girl initially diagnosed with CKD stage 5, with the former variant causing exon 19 skipping and early translation termination. c.1311 + 1(IVS15) G > A and c.1790 C > T were identified in the second affected girl, with the former causing exon 15 skipping and an in-frame loss of aa417-438, which disrupted the stability of NUP107 and interaction with NUP133. Our findings expand the spectrum of phenotypes and genotypes of NUPs-associated SRNS and suggest its possible pathogenic mechanism in nuclear and ER homeostasis. Show less
Nucleoporins (Nups) are a class of proteins that assemble to form nuclear pore complexes, which are related to nucleocytoplasmic transport, gene expression, and the cell cycle. Pathogenic variants in Show more
Nucleoporins (Nups) are a class of proteins that assemble to form nuclear pore complexes, which are related to nucleocytoplasmic transport, gene expression, and the cell cycle. Pathogenic variants in six genes encoding Nups, NUP85, NUP93, NUP107, NUP133, NUP160, and NUP205, cause monogenic steroid-resistant nephrotic syndrome (SRNS), referred to as nucleoporin-associated SRNS. In this paper, we review the epidemiology, structure and function of Nups, pathogenesis, phenotypes and genotypes, and management of nucleoporin-associated SRNS as well as implications for genetic counseling. Affected individuals exhibit autosomal recessive isolated and syndromic SRNS, whose extrarenal manifestations include neurological disorders, growth and development disorders, cardiovascular disorders, and congenital malformations. The median ages at onset of NUP85-, NUP93-, NUP107-, NUP133-, NUP160-, and NUP205-associated SRNS are 7, 3, 4.1, 9, 7, and 2 years, respectively. Kidney biopsies reveal focal segmental glomerulosclerosis in 89% of patients. Most affected individuals are resistant to immunosuppressants. For the six subtypes of nucleoporin-associated SRNS, patients show progression to kidney failure at median ages of 8.5, 3.7, 6.9, 13, 15, and 7 years, respectively. Only two patients with NUP93-associated SRNS with nephrotic syndrome relapse post-transplant have been reported, and the recurrence rate is 12.5%. Next-generation sequencing using a targeted gene panel is recommended in cases of suspected nucleoporin-associated SRNS for genetic diagnosis. Renin-angiotensin-aldosterone system inhibitors are recommended for patients with nucleoporin-associated SRNS. Once genetic diagnosis is confirmed, immunosuppressant discontinuation should be considered, and kidney transplant is preferred when patients progress to kidney failure. Genetic counselling should be provided for asymptomatic siblings and future siblings of an affected individual. Further studies on the pathogenesis of nucleoporin-associated SRNS are needed to seek new therapeutic interventions. Show less
Alpha-enolase (ENO1), the enzyme catalyzing 2-phosphoglycerate conversion to phosphoenolpyruvate, is highly expressed in diffuse large B-cell lymphoma (DLBCL) and correlates with adverse clinical outc Show more
Alpha-enolase (ENO1), the enzyme catalyzing 2-phosphoglycerate conversion to phosphoenolpyruvate, is highly expressed in diffuse large B-cell lymphoma (DLBCL) and correlates with adverse clinical outcomes. Thus, understanding the relationship between ENO1-related gene (ERG) network and DLBCL is imperative. Here, we integrated multi-omics profiling (RIP-seq, RNA-seq, and protein interactome analysis) to identify ERGs and established a prognostic model by machine learning algorithms. We identified eleven hub genes (CHERP, SYNE2, INTS1, FAP, MMP9, LRP5, RBM8A, PRMT5, SLC25A6, PABPC4, PSTPIP2) using RNA sequencing, RNA immunoprecipitation sequencing, and protein interaction profiling. A prognostic model was constructed using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression in the GSE10846 dataset and validated in two independent cohorts. DLBCL patients were stratified into high- and low-risk groups based on the model, and clinical characteristics were compared. The tumor immune microenvironment (TIME) was analyzed using CIBERSORT and xCell algorithms to explore correlations with the ERG score. Drug sensitivity assays in DLBCL cell lines were performed to validate the model's predictive capacity for chemotherapy response. Furthermore, the functional role of PABPC4, a key gene in the scoring system, was investigated through A prognostic model including 11 hub genes was established. Patients in the high-risk group exhibited worse clinical outcomes and an immunosuppressive TIME, characterized by altered expression of immune checkpoint-related proteins. This group demonstrated increased sensitivity to vincristine, etoposide, and oxaliplatin. Knockdown of PABPC4 significantly inhibited cell proliferation, reduced colony formation, and delayed tumor growth The ERG scoring system offers a robust and precise tool for predicting survival and guiding personalized treatment in DLBCL patients. Show less
Poly(A) binding protein cytoplasmic 4 (PABPC4) has been regarded as a prognostic marker in many malignancies. In this study, we evaluated PABPC4 expression at both messenger ribonucleic acid (mRNA) an Show more
Poly(A) binding protein cytoplasmic 4 (PABPC4) has been regarded as a prognostic marker in many malignancies. In this study, we evaluated PABPC4 expression at both messenger ribonucleic acid (mRNA) and protein levels. The prognostic value of PABPC4 in patients with prostate cancer (PCa) was also investigated. The Cancer Genome Atlas (TCGA) database, Gene Expression Omnibus (GEO) database, our analysis of Chinese Prostate Cancer Genome and Epigenome Atlas (CPGEA), and 65 pairs of ribonucleic acid (RNA) sequencing data from our center were employed to detect the expression of PABPC4 in PCa tissues. Tissue microarrays (TMAs) were utilized to detect the expression of the PABPC4 protein, and survival analysis as well as risk factor analysis were conducted. In the 65 pairs of sequencing data, the expression of PABPC4 in tumor tissues was significantly higher than that in paired adjacent tissues (P<0.001), and its expression also presented significant differences among different Gleason groups (P=0.041). In the CPGEA data, the expression of PABPC4 in tumor tissues was significantly higher than that in control tissues (P<0.001), and the expression of PABPC4 in M1 patients was higher than that in M0 patients, although no significant statistical difference was shown (P=0.051). In the TCGA data, the expression of PABPC4 in tumor tissues was significantly higher than that in control tissues (P<0.001). The expression of pT3/4 (pathological tumor stage 3 and pathological tumor stage 4) in high-stage tumor tissues was significantly higher than that in low-stage tumor tissues (pT2) (P=0.02), the expression of pT3/4 in GSE21034 and GSE32571 tumor tissues was significantly higher than that in control tissues (P<0.001), and the expression of pT3/4 in primary tumor tissues was higher than that in metastatic tissues in GSE6752 (P<0.001). The TCGA data revealed that patients with high PABPC4 expression had poorer overall survival (OS) than those with low PABPC4 expression (P=0.04), and the TMA data indicated that patients with high PABPC4 expression had a poor prognosis (P=0.004). Our study demonstrated that PABPC4 was overexpressed at mRNA and protein levels in PCa. We found that patients with high PABPC4 expression had a shorter biochemical recurrence (BCR)-free survival and OS, showing its value as a prognostic biomarker in patients with PCa. Show less
Signal-induced proliferation-associated 1 like 3 (SIPA1L3) is a member of the protein family. Very limited data are currently available regarding the role of SIPA1L3 in human carcinoma. Therefore, in Show more
Signal-induced proliferation-associated 1 like 3 (SIPA1L3) is a member of the protein family. Very limited data are currently available regarding the role of SIPA1L3 in human carcinoma. Therefore, in this study, we investigated the expression pattern and function of SIPA1L3 in non-small cell lung cancer (NSCLC). We analyzed the distribution of SIPA1L3 in NSCLC specimens by immunohistochemistry, the relationship between SIPA1L3 expression and patient clinicopathological features, and investigated the effect of SIPA1L3 on cell growth and invasion in vivo and in vitro using small interfering RNA. Western blotting and immunoprecipitation were performed to demonstrate the interaction between SIPA1L3 and tight junction-associated angiomotin (AMOT) and Pals1-associtated tight junction protein. We found that SIPA1L3 was overexpressed in NSCLC clinical tissue samples and was associated with several clinicopathological factors. SIPA1L3 affects the proliferation and invasion of cancer cells both in vivo and in vitro. Using a SIPA1L3 mutant, we found that SIPA1L3 interacts with AMOT through its PDZ domain, which inhibits the binding of AMOT to Pals1-associtated tight junction protein and further decreases AMOT anchoring to tight junctions. Our findings suggested that SIPA1L3 promotes tumorigenesis in lung cancer cells through its PDZ domain-mediated interaction with AMOT, suggesting that SIPA1L3 is a novel candidate gene that contributes to the malignant phenotype of lung cancer. Show less
The highly organized structures of the immunological synapse (IS) are crucial for T cell activation. PDZ domains might be involved in the formation of the IS by serving as docking sites for protein in Show more
The highly organized structures of the immunological synapse (IS) are crucial for T cell activation. PDZ domains might be involved in the formation of the IS by serving as docking sites for protein interactions. In this study, we investigate the role of the PALS1-associated tight junction protein (PATJ), which contains 10 PDZ domains, in the formation of IS and its subsequent impact on T cell activation. To elucidate the function of PATJ, we generated murine models with conditional T cell-specific knockout of We observed a rapid increase in PATJ expression during T cell activation. Conditional knockout of Our study reveals an important role of PATJ in the formation of IS and provides an approach to improve the efficacy of CAR-T therapy. Show less
The persistent issues of drug resistance and tumor recurrence remain major challenges in bladder cancer (BCa) treatment, severely impacting patient outcomes. In this study, we found that Triosephospha Show more
The persistent issues of drug resistance and tumor recurrence remain major challenges in bladder cancer (BCa) treatment, severely impacting patient outcomes. In this study, we found that Triosephosphate isomerase 1 (TPI1) plays a crucial role in influencing gemcitabine (Gem) resistance in BCa. TPI1 is significantly upregulated in Gem-resistant BCa tissues, and the knockdown of TPI1 markedly increases Gem sensitivity and chemotherapy-induced apoptosis both in vivo and in vitro. Meanwhile, the same was validated in Gem-resistant strains. Mechanistically, transcriptome sequencing and transmission electron microscopy, among others, revealed that TPI1 promoted Gem-associated autophagy. Furthermore, mass spectrometry and co-immunoprecipitation assays demonstrated that TPI1 directly binds to the BH3 domain of Beclin-1. This interaction competitively disrupts the binding between Bcl-2 and Beclin-1, thereby relieving Bcl-2-mediated inhibition of Beclin-1. Furthermore, the interaction between TPI1 and Beclin-1 promotes the formation of PIK3C3-C1, which in turn enhances the interaction between PIK3C3-C1 and the ULK1 complex, thereby increasing the phosphorylation of Beclin-1 at Ser15. In addition, TPI1 also enhanced mitochondrial autophagy induced by Gem in BCa cells and tissues. Importantly, a transcription factor, c-Myc, that regulates TPI1 expression was also identified, and dual luciferase and Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) analysis showed that c-Myc binds primarily to the promoter region of TPI1. Our results suggest that TPI1 plays an important role in regulating the formation of autophagic complexes, and that promoting autophagy significantly increased Gem resistance in BCa. Show less
Dysregulation of macrophage autophagy plays a critical role in sepsis-induced acute lung injury (ALI); however, its underlying mechanism remains unclear. In this study, we aimed to identify the regula Show more
Dysregulation of macrophage autophagy plays a critical role in sepsis-induced acute lung injury (ALI); however, its underlying mechanism remains unclear. In this study, we aimed to identify the regulatory pathway involving the PIK3C3-MAPK14 signaling axis that drives ALI progression by controlling autophagy and macrophage polarization. Using machine learning transcriptomic analysis, MAPK14 was identified as a core gene associated with ALI, and multi-omics integration confirmed its upregulated expression in ALI tissues. MAPK14 localization to pro-inflammatory macrophages was determined using single-cell sequencing. Furthermore, we observed a significant positive correlation between MAPK14 and autophagy-related genes. Molecular docking and kinetic simulations revealed high-affinity interactions between PIK3C3 and MAPK14 (ΔG-bind = -127.722 ± 33.269 kJ/mol). In vitro experiments followed by Western Blot(WB) and RT-q polymerase chain reaction (PCR) assays demonstrated that lipopolysaccharide stimulation upregulated MAPK14 expression through downregulation of PIK3C3 expression, resulting in impaired autophagic flux (LC3-II/Ⅰ↓, TOM20↑, P62↑, HSP60↑). Flow cytometry and enzyme-linked immunosorbent assay (ELISA) confirmed a shift toward pro-inflammatory (M1) macrophage polarization. RNA pull-down assay directly captured the PIK3C3-MAPK14 complex, and functional validation showed that PIK3C3 overexpression significantly inhibited MAPK14 protein expression, whereas PIK3C3 knockdown enhanced it. In conclusion, targeting the PIK3C3-MAPK14 axis is a promising therapeutic strategy for ALI. Show less
Cancer persists as one of the most formidable global public health crises and socioeconomic burdens of our era, compelling the scientific community to develop innovative and diversified therapeutic mo Show more
Cancer persists as one of the most formidable global public health crises and socioeconomic burdens of our era, compelling the scientific community to develop innovative and diversified therapeutic modalities to revolutionize clinical management and enhance patient outcomes. The recent seminal discovery by Swamynathan et al. has unveiled menadione, a vitamin K precursor, as a potent inducer of triaptosis-a novel regulated cell death pathway mediated through the oxidative modulation of phosphatidylinositol 3-kinase PIK3C3/VPS34. This mechanistically distinct cell death paradigm, characterized by its intimate association with endosomal dysfunction and oxidative stress-induced cellular catastrophe, has demonstrated remarkable therapeutic efficacy in preclinical prostate cancer models, outperforming conventional therapeutic regimens and emerging as a potential paradigm-shifting strategy in oncology. This comprehensive review provides a critical synthesis of the triaptosis discovery landscape, elucidating its molecular intricacies and pathophysiological implications. We systematically examine the multifaceted roles of endosomal biology in oncogenesis and tumor progression, while offering a nuanced perspective on redox homeostasis in malignant cells and the therapeutic potential of oxidative stress modulation. Furthermore, we address the inherent dichotomy of oxidative stress induction in cancer therapy, balancing its therapeutic promise against potential adverse effects. Looking toward the horizon of cancer research, we explore transformative therapeutic strategies leveraging triaptosis induction and its potential applications beyond oncology, aiming to catalyze a new era of precision medicine that ultimately enhances patient survival and quality of life. Show less
While spermatogenesis has been extensively characterized in mammals, its molecular underpinnings in avian species remain largely unexplored. To address this knowledge gap, we performed single-cell tra Show more
While spermatogenesis has been extensively characterized in mammals, its molecular underpinnings in avian species remain largely unexplored. To address this knowledge gap, we performed single-cell transcriptomic profiling of duck testes across developmental stages (10-week immature vs. 23-week mature). Our analysis generated a comprehensive cellular atlas comprising 54,702 cells, resolving eight germ cell clusters (three spermatogonia [SPG], three spermatocytes [SPC], two spermatozoa [SPT]) and nine somatic populations, including peritubular myoid cells, immune subsets (T cells, macrophages, granulocytes), endothelial cells, Leydig cells, and three Sertoli cell subtypes, each defined by unique marker gene signatures. Furthermore, novel marker genes were identified, including EXFABP for granulocyte, ARHGAP15 for T cell regulation, FDX1 specific to Leydig cells (LC), and TSSK3/TSSK2 linked to elongated spermatid formation (SPT). Notably, we identified some novel molecular markers distinguishing these populations. Pseudotemporal trajectory reconstruction of germline development revealed stage-specific enrichment of ribosome, endoplasmic reticulum protein processing, and autophagy pathways. Core regulators MRPL13, MRPL2, MRPL22, MRPS14, MRPS7 (ribosome), HSPA5 (ER stress response), and PIK3C3 (autophagy) emerged as molecular hubs showing progressive downregulation during differentiation. Comparative transcriptomic analysis of germ cells and Sertoli cells between immature (IMT) and mature (MT) testes revealed significant enrichment of the spliceosome pathway in both germ and Sertoli cells. Critical spliceosome components SNRPG, SF3B3, and SNRPF exhibited coordinated downregulation during testicular maturation, suggesting their role as negative regulators of spermatogenic progression. This study establishes the first high-resolution cellular blueprint of avian spermatogenesis, delineating regulatory networks of duck testis cell development. Our findings provide valuable datasets and mechanistic insights into the evolutionary specialization of reproductive strategies in poultry. Show less
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a substantial global threat. SARS-CoV-2 nonstructural proteins (NSPs) are essential for impeding the host replication mechanism while Show more
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a substantial global threat. SARS-CoV-2 nonstructural proteins (NSPs) are essential for impeding the host replication mechanism while also assisting in the production and organization of new viral components. However, NSPs are not incorporated into viral particles, and their subsequent fate within host cells remains poorly understood. Additionally, their role in viral pathogenesis requires further investigation. This study aimed to discover the ultimate fate of NSP6 in host cells and to elucidate its role in viral pathogenesis. We investigated the effects of NSP6 on cell death and explored the underlying mechanism; moreover, we examined the degradation mechanism of NSP6 in human cells, along with analysing its correlation with coronavirus disease 2019 (COVID-19) severity in patient peripheral blood mononuclear cells (PBMCs). NSP6 was demonstrated to induce cell death. Specifically, NSP6 interacted with EI24 autophagy-associated transmembrane protein (EI24) to increase intracellular Ca This study reveals that KLHL22-mediated ubiquitination controls NSP6 stability and that NSP6 induces autophagic cell death via calcium overload, highlighting its cytotoxic role and suggesting therapeutic strategies that target calcium signaling or promote NSP6 degradation as potential interventions against COVID-19. Show less
Autophagy is essential in DNA damage response by limiting damage, but its responsive activation remains unclear. RBM38 (RBM38a), an RNA-binding protein, regulates mRNA metabolism and plays a key role Show more
Autophagy is essential in DNA damage response by limiting damage, but its responsive activation remains unclear. RBM38 (RBM38a), an RNA-binding protein, regulates mRNA metabolism and plays a key role in controlling cell cycle progression, senescence, and cancer. In this study, we uncovered a novel primate-specific isoform, RBM38c, with 32 extra amino acids from exon 2, which imparts a distinct capacity to promote autophagy upon DNA damage. TP53 increases RBM38c expression upon DNA damage, while TRIM21 facilitates its K63-linked ubiquitination at lysine (K) 35. Activated RBM38c enhances its interaction with BECN1, promoting the formation of the ATG14-containing PtdIns3K-C1 complex and thus autophagy initiation. A K35R mutation or TRIM21 deficiency impairs RBM38c ubiquitination, preventing autophagy activation upon DNA damage. Moreover, RBM38c-driven autophagy protects cells from DNA damage-induced apoptosis and promotes survival, with this beneficial effect susceptible to suppression by the autophagy inhibitor 3-methyladenine. Consequently, depleting RBM38c enhances the efficacy of DNA-damaging drugs by impairing autophagy and increasing DNA damage. Clinical lung cancer samples show a positive correlation between RBM38c expression and LC3 expression, and this correlation is linked to chemotherapy resistance. Together, our study reveals a novel mechanism for DNA damage-induced autophagy, involving K63-linked ubiquitination of RBM38c as a critical interactor with BECN1. Show less
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide. This study aimed to identify key genes involved in HCC development and elucidate their molecular mech Show more
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide. This study aimed to identify key genes involved in HCC development and elucidate their molecular mechanisms, with a particular focus on mitochondrial function and apoptosis. Differential expression analyses were performed across three datasets-The Cancer Genome Atlas (TCGA)-Liver Hepatocellular Carcinoma (LIHC), GSE36076, and GSE95698-to identify overlapping differentially expressed genes (DEGs). A prognostic risk model was then constructed. Cysteine/serine-rich nuclear protein 1 ( A six-gene prognostic model was established, comprising downregulated genes ( Show less
Centrioles undergo marked transformations during spermatogenesis that are essential for sperm motility and male fertility. Despite their importance, the molecular mechanisms and ultrastructural dynami Show more
Centrioles undergo marked transformations during spermatogenesis that are essential for sperm motility and male fertility. Despite their importance, the molecular mechanisms and ultrastructural dynamics underlying these transformations remain largely unknown. Here, we apply ultrastructure expansion microscopy and reveal previously unrecognized centriolar architectural changes in mouse male germ cells, including geometry switching between the two centrioles and stage-specific removal of distal tip proteins such as centrin and SFI1. We further identify the centrin-POC5 inner scaffold as a key structure selectively augmented at the distal centriole, which directly forms and anchors the flagellum. Functional analyses of Show less
Obesity is a major public health crisis associated with high mortality rates. Previous genome-wide association studies (GWAS) investigating body mass index (BMI) have largely relied on imputed data fr Show more
Obesity is a major public health crisis associated with high mortality rates. Previous genome-wide association studies (GWAS) investigating body mass index (BMI) have largely relied on imputed data from European individuals. This study leveraged whole-genome sequencing (WGS) data from 88,873 participants from the Trans-Omics for Precision Medicine (TOPMed) Program, of which 51% were of non-European population groups. We discovered 18 BMI-associated signals (P < 5 × 10 Show less
Centrioles have a unique, conserved architecture formed by three linked, 'triplet', microtubules arranged in ninefold symmetry. The mechanisms by which these triplet microtubules are formed remain unc Show more
Centrioles have a unique, conserved architecture formed by three linked, 'triplet', microtubules arranged in ninefold symmetry. The mechanisms by which these triplet microtubules are formed remain unclear but likely involve the noncanonical tubulins delta-tubulin and epsilon-tubulin. Previously, we found that human cells lacking delta-tubulin or epsilon-tubulin form abnormal centrioles, characterized by an absence of triplet microtubules, lack of central core protein POC5, and a futile cycle of centriole formation and disintegration (Wang et al., 2017). Here, we show that human cells lacking either TEDC1 or TEDC2 have similar abnormalities. Using ultrastructure expansion microscopy, we observed that mutant centrioles elongate to the same length as control centrioles in G2 phase and fail to recruit central core scaffold proteins. Remarkably, mutant centrioles also have an expanded proximal region. During mitosis, these mutant centrioles further elongate before fragmenting and disintegrating. All four proteins physically interact and TEDC1 and TEDC2 can form a subcomplex in the absence of the tubulins, supporting an AlphaFold Multimer model of the tetramer. TEDC1 and TEDC2 localize to centrosomes and are mutually dependent on each other and on delta-tubulin and epsilon-tubulin for localization. Our results demonstrate that delta-tubulin, epsilon-tubulin, TEDC1, and TEDC2 function together to promote robust centriole architecture, laying the foundation for future studies on the mechanisms underlying the assembly of triplet microtubules and their interactions with centriole structure. Show less
Colorectal cancer (CRC) is a globally prevalent malignancy associated with high mortality rates. Despite the existence of various treatment modalities, the prognosis for CRC remains relatively poor. T Show more
Colorectal cancer (CRC) is a globally prevalent malignancy associated with high mortality rates. Despite the existence of various treatment modalities, the prognosis for CRC remains relatively poor. This study aims to explore the role of RNA-binding proteins (RBPs) in CRC progression and their potential as prognostic biomarkers and therapeutic targets. We first identified 166 prognosis-related RBPs, including LIN28B, PPARGC1A, RBM47, and AFF3, by performing univariate Cox regression analysis on bulk transcriptomic and clinical data from The Cancer Genome Atlas (TCGA). Next, single-cell RNA sequencing data from normal, adenoma, and CRC tissues of four patients were analyzed to determine cell type-specific expression patterns of RBPs. Ten upregulated RBPs (HSPB1, RBM47, HMGN2, BRD2, BST2, RBM6, YBX3, CANX, PLEC, and RNASET2) were identified as CRC-associated. Among them, HSPB1, RBM47, HMGN2, BRD2, BST2, and PLEC were predominantly expressed in epithelial cell subsets, whereas RNASET2, RBM6, YBX3, and G3BP2 showed higher expression in T cell subpopulations. Aberrant expression of these RBPs was significantly associated with clinical features such as age, cancer stage, and overall survival ( The online version contains supplementary material available at 10.1038/s41598-025-29678-9. Show less
Increasing evidence suggests a complex interplay between psychiatric disorders and metabolic dysregulations. However, most research has been limited to specific disorder pairs, leaving a significant g Show more
Increasing evidence suggests a complex interplay between psychiatric disorders and metabolic dysregulations. However, most research has been limited to specific disorder pairs, leaving a significant gap in our understanding of the broader psycho-metabolic nexus. This study leveraged large-scale cohort data and genome-wide association study (GWAS) summary statistics, covering 8 common psychiatric disorders and 43 metabolic traits. We introduced a comprehensive analytical strategy to identify shared genetic bases sequentially, from key genetic correlation regions to local pleiotropy and pleiotropic genes. Finally, we developed polygenic risk score (PRS) models to translate these findings into clinical applications. We identified significant bidirectional clinical risks between psychiatric disorders and metabolic dysregulations among 310,848 participants from the UK Biobank. Genetic correlation analysis confirmed 104 robust trait pairs, revealing 1088 key genomic regions, including critical hotspots such as chr3: 47588462-50387742. Cross-trait meta-analysis uncovered 388 pleiotropic single nucleotide variants (SNVs) and 126 shared causal variants. Among variants, 45 novel SNVs were associated with psychiatric disorders and 75 novel SNVs were associated with metabolic traits, shedding light on new targets to unravel the mechanism of comorbidity. Notably, RBM6, a gene involved in alternative splicing and cellular stress response regulation, emerged as a key pleiotropic gene. When psychiatric and metabolic genetic information were integrated, PRS models demonstrated enhanced predictive power. The study highlights the intertwined genetic and clinical relationships between psychiatric disorders and metabolic dysregulations, emphasising the need for integrated approaches in diagnosis and treatment. The National Key Research and Development Program of China (2023YFC2506200, SHH). The National Natural Science Foundation of China (82273741, SY). Show less
The Regulator of G Protein Signaling (RGS) gene family, known as critical negative regulators of G protein-coupled receptor (GPCR) signaling pathways, has emerged as a potential therapeutic target in Show more
The Regulator of G Protein Signaling (RGS) gene family, known as critical negative regulators of G protein-coupled receptor (GPCR) signaling pathways, has emerged as a potential therapeutic target in various malignancies. This study aims to comprehensively evaluate the expression profiles of RGS genes in breast cancer, exploring their diagnostic, prognostic, and chemotherapeutic sensitivity-related roles. Pan-cancer RNA-seq data, immune phenotype data, stemness indices, and breast cancer data from the TCGA and GTEx databases (via UCSC Xena) were integrated to analyze the expression patterns of RGS genes across different cancers. Associations with immune microenvironment factors (e.g., stromal and immune scores), tumor stemness (mRNAsi/mDNAsi), and chemotherapy drug sensitivity (cyclophosphamide, neratinib, clobutin, etc.) were assessed. The relationship between RGS gene expression and overall survival (OS) as well as progression-free survival (PFS) in breast cancer patients was analyzed using the KM-Plotter database, leading to the identification of potential diagnostic and prognostic biomarkers. Pan-cancer analyses revealed significant positive correlations between the expression of RGS1, RGS13, RGS18, and RGS19 and both stromal and immune scores ( The RGS gene family plays a crucial role in breast cancer progression through modulation of the immune microenvironment and chemotherapy resistance. Their expression profiles hold promise as novel biomarkers for personalized prognostic stratification and targeted therapy, particularly for guiding chemotherapy drug selection. Show less
Diabetic retinopathy (DR), a microvascular disease, also involves retinal neurodegeneration. Müller cells exert an important role in the retina, and their destabilization and reduction affect the phys Show more
Diabetic retinopathy (DR), a microvascular disease, also involves retinal neurodegeneration. Müller cells exert an important role in the retina, and their destabilization and reduction affect the physiological function of the retina. To investigate the effect and mechanism of hedgehog acyltransferase-like (Hhatl) on Müller cells in DR. The differentially expressed genes (DEGs) in Müller cells of DR rats were first analyzed by single-cell transcriptomics techniques (scRNA-seq). Regulating Hhatl expression, cell viability was detected using cell counting kit-8 (CCK-8) assay; apoptosis was detected by terminal deoxynucleotidyl transferase nick-end labeling (TUNEL); the expression of B-cell lymphoma 2 (Bcl2), Bcl2-associated X protein (Bax), activating transcription factor 6 (ATF6), C/EBP homologous protein (CHOP), and glucose-regulated protein 78 (GRP78) was assessed by immunofluorescence; and Ca scRNA-seq analysis revealed that Hhatl was low-expressed in Müller cells of DR rats. In vitro assays confirmed that upregulation of Hhatl could increase rMC-1 Bcl2 expression, decrease Bax expression, and reduce apoptosis in HG environments. In addition, Hhatl did downregulate ATF6 expression, decrease CHOP and GRP78 levels, and reduce Ca Hhatl reduces apoptosis of Müller cells in DR by alleviating ATF6-related ERS signaling. Show less
Liya Deng, Ying Wang · 2025 · Stem cell research & therapy · BioMed Central · added 2026-04-24
Diabetic retinopathy (DR) is a leading cause of blindness in adults, which is characterized by neurovascular dysfunction. Retinal neurodegeneration was involved in the pathogenesis of early-stage DR. Show more
Diabetic retinopathy (DR) is a leading cause of blindness in adults, which is characterized by neurovascular dysfunction. Retinal neurodegeneration was involved in the pathogenesis of early-stage DR. This research aims to reveal the therapeutic effects and potential molecule mechanism of Mesenchymal stem cells-derived exosomes (MSCs-EXOs) in Müller cells at the early stage of DR. More specifically, we investigated in the rat retinal Müller cell line rMC-1. We cultured rMC-1 in high glucose (HG) medium mixed with MSCs-EXOs to observe the changes in cell proliferative capacity and function. EdU assay, Immunofluorescence staining and Cell viability were used to assess cell proliferative capacity and function. Western blot and Quantitative Real-Time polymerase chain reaction (qRT-PCR) were used to assess the expression of cell proliferation-related proteins and cell cycle-related protein. Finally, dual-luciferase reporter assay, miRNA sequencing and cell transfection were used to assess the relationships between MSCs-EXOs and binding site. Here our results displayed that MSCs-EXOs promoted HG-induced cell proliferation in rMC-1. Furthermore, MSCs-EXOs protected HG-induced function of rMC-1. Mechanistically, MSCs-EXOs promoted the proliferation of rMC-1 by inhibiting the Hippo pathway to decrease the expression of Large tumor suppressor 1 (LATS1) and p-YAP and increase the expression of cell proliferation-related proteins Yes-associated protein (YAP), EGFR and cell cycle-related protein CYCLIN D1. In addition, LATS1 knockdown inhibited p-YAP expression and promoted HG-induced cell proliferation and YAP, EGFR and CYCLIN D1 expression in rMC-1. We subsequently performed bioinformatics sequencing analysis of MSCs-EXOs and confirmed that LATS1 was the target of miR-21a-5p. Our research proved that MSCs-EXOs containing miR-21a-5p increased the expression of YAP via targeting LATS1, and ultimately promoted the cell proliferation in rMC-1. Our current study clarified the molecular mechanism of MSCs-EXOs-regulated cell proliferation and function protection in rMC-1 and provided a novel strategy for the treatment of DR. Show less
Glucose homeostasis, essential for metabolic health, requires coordinated insulin and glucagon activity to maintain blood glucose balance. Dysregulation of glucose homeostasis causes hyperglycaemia an Show more
Glucose homeostasis, essential for metabolic health, requires coordinated insulin and glucagon activity to maintain blood glucose balance. Dysregulation of glucose homeostasis causes hyperglycaemia and glucose intolerance, hallmark features of type 2 diabetes. While SEC16 homologue B (SEC16B), an endoplasmic reticulum export factor, has been linked to obesity, type 2 diabetes and lipid metabolism, its role in glucose regulation remains poorly defined. This study aims to investigate SEC16B's contribution to glucose homeostasis by systematically dissecting its conserved physiological mechanisms across species. To interrogate SEC16B's role, we combined Drosophila genetics (RNA interference-mediated dSec16 knockdown) with murine models (Sec16b deletion) under standard or high-fat diet conditions. Glucose and insulin tolerance tests assessed glucose homeostasis. Mechanistic insights into beta cell dysfunction were derived from immunostaining, glucose-stimulated insulin secretion assays and RNA-seq profiling of murine pancreatic islets. Both disruption of dSec16 in Drosophila and Sec16b deletion in mice triggered glucose intolerance under standard diet conditions, recapitulating conserved metabolic dysfunction. In addition, Sec16b loss impaired glycaemic control in mice fed a high-fat diet. Mechanistically, Sec16b deficiency impairs insulin secretion by downregulating cholinergic signalling and compromising intracellular Ca Our study reveals SEC16B, a genome-wide association study-identified obesity risk gene, as an evolutionarily conserved regulator of glucose homeostasis. By linking SEC16B to cholinergic-driven insulin secretion and calcium dynamics, we resolve a mechanistic gap in beta cell dysfunction and metabolic disease. This finding provides novel insights into the mechanisms underlying glucose homeostasis and may enhance our understanding of potential treatments for metabolic diseases. Show less
The development of an immunosuppressive microenvironment is a critical factor in stomach carcinogenesis. Polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) serve a pivotal function in medi Show more
The development of an immunosuppressive microenvironment is a critical factor in stomach carcinogenesis. Polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) serve a pivotal function in mediating immune suppression. However, the precise mechanisms underlying PMN-MDSCs infiltration into the tumor immune microenvironment (TIME) and their immunosuppressive functions remain poorly understood. In this investigation, we observed that PMN-MDSCs were up-regulated during stomach carcinogenesis, with gastric cancer (GC) cells secreting CCL26 to promote the infiltration of PMN-MDSCs into the TIME via the CX3CR1 receptor. The infiltrating CX3CR1 Show less