PURPOSE:This study aims to investigate whether matrix metalloproteinases (MMPs) are associated with the risk of metabolic syndrome (MetS) and its components. METHODS:We conducted a two-sample Mendelian randomization (MR) study by using 9 types of MMPs as exposures and MetS and its components (waist circumference, essential hypertension, fasting blood glucose [FBG], high-density lipoprotein [HDL] cholesterol, and triglycerides) as outcomes. The genome-wide association study summary data of exposure and outcome were both obtained from publicly published research. Four MR analytical methods, including inverse variance weighted, MR-Egger, weighted median, and weighted mode, were applied to analyze the causality between exposure and outcome, in which IVW was employed as the primary analytical method. MR-Egger, Cochran's Q, leave-one-out (LOO), and MR pleiotropy residual sum and outlier (MR-PRESSO) were used to assess the reliability of the results of the MR analysis. RESULTS:Genetically determined MMP12 showed significant negative associations to the risk of essential hypertension (OR = 0.996, 95% CI: 0.993-0.998, p = 0.001). Results that were analyzed with the MR-Egger, weighted median, and weight mode were consistent with those analyzed with IVW. Although MMP12 may have a suggestive protective effect on FBG levels (OR = 0.993, 95% CI: 0.986-1, p = 0.049), this finding may be affected by potential horizontal pleiotropy and requires further validation. No causal associations were identified between other MMPs and the risk of MetS or its components. CONCLUSIONS:This MR analysis provides evidence of causal links between MMP12 and the risk of essential hypertension, indicating that MMP12 might inform early risk stratification for specific cardiometabolic components (e.g., essential hypertension), rather than serving as a diagnostic biomarker for the composite metabolic syndrome.
BACKGROUND:Epstein-Barr virus-associated gastric cancer (EBVaGC) is a distinct molecular subtype of gastric cancer, but reliable biomarkers linking EBV-related biology, prognosis, and microenvironmental remodeling remain limited. METHODS:Differentially expressed genes associated with EBVaGC were identified from TCGA and GEO datasets. Weighted gene co-expression network analysis and machine learning were used to screen core genes. Functional enrichment, diagnostic and prognostic modeling, immune infiltration analysis, single-cell transcriptomic analysis of a public scRNA-seq dataset, cell-cell communication analysis, drug sensitivity prediction, external cohort validation, and RT-qPCR validation in gastric cancer cell lines were subsequently performed. RESULTS:Five core genes (ASPA, CHODL, GNG7, P2RY14, and PI16) were identified. The combined classifier showed high apparent diagnostic performance in the discovery datasets (AUC = 1.000 in the EBV cohort and 0.981 in TCGA-STAD) and retained value in GSE27342 (AUC = 0.771). RT-qPCR confirmed differential expression of these genes between a gastric epithelial cell line and a gastric cancer cell line, providing general tumor-versus-normal experimental support rather than EBV-specific validation. A five-gene risk signature stratified overall survival, with 1-, 2-, and 3-year AUCs of 0.634, 0.645, and 0.622, which improved to 0.716, 0.768, and 0.693 after integration with age and stage. Single-cell analysis localized the strongest signature signal to fibroblasts and B cells and revealed enhanced MIF-, PTN-, and TNFSF13B-related communication in tumors. High-risk tumors showed higher predicted IC50 values for paclitaxel and 5-fluorouracil. CONCLUSION:We identified a five-gene signature with strong diagnostic value and biologically meaningful prognostic relevance in EBVaGC, highlighting fibroblast- and B-cell-associated microenvironmental programs in aggressive disease.
OBJECTIVE:To detect the expression level of cell division cycle 20 homolog (CDC20) in clear cell renal cell carcinoma (ccRCC) and to study the biological function of CDC20 in ccRCC. METHODS:CDC20 expression levels and clinical significance of ccRCC were determined using the Cancer Genome Atlas (TCGA) database. We detected the expression level of CDC20 in ccRCC with the help of immunohistochemistry (IHC). The effect of CDC20 on the proliferation of renal cancer cells was investigated using EDU and CCK-8 proliferation assays. We used wound healing assays and Transwell assays to determine the effects of CDC20 on renal cancer cell migration and invasion and Wnt signaling pathway agonists in recovery experiments. The mechanism of CDC20 in ccRCC was detected using western blotting. Finally, the effect of CDC20 on renal cancer cells was verified in vivo in a nude mouse xenograft model. RESULTS:Bioinformatics analysis found that CDC20 was upregulated in ccRCC, and its high expression was associated with poor prognosis in kidney renal cell carcinoma (KIRC) patients. In addition, we detected high expression of CDC20 in KIRC tissues, consistent with the results of bioinformatics analysis. Besides, knockdown of CDC20 can inhibit the biological functions of renal cancer cells. The recovery experiment proved that the biological function of the originally inhibited renal cancer cells was restored. In vivo, low expression of CDC20 can inhibit tumor growth. CONCLUSIONS:As CDC20 is highly expressed in KIRC tissues, it can be used as both a therapeutic target and a prognostic marker.
BACKGROUND:The significance of M2 macrophages in cancer is well established, yet their specific role and the regulatory molecules involved in colorectal cancer remain unclear. METHODS:Using publicly available single-cell RNA-seq data from four colorectal cancer datasets (EMTAB8107, GSE139555, GSE146771, and GSE166555), we evaluated macrophage proportions and their functional enrichment. Immune cell infiltration was quantified by CIBERSORT, quanTIseq, and xCell on TCGA-COAD bulk transcriptomes, with immune correlations adjusted for tumor purity. GSEA was performed with MSigDB v7.4 gene sets (Hallmark, GO, KEGG). Prognostic models were built using Kaplan-Meier and multivariate Cox regression. In vitro, CCBE1 was silenced in SW480 and HCT116 cells; proliferation was measured by CCK-8, colony formation, and EdU assays, and migration/invasion were measured by transwell assays. M2 polarization was assessed by flow cytometry. RESULTS:Macrophages represented a substantial fraction (20%-35% across datasets) of the tumor microenvironment and were associated with upregulated coagulation and KRAS signaling. Consensus M2 macrophage infiltration was linked to 91 upregulated genes, among which CCBE1 emerged as an independent prognostic risk factor (multivariate Cox: HR = 1.305 [95% CI: 1.039-1.639], p < 0.05). CCBE1 was overexpressed in colorectal cancer cell lines compared to NCM460. Silencing CCBE1 significantly suppressed cell proliferation, migration, and invasion. Moreover, the conditioned medium from CCBE1-knockdown cancer cells decreased the proportion of CD206+ M2 macrophages and upregulated M1 markers while downregulating M2 markers, indicating that CCBE1 promotes M2 polarization. CONCLUSIONS:CCBE1 is an oncogenic driver in colorectal cancer that independently predicts poor survival and functionally enhances tumor cell proliferation, invasion, and M2 macrophage polarization. Targeting CCBE1 may represent a potential therapeutic strategy for colorectal cancer.
Ataxia-telangiectasia (A-T) is a heterogeneous genetic disorder with a recessive mode of inheritance resulting from biallelic variants in the A-T mutated gene (ATM). Besides ataxia, the disorder involves compromised immunity and an increased risk of malignancies. We recruited a consanguineous Pakistani family with multiple individuals having adolescent-onset ataxia. Phenotyping and clinical testing were completed for the patients. DNA samples from multiple individuals were used for bidirectional exome sequencing at 100X coverage, and data were aligned to the hg19 genome assembly. Sanger sequencing was completed to confirm the segregation of the variants. Multiple sequence alignments of orthologous proteins from diverse species were performed using ClustalO to check the amino acid conservation. Patients in the family manifested gait and limb ataxia, postural instability, and dystonia. A known heterozygous pathogenic nonsense ATM variant, c.2413C > T, p.(Arg805Ter), in trans with a new unreported missense variant, c.8708C > T, p.(Pro2903Leu), was identified, which segregated with the disease. The missense variant affected an amino acid, which was conserved in evolution. Telangiectasia of the eyes and skin was absent in the affected individuals, which led to the initial misdiagnosis of the disease as cerebellar ataxia. There were no reports of malignancies in the family, and affected individuals were alive in their third and fourth decades of life. Thus, molecular analyses resulted in the reclassification of the disease as A-T, an example of reverse phenotyping. The study expands the phenotypic heterogeneity of A-T and extends the allelic spectrum of ATM variants.
BACKGROUND:The CCDC22 gene is a key regulator of endosomal trafficking and NF-κB signaling, and its dysfunction is implicated in a spectrum of X-linked neurodevelopmental disorders, including Ritscher-Schinzel syndrome 2, intellectual disability, and epilepsy. Despite the identification of CCDC22 variants having increased, a comprehensive biological characterization, including its spatiotemporal expression and functional molecular networks, remains to be systematically delineated. Furthermore, the rarity of CCDC22 variants created a significant challenge in distinguishing their pathogenicity. This study aimed to explore the integration of biological context-informed and clinical genetic analysis workflows and to perform an exploratory evaluation of prediction algorithms to better optimize the genetic diagnosis process for CCDC22. METHODS:Multilevel biological analysis was performed to evaluate the spatiotemporal expression patterns of CCDC22 across developmental stages. A protein-protein interaction network was constructed to identify key functional modules and pathway enrichments. Additionally, an expert-classified dataset of CCDC22 missense variants was utilized to conduct an exploratory performance evaluation of twenty prediction algorithms, specifically assessing the effect of filtering out variants observed as population hemizygotes. RESULT:CCDC22 exhibits distinct spatiotemporal expression dynamics and chromatin accessibility patterns closely associated with neurodevelopmental processes. PPI and functional enrichment analyses highlighted its core involvement in endocytic recycling and vesicle transport. In the exploratory missense variant evaluation, meta-predictors, notably ClinPred and MetaRNN, demonstrated the highest predictive potential within this limited cohort. After filtering out variants observed as hemizygotes in the gnomAD database, most of the algorithms' performance improved in distinguishing the pathogenicity of variants and genetic diagnosis. ClinPred, M-CAP, MetaRNN, and SIFT achieved the highest balanced accuracy (84.6%, 80.8%, 78.7%, and 76.1%, respectively). ClinPred, M-CAP, and MetaRNN achieved the highest AUC value (> 0.9). CONCLUSION:This study delineates the spatiotemporal and functional molecular network of CCDC22 in neurodevelopment. A combination of population-based strategy and prediction enhanced the performance of most algorithms. ClinPred and MetaRNN showed higher predictive potential. This study may provide insights into the evaluation of variants in CCDC22-related diseases.
PurposeThe p47ING1a isoform of the ING1 tumor suppressor regulates cellular senescence through Rb-dependent pathways via its plant homeodomain (PHD) zinc-finger, which recognizes the H3K4me3 histone mark. However, the mutational landscape of p47ING1a and the functional consequences of PHD-domain nonsynonymous single-nucleotide polymorphisms (nsSNPs) remain poorly characterized. This study aimed to identify and structurally evaluate the most deleterious nsSNPs in p47ING1a and clarify their potential role in disrupting ING1 tumor-suppressor activity.MethodsA total of 347 missense nsSNPs were retrieved from the NCBI dbSNP database and screened using 12 sequence-based computational tools. Variants consistently predicted as deleterious were further evaluated by I-Mutant stability analysis and ConSurf evolutionary conservation profiling. Three-dimensional structural modeling was performed using AlphaFold3, refined through GalaxyRefine, and validated by ERRAT, PROCHECK, and TM-align. Mutation-induced structural and binding effects were assessed using Missense3D, mCSM, and BeAtMuSiC. Post-translational modification sites were predicted via NetPhos 3.1, GPS 3.0, BDM-PUB, and NetOGlyc 4.0. Protein-protein interaction networks were constructed using STRING and Gene MANIA. Pan-cancer expression was analyzed through UALCAN and the Human Protein Atlas.ResultsTwelve computational tools converged on six high-priority variants, namely, C358S, C374G, W378G, F379V, S382L, and R400P. All localized exclusively within the PHD zinc-finger domain, residues 353-402. All six mutations were consistently predicted to destabilize the p47ING1a protein across multiple stability analyses.ConclusionsSix nsSNPs in the PHD domain of p47ING1a are predicted to disrupt protein stability, H3K4me3 binding, and Sin3A/HDAC complex interactions, thereby impairing ING1 tumor-suppressor function. These findings provide a computational basis for prioritizing variants for experimental validation through site-directed mutagenesis, chromatin-binding assays, and structure-guided therapeutic targeting of the PHD-H3K4me3 interface.
Congenital contractural arachnodactyly (CCA) is a rare, autosomal dominant connective tissue disease characterized by arachnodactyly, camptodactyly, multiple joint contractures, tall and slender habitus, crumpled ears, and scoliosis. It shares overlapping features with Marfan syndrome (MFS). This condition is caused by pathogenic variants in the fibrillin 2 (FBN2) gene. Currently, approximately 200 variants in FBN2 have been identified, with most of the variants located in the middle region of the gene (Exons 24-35). Here, we investigated the genetic etiology of CCA in two unrelated Chinese families. Whole-exome sequencing (WES) identified a novel in-frame deletion variant, NM_001999.4: c.4195_4209del, p.Trp1399_Gly1403del, in Exon 32 of FBN2 that was detected in all 3 affected patients but absent in 6 unaffected family members. The other novel missense variant in Exon 27 of FBN2 (c.3521G > A, p.Cys1174Tyr) was identified in an 8-month-old female patient who was diagnosed with CCA. This variant was verified to be inherited from her unaffected mother with low-level mosaicism. Our study expands the mutation spectrum of FBN2 and provides insights into the genotype-phenotype relationship in CCA as well as a foundation for its genetic diagnosis, counseling, and management.
BackgroundSystemic lupus erythematosus (SLE) is a complex and heterogeneous systemic autoimmune disease associated with poor treatment outcomes. While previous studies have indicated a genetic predisposition to SLE, the underlying mechanisms remain poorly understood.ObjectiveThis study aimed to identify diagnostic targets with potential genetic associations to SLE by leveraging bioinformatics and the Mendelian randomization (MR) approach.MethodsSix datasets (GSE30153, GSE39088, GSE50635, GSE50772, GSE61635, and GSE110169) were obtained from the GEO database for differential expression analysis to identify differentially expressed genes (DEGs). Weighted gene coexpression network analysis (WGCNA) was then performed, and the most relevant module was intersected with the DEGs to identify candidate genes with potential diagnostic value. Subsequently, machine learning algorithms were applied to screen diagnostic genes, and their performance was evaluated using receiver operating characteristic (ROC) curves and confusion matrices. MR analysis was conducted to identify diagnostic genes with genetic associations. A protein-protein interaction (PPI) network was constructed to identify core genes. Finally, gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), and immune infiltration analysis were performed.ResultsDifferential expression analysis identified 244 DEGs, and WGCNA revealed a highly relevant module. Intersecting this module with the DEGs produced 136 candidate genes. Machine learning algorithms and MR analysis further refined the selection, identifying five diagnostic genes: GBP1, IFI6, KLHDC8B, OAS3, and ZCCHC2, all of which were shown to be well-aligned with their respective drugs. The PPI network highlighted GBP1, IFI6, and OAS3 as core genes, which showed significant correlations with immune cell infiltration.ConclusionsOur study identified GBP1, IFI6, and OAS3 as core genes implicated in SLE pathogenesis, providing novel insights into its molecular mechanisms and potential therapeutic targets.
Plant tissue development often relies on the specification of cell type initials with stem cell-like properties. These later undergo differentiation, losing division potential and acquiring specific identities and functions. In the stomatal lineage, protodermal cells develop into guard cells (GCs) through the action of the bHLH transcription factors (TFs) SPEECHLESS (SPCH), MUTE and FAMA. Existing models support that these regulators act sequentially, but recent evidence indicates that SPCH expression and function are retained in late stomatal cells. Here, we combine transcriptomic and genetic approaches to define the function of SPCH during the late stomatal lineage. We show that relative levels and activities of SPCH and FAMA control GC division and expansion. Through cell type-specific TF induction and mRNA sequencing, we identify late-lineage targets of both TFs, and through genetic perturbation of these targets we demonstrate that their precise temporal regulation is required for proper GC morphology and function. Our findings reveal a previously unrecognized role for SPCH in late stomatal development and support a revised model in which the functions of stomatal bHLH factors are not strictly separated in time.
BackgroundOsteoporosis (OP) and its associated complications have emerged as critical public health challenges worldwide, primarily due to the high rates of disability and mortality they cause. In terms of its complex pathogenesis, epigenetic mechanisms play significant roles. Against this backdrop, this study aims to clarify the current research trends and hotspots in OP.MethodsLiterature was retrieved from the "Web of Science," "PubMed," and "Scopus." Subsequently, publication counts, country distribution, regional collaborations, and keyword analyses were conducted by using the "Bibliometrix" and "ggplot2" packages in R Studio. For visualization analysis, institutional cooperation and keyword relationships were examined using "CiteSpace" and "VOSviewer."ResultsA total of 464 publications were included in this analysis. The five most frequently cited keywords were "postmenopausal osteoporosis (PMOP)," "expression," "mesenchymal stem-cells (MSCs)," "osteogenic differentiation," and "differentiation." Keyword co-occurrence analysis further identified "expression," "PMOP," and "MSCs" as predominant research themes. Moving forward, the findings suggest that future research will focus on elucidating the role of miRNAs in the epigenetic mechanisms of OP and identifying potential therapeutic targets. Regarding global collaboration, China led in international partnerships, particularly with the United States.ConclusionEpigenetic mechanisms constitute a core regulatory factor in OP, serving as the critical link between genetic predisposition and environmental influences. Emerging research emphasizes the combined analysis of epigenetics and metabolomics, artificial intelligence (AI)-based prediction of epigenetic regulatory networks, and gene editing therapies targeting epigenetic factors. Furthermore, therapeutic strategies-including gene therapy, stem cell-based interventions, and small-molecule targeted compounds-represent pivotal future directions for OP therapeutics.
The presomitic mesoderm is a transient embryonic tissue patterned along the anterior-posterior axis of vertebrates that periodically generates somites at its anterior end. Somitogenesis is driven by waves of gene expression that propagate from the posterior to the anterior end of the presomitic mesoderm under the control of the segmentation clock, a molecular oscillator. Using a mouse primary culture system, we performed a small-scale chemical screen targeting pathways implicated in cellular mechanics and we identified Rac1-dependent signaling as a modulator of segmentation clock dynamics. Pharmacological perturbation of Rac1 signaling reproducibly slowed oscillatory dynamics without disrupting intercellular synchrony. These changes were reversible and associated with increased somite length and reduced somite number. In addition, inhibition of Rac1 signaling was associated with changes in the expression of selected Wnt and Notch target genes in tail explants. These findings identify Rac1-dependent signaling as a candidate modulator of segmentation clock dynamics and somite morphogenesis, linking mechanical and molecular aspects of segmentation dynamics.
Regulatory networks that maintain cardiomyocyte identity are not completely understood. Here, we have examined the relationship of the transcription factors Nr2f1a and Isl1, which, respectively, repress and promote pacemaker cardiomyocyte (PC) differentiation within the venous pole of zebrafish atria. Using zebrafish nr2f1a;isl1 mutants, we found that loss of Isl1 exacerbates the inability to maintain the atrial cardiomyocyte (AC) identity found in nr2f1a mutant hearts. Subsequently, while nr2f1a;isl1 mutants have a failure of PC differentiation and their ACs are unable to transdifferentiate into PC identity, ACs in nr2f1a;isl1 mutant hearts lose myocardial marker expression, gain epicardial cell (EC) gene expression and exit the myocardial layer. Single-cell RNA-sequencing analysis of hearts supports the observation that the ACs and ECs of nr2f1a;isl1 mutant embryos share common myocardial and EC transcriptomic signatures. Depletion of tcf21 and tbx18 in nr2f1a;isl1 mutants was sufficient to prevent the acquisition of EC identity within putatively transdifferentiating ACs. Thus, our results reveal reiterative requirements for Nr2f and Isl1 transcription factors in binary fate decisions within the genetic hierarchy that maintains distinct AC, PC and EC identities at the venous pole of vertebrate hearts.
BackgroundWhether hypertension and dyslipidemia are risk factors for adhesive capsulitis (AC) remains controversial. Many observational studies have reported conflicting results. However, observational studies are susceptible to confounding and reverse causation, limiting the ability to establish causality. Therefore, a robust method is needed to clarify these relationships. MethodsWe first conducted a hospital-based case-control study that included 200 AC patients and 200 controls. Multivariate logistic regression was used to examine the associations of hypertension and dyslipidemia with AC after adjusting for potential confounders. To address the inherent limitations of observational studies, we then performed a two-sample Mendelian randomization (MR) analysis. We obtained datasets related to essential hypertension, dyslipidemia, and AC from a public genome-wide association study (GWAS) database. Inverse variance weighted (IVW) served as the primary analysis method. Sensitivity analyses included MR-PRESSO to detect outliers and pleiotropy and Cochran's Q test (combined with MR-Egger and IVW) to assess heterogeneity. The robustness of the findings was evaluated using a leave-one-out analysis. Finally, a bidirectional MR analysis was conducted by swapping the exposures and outcomes to test for reverse causality. ResultsIn the clinical case-control study, multivariate logistic regression revealed that age (OR: per year: 1.061, 95% CI: 1.034-1.089, p < 0.001) and diabetes (OR: 2.153, 95% CI: 1.271-3.646, p = 0.004) were independently associated with AC, whereas neither hypertension (OR: 1.406, 95% CI: 0.870-2.274, p = 0.164) nor dyslipidemia (OR: 1.760, 95% CI: 0.912-3.395, p = 0.092) showed a significant association with AC. Consistent with the observational findings, MR analysis detected no causal effect of hypertension or dyslipidemia on AC. However, reverse MR analysis identified a significant negative causal effect of AC on high-density lipoprotein (HDL) cholesterol (OR: 0.989, 95% CI: 0.982-0.997, p = 0.008) and a positive causal effect of AC on the apolipoprotein B/A1 ratio (OR: 1.018, 95% CI: 1.001-1.034, p = 0.033). ConclusionOur MR analysis revealed a negative causal effect from AC to HDL cholesterol and a positive causal effect from AC to the apolipoprotein B/A1 ratio. These findings provide evidence for the temporal sequence and reverse causal relationship between AC and dyslipidemia. The convergent results from both clinical and genetic analyses support the robustness of this causal relationship and highlight AC as a potential driver of lipid abnormalities. Therefore, these findings underscore the need for further experimental and mechanistic studies to elucidate the underlying biological mechanisms.
OBJECTIVE:This study aims to examine the frequency and distribution of incidental chromosomal abnormalities identified through peripheral blood karyotype analysis and to evaluate their associations with sex, age, and chromosomal characteristics. METHODS:This retrospective study conducted an analysis of 2397 peripheral blood karyotype assessments carried out between September 2023 and February 2025. The study employed conventional lymphocyte culture and G-banding techniques, with karyotypes characterized in accordance with the International System for Human Cytogenomic Nomenclature (ISCN) 2024 guidelines. Chromosomal abnormalities that did not satisfy clinical reporting criteria were systematically documented. Detection rates were evaluated and compared across different sex and age groups, as well as chromosomal categories, utilizing chi-square tests and linear trend analysis. RESULTS:A total of 511 cases of incidental chromosomal abnormalities were identified, yielding an overall detection rate of 21.32%. No statistically significant difference was observed in the detection rates of abnormalities between females and males (p > 0.05). However, significant differences were noted among various age groups, with detection rates exhibiting an increasing trend with advancing age (p < 0.05). The distribution of abnormalities was uneven across chromosomes, predominantly concentrated in the C and D chromosome groups. Chromosomes 7, 9, and 14 were the most frequently affected. The most prevalent types of abnormalities included balanced translocations, deletions, and inversions, with t(7; 14) and del(9) (q13) being the most commonly observed. Additionally, 23 marker chromosomes were identified, displaying considerable morphological variability. CONCLUSION:Incidental chromosomal abnormalities identified through peripheral blood karyotype analysis exhibit nonrandom distributions associated with variables such as age and specific chromosomes. These low-frequency occurrences may represent underlying somatic chromosomal variation and offer valuable reference data for the interpretation of karyotypes and the enhancement of laboratory quality control.
Embryonic livers undergo extensive vascular expansion after midgestation to support rapid growth and evolving functions. Immature embryonic vessels receive structural support from extracellular matrix (ECM), which is also essential for normal liver development and function. Meanwhile, pro-inflammatory cytokines that promote hematopoiesis and hepatic organogenesis must be tightly regulated to prevent sterile inflammation. However, endothelial contributions to ECM and cytokine production during liver development remain poorly understood. Here, we demonstrate that the chromatin remodelers CHD4 and BRG1 act antagonistically in embryonic endothelial cells to protect developing livers from lethal degeneration. Transcriptomic analysis of endothelial Chd4 mutant livers revealed increased activity of plasmin (an ECM protease) and sterile inflammation before the onset of overt phenotypes. Within these pathways, we found that endothelial CHD4 and BRG1 antagonistically regulate transcription of the plasmin activator uPAR and of the inflammatory adhesion molecule ICAM1 in developing livers. Our genetic and pharmacological data demonstrate that elevated plasmin activity and sterile inflammation synergistically contribute to hepatic degeneration. These findings highlight endothelial transcriptional control of plasmin activity and sterile inflammation and reveal their detrimental synergy during liver development.
Mitophagy is essential for cancer formation and invasion, but its role in colorectal cancer (CRC) remains unclear. We obtained sequencing data and mitophagy-related genes (MP-RGs) from public databases. Differential expression analysis and weighted gene coexpression network analysis (WGCNA) identified mitophagy-related differentially expressed genes (DE-MPGs). Mendelian randomization (MR) analysis identified candidate genes with genetically supported causal relevance to CRC. Biomarkers were identified using machine learning, receiver operating characteristic (ROC) analysis and expression studies. Single-cell RNA sequencing (scRNA-seq) analyzed biomarker expression profiles in various CRC cell types. Quantitative PCR (qPCR) validated biomarker expression in clinical CRC samples. 147 DE-MPGs were identified. MR analysis revealed seven genes with potential causal contributions to CRC susceptibility. Three genes, SGCE (IVW: OR = 1.00041, p=0.011), ATP8B2 (IVW: OR = 0.99920, p=0.042), and RANGAP1 (IVW: OR = 0.99861, p=0.002), were selected as biomarkers. Immune microenvironment and checkpoint differences were observed between CRC and controls. Biomarker expression varied among cell types. qPCR showed decreased SGCE and ATP8B2 and increased RANGAP1 in CRC. SGCE, ATP8B2, and RANGAP1 can serve as mitophagy-related biomarkers with genetically supported causal relevance to CRC, providing new insights for CRC diagnosis and therapy.
High-grade serous ovarian cancer (HGSOC) exhibits homologous recombination deficiency (HRD), but its impact on the immune microenvironment remains unclear. Using single-cell RNA sequencing, spatial transcriptomic inference, and survival analyses, we characterized 166,895 macrophages across HRD subtypes: functional BRCA1/2 inactivation (FBI), HRD-Del (deletions), and HRD-Dup (duplications). FBI macrophages showed lipid metabolism enrichment (S100A8, CD36), HRD-Del macrophages upregulated antigen presentation (HLA-DQA1, HLA-DPB1), and HRD-Dup macrophages displayed interferon-stimulated gene expression (ISG15, MX1). Six macrophage subtypes (C1Q, FCN1, MARCO, MKI67, MMP9, S100A9) exhibited distinct spatial distributions and functions. MKI67+ macrophages correlated with improved survival, while C1Q + subsets predicted worse outcomes. HRD-Dup tumors with high macrophage signatures had better survival, suggesting a favorable immune landscape. Our findings reveal HRD-driven macrophage reprogramming as a key determinant of immune microenvironment composition and clinical outcomes, supporting HRD-specific macrophage-targeted therapies for HGSOC.
Intracytoplasmic sperm injection (ICSI) is widely used to treat human infertility, yet its effects on offspring fertility remain unclear. As infertile gametes are used in human ICSI procedures, it has remained unclear whether the procedure per se influences fertility of the resulting offspring. Here, we report on increased abortion rates and the induction of immunotolerance breakdown in mice following ICSI. Although sperm concentration was normal, sperm from ICSI-derived males showed higher curvilinear velocity and greater amplitude of lateral head displacement, suggesting a potentially increased fertilization capacity. However, when ICSI-produced males were naturally mated with wild-type females, 27.1% of the fetuses were aborted, compared to a loss of 7.5% of fetuses in control pregnancies, despite identical H2 haplotypes. Analysis of the placenta revealed infiltrating macrophages and granulocytes, as well as increased levels of 8-oxoguanine. This was accompanied by activation of innate immunity and significant downregulation of microRNAs located in the Dlk1-Dio3 microRNA cluster. Several organs of the grand-offspring exhibited inflammation. Therefore, ICSI procedure using wild-type gametes impairs the fertility of ICSI-derived male offspring by activating innate immunity during pregnancy.
Arterial-venous specification of endothelial cells during vascular development requires coordination between intracellular signaling, cell cycle state and transcription factor activity. However, the intrinsic regulatory mechanisms that govern these processes are poorly understood. To investigate this, we assessed endothelial chromatin accessibility during vascular development. Murine postnatal day (P) 6 and P15 retinal endothelial cells were analyzed by single cell assay for transposase accessible chromatin sequencing, revealing heterogeneous chromatin accessibility across an arterial-venous continuum and in distinct cell cycle states. Enhancer regulatory network analysis predicted transcription factors with differential cell cycle and arterial-venous activity, and many with dual activator and repressor functions, including SOX17. We then validated SOX17 function in human endothelial cells, identifying that it inhibits proliferation and promotes arterial gene expression. Our findings suggest that dual roles of key endothelial transcription factors are regulated by chromatin accessibility in a cell cycle- and subtype-specific manner to control arterial-venous specification.
