Hereditas最新文献

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Insight into the shared pathogenic link between COVID-19 and pterygium: a systematic bioinformatics analysis with experimental validation. 洞察COVID-19与翼状胬肉之间的共同致病联系:具有实验验证的系统生物信息学分析。
IF 2.7 3区 生物学
Hereditas Pub Date : 2025-07-14 DOI: 10.1186/s41065-025-00500-w
Tianyi Zhou, Xueyao Cai, Wenjun Shi, Xia Ding, Yuchen Cai
{"title":"Insight into the shared pathogenic link between COVID-19 and pterygium: a systematic bioinformatics analysis with experimental validation.","authors":"Tianyi Zhou, Xueyao Cai, Wenjun Shi, Xia Ding, Yuchen Cai","doi":"10.1186/s41065-025-00500-w","DOIUrl":"10.1186/s41065-025-00500-w","url":null,"abstract":"<p><p>The outbreak of coronavirus disease 2019 (COVID-19) has resulted in a remarkable threat to global public health over the past few years. Despite the tremendous studies of COVID-19 ongoing, few have focused on the viral impact on the ocular surface. As one of the most common inflammatory diseases of the ocular surface, pterygium could be triggered under multiple environmental exposures. In the present work, we aimed at investigating the potential interactions between pterygium and COVID-19. Based on bioinformatic tools, we compared databases of COVID-19 and pterygium and screened for common differentially expressed genes (DEGs). Multifactor regulatory network and co-expression network of the common DEGs were analyzed. In vitro experiments, including siRNA knockdown using human conjunctival fibroblasts (HConFs) confirmed the bioinformatics results. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis implied that immune response was associated with COVID-19-induced ocular events. We then identified five common DEGs, including ERP27, SYTL5, STXBP6, EXTL1 and DIO2, which was further validated by in vitro experiments. Three hub genes were further extracted which included SYTL5, STXBP6 and ERP27 through protein-protein interactions (PPI) network. Furthermore, we illustrated a regulatory network consisting of eight transcription factors (STAT6B, GATA1, POU2F2, PGR, RBPJ, STAT3, CRTC1 and HMGA1) and one microRNA (hsa-miR-384). Overall, we investigated the common link between SARS-CoV-2 and pterygium in the modulation of gene profiles on the ocular surface. Our study proposed a novel insight into the common pathogenic mechanisms between COVID-19 and pterygium, which are associated with immune dysregulation and pathological proliferation, indicating a viral impact on pterygium susceptibility. This innovative perspective may enable a more comprehensive understanding and advance towards improved clinical prevention and treatment.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"162 1","pages":"128"},"PeriodicalIF":2.7,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12261744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144636893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reduced miR-338-3p contributes to polycystic ovarian syndrome by inhibiting proliferation and enhancing apoptosis. miR-338-3p降低通过抑制增殖和增强细胞凋亡参与多囊卵巢综合征。
IF 2.7 3区 生物学
Hereditas Pub Date : 2025-07-12 DOI: 10.1186/s41065-025-00498-1
Lin Liang, Jie Lv, Wei Li, Chengwen Song, Ying Chen, Huafang Wei
{"title":"Reduced miR-338-3p contributes to polycystic ovarian syndrome by inhibiting proliferation and enhancing apoptosis.","authors":"Lin Liang, Jie Lv, Wei Li, Chengwen Song, Ying Chen, Huafang Wei","doi":"10.1186/s41065-025-00498-1","DOIUrl":"10.1186/s41065-025-00498-1","url":null,"abstract":"<p><strong>Background: </strong>Polycystic ovarian syndrome (PCOS) is a frequently occurring disorder affecting reproductive and metabolic health. miR-338-3p is implicated in early follicular development. We aimed to investigate the expression of miR-338-3p in PCOS patients and its effects on proliferation and apoptosis of ovarian granulosa cells.</p><p><strong>Methods: </strong>The study included 100 healthy women and 110 women diagnosed with PCOS as participants. Reverse transcription quantitative PCR (RT-qPCR) was used to detect the expression of miR-338-3p and phosphatase and tensin homolog (PTEN), and receiver operating characteristic (ROC) was employed to evaluate the diagnostic efficacy of miR-338-3p. Cell proliferation and apoptosis were detected by Cell Counting Kit-8 (CCK-8) and flow cytometry. Pearson correlation analysis was used to assess the correlations between miR-338-3p and luteinizing hormone (LH), testosterone, or PTEN. The target relationship of miR-338-3p and PTEN was confirmed via dual-luciferase assay.</p><p><strong>Results: </strong>Serum miR-338-3p was decreased in PCOS patients, and it was negatively correlated with both LH and testosterone. Downregulation of miR-338-3p inhibits the proliferation of ovarian granulosa cells and enhances cell apoptosis, whereas upregulation produces the opposite effect. PTEN inhibition subverted the inhibited proliferation and enhanced apoptosis regulated by miR-338-3p inhibitor.</p><p><strong>Conclusions: </strong>Reduced miR-338-3p levels have potential predictive value in distinguishing individuals with PCOS patients from normal population. Mechanistically, this microRNA regulates the PTEN gene to inhibit granulosa cell proliferation and promote apoptosis, thereby contributing to the pathological processes of PCOS.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"162 1","pages":"126"},"PeriodicalIF":2.7,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12254983/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144617150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Prognostic value of LncRNA PSMA3-AS1 in prostate cancer and its potential regulatory mechanism. LncRNA PSMA3-AS1在前列腺癌中的预后价值及其潜在调控机制
IF 2.7 3区 生物学
Hereditas Pub Date : 2025-07-12 DOI: 10.1186/s41065-025-00485-6
Muyang Cao, Jin Li, Jianbin Zhang, Wenlong Lu
{"title":"Prognostic value of LncRNA PSMA3-AS1 in prostate cancer and its potential regulatory mechanism.","authors":"Muyang Cao, Jin Li, Jianbin Zhang, Wenlong Lu","doi":"10.1186/s41065-025-00485-6","DOIUrl":"10.1186/s41065-025-00485-6","url":null,"abstract":"<p><strong>Objective: </strong>Prostate adenocarcinoma (PRAD) is asymptomatic in the early stages and most patients are diagnosed at an advanced stage, which leads to a poor prognosis. Therefore, an effective prognostic marker is required to improve PRAD prognosis.</p><p><strong>Methods: </strong>A total of 128 patients with PRAD were included in the study. PSMA3-AS1 and miR-29a-3p expression in tissues was detected using RT-qPCR. CCK-8 and Transwell assays were then used to evaluate the proliferative, migratory, and invasive capacities of prostate cancer cell lines. A DLR assay confirmed the binding relationship between PSMA3-AS1 and miR-29a-3p. The five-year prognosis of PRAD patients was analyzed using a Kaplan-Meier plotter curve.</p><p><strong>Results: </strong>PSMA3-AS1 was highly expressed in PRAD tissues, and patients with high expression had poor 5-year survival. In contrast, miR-29a-3p was poorly expressed in PRAD tissues. PSMA3-AS1 bound to miR-29a-3p in a targeted manner and the levels showed a negative correlation. Knocking down PSMA3-AS1 could increase the level of miR-29a-3p and slow the proliferation of PRAD cell lines, as well as inhibiting their migration and invasion ability.</p><p><strong>Conclusion: </strong>A high level of PSMA3-AS1 was strongly linked to a poor prognosis for patients and is expected to serve as a prognostic marker for PRAD. Furthermore, PSMA3-AS1 knockdown increased the level of miR-29a-3p and reduced the physiological activity of cancer cells. Therefore, regulating the expression of the PSMA3-AS1/miR-29a-3p axis could influence PRAD development.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"162 1","pages":"127"},"PeriodicalIF":2.7,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12255973/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144617149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
In silico and in vitro assessment of TP53, ATM, RAD51, and BAX genes in gastric cancer and their contribution to radiotherapy resistance. 胃癌组织中TP53、ATM、RAD51、BAX基因的体内和体外研究及其对放疗耐药的影响
IF 2.7 3区 生物学
Hereditas Pub Date : 2025-07-12 DOI: 10.1186/s41065-025-00496-3
Junwei Zhang, Pengtao He
{"title":"In silico and in vitro assessment of TP53, ATM, RAD51, and BAX genes in gastric cancer and their contribution to radiotherapy resistance.","authors":"Junwei Zhang, Pengtao He","doi":"10.1186/s41065-025-00496-3","DOIUrl":"10.1186/s41065-025-00496-3","url":null,"abstract":"<p><strong>Background: </strong>Gastric cancer remains a leading cause of cancer-related morbidity and mortality worldwide. The genetic factors contributing to gastric cancer progression and resistance to therapies, particularly radiotherapy, are not fully understood. TP53, ATM, RAD51, and BAX are genes involved in DNA repair, apoptosis, and response to stress. The aim of this study was to investigate the expression patterns of these genes in gastric cancer, their potential role in radiotherapy resistance, and their diagnostic value.</p><p><strong>Methodology: </strong>Gene expression levels of TP53, ATM, RAD51, and BAX were assessed using RT-qPCR across 9 gastric cancer cell lines and 6 normal control cell lines. Additionally, protein expression was confirmed via IHC and TCGA dataset analysis. Methylation levels of these genes were evaluated in gastric cancer tissues using the GSCA database. Mutational analysis was conducted using cBioPortal, and survival analysis was performed using Kaplan-Meier and meta-analysis. The radiotherapy resistance study was carried out by knocking down TP53, RAD51, and BAX in AGS and MKN-45 gastric cancer cell lines, followed by expression analysis, colony formation, and wound healing assays.</p><p><strong>Results: </strong>The expression of TP53, RAD51, and BAX was significantly upregulated, while ATM was downregulated in gastric cancer cell lines compared to normal controls. All four genes demonstrated good discriminatory power (AUC = 1) in distinguishing gastric cancer from normal samples. Methylation analysis revealed significant hypomethylation of TP53, RAD51, and BAX, and hypermethylation of ATM in gastric cancer tissues. Mutational analysis showed that TP53 was altered in 88% of gastric cancer samples, while ATM, RAD51, and BAX exhibited lower mutation rates. Survival analysis suggested that elevated expression of TP53, RAD51, and BAX may be linked to poorer survival outcomes, while reduced ATM expression appeared to associate with decreased overall survival. However, these associations require further validation through additional studies. Knockdown of TP53, RAD51, and BAX in AGS and MKN-45 cells resulted in significantly reduced cell proliferation and slower wound healing, highlighting their role in radiotherapy resistance.</p><p><strong>Conclusion: </strong>The TP53, RAD51, and BAX genes are significantly involved in gastric cancer progression and resistance to radiotherapy. Their expression and mutation status provide valuable diagnostic and prognostic information.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"162 1","pages":"125"},"PeriodicalIF":2.7,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12255106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144617148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
LncRNA SDCBP2-AS1 is a putative biomarker for postmenopausal osteoporosis and promotes osteogenic differentiation of BMSCs by regulating miR-361-3p. LncRNA SDCBP2-AS1被认为是绝经后骨质疏松症的生物标志物,并通过调节miR-361-3p促进BMSCs的成骨分化。
IF 2.7 3区 生物学
Hereditas Pub Date : 2025-07-10 DOI: 10.1186/s41065-025-00494-5
Jindong Chen, Shilong Zhang, Dixin Cai, Qing Yin, Qian Xie, Pengfang Xu, Junling Zhu
{"title":"LncRNA SDCBP2-AS1 is a putative biomarker for postmenopausal osteoporosis and promotes osteogenic differentiation of BMSCs by regulating miR-361-3p.","authors":"Jindong Chen, Shilong Zhang, Dixin Cai, Qing Yin, Qian Xie, Pengfang Xu, Junling Zhu","doi":"10.1186/s41065-025-00494-5","DOIUrl":"10.1186/s41065-025-00494-5","url":null,"abstract":"<p><strong>Background: </strong>Numerous long noncoding RNAs (lncRNAs) have been proven to participate in osteogenesis and postmenopausal osteoporosis (PMOP). We measured serum SDCBP2-AS1 expression changes in patients with PMOP and investigated its effects on osteoblast differentiation in human bone marrow-derived mesenchymal stem cells (hBMSC) cells.</p><p><strong>Methods: </strong>RT-qPCR was used to measure SDCBP2-AS1 levels and the expression of osteogenic differentiation indicators. The diagnostic efficacy of SDCBP2-AS1 was assessed using a receiver operating characteristic (ROC) analysis. CCK-8 and flow cytometry methods were employed to investigate the functional impact of SDCBP2-AS1 on hBMSC cell proliferation and apoptosis during osteoblast differentiation. The bioinformatics, dual-luciferase reporter assay, and RNA Immunoprecipitation (RIP) assay were used to identify and confirm SDCBP2-AS1/miR-361-3p interaction.</p><p><strong>Results: </strong>Serum SDCBP2-AS1 was decreased in patients with PMOP, especially in those with fractures. The SDCBP2-AS1 levels were positively correlated with patients' T scores and BMDs. Decreased SDCBP2-AS1 had a certain high area under the ROC curve (AUC) value (AUC = 0.81) in distinguishing PMOP patients with fractures from those without fractures. SDCBP2-AS1 levels gradually increased after four weeks of treatment in PMOP patients and hBMSCs during cell differentiation. Enhanced SDCBP2-AS1 promoted cell proliferation and the levels of osteoblast differentiation markers, including ALP, OCN, RUNX2, and Collagen I, while decreasing cell apoptosis. miR-361-3p was a direct target of SDCBP2-AS1. The influence of SDCBP2-AS1 on cell activities and hBMSCs differentiation was diminished by miR-361-3p.</p><p><strong>Conclusions: </strong>SDCBP2-AS1 might be a diagnostic biomarker in predicting PMOP patients with fractures. By measuring the levels of SDCBP2-AS1 in patient samples, clinicians may be able to identify those who are more susceptible to bone fractures, enabling earlier and more targeted preventive measures. SDCBP2-AS1 targeting miR-361-3p regulates the osteogenic differentiation of hBMSCs, which might be a new target for the treatment of PMOP.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"162 1","pages":"124"},"PeriodicalIF":2.7,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12247319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144608173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
METTL3 mediates m6A methylation modification of ULBP2 and affects the progression of cervical cancer. METTL3介导ULBP2的m6A甲基化修饰,影响宫颈癌的进展。
IF 2.7 3区 生物学
Hereditas Pub Date : 2025-07-10 DOI: 10.1186/s41065-025-00483-8
Hongtao Ren, Yuting Wang, Jiao Yu, Lei An, Xiulong Ma, Jiyuan Pan
{"title":"METTL3 mediates m6A methylation modification of ULBP2 and affects the progression of cervical cancer.","authors":"Hongtao Ren, Yuting Wang, Jiao Yu, Lei An, Xiulong Ma, Jiyuan Pan","doi":"10.1186/s41065-025-00483-8","DOIUrl":"10.1186/s41065-025-00483-8","url":null,"abstract":"<p><strong>Background: </strong>Cervical cancer (CC) is one of the most prevalent malignancies in women, posing a significant challenge globally. However, the precise molecular mechanism regulating CC progression through methyltransferase-like protein 3 (METTL3) and UL16 Binding Protein 2 (ULBP2) remains largely unknown.</p><p><strong>Methods: </strong>Bioinformatic analysis was used to identify the effect of ULBP2 expression in CC tissues. RT-qPCR and western blotting were employed to assess the mRNA and protein expression in CC cells and tissues. Methylthiazolyldiphenyl-tetrazolium bromide (MTT), 5‑Ethynyl‑2'‑deoxyuridine (EdU), wound healing, and transwell assays were utilized to estimate cell viability, proliferation, and metastasis, respectively. Cell apoptosis was detected by flow cytometry. CC cells were treated with different doses of radiotherapy. The m6A level was measured using methylated RNA immunoprecipitation (MeRIP) assay. A xenograft assay was conducted to further verify the roles of ULBP2 in CC.</p><p><strong>Results: </strong>ULBP2 was upregulated in CC. Downregulation of ULBP2 restrained the proliferation, metastasis and radiotherapy resistance of CC cells. METTL3 regulated m6A methylation modification of ULBP2. Insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) promoted m6A methylation modification of ULBP2. METTL3 influenced the expression of ULBP2 and impacted the biological function of the CC cells. Silencing ULBP2 reduced the radioresistance of CC in vivo. Radiotherapy altered the gut microbiota in CC patients.</p><p><strong>Conclusion: </strong>METTL3 modulated the m6A methylation of ULBP2, affecting the oncogenic properties and radioresistance of CC cells.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"162 1","pages":"123"},"PeriodicalIF":2.7,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12243326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144608174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Translocations associated with colour-sidedness are common in northern Swedish cattle breeds. 与偏色性相关的易位在瑞典北部的牛品种中很常见。
IF 2.7 3区 生物学
Hereditas Pub Date : 2025-07-07 DOI: 10.1186/s41065-025-00481-w
Julia Hinken, Tytti Vanhala, Marta Gòdia, Martin Johnsson, Anna M Johansson
{"title":"Translocations associated with colour-sidedness are common in northern Swedish cattle breeds.","authors":"Julia Hinken, Tytti Vanhala, Marta Gòdia, Martin Johnsson, Anna M Johansson","doi":"10.1186/s41065-025-00481-w","DOIUrl":"10.1186/s41065-025-00481-w","url":null,"abstract":"<p><p>The Swedish Mountain cattle and four other native Swedish cattle breeds show the phenotype of colour-sidedness. The causes of this phenotype are either a translocation and duplication from chromosome 6 to chromosome 29 (known as Cs<sub>29</sub>) including the KIT gene, or an additional translocation allele where part of Cs<sub>29</sub> has been translocated back to chromosome 6 (Cs<sub>6</sub>). Besides the colour-sidedness, the Cs<sub>29</sub> translocation has been associated with gonadal hypoplasia which can cause fertility problems. Despite breeding efforts during more than 80 years to reduce the prevalence of gonadal hypoplasia, there are still individuals with gonadal hypoplasia. We genotyped the Cs<sub>29</sub> and Cs<sub>6</sub> alleles in Swedish Mountain cattle and five other Swedish native breeds. Whole-genome sequence data of 30 cattle were analysed for the translocations, and 115 DNA samples were analysed using multiplex PCR. The current allele frequency of the Cs<sub>29</sub> allele in Swedish mountain cattle was estimated to be 44%. The results indicate that the Cs<sub>29</sub> translocation is also present in the four other native Swedish cattle breeds with colour-sidedness, and the Cs<sub>6</sub> translocation in at least three of them.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"162 1","pages":"122"},"PeriodicalIF":2.7,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235870/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144583759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
WMRCA + : a weighted majority rule-based clustering method for cancer subtype prediction using metabolic gene sets. WMRCA +:基于加权多数规则的聚类方法,用于使用代谢基因集预测癌症亚型。
IF 2.7 3区 生物学
Hereditas Pub Date : 2025-07-07 DOI: 10.1186/s41065-025-00487-4
Guojun Liu, Zhaopo Zhu, Yongqiang Xing, Hu Meng, Khyber Shinwari, Ningkun Xiao, Guoqing Liu
{"title":"WMRCA + : a weighted majority rule-based clustering method for cancer subtype prediction using metabolic gene sets.","authors":"Guojun Liu, Zhaopo Zhu, Yongqiang Xing, Hu Meng, Khyber Shinwari, Ningkun Xiao, Guoqing Liu","doi":"10.1186/s41065-025-00487-4","DOIUrl":"10.1186/s41065-025-00487-4","url":null,"abstract":"<p><p>Accurate classification of cancer subtypes plays a pivotal role in advancing precision medicine. In this study, we introduce WMRCA + , a novel clustering approach based on a weighted majority rule that integrates multi-omics data and incorporates metabolic gene sets to robustly determine the optimal number of clusters for tumor subtype identification. WMRCA + evaluates clustering performance using ten internal metrics and offers comprehensive functionalities for data preprocessing and visualization. When applied to The Cancer Genome Atlas (TCGA) lung cancer dataset using lipid metabolism-related gene sets, WMRCA + outperformed widely used clustering algorithms-including iCluster, SNF, NMF, CC, and CNMF-achieving an AUC of 0.947. WMRCA + provides robust, interpretable, and biologically meaningful clustering results, offering a valuable tool for improving the accuracy of cancer subtype prediction. The WMRCA + R package is freely available at https://github.com/guojunliu7/WMRCA .</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"162 1","pages":"121"},"PeriodicalIF":2.7,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144583760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of components in scorpion and centipede traditional Chinese medicine formulations with potentially beneficial actions in asthma: network pharmacology and molecular docking. 对哮喘有潜在有益作用的蝎子和蜈蚣中药制剂成分的鉴定:网络药理学和分子对接。
IF 2.7 3区 生物学
Hereditas Pub Date : 2025-07-02 DOI: 10.1186/s41065-025-00490-9
Yi-Ren Chen, Ya-Da Zhang, Wei Zhang, Bin-Qing Tang
{"title":"Identification of components in scorpion and centipede traditional Chinese medicine formulations with potentially beneficial actions in asthma: network pharmacology and molecular docking.","authors":"Yi-Ren Chen, Ya-Da Zhang, Wei Zhang, Bin-Qing Tang","doi":"10.1186/s41065-025-00490-9","DOIUrl":"10.1186/s41065-025-00490-9","url":null,"abstract":"<p><strong>Background: </strong>The aim of this study is to identify the principal active components of scorpion and centipede-derived traditional Chinese medicine (TCM) ingredients using network pharmacology and explore their mechanisms of action in the treatment of asthma.</p><p><strong>Methods: </strong>The chemical constituents and target information pertaining to scorpion and centipede-derived TCM components were obtained from the Traditional Chinese Medicine System Pharmacology (TCMSP) database and an herbal database. Asthma-related target genes were retrieved from the GeneCards and the Online Mendelian Inheritance in Man (OMIM) databases. The \"component-target\" network was constructed with the identified target genes using \"Cytoscape 3.9.2\" software, and the protein-protein interaction (PPI) network was generated in conjunction with the String database to further identify the core targets. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and gene ontology (GO) functional enrichment analysis were carried out on the targets associated with scorpion and centipede-derived TCM components. Molecular docking was subsequently performed using Autodock Vina software to validate the results. Asthma mouse model was established, and mouse lung tissues were collected for histopathological examination. The levels of TP53, HSP90AA1, and IL-17 mRNA in the mouse lung tissues were evaluated.</p><p><strong>Results: </strong>A total of 11 active components met the screening conditions, including 4 centipede-derived components and 7 scorpion-derived components. The key components identified included histamine, L-histidine, stearin, cholesteryl ferulate, and cholesterol, among others. Targets with degree values ≥ 16 included TP53, HSP90AA1, HSP90AB1, steroid receptor coactivator (SRC), epidermal growth factor receptor (EGFR), estrogen receptor 1 (ESR1), mitogen-activated protein kinase 1 (MAPK1), mitogen-activated protein kinase 3 (MAPK3), and histone deacetylase 1 (HDAC1). The pathways involved comprised calcium signaling, estrogen signaling, arachidonic acid metabolism, inflammatory mediator and transient receptor potential (TRP) signaling, vascular smooth muscle contraction, thyroid hormone signaling, sphingolipid signaling, IL-17 signaling, insulin resistance, and human cytomegalovirus infection pathways. Furthermore, the mouse experiments showed that SC improved inflammatory cell infiltration and mucus secretion in mouse lung tissues and significantly suppressed the expression of TP53, HSP90AA1, and IL-17 mRNA (all p < 0.05).</p><p><strong>Conclusion: </strong>Scorpion and centipede-derived active components may exert therapeutic effects in asthma treatment through potential targets such as TP53, HSP90AA1, HSP90AB1, SRC, EGFR, ESR1, MAPK1, MAPK3, and HDAC1.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"162 1","pages":"120"},"PeriodicalIF":2.7,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12217821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
TIMP1 promotes microglia M2 polarization through MAPK pathway to ameliorate early brain injury after ischemia. TIMP1通过MAPK通路促进小胶质细胞M2极化,改善缺血后早期脑损伤。
IF 2.7 3区 生物学
Hereditas Pub Date : 2025-07-02 DOI: 10.1186/s41065-025-00491-8
Kangkang Zhao, Zizhao Huang
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