BMC Medical Genomics最新文献

{"title":"Dynamic clustering of genomics cohorts beyond race, ethnicity-and ancestry.","authors":"Hussein Mohsen, Kim Blenman, Prashant S Emani, Quaid Morris, Jian Carrot-Zhang, Lajos Pusztai","doi":"10.1186/s12920-025-02154-z","DOIUrl":"10.1186/s12920-025-02154-z","url":null,"abstract":"<p><strong>Background: </strong>Recent decades have witnessed a steady decrease in the use of race categories in genomic studies. While studies that still include race categories vary in goal and type, these categories already build on a history during which racial color lines have been enforced and adjusted in the service of social and political systems of power and disenfranchisement. For early modern classification systems, data collection was also considerably arbitrary and limited. Fixed, discrete classifications have limited the study of human genomic variation and disrupted widely spread genetic and phenotypic continuums across geographic scales. Relatedly, the use of broad and predefined classification schemes-e.g. continent-based-across traits can risk missing important trait-specific genomic signals.</p><p><strong>Methods: </strong>To address these issues, we introduce a dynamic approach to clustering human genomics cohorts based on genomic variation in trait-specific loci and without using a set of predefined categories. We tested the approach on whole-exome sequencing datasets in ten cancer types and partitioned them based on germline variants in cancer-relevant genes that could confer cancer type-specific disease predisposition.</p><p><strong>Results: </strong>Results demonstrate clustering patterns that transcend discrete continent-based categories across cancer types. Functional analysis based on cancer type-specific clusterings also captures the fundamental biological processes underlying cancer, differentiates between dynamic clusters on a functional level, and identifies novel potential drivers overlooked by a predefined continent-based clustering.</p><p><strong>Conclusions: </strong>Through a trait-based lens, the dynamic clustering approach reveals genomic patterns that transcend predefined classification categories. We propose that coupled with diverse data collection, new clustering approaches have the potential to draw a more complete portrait of genomic variation and to address, in parallel, technical and social aspects of its study.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"87"},"PeriodicalIF":2.1,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exome sequencing revealed a novel homozygous variant in TRMT61 A in a multiplex family with atypical Cornelia de Lange Syndrome from Rwanda.","authors":"Esther Uwibambe, Abdoulaye Yalcouyé, Elvis Twumasi Aboagye, Lettilia Xhakaza, Kalinka Popel, Norbert Dukuze, Thashi Bharadwaj, Carmen de Kock, Isabelle Schrauwen, Suzanne M Leal, Leon Mutesa, Ambroise Wonkam","doi":"10.1186/s12920-025-02153-0","DOIUrl":"10.1186/s12920-025-02153-0","url":null,"abstract":"<p><strong>Background: </strong>In 30% of patients who exhibit the clinical profile of Cornelia de Lange Syndrome (CdLS), the genetic cause remains undetermined. This proportion tends to be higher in low-resource settings including Africa. We performed a molecular characterization of CdLS in a multiplex Rwandan family.</p><p><strong>Methods: </strong>After a clinical evaluation of two affected siblings, DNA isolated from peripheral whole blood of the affected patients and their parents underwent Exome Sequencing (ES). Sanger sequencing validated the variant segregating with CdLS. In silico predictive tools, protein modelling, and cell-based experiments using HEK293T cells were used to investigate the pathogenicity of the variant found.</p><p><strong>Results: </strong>We identified a family with two parents and their two offspring (male and female), who were referred for hearing impairment. The 17-year-old female presented bilateral profound hearing impairment with moderate hypertelorism, progressive visual impairment, and secondary amenorrhea. The 14-year-old male displayed intellectual disability and a bilateral profound hearing impairment with no noticeable facial dysmorphism. Following exome sequencing (ES) of DNA samples obtained from the four family members, we found that the siblings harbored a novel likely pathogenic homozygous missense variant in the TRMT61 A gene [NM_152307.3:c.665C > T p.(Ala222Val)] inherited from both heterozygous parents. In silico analysis suggested that the variant substitutes a highly conserved amino acid, and 2-D structure modelling revealed a significant decrease in the stability of the protein. Cell-based experiment in HEK293T showed that the variant significantly affected the TRMT61 A protein localization which is thought to impact the mitochondrial and cytosolic functions.</p><p><strong>Conclusion: </strong>We reported a novel biallelic variant in TRMT61 A, [NM_152307.3:c.665C > T p.(Ala222Val)], which is associated with autosomal recessive atypical CdLS in a multiplex Rwandan family, the first report from Africa, and the second globally. The study emphasizes the need to expand the availability of ES for molecular characterization of rare diseases for the understudied genetically diverse population of Africa.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"85"},"PeriodicalIF":2.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12070710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143975943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomics-based exploration of ubiquitination-related biomarkers and potential molecular mechanisms in laryngeal squamous cell carcinoma.","authors":"Qiu Chen, Zhimin Wu, Yifei Ma","doi":"10.1186/s12920-025-02148-x","DOIUrl":"10.1186/s12920-025-02148-x","url":null,"abstract":"<p><strong>Background: </strong>One of the most common and prevalent cancers is laryngeal squamous cell carcinoma (LSCC), which poses a great threat to the life and health of the patient. Nonetheless, it has been demonstrated that ubiquitination is crucial for the development and course of LSCC. Therefore, it is particularly important to identify biomarkers for ubiquitination-related genes (UbRGs) in LSCC.</p><p><strong>Methods: </strong>Differentially expressed genes (DEGs) in the LSCC versus controls were obtained by differential expression analysis. Also, key modular genes associated with LSCC were obtained using weighted gene co-expression network analysis (WGCNA). Next, DEGs, key module genes, and UbRGs were taken to intersect to obtain candidate genes. And then machine algorithms were to screen potential biomarkers, further their diagnostic value were analyzed and validated. Then, therapeutic agents for biomarkers were predict. In addition, the regulatory networks of the biomarkers were mapped. The expression levels of biomarkers were detected in clinical samples using reverse transcription-quantitative PCR (RT-qPCR).</p><p><strong>Results: </strong>A total of eight candidate genes were acquired by the overlap 1,911 DEGs, the key modular genes of WGCNA, and 1,393 UbRGs. A sum of four biomarkers (WDR54, KAT2B, NBEAL2 and LNX1) were identified by two machine learning, then these four biomarkers were validated in GSE127165 and the expression trend was consistent with TCGA-LSCC, they were recorded as biomarkers. Moreover, the accuracy of the biomarkers in predicting clinical aspects of LSCC was confirmed by the receiver operating characteristic (ROC) curves. Subsequently, cancers such as malignant neoplasms, colorectal cancers, tumors, and primary malignant neoplasms were significantly associated with the biomarkers, which further suggests that these four biomarkers were strongly associated with cancer. Meanwhile, the drugs garcinol, cocaine, and triazolam, among others, used for LSCC treatment were predicted. Finally, transcription factors (TFs) (BRD4, MYC, AR, and CTCF) were predicted to regulate the biomarkers. RT-qPCR assays illustrated that the expression trends of KAT2B, LNX1 and NBEAL2 remained consistent with the dataset.</p><p><strong>Conclusion: </strong>The identification of four biomarkers (WDR54, KAT2B, NBEAL2 and LNX1) associated with UbRGs could ultimately serve as a predictive clinical diagnosis of LSCC and provide insight into the molecular mechanisms of LSCC.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"84"},"PeriodicalIF":2.1,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12070575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic analysis of three patients from two unrelated Chinese families with autosomal recessive spastic ataxia of Charlevoix-Saguenay.","authors":"Hui Liu, Ranran Li, Chen Chen, Lin Shang, Ying Bai, Duo Chen, Xiangdong Kong, Qianqian Li","doi":"10.1186/s12920-025-02151-2","DOIUrl":"https://doi.org/10.1186/s12920-025-02151-2","url":null,"abstract":"<p><p>Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a rare early-onset neurodegenerative disorder characterized by progressive cerebellar ataxia, spasticity, and sensorimotor peripheral neuropathy. This disorder is caused by homozygous or compound heterozygous variants in the sacsin (SACS) gene on chromosome 13q12.12. Three patients with ARSACS from two unrelated Chinese families were recruited for this study. Patient #1 was an 18-year-old male who had been walking unstably for 12 years. Patient #2, the younger sister of Patient #1, was a 5-year-old girl who had been walking unstably for 2 years. Patient #3 was a 19-year-old female who had been walking unstably and a tendency to fall for 17 years. For Patient #1, whole-exome sequencing (WES) identified a hemizygous variant c.8310_8313delAGAT (p.Asp2771fs4*) in SACS (NM_014363.6), with the father being heterozygous, the mother wild-type, and Patient #2 hemizygous, as verified by Sanger sequencing. Additional copy number variant analysis of the WES data indicated that Patient #1 had a heterozygous gross deletion of chr13q12.12 (chr13:23,808,732 - 24,890,322). Low-coverage whole-genome sequencing results revealed that Patient #2 carried a chr13q12.12 deletion (chr13:23,520,000-24,940,000). Together with Sanger sequencing results, this gross deletion was speculated to have been inherited from the mother, further explaining the hemizygous state of c.8310_8313delAGAT (p.Asp2771fs4*) in Patients #1 and #2. Through WES, Patient #3 was identified as having suspected compound heterozygous variants of c.2881 C > T (p.Arg961*) and c.6409 C > T (p.Gln2137*), inherited from the father and mother, respectively, as confirmed by Sanger sequencing. This study identified three variants in SACS. The c.8310_8313delAGAT (p.Asp2771fs4*) is novel, whereas c.2881 C > T (p.Arg961*) and c.6409 C > T (p.Gln2137*) have been reported previously. Moreover, this study highlights the growing trend that ARSACS has become increasingly prevalent worldwide rather than being localized to a specific region or race. As an increasing number of patients with ARSACS are diagnosed, the genetic spectrum of ARSACS will gradually broaden, providing an accurate genetic basis for prenatal diagnosis of mothers in the years ahead, if possible.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"83"},"PeriodicalIF":2.1,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12049771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143975368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the c.406 C > T variant in TNNI3 gene: pathogenic insights into restrictive cardiomyopathy.","authors":"Tannaz Masoumi, Hamed Hesami, Majid Maleki, Samira Kalayinia","doi":"10.1186/s12920-025-02150-3","DOIUrl":"https://doi.org/10.1186/s12920-025-02150-3","url":null,"abstract":"<p><strong>Background: </strong>Restrictive cardiomyopathy (RCM) is a rare cardiac disorder characterized by diastolic dysfunction and myocardial stiffness, frequently associated with genetic variants. We aimed to explore the genetic basis of RCM in a diagnosed patient through comprehensive genetic analysis.</p><p><strong>Methods: </strong>Whole exome sequencing (WES) was conducted on the proband, followed by Sanger sequencing for variant confirmation and familial segregation analysis. In silico tools and structural protein modeling were employed to assess the functional impact of the identified variant.</p><p><strong>Results: </strong>The c.406 C > T variant, classified as likely pathogenic, results in a truncated TNNI3 protein. Bioinformatics analysis highlighted significant structural disruptions, likely impairing sarcomere function. The patient presented with growth retardation, progressive dyspnea, and echocardiographic findings consistent with RCM. Both parents were heterozygous carriers, supporting an autosomal recessive inheritance pattern. The homozygosity of the novel variant identified in this study is a critical factor in the genotype-phenotype correlation observed in this case.</p><p><strong>Conclusion: </strong>This study identified the novel c.406 C > T variant in TNNI3 as a potential pathogenic driver of RCM, emphasizing the critical role of genetic evaluations in early diagnosis and management of inherited cardiomyopathies. Further studies are warranted to explore therapeutic interventions targeting TNNI3-related pathologies.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"82"},"PeriodicalIF":2.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12044743/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive chromosomal abnormality detection: integrating CNV-Seq with traditional karyotyping in prenatal diagnostics.","authors":"Yan Huang, Shuai Fu, Di Shao, Yanhua Yao, Fangyan Wu, Minrong Yao","doi":"10.1186/s12920-025-02139-y","DOIUrl":"https://doi.org/10.1186/s12920-025-02139-y","url":null,"abstract":"<p><strong>Background: </strong>This study aimed to evaluate the efficacy of copy number variation sequencing (CNV-Seq) in detecting chromosomal abnormalities in prenatal diagnosis, comparing its performance with traditional karyotype analysis.</p><p><strong>Methods: </strong>A retrospective analysis was conducted on 1001 prenatal samples collected between April 2021 and December 2023. Samples were analyzed using both CNV-Seq and karyotype analysis. The detection rates of chromosomal abnormalities were compared between the two methods across various prenatal diagnostic indications. Clinical follow-up was performed to assess pregnancy outcomes.</p><p><strong>Results: </strong>CNV-Seq detected chromosomal abnormalities in 89 of 1,001 cases (8.9%), compared to 50 cases (5.0%) identified by traditional karyotyping. CNV-Seq not only detected all abnormalities identified by karyotyping, including common aneuploidies such as trisomy 21 and sex chromosome abnormalities, but also uncovered 53 additional pathogenic submicroscopic CNVs associated with 33 known syndromes. The detection rates of CNV-Seq were significantly higher in high-risk groups, such as those identified by non-invasive prenatal testing (HR-NIPT) and maternal serum screening (HR-MSS), demonstrating superior sensitivity and accuracy in prenatal diagnostics.</p><p><strong>Conclusion: </strong>CNV-Seq demonstrated superior sensitivity in detecting chromosomal abnormalities, particularly submicroscopic alterations, compared to traditional karyotyping. The study highlights the potential of CNV-Seq as a valuable tool in prenatal diagnostics, offering improved detection of genetic abnormalities and guiding clinical decision-making. However, a combined approach using both CNV-Seq and karyotype analysis is recommended for comprehensive prenatal genetic screening.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"81"},"PeriodicalIF":2.1,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TPX2 promotes papillary renal cell carcinoma progression by forming a ceRNA with LINC00894.","authors":"Zhenshan Ding, Wenwei Ying, Ye Yan, Ying Zhao, Cheng Liu, Lulin Ma","doi":"10.1186/s12920-025-02120-9","DOIUrl":"https://doi.org/10.1186/s12920-025-02120-9","url":null,"abstract":"<p><strong>Purpose: </strong>Papillary renal cell carcinoma (pRCC), particularly type 2, is associated with a poor prognosis. This study aimed to identify molecular mechanisms underlying pRCC progression and explore potential therapeutic targets to improve patient outcomes.</p><p><strong>Methods: </strong>TPX2 expression was analyzed in tumor samples from patients with type 2 pRCC. In vitro experiments were conducted to assess the effects of TPX2 and LINC00894 knockdown and overexpression on the proliferation and migration of Caki-2 and ACHN cells. Immunohistochemical analysis of tissue microarrays was performed to evaluate the associations between TPX2 expression and clinicopathological characteristics in type 2 pRCC patients.</p><p><strong>Results: </strong>Elevated TPX2 expression was significantly associated with a worse prognosis in type 2 pRCC patients and served as an independent risk factor for overall survival. Knockdown of TPX2 in Caki-2 and ACHN cells significantly reduced cell proliferation and migration. Additionally, LINC00894 was highly expressed in type 2 pRCC and correlated with poor prognosis. Mechanistically, miR-660-5p targeted the TPX2 3' UTR, promoting TPX2 degradation, while LINC00894 competitively bound to miR-660-5p, protecting TPX2 from miRNA-mediated degradation and exerting a pro-oncogenic effect. Immunohistochemical analysis revealed significant correlations between TPX2 expression and clinicopathological features, including tumor thrombus volume, tumor diameter, pathological TNM stage, and Fuhrman grade.</p><p><strong>Conclusion: </strong>This study underscores the critical role of TPX2 in type 2 pRCC progression and highlights its potential as a prognostic biomarker and therapeutic target. The TPX2/LINC00894/miR-660-5p regulatory axis provides novel insights into the molecular mechanisms driving pRCC and offers a promising avenue for improving patient prognosis.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"80"},"PeriodicalIF":2.1,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12036302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The frequency of the ACTN3 polymorphism in Brazil: a systematic review and meta-analysis.","authors":"Valmir Oliveira Silvino, Cirley Pinheiro Ferreira, Helen Matias Apaza, Valtemir Silvino de Souza-Junior, Sérgio Luís Galan Ribeiro, Sandro Soares Almeida, Marcos Antonio Pereira Dos Santos","doi":"10.1186/s12920-025-02136-1","DOIUrl":"https://doi.org/10.1186/s12920-025-02136-1","url":null,"abstract":"<p><strong>Background: </strong>The ACTN3 gene encodes the protein alpha-actinin-3, which is crucial for fast-twitch muscle fibers, contributing to rapid and forceful contractions. The distribution of these genotypes and their impact on sports performance in Brazilian populations are not well-documented. This study aimed to determine the allelic and genotypic frequency of the ACTN3 R/X polymorphism in Brazil and its association with sports performance.</p><p><strong>Methods: </strong>A systematic review was conducted, including studies sourced from PubMed, Scielo, LILACS, LIPECS, Coleciona SUS, CUMED, BINACIS, IBECS, and MEDLINE databases, resulting in 42 studies included. The quality of these studies was assessed using the Strengthening the Reporting of Genetic Association (STREGA) guidelines.</p><p><strong>Results: </strong>Among all the 8,746 participants, 35.2% had the RR genotype, 46.2% had the RX genotype, and 18.6% had the XX genotype. Regarding allelic frequency, 58.3% were R allele carriers, while 41.7% were X allele carriers. Meta-analysis showed that there was no consistent association between the ACTN3 genotypes and sports performance, although some data suggested potential benefits in athletic performance.</p><p><strong>Conclusion: </strong>This study revealed that the RX genotype of the ACTN3 R577X polymorphism is the most prevalent in Brazil, followed by the RR and XX genotypes. While the R allele was more frequent, the meta-analysis did not confirm a consistent association between ACTN3 genotypes and sports performance, suggesting that other genetic and environmental factors contribute to athletic success.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"79"},"PeriodicalIF":2.1,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12034205/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143962892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LIMA1 inhibits cisplatin resistance and malignant biological behavior of bladder cancer cells by suppressing the Wnt/β-catenin pathway.","authors":"Zhong Lv, Shuchen Zhao, Haoran Wu","doi":"10.1186/s12920-025-02146-z","DOIUrl":"10.1186/s12920-025-02146-z","url":null,"abstract":"<p><strong>Objective: </strong>This study aimed to explore the effect of LIM domain and actin binding 1 (LIMA1) on bladder cancer (BCa) cells and to investigate its underlying molecular mechanisms.</p><p><strong>Methods: </strong>The expression of LIMA1 gene in clinical BCa tissue samples and BCa cell models was detected using real-time quantitative PCR and western blot. Subsequently, LIMA1 knockdown experiments were performed exclusively in the BCa J82 cell line, while LIMA1 overexpression was conducted only in the cisplatin-resistant J82/CR cell line. The proliferation of the cells was assessed by colony formation assay. Cisplatin resistance was evaluated by MTT assay. Migration and invasion of the cells were tested by Transwell assay. Additionally, the levels of key proteins in the Wnt/β-catenin signaling pathway were examined by western blotting.</p><p><strong>Results: </strong>We found that LIMA1 was underexpressed in BCa tissues and cells (P < 0.01). Overexpression of LIMA1 inhibited the proliferation, migration, invasion, and epithelial-mesenchymal transition of BCa cells (P < 0.01) and improved their cisplatin resistance (P < 0.01), whereas knocking down LIMA1 produced opposite results (P < 0.01). Furthermore, overexpression of LIMA1 could suppress the Wnt/β-catenin signaling pathway in BCa cells (P < 0.01), and activation of this pathway partially reversed the anti-tumor effects produced by overexpression of LIMA1 (P < 0.01).</p><p><strong>Conclusion: </strong>LIMA1 could inhibit the malignant biological behavior of BCa cells and weaken their cisplatin resistance by negatively regulating the Wnt/β-catenin signaling pathway. Our findings provide new insights for the clinical treatment of BCa.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"78"},"PeriodicalIF":2.0,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CCT8 drives colorectal cancer progression via the RPL4-MDM2-p53 axis and immune modulation.","authors":"Yangyang Teng, Hao Lin, Zijian Lin, Xichen Li, Yejiao Ruan, Binhui Pan, Jinlin Ge, Yuesheng Zhu, Daopo Lin, Qingji Ying, Zhenzhai Cai, Xuanping Xia","doi":"10.1186/s12920-025-02133-4","DOIUrl":"https://doi.org/10.1186/s12920-025-02133-4","url":null,"abstract":"<p><strong>Purpose: </strong>Colorectal cancer (CRC) ranks high in global mortality, emphasizing the need for effective interventions. The aim of the research is to elucidate the oncogenic role of CCT8 in CRC and its interaction with RPL4 in the RPL4-MDM2-p53 axis.</p><p><strong>Methods: </strong>TIMER 2.0, TCGA, and GTEx databases were used to analyze CCT8 expression patterns in CRC. Immunohistochemistry was performed to examine CCT8 distribution in CRC tissues and adjacent non-tumor tissues. Functional assays, including CCK-8, transwell, wound-healing, and flow cytometry, were conducted using DLD-1 and HCT116 cell lines to assess the effects of CCT8 on cell proliferation, migration, invasion, and apoptosis. Gene set enrichment analysis, protein-protein interaction network analysis, and co-immunoprecipitation were performed to explore the interaction between CCT8 and RPL4 and their role in the RPL4-MDM2-p53 pathway. Additionally, gene set variation analysis was applied to investigate the relationship between CCT8/RPL4 expression and immune infiltration patterns in CRC.</p><p><strong>Results: </strong>CCT8 was significantly upregulated in CRC and associated with tumor progression. Mechanistically, CCT8 potentially synergizes with RPL4 concluded from their positive correlation and similar immune infiltration patterns, influencing the RPL4-MDM2-p53 axis and contributing to p53 ubiquitination and degradation.</p><p><strong>Conclusion: </strong>These findings underscore the oncogenic significance of CCT8 in CRC and shed light on its molecular mechanisms, paving the way for potential therapeutic applications.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"77"},"PeriodicalIF":2.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143965367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}