BMC Medical Genomics最新文献

{"title":"MicroRNA-486: a dual-function biomarker for diagnosis and tumor immune microenvironment characterization in non-small cell lung cancer.","authors":"Jun Yu, Yi Shen, Yao Xu, Zhengyang Feng, Yuntian Shen, Yaqun Zhu, Jian Huan, Qiliang Peng","doi":"10.1186/s12920-025-02158-9","DOIUrl":"10.1186/s12920-025-02158-9","url":null,"abstract":"<p><strong>Background: </strong>This investigation evaluates the clinical significance and molecular mechanisms of microRNA-486 (miR-486) as a potential biomarker in non-small cell lung cancer (NSCLC) through an integrative analytical approach.</p><p><strong>Methods: </strong>We conducted systematic search and meta-analysis of diagnostic studies from major biomedical databases from inception through April 04, 2025, followed by comprehensive bioinformatics interrogation. Protein-protein interaction (PPI) networks were constructed using STRING to identify key hub genes regulated by miR-486. Validation of hub genes employed TCGA datasets, while immune infiltration analysis utilized TIMER2.0 platform.</p><p><strong>Results: </strong>The meta-analysis indicated that miR-486, both individually and in combination, could be effective biomarkers for NSCLC detection. Afterwards, functional enrichment analyses of miR-486 target genes highlighted significant ontology terms and pathways crucial to the initiation and progression of NSCLC. PPI networks revealed key proteins and modules that participate in multiple essential pathways associated with NSCLC pathogenesis. Furthermore, the identified hub genes were validated for differential expression in cancerous versus normal tissues, suggesting their potential diagnostic utility, while subsequent survival analyses confirmed their prognostic value through significant associations with overall survival. Notably, these hub genes were found to be significantly associated with immune infiltration levels, immune microenvironment scores, and immune-related proteins in NSCLC.</p><p><strong>Conclusions: </strong>This dual-modality investigation establishes miR-486 as a multi-functional biomarker in NSCLC, demonstrating both diagnostic utility and immunoregulatory potential through tumor microenvironment modulation.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"92"},"PeriodicalIF":2.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101321","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":"Predicting breast cancer risk and its association to biopsychosocial factors among Taiwanese women with a family history of breast cancer: an investigation based on the Gail model.","authors":"Sabiah Khairi, Nur Aini, Lalu Muhammad Harmain Siswanto, Min-Huey Chung","doi":"10.1186/s12920-025-02149-w","DOIUrl":"10.1186/s12920-025-02149-w","url":null,"abstract":"<p><strong>Background: </strong>First-degree relatives with breast cancer have a two-fold higher risk than women without a family history. The Gail model approach has been employed in numerous studies to investigate the risk of breast cancer among women in a variety of countries. Nevertheless, the studies investigating the correlation between the level of breast cancer risk and biopsychosocial factors among Taiwanese women with a family history of breast cancer (FHBC) are limited. By using the Gail model, we explored the breast cancer risk score and its relationship to biopsychosocial factors among Taiwanese women with FHBC.</p><p><strong>Methods: </strong>The present study was a cross-sectional study from secondary data of the Taiwan Biobank from 2008 to 2018. Self-reports were conducted to determine biopsychosocial factors. A total of 3,060 women aged 35-70 years with and without FHBC were considered eligible for enrollment. The Gail model, which utilizes six questions, was used to estimate individual five-year absolute breast cancer risk. Women with scores at least 1.66% and above were categorized as high risk. In addition, we performed bivariate and multivariate logistic regression analysis using SPSS version 27 to predict the associations between biopsychosocial factors and the risk of breast cancer based on the Gail model. All analyses were stratified by age.</p><p><strong>Results: </strong>Among the 3,060 Taiwanese women, there was a statistically significant difference in breast cancer risk score between the groups with and without FHBC (p = < 0.001), stratified by age, of which 574 in FHBC group (34.2%) were identified as having a high breast cancer risk based on the Gail model. Furthermore, six out of 15 biopsychosocial factors were significantly associated with breast cancer risk in women under 50 years of age, while seven factors showed significant associations in women aged 50 years and older. Logistic regression analysis identified five biopsychosocial factors as consistent and significant predictors of breast cancer risk in women aged 50 years and older, highlighting this group as particularly vulnerable.</p><p><strong>Conclusions: </strong>This study concludes that the Gail model identifies Taiwanese women who have a higher estimated risk of breast cancer based on cross-sectional data. Various biopsychosocial factors are associated with higher risk estimates in this population particularly in older women. Professionals can assist women in recognizing risk factors beyond the inevitable risk by encouraging regular screenings, positive behavior, and health promotion.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"88"},"PeriodicalIF":2.1,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144085718","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":"Discovering diabetes complications-related microRNAs: meta-analyses and pathway modeling approach.","authors":"Ruiyang Yin, Yanjiao Zhang, Xinyi Fang, Yuxin Zhang, Runyu Miao, Yiqi Yao, Huifang Guan, Jiaxing Tian","doi":"10.1186/s12920-025-02144-1","DOIUrl":"10.1186/s12920-025-02144-1","url":null,"abstract":"<p><strong>Purpose: </strong>MicroRNAs(miRNA) play an important role in the pathogenesis of diabetic complications by regulating gene expression. The objective of this paper is to investigate micoRNA expression in diabetic nephropathy (DN), diabetic retinopathy (DR), diabetic neuropathy (DNP), and diabetic cardiopathy (DC).</p><p><strong>Methods: </strong>We conducted this systematic review according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement and retrieved eligible microRNA-related studies of diabetic complications from PubMed, Embase, and Web of science databases. We enriched pathways corresponding to differentially expressed miRNAs using the miRPath tool on the DIANA website, and predicted their target genes with DIANA microT-CDS and TargetScan.</p><p><strong>Results: </strong>Although many of the selected studies were of high scientific quality, the results were heterogeneous. Among the 71 selected articles, 79 miRNAs were differentially expressed in various complications of diabetes, of which miRNA126, miRNA192 and 17 others were reported in at least two or more studies. A total of 156 target genes were predicted and 103 pathways were obtained by KEGG enrichment analysis.</p><p><strong>Conclusion: </strong>This comprehensive systematic evaluation provides experimental evidence statistics for miRNAs as circulating biomarkers and highlights promising biomarkers. These results provide preliminary data to further investigate the role of miRNAs in the diagnosis and therapeutic targets of human diabetic complications and support future broader longitudinal studies to better substantiate the role of dysregulated miRNAs as potential biomarkers and therapeutic targets of diabetic complications.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"86"},"PeriodicalIF":2.1,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075622","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":"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}