Human Genomics最新文献

筛选
英文 中文
Parents' perspectives on expanded newborn genomic screening in Abu Dhabi, United Arab Emirates. 阿拉伯联合酋长国阿布扎比父母对扩大新生儿基因组筛查的看法
IF 3.8 3区 医学
Human Genomics Pub Date : 2025-06-06 DOI: 10.1186/s40246-025-00766-1
Yasir Ahmed Mohammed Elhadi, Marwa Alkatheeri, Maryam Alktifan, Fatma Alhammadi, Taif Sultan, Yousef M Abu Alqumboz, Ahmed Jihad, M Islam Shaidul, Mohammed Al Saadi, Meera Saeed Nhayah Alkaabi, Khalid Almaamari, Khalifa Alseiari, Naser Alshamsi, Omar Alzaabi, Saoud Al Tamimi, Mohamed Salem Alameri, Emad Masuadi, Azhar T Rahma
{"title":"Parents' perspectives on expanded newborn genomic screening in Abu Dhabi, United Arab Emirates.","authors":"Yasir Ahmed Mohammed Elhadi, Marwa Alkatheeri, Maryam Alktifan, Fatma Alhammadi, Taif Sultan, Yousef M Abu Alqumboz, Ahmed Jihad, M Islam Shaidul, Mohammed Al Saadi, Meera Saeed Nhayah Alkaabi, Khalid Almaamari, Khalifa Alseiari, Naser Alshamsi, Omar Alzaabi, Saoud Al Tamimi, Mohamed Salem Alameri, Emad Masuadi, Azhar T Rahma","doi":"10.1186/s40246-025-00766-1","DOIUrl":"10.1186/s40246-025-00766-1","url":null,"abstract":"<p><strong>Background: </strong>Newborn genomic screening offers the potential for early detection and management of genetic disorders. Understanding parental perspectives is essential before integrating genomic testing into standard newborn screening.</p><p><strong>Methods: </strong>This was a descriptive cross-sectional study surveyed 568 parents in Abu Dhabi, United Arab Emirates (UAE). An online self-administered validated and piloted questionnaire was used to gather information on demographic characteristic and perspectives regarding newborn genomic screening. Data were analysed using R version 4.4.3.</p><p><strong>Results: </strong>Most parents (78.2%) supported integrating genomics into newborn screening programs, with 63.5% stating it requires distinct management from standard screening. Females preferred geneticists (38.2% vs. 32.5%, p < 0.001) and hospitals (45.1% vs. 39.2%, p < 0.001) for discussions, with 74.2% emphasizing explicit consent compared to 68.5% of males (p < 0.002). Treatability (82.7%), age of symptom onset (74.1%), and severity (72.2%) were key decision-making factors. Additionally, 66.7% preferred genomic testing to be covered by insurance, and 82.2% supported storing genomic data for future use.</p><p><strong>Conclusion: </strong>Parents participated in the study strongly support genomic newborn screening. Gender-based differences emphasize the need for tailored communication and culturally sensitive strategies to inform policy development and implementation of newborn genomic screening program in the UAE and similar contexts.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":"19 1","pages":"63"},"PeriodicalIF":3.8,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12144800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Human Genomics Brief Reports: embracing concise dissemination for rapid and impactful discoveries. 人类基因组学简报:拥抱简明传播快速和有影响力的发现。
IF 3.8 3区 医学
Human Genomics Pub Date : 2025-06-06 DOI: 10.1186/s40246-025-00777-y
Vasilis Vasiliou, Juergen K V Reichardt, Bassam R Ali
{"title":"Human Genomics Brief Reports: embracing concise dissemination for rapid and impactful discoveries.","authors":"Vasilis Vasiliou, Juergen K V Reichardt, Bassam R Ali","doi":"10.1186/s40246-025-00777-y","DOIUrl":"https://doi.org/10.1186/s40246-025-00777-y","url":null,"abstract":"","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":"19 1","pages":"64"},"PeriodicalIF":3.8,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12144796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Proof of principle concept for the analysis and functional prediction of rare genetic variants in the CYP2C19 and CYP2D6 genes. CYP2C19和CYP2D6基因罕见遗传变异分析和功能预测的原理概念证明。
IF 3.8 3区 医学
Human Genomics Pub Date : 2025-05-28 DOI: 10.1186/s40246-025-00765-2
Inger Johansson, Yuchen Lu, Yitian Zhou, Kristi Krebs, Martina Akcan, Lili Milani, Magnus Ingelman-Sundberg
{"title":"Proof of principle concept for the analysis and functional prediction of rare genetic variants in the CYP2C19 and CYP2D6 genes.","authors":"Inger Johansson, Yuchen Lu, Yitian Zhou, Kristi Krebs, Martina Akcan, Lili Milani, Magnus Ingelman-Sundberg","doi":"10.1186/s40246-025-00765-2","DOIUrl":"10.1186/s40246-025-00765-2","url":null,"abstract":"<p><strong>Background: </strong>Variations in pharmacogenes that regulate drug absorption, distribution, metabolism, and excretion (ADME) contribute to approximately 20-30% of interindividual differences in drug response. While many common variants are successfully utilized in clinical settings to predict individual drug responses, a significant portion of the genetic basis underlying this variability remains unidentified. This includes rare variants, which are estimated to account for 4-6% of drug response variability.</p><p><strong>Results: </strong>To comprehensively elucidate the functional consequences and molecular mechanisms of rare variants, we conducted in vitro enzyme expression studies combined with in silico structure-function analyses. We selected 11 rare variants in the CYP2C19 and CYP2D6 genes identified among participants within the Estonian Biobank. Variant cDNAs were heterologously expressed in HEK-293 cells, and detailed enzyme activity analyses were performed. The experimental results were further validated against average scores from five optimized in silico prediction models: LRT, Mutation Assessor, PROVEAN, VEST3, and CADD. To explore structure-activity relationships, we performed in silico docking of substrates into available 3D enzyme structures. Our findings reveal that most of the rare genetic variants caused significant functional alterations, including: (i) Likely impairments in substrate transport to the active site due to narrowing of access channels; (ii) Changes in catalytic rates; and (iii) Potential effects on substrate extrusion rates from the active site. The in silico prediction tools accurately anticipated the functional impact of 6 out of the 11 variants (54%).</p><p><strong>Conclusions: </strong>Evaluating the functionality of rare variants will become increasingly essential as rapid and cost-effective whole-genome sequencing technologies continue to advance. Our results highlight the need for further refinement of in silico prediction models, particularly those leveraging 3D crystal enzyme structures, to enhance the accuracy of functional predictions for rare genetic variants.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":"19 1","pages":"62"},"PeriodicalIF":3.8,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Causal impact of genetically-determined fish and fish oil intake on epigenetic age acceleration and related serum markers. 遗传决定的鱼和鱼油摄入量对表观遗传年龄加速和相关血清标志物的因果影响。
IF 3.8 3区 医学
Human Genomics Pub Date : 2025-05-24 DOI: 10.1186/s40246-025-00756-3
Paul Fabian, Gil Blander, Renee Deehan, Ali Torkamani, Bartek Nogal
{"title":"Causal impact of genetically-determined fish and fish oil intake on epigenetic age acceleration and related serum markers.","authors":"Paul Fabian, Gil Blander, Renee Deehan, Ali Torkamani, Bartek Nogal","doi":"10.1186/s40246-025-00756-3","DOIUrl":"10.1186/s40246-025-00756-3","url":null,"abstract":"<p><strong>Background: </strong>The interplay between diet and healthspan is a topic of great interest in biomedical research. Toward this end, consumption of marine omega-3 fatty acids is of particular significance, as reports suggest that diets focused on seafood can prolong the disease-free portion of the human lifespan. Fish consumption has also been linked to reduced biological aging as measured by epigenetic clocks, but there is no conclusive evidence of a causal relationship. Moreover, fish oils reduce triglycerides, and may affect other lipid profiles, as well as systemic inflammation. To investigate further, we used two-sample Mendelian randomization to investigate potential causality between fish intake and healthspan markers.</p><p><strong>Methods: </strong>Bidirectional Mendelian randomization was performed in the two-sample setting with publicly available GWAS summary statistics. GWAS data from the UK Biobank for oily fish consumption (n = 460,443) and fish oil supplementation (n = 461,384) were used as the primary exposures. First-generation epigenetic clocks Hannum age and intrinsic epigenetic age acceleration (IEAA), as well as second-generation clocks GrimAge and PhenoAge were collected from an independent dataset of individuals of European ancestry (n = [34,449-34,667]). Finally, data from the Integrative Epidemiology Unit database was used for serum proxies of lipidemia and systemic inflammation (n = [61,308-78,700]). Additional sensitivity analyses, such as reverse causation testing and the Cochran's Q test were performed for exposure-outcome pairs where the inverse variance weighted (IVW) method was significant (p-value < 0.05), and where the MR Egger method indicated an effect in the same direction as the IVW result.</p><p><strong>Results: </strong>We report that oily fish consumption appears to decrease PhenoAge acceleration (p < 0.0086), whereas fish oil supplementation appears to decrease GrimAge (p <math><mo>=</mo></math> 0.037). Both omega-3 exposures modify the epigenetic clocks in the expected negative, or age-decelerating, direction. For the serum biomarkers, we find evidence that fish oil consumption leads to a reduction in triglycerides (p <math><mo>=</mo></math> 0.004), although HDL and LDL were not significantly modified. Finally, we also detected a suggestive inverse relationship between oily fish consumption and hsCRP (p <math><mo>=</mo></math> 0.064).</p><p><strong>Conclusions: </strong>Our analysis shows that consuming fish oil, whether through whole food or as a supplement, can have a rejuvenating impact as measured by PhenoAge and GrimAge acceleration. We have also provided evidence further linking fish oil intake and lower triglyceride levels. These results, based on robust MR-based analyses, emphasize the effectiveness of dietary choices in modifying emerging measures of healthspan.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":"19 1","pages":"61"},"PeriodicalIF":3.8,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CLPP Gene Variants Causing Perrault Syndrome Type 3 in Han Chinese Families: A Genotype-Phenotype Study. 中国汉族家庭CLPP基因变异导致佩诺特综合征3型:一项基因型-表型研究
IF 3.8 3区 医学
Human Genomics Pub Date : 2025-05-23 DOI: 10.1186/s40246-025-00762-5
Xicui Long, Bingqian Yang, Wei Wang, Wan Peng, Xiaolu Wang, Wenyu Xiong, Man Liu, Huijun Yuan, Yu Lu
{"title":"CLPP Gene Variants Causing Perrault Syndrome Type 3 in Han Chinese Families: A Genotype-Phenotype Study.","authors":"Xicui Long, Bingqian Yang, Wei Wang, Wan Peng, Xiaolu Wang, Wenyu Xiong, Man Liu, Huijun Yuan, Yu Lu","doi":"10.1186/s40246-025-00762-5","DOIUrl":"10.1186/s40246-025-00762-5","url":null,"abstract":"<p><strong>Background: </strong>Perrault syndrome is a rare autosomal recessive disorder characterized by sensorineural hearing loss (SNHL) and primary ovarian insufficiency (POI) secondary to ovarian dysgenesis. However, the mutation spectrum of disease-causing genes for Perrault syndrome in the Chinese population remains poorly understood. In this study, we report on two Chinese families with Perrault syndrome type 3 caused by novel CLPP gene variants. We also conducted a comprehensive literature review of CLPP gene variants in Perrault syndrome type 3 to elucidate genotype-phenotype associations.</p><p><strong>Methods: </strong>Using Whole Genome Sequencing (WGS) data, two pedigrees with Perrault syndrome type 3 were ascertained in the Chinese Deafness Genetics Cohort through genotype-driven analysis. Variants were validated using Sanger sequencing and copy number quantification methods. In vitro analysis of splice site variants in the CLPP gene using the minigene assay.</p><p><strong>Results: </strong>Two Han Chinese families were ascertained: one with compound heterozygous variants (c.270 + 1G > C and c.355A > C [p. Ile119Leu]) and the other with missense variant (c.400G > C [p. Asp134His]) together with a large deletion in CLPP. In vitro minigene assays confirmed that the c.270 + 1G > C variant causes intron 2 retention and an alternative 5' splice site in exon 2, leading to protein alteration. Among 33 Perrault syndrome type 3 patients in literature, 97% (31/32) had hearing loss, 55% (16/29) neurological disease, and 71% (15/21) females had POI. Including our 4 novel variants, 21 pathogenic CLPP gene variants have been reported, with 57% (12/21) missense and 43% (9/21) truncating variants, mainly in the ATP-dependent Clp protease proteolytic subunit. Biallelic truncating or missense plus truncating genotypes showed higher rates of neurological disease (p = 0.001), but no significant difference in hearing loss incidence compared to biallelic missense genotypes was observed.</p><p><strong>Conclusion: </strong>This study highlights the challenges in diagnosing Perrault syndrome due to its genetically and clinically heterogeneity. By exploring novel variants and establishing genotype-phenotype correlations, we aim to improve the genetic diagnosis and consultation for this complex disorder.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":"19 1","pages":"60"},"PeriodicalIF":3.8,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102955/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic counseling in the Middle East: provider perspectives of patient attitudes and cultural challenges. 中东的遗传咨询:提供者对病人态度和文化挑战的看法。
IF 3.8 3区 医学
Human Genomics Pub Date : 2025-05-20 DOI: 10.1186/s40246-025-00770-5
Shruti Shenbagam, Alan Taylor, Ruchi Jain, Khalid Fakhro, Fowzan Alkuraya, Ahmad Abou Tayoun
{"title":"Genetic counseling in the Middle East: provider perspectives of patient attitudes and cultural challenges.","authors":"Shruti Shenbagam, Alan Taylor, Ruchi Jain, Khalid Fakhro, Fowzan Alkuraya, Ahmad Abou Tayoun","doi":"10.1186/s40246-025-00770-5","DOIUrl":"10.1186/s40246-025-00770-5","url":null,"abstract":"<p><p>Genomic advancements have led to increased utilization of genetic testing in clinical care, yet barriers to accessing genetic counseling and genomics services remain, particularly in the Middle East where inherited diseases are highly prevalent due to consanguinity. Limited knowledge of healthcare professionals' experiences in genetic counseling in the Middle East necessitates understanding their perspectives for better service improvement in the region. As a pilot, a survey of 32 healthcare professionals providing genetic counseling services in the Middle East explored provider experiences, patient attitudes and cultural/psychosocial factors related to genetic testing. Among the participants, 21 providers (65.6%), caring for patients of multiple ethnicities, including Arabs, recognised that there are unique challenges to counseling between these patient groups. Thematic data analysis identified that higher levels of consanguinity and stoic nature of the people are unique cultural considerations in the region. Language barriers and limited resources were identified as genetic counseling challenges. Overall, patients demonstrated good coping abilities with a genetic diagnosis. Eighteen responses (56%) highlighted an overall positive attitude, with increasing awareness and acceptance towards genetic testing. This study highlights the need for further research and interventions to address the unique challenges and improve genetic counseling services in the Middle East.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":"19 1","pages":"59"},"PeriodicalIF":3.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144110433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","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 loci associated with women's reproductive traits and exploration of a shared genetic basis with obesity. 鉴定与女性生殖特征相关的基因座,探索与肥胖的共同遗传基础。
IF 3.8 3区 医学
Human Genomics Pub Date : 2025-05-20 DOI: 10.1186/s40246-025-00773-2
Seong-Ah Kwon, Yoon Shin Cho
{"title":"Identification of loci associated with women's reproductive traits and exploration of a shared genetic basis with obesity.","authors":"Seong-Ah Kwon, Yoon Shin Cho","doi":"10.1186/s40246-025-00773-2","DOIUrl":"10.1186/s40246-025-00773-2","url":null,"abstract":"<p><strong>Background: </strong>The timing of menarche and menopause significantly affects women's health, with influences on cancer, cardiovascular disease, obesity, type 2 diabetes, and psychosocial problems. In addition, observational studies have reported that ages at menarche (AAM) and natural menopause (ANM) are correlated with obesity. To understand the genetic bases of these reproductive traits, we conducted a genome-wide association study (GWAS) of AAM and ANM in the Korean population. We also investigated the genetic correlation and causal relationship to explore the shared genetic architecture between reproductive traits and obesity in women.</p><p><strong>Results: </strong>Our GWA analyses of 45,608 and 21,599 adult women identified two and six genome-wide significant associations (P-value < 5 × 10<sup>- 8</sup>) for AAM and ANM, respectively. Although most of the loci that we detected have been reported in previous studies, we have newly linked the JHY locus containing the SNP rs11605693 to AAM. Leveraging the GWAS results, we tested the shared genetic basis underlying AAM and ANM, which appear to be closely related to female hormone activity. Linkage disequilibrium score regression (LDSC) analysis did not identify a significant genetic correlation between the two traits. Our LDSC analyses indicated that AAM was inversely correlated with two obesity traits, body mass index (BMI) and waist circumference (WC). However, Mendelian randomization (MR) analyses did not provide evidence of a causal relationship between AAM and obesity traits.</p><p><strong>Conclusions: </strong>Overall, our study provides insights into the genetic architecture of women's reproductive traits and the shared genetic basis between AAM and obesity. Our MR analyses suggest that the genetic correlation between AAM and obesity traits results from the direct effects of genetic variants on both traits rather than a causal relationship between them.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":"19 1","pages":"58"},"PeriodicalIF":3.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144110488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
BAX-mediated ammonia-driven cell death: a novel prognostic and therapeutic target in clear cell renal cell carcinoma. bax介导的氨驱动细胞死亡:透明细胞肾细胞癌的一个新的预后和治疗靶点。
IF 3.8 3区 医学
Human Genomics Pub Date : 2025-05-17 DOI: 10.1186/s40246-025-00764-3
Xi Zhang, Zijie Yu, Lu Yin, Qiang Li, Shaohua He, Heng Li, Jian Li, Lian Sheng, Hongfei Wu, Hongqi Chen, Xiaoxu Zhu, Yang Lv
{"title":"BAX-mediated ammonia-driven cell death: a novel prognostic and therapeutic target in clear cell renal cell carcinoma.","authors":"Xi Zhang, Zijie Yu, Lu Yin, Qiang Li, Shaohua He, Heng Li, Jian Li, Lian Sheng, Hongfei Wu, Hongqi Chen, Xiaoxu Zhu, Yang Lv","doi":"10.1186/s40246-025-00764-3","DOIUrl":"10.1186/s40246-025-00764-3","url":null,"abstract":"<p><strong>Background: </strong>ccRCC (clear cell renal cell carcinoma) is characterized by metabolic reprogramming and immunosuppression, leading to poor clinical prognosis. In recent years, ammonia-related cell death has attracted increasing attention as a novel mechanism related to tumor progression, but its role in ccRCC has not been clarified.</p><p><strong>Methods: </strong>In this study, the Ammonia-related Signature (AS) of ccRCC was constructed by integrating bioinformatics analysis and experimental verification. Multiple independent cohorts including TCGA, PMID 35,440,542 cohort, E-MTAB-1980, and GSE29609 were used to evaluate prognostic accuracy and clinical relevance, and biological functions of key ammonia related genes were explored by cell proliferation, clonal formation, migration, and invasion assays. ScRNA-seq was used to analyze interaction between AS and immune cells in ccRCC.</p><p><strong>Results: </strong>The ammonia-related prognostic model demonstrated robust predictive power in multiple datasets. The high AS group of patients with poor prognosis, and the tumor mutation load, immunosuppressive cell infiltration level and immune checkpoint molecular expression were higher. BAX was a key ammonia-related gene closely related to tumor progression, and its knockdown obviously inhibit proliferation, migration and invasion of ccRCC cells. Single-cell analysis confirmed the activation of ammonia-related signaling pathways in the tumor microenvironment, in particular revealing specific interactions between BAX-positive tumor cells and immunosuppressive cell populations.</p><p><strong>Conclusion: </strong>The ammonia-related cell death pathway, especially BAX, can be employed as a potential prognostic marker and therapeutic target for ccRCC, providing new ideas for individualized treatment strategies to overcome immunosuppression and improve clinical prognosis.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":"19 1","pages":"57"},"PeriodicalIF":3.8,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144093477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring potential methylation markers for ovarian cancer from cervical scraping samples. 从宫颈刮痧样本中探索卵巢癌潜在的甲基化标志物。
IF 3.8 3区 医学
Human Genomics Pub Date : 2025-05-17 DOI: 10.1186/s40246-025-00763-4
Ju-Yin Lien, Lu Ann Hii, Po-Hsuan Su, Lin-Yu Chen, Kuo-Chang Wen, Hung-Cheng Lai, Yu-Chao Wang
{"title":"Exploring potential methylation markers for ovarian cancer from cervical scraping samples.","authors":"Ju-Yin Lien, Lu Ann Hii, Po-Hsuan Su, Lin-Yu Chen, Kuo-Chang Wen, Hung-Cheng Lai, Yu-Chao Wang","doi":"10.1186/s40246-025-00763-4","DOIUrl":"10.1186/s40246-025-00763-4","url":null,"abstract":"<p><strong>Background: </strong>Ovarian cancer has the highest mortality rate among gynecological cancers, making early detection crucial, as the five-year survival rate drops from 92% with early-stage diagnosis compared to 31% with late-stage diagnosis. Current diagnostic methods such as histopathological examination and detection of cancer antigen 125 and human epididymis protein 4 biomarkers are either invasive or lack specificity and sensitivity. However, the Papanicolaou (Pap) test, which is widely used for cervical cancer screening, shows the potential for detecting ovarian cancer by identifying tumor DNA in cervical scrapings. Since aberrant DNA methylation patterns are linked to cancer progression, DNA methylation offers a promising avenue for early diagnosis. Therefore, this study aimed to develop a methylation-based machine-learning model to stratify patients with ovarian cancer from the cervical scraping samples collected via Pap test.</p><p><strong>Results: </strong>Cervical scrapings were collected by gynecologists using conventional Pap smears. In total, 160 samples were collected: 95 normal, 37 benign, and 28 malignant. Methylation data were generated using the Illumina Infinium MethylationEPIC BeadChip array, which contains approximately 850,000 CpG loci. Methylation data were initially divided into training and testing sets in a 3:1 ratio comprising 120 and 40 samples, respectively. A two-step methylation-based model was trained using the training data for classification: a principal component analysis (PCA) model, consisting of 30 features, to classify samples as normal or tumor; then a gradient boosting model, containing 16 features, to further stratify tumor samples as benign or malignant. The two-step model achieved an accuracy of 0.88 and an F1-score of 0.86 on the testing data. Furthermore, an over-representation analysis was conducted to explore the functions associated with genes mapped from differentially methylated positions (DMPs) in comparisons between normal and tumor samples, as well as between benign and malignant samples. These results suggest that DMPs may be associated with olfactory transduction when comparing normal versus tumor samples, and immune regulation when comparing benign and malignant samples.</p><p><strong>Conclusions: </strong>Our two-step model shows promise for predicting ovarian cancer and suggests that cervical scrapings may be a viable alternative for sample collection during screening.</p>","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":"19 1","pages":"56"},"PeriodicalIF":3.8,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144093478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
On the aspiration to decode the impact of genomics on performance in power and endurance sports. 关于解码基因组学对力量和耐力运动表现的影响的愿望。
IF 3.8 3区 医学
Human Genomics Pub Date : 2025-05-16 DOI: 10.1186/s40246-025-00750-9
Martin Flück, Benedikt Gasser, Alain Dössegger
{"title":"On the aspiration to decode the impact of genomics on performance in power and endurance sports.","authors":"Martin Flück, Benedikt Gasser, Alain Dössegger","doi":"10.1186/s40246-025-00750-9","DOIUrl":"10.1186/s40246-025-00750-9","url":null,"abstract":"","PeriodicalId":13183,"journal":{"name":"Human Genomics","volume":"19 1","pages":"55"},"PeriodicalIF":3.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信