Frontiers in Genetics最新文献

{"title":"Retraction: Mitochondrial-associated protein LRPPRC is related with poor prognosis potentially and exerts as an oncogene via maintaining mitochondrial function in pancreatic cancer.","authors":"","doi":"10.3389/fgene.2024.1495469","DOIUrl":"https://doi.org/10.3389/fgene.2024.1495469","url":null,"abstract":"<p><p>[This retracts the article DOI: 10.3389/fgene.2021.817672.].</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380614","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}

{"title":"Case report: A novel FBXW7 gene variant causes global developmental delay.","authors":"Yu Wang, Xiaoping Ma, Hua Li, Yanrui Dai, Xiaochen Wang, Li Liu","doi":"10.3389/fgene.2024.1436462","DOIUrl":"10.3389/fgene.2024.1436462","url":null,"abstract":"<p><p><b>Objective:</b> To investigate a case of neurodevelopmental disorder caused by mutation of <i>FBXW7</i>. <b>Methods:</b> Clinical data were collected from the patient, trio-WES (whole-exome sequencing) was performed on the patient and his parents (trio), and the results were verified by Sanger sequencing. RESULTS: The patient was a 2-year and 1-month old male who presented with facial dysmorphism (prominent forehead, ocular hypertelorism, and low nasal bridge), global developmental delay, language impairment, hypertonia, labial hemangioma, hydrocele, and overgrowth. The trio-WES confirmed that the child had a pathogenic <i>de novo FBXW7</i> gene variant, c.1612C>T (p.G1n538*), a heretofore unreported locus. <b>Conclusion:</b> This case of developmental delay, hypotonia, and impaired language (OMIM: #620012) related to a mutation in <i>FBXW7</i>, is a rare genetic disorder, newly identified in recent years, and seldom reported. The presence of hypertonia, labial hemangioma, and hydrocele in this child suggests significant phenotypic heterogeneity of the disease, and the discovery of new mutant loci enriches the spectrum of pathogenic variants of the disease.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11446863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371642","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}

{"title":"Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production.","authors":"Kiran D Rasal, Pokanti Vinay Kumar, Shasti Risha, Prachi Asgolkar, M Harshavarthini, Arpit Acharya, Siba Shinde, Siyag Dhere, Avinash Rasal, Arvind Sonwane, Manoj Brahmane, Jitendra K Sundaray, Naresh Nagpure","doi":"10.3389/fgene.2024.1398084","DOIUrl":"10.3389/fgene.2024.1398084","url":null,"abstract":"<p><p>Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11446788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371644","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}

{"title":"A proteogenomic atlas of the human neural retina.","authors":"Tabea V Riepe, Merel Stemerdink, Renee Salz, Alfredo Dueñas Rey, Suzanne E de Bruijn, Erica Boonen, Tomasz Z Tomkiewicz, Michael Kwint, Jolein Gloerich, Hans J C T Wessels, Emma Delanote, Elfride De Baere, Filip van Nieuwerburgh, Sarah De Keulenaer, Barbara Ferrari, Stefano Ferrari, Frauke Coppieters, Frans P M Cremers, Erwin van Wyk, Susanne Roosing, Erik de Vrieze, Peter A C 't Hoen","doi":"10.3389/fgene.2024.1451024","DOIUrl":"10.3389/fgene.2024.1451024","url":null,"abstract":"<p><p>The human neural retina is a complex tissue with abundant alternative splicing and more than 10% of genetic variants linked to inherited retinal diseases (IRDs) alter splicing. Traditional short-read RNA-sequencing methods have been used for understanding retina-specific splicing but have limitations in detailing transcript isoforms. To address this, we generated a proteogenomic atlas that combines PacBio long-read RNA-sequencing data with mass spectrometry and whole genome sequencing data of three healthy human neural retina samples. We identified nearly 60,000 transcript isoforms, of which approximately one-third are novel. Additionally, ten novel peptides confirmed novel transcript isoforms. For instance, we identified a novel <i>IMPDH1</i> isoform with a novel combination of known exons that is supported by peptide evidence. Our research underscores the potential of in-depth tissue-specific transcriptomic analysis to enhance our grasp of tissue-specific alternative splicing. The data underlying the proteogenomic atlas are available via EGA with identifier EGAD50000000101, via ProteomeXchange with identifier PXD045187, and accessible through the UCSC genome browser.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380610","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}

{"title":"Analysis of codon usage patterns in complete plastomes of four medicinal <i>Polygonatum</i> species (Asparagaceae).","authors":"Naixing Shi, Yiwen Yuan, Renjie Huang, Guosong Wen","doi":"10.3389/fgene.2024.1401013","DOIUrl":"10.3389/fgene.2024.1401013","url":null,"abstract":"<p><p>Polygonati Rhizoma and Polygonati odorati Rhizoma, known as \"Huangjing\" and \"Yuzhu\" in China, are medicinal <i>Polygonatum</i> species resources with top-grade medical and edible properties. The chloroplast (cp) genome has been used to study species diversity, evolution, and breeding of species for applications in genetic engineering. Codon usage bias (CUB), a common and complex natural phenomenon, is essential for studies of codon optimization of exogenous genes, genetic engineering, and molecular evolution. However, the CUB of medicinal <i>Polygonatum</i> species chloroplast genomes has not been systematically studied. In our study, a detailed analysis of CUB was performed in the medicinal <i>Polygonatum</i> species chloroplast genomes. We investigated the codon bias of 204 plastid protein-coding genes (PCGs) in 4 medicinal <i>Polygonatum</i> species using CodonW and CUSP online software. Through the analysis of the codon bias index, we found that the medicinal <i>Polygonatum</i> species chloroplast genomes had weak codon usage bias. In addition, our results also showed a high preference for AT bases in medicinal <i>Polygonatum</i> species chloroplast genomes, and the preference to use AT-ending codons was observed in these species chloroplast genomes. The neutrality plot, ENC plot, PR2-Bias plot, and correspondence analysis showed that compared with mutation pressure, natural selection was the most important factor of CUB. Based on the comparative analysis of high-frequency codons and high expression codons, we also determined the 10-11 optimal codons of investigative medicinal <i>Polygonatum</i> species. Furthermore, the result of RSCU-based cluster analysis showed that the genetic relationship between different medicinal <i>Polygonatum</i> species could be well reflected. This study provided an essential understanding of CUB and evolution in the medicinal <i>Polygonatum</i> species chloroplast genomes.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11447317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371641","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}

{"title":"Methods for multi-omic data integration in cancer research.","authors":"Enrique Hernández-Lemus, Soledad Ochoa","doi":"10.3389/fgene.2024.1425456","DOIUrl":"10.3389/fgene.2024.1425456","url":null,"abstract":"<p><p>Multi-omics data integration is a term that refers to the process of combining and analyzing data from different omic experimental sources, such as genomics, transcriptomics, methylation assays, and microRNA sequencing, among others. Such data integration approaches have the potential to provide a more comprehensive functional understanding of biological systems and has numerous applications in areas such as disease diagnosis, prognosis and therapy. However, quantitative integration of multi-omic data is a complex task that requires the use of highly specialized methods and approaches. Here, we discuss a number of data integration methods that have been developed with multi-omics data in view, including statistical methods, machine learning approaches, and network-based approaches. We also discuss the challenges and limitations of such methods and provide examples of their applications in the literature. Overall, this review aims to provide an overview of the current state of the field and highlight potential directions for future research.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11446849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371646","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}

{"title":"Improved species assignments across the entire <i>Anopheles</i> genus using targeted sequencing.","authors":"Marilou Boddé, Alex Makunin, Fiona Teltscher, Jewelna Akorli, Nana Efua Andoh, Amy Bei, Victor Chaumeau, Ife Desamours, Uwem F Ekpo, Nicodem J Govella, Jonathan Kayondo, Kevin Kobylinski, Elhadji Malick Ngom, El Hadji Amadou Niang, Fredros Okumu, Olaitan O Omitola, Alongkot Ponlawat, Malala Nirina Rakotomanga, Mialy Tatamo Rasolonjatovoniaina, Diego Ayala, Mara Lawniczak","doi":"10.3389/fgene.2024.1456644","DOIUrl":"10.3389/fgene.2024.1456644","url":null,"abstract":"<p><p>Accurate species identification of the mosquitoes in the genus <i>Anopheles</i> is of crucial importance to implement malaria control measures and monitor their effectiveness. We use a previously developed amplicon panel (ANOSPP) that retrieves sequence data from multiple short nuclear loci for any species in the genus. Species assignment is based on comparison of samples to a reference index using <i>k</i>-mer distance. Here, we provide a protocol to generate version controlled updates of the reference index and present its latest release, NNv2, which contains 91 species, compared to 56 species represented in its predecessor NNv1. With the updated reference index, we are able to assign samples to species level that previously could not be assigned. We discuss what happens if a species is not represented in the reference index and how this can be addressed in a future update. To demonstrate the increased power of NNv2, we showcase the assignments of 1789 wild-caught mosquitoes from Madagascar and demonstrate that we can detect within species population structure from the amplicon sequencing data.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11446804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371645","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}

{"title":"Driver gene alterations in NSCLC patients in southern China and their correlation with clinicopathologic characteristics.","authors":"Lingna Deng, Jinbang Li, Zhanlong Qiu, Yanfen Wang","doi":"10.3389/fgene.2024.1455502","DOIUrl":"10.3389/fgene.2024.1455502","url":null,"abstract":"<p><strong>Introduction: </strong>In this study, we aimed to explore the relationship between clinicopathological features and driver gene changes in Chinese NSCLC patients.</p><p><strong>Methods: </strong>Amplification refractory mutation system PCR was used to detect the aberrations of 10 driver oncogenes in 851 Chinese NSCLC patients, and their correlation with clinicopathological characteristics was also analyzed. Moreover, three models of logistic regression were used to analyze the association between histopathology and <i>EGFR</i> or <i>KRAS</i> mutations.</p><p><strong>Results: </strong>The top two most frequently aberrant target oncogenes were <i>EGFR</i> (48.06%) and <i>KRAS</i> (9.51%). These were followed by <i>ALK</i> (5.41%), <i>HER2</i> (2.35%), <i>MET</i> (2.23%), <i>RET</i> (2.11%), <i>ROS1</i> (1.88%), <i>BRAF</i> (0.47%), <i>NRAS</i> (0.24%), and <i>PIK3CA</i> (0.12%). Additionally, 11 (1.29%) patients had synchronous gene alterations in two genes. The main <i>EGFR</i> mutations were exon 21 L858R and exon 19-Del, which accounted for 45.97% and 42.79% of all <i>EGFR</i> mutations, respectively. Logistic regression analysis showed that the frequency of <i>EGFR</i> mutations was positively correlated with women, non-smokers, lung adenocarcinoma, and invasive non-mucinous adenocarcinoma (IA), and negatively correlated with solid nodule, micro-invasive adenocarcinoma, and solid-predominant adenocarcinoma. <i>KRAS</i> mutations were positively associated with men and longer tumor long diameters and negatively correlated with lung adenocarcinoma (<i>P < 0.05</i> for all).</p><p><strong>Conclusion: </strong>Our findings suggest that the <i>EGFR</i> mutation frequency was higher in women, non-smokers, lung adenocarcinoma, and the IA subtype in lung adenocarcinoma patients, while the <i>KRAS</i> mutation rate was higher in men and patients with longer tumor long diameter and lower in lung adenocarcinoma patients.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11446855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371643","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}

{"title":"Monozygotic triplets with juvenile-onset autoimmunity and 18p microdeletion involving PTPRM","authors":"Morten Krogh Herlin, Jens Magnus Bernth Jensen, Lotte Andreasen, Mikkel Steen Petersen, Jonas Lønskov, Mette Bendixen Thorup, Niels Birkebæk, Trine H. Mogensen, Troels Herlin, Bent Deleuran","doi":"10.3389/fgene.2024.1437566","DOIUrl":"https://doi.org/10.3389/fgene.2024.1437566","url":null,"abstract":"Abnormal gene dosage from copy number variants has been associated with susceptibility to autoimmune disease. This includes 18p deletion syndrome, a chromosomal disorder with an estimated prevalence of 1 in 50,000 characterized by intellectual disability, facial dysmorphology, and brain abnormalities. The underlying causes for autoimmune manifestations associated with 18p deletions, however, remain unknown. Our objective was to investigate a distinctive case involving monozygotic triplets concordant for developmental delay, white matter abnormalities, and autoimmunity, specifically juvenile-onset Graves’ thyroiditis. By chromosomal microarray analysis and whole genome sequencing, we found the triplets to carry a <jats:italic>de novo</jats:italic> interstitial 5.9 Mb deletion of chromosome 18p11.31p11.21 spanning 19 protein-coding genes. We conducted a literature review to pinpoint genes affected by the deletion that could be associated with immune dysregulation and identified PTPRM as a potential candidate. Through dephosphorylation, PTPRM serves as a negative regulator of STAT3, a key factor in the generation of Th17 cells and the onset of specific autoimmune manifestations. We hypothesized that PTPRM hemizygosity results in increased STAT3 activation. We therefore performed assays investigating PTPRM expression, STAT3 phosphorylation, Th1/Th2/Th17 cell fractions, Treg cells, and overall immunophenotype, and in support of the hypothesis, our investigations showed an increase in cells with phosphorylated STAT3 and higher levels of Th17 cells in the triplets. We propose that PTPRM hemizygosity can serve as a contributing factor to autoimmune susceptibility in 18p deletion syndrome. If confirmed in unrelated 18p/PTPRM deletion patients, this susceptibility could potentially be treated by targeted inhibition of IL-17.","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142250589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bidirectional two-sample Mendelian randomization analysis investigates causal associations between cathepsins and inflammatory bowel disease","authors":"Na Wang, Jun Liu, Bao Chai, Jianhong Yao, Xufang Du, Qi Mei, Xuena Wang","doi":"10.3389/fgene.2024.1436407","DOIUrl":"https://doi.org/10.3389/fgene.2024.1436407","url":null,"abstract":"BackgroundCathepsins, key regulators of the pathology of gastrointestinal disorders such as inflammatory bowel disease (IBD), are a target protease that has attracted much attention in recent years. IBD is a chronic and relapsing inflammatory disorder of the gut. Traditional studies have shown a correlation between cathepsin and the risk of IBD, while the causal relationship remains unclear.MethodsThis study utilized Mendelian randomization techniques to evaluate the causal relationships between eleven cathepsins and the subtypes of IBD, such as ulcerative colitis (UC) and Crohn’s disease (CD). We also performed a series of sensitivity analyses to validate the primary Mendelian randomization (MR) results, including Cochran’s Q test, the MR-PRESSO global test, and the MR pleiotropy test.ResultsThe forward MR analyses showed no significant association between cathepsins and IBD. Reverse Mendelian randomization analyses suggested that UC might lead to elevated cathepsin G levels [inverse-variance weighted (IVW): <jats:italic>p</jats:italic> = 0.038, b = 9.966], and CD might cause a decrease in cathepsin B levels [IVW: <jats:italic>p</jats:italic> = 0.002, b = −10.525] and cathepsin L1 levels [IVW: <jats:italic>p</jats:italic> = 0.045, b = −4.742].ConclusionsOur findings offer novel and comprehensive evidence on the impact of UC or CD on cathepsins, potentially providing valuable insights into the treatment and prognosis of IBD.","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142250631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}