Frontiers in Genetics最新文献

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The risk status, signatures of adaptation, and environmental suitability of village-based indigenous chickens from certain regions of Limpopo and KwaZulu-Natal provinces of South Africa.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2024-12-18 eCollection Date: 2024-01-01 DOI: 10.3389/fgene.2024.1450939
Reneilwe Rose Mogano, Takalani Judas Mpofu, Bohani Mtileni, Khanyisile Hadebe
{"title":"The risk status, signatures of adaptation, and environmental suitability of village-based indigenous chickens from certain regions of Limpopo and KwaZulu-Natal provinces of South Africa.","authors":"Reneilwe Rose Mogano, Takalani Judas Mpofu, Bohani Mtileni, Khanyisile Hadebe","doi":"10.3389/fgene.2024.1450939","DOIUrl":"https://doi.org/10.3389/fgene.2024.1450939","url":null,"abstract":"<p><p>Indigenous chickens are an important Farm Animal Genetic Resource (FAnGR) in South Africa as they alleviate poverty and are a source of protein. Climate change and market demand for high-performing exotic breeds threaten and undermine locally adapted village chickens. The current study explored the risk status and signatures of adaptation of village-based indigenous chickens from two provinces and mapped their environmental suitability across the country. A total of 244 village chickens from rural areas of the Capricorn (n = 85) and Sekhukhune (n = 113) districts of Limpopo province; the Harry Gwala (n = 21) and uMzinyathi (n = 25) districts of KwaZulu-Natal province were genotyped using the Illumina 60K BeadChip. The conservation flock comprised Ovambo (OV; n = 10), Potchefstroom KoeKoek (PK; n = 20), and Venda (VD; n = 20). Naked Neck (NN; n = 20), New Hampshire (NH; n = 10), White Leghorn (WL; n = 10), and White Plymouth Rock (WR; n = 10) from the Agricultural Research Council Poultry Breeding Unit were used as reference populations and representative of flocks under conservation. The effective population size (<i>Ne</i>) in village chickens and conserved flocks ranged from 18 to 53 and 26 to 38 at 12 generations ago, respectively. PC1 and PC2 explained 5.64% of the total variation, which resulted in five clusters with the Venda, Naked Neck, and White Leghorn being separated from village chickens. The first three redundancy analysis (RDA) axes capture 46.8% of the total genetic variation used to detect significant outlier SNPs. A total of 386 outlier SNPs associated with all 10 environmental variables were detected. Using ecological niche modeling, chickens from Dipakakeng, Mgababa, and Podu villages, Limpopo, had a localized predicted suitability probability, while chickens originating from Nhlonga village, KwaZulu-Natal, had a broader distribution of predicted suitability habitats with elevation and BIO6 being important variables. The results of this study provide insight into the risk status, geographic suitability, and contributing environmental factors of indigenous chickens that can be used to influence conservation and improvement decisions.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1450939"},"PeriodicalIF":2.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11688331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genome-wide identification and expression analysis of the PsKIN gene family in pea.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2024-12-18 eCollection Date: 2024-01-01 DOI: 10.3389/fgene.2024.1510864
Hao Yuan, Baoxia Liu, Guwen Zhang, Zhijuan Feng, Bin Wang, Yuanpeng Bu, Yu Xu, Yaming Gong, Zhihong Sun, Na Liu
{"title":"Genome-wide identification and expression analysis of the <i>PsKIN</i> gene family in pea.","authors":"Hao Yuan, Baoxia Liu, Guwen Zhang, Zhijuan Feng, Bin Wang, Yuanpeng Bu, Yu Xu, Yaming Gong, Zhihong Sun, Na Liu","doi":"10.3389/fgene.2024.1510864","DOIUrl":"https://doi.org/10.3389/fgene.2024.1510864","url":null,"abstract":"<p><p>Peas (<i>Pisum sativum</i> L.) serve as a vital model for plant development and stress research. The <i>kinesin</i> (<i>KIN</i>) gene family, encoding essential motor proteins, remains understudied in peas. Our research conducted a comprehensive genomic analysis of the <i>KIN</i> genes in peas, identifying 105 genes categorized into seven subfamilies based on evolutionary relationships, gene structures, conserved motifs, and interaction networks. A comparative analysis with <i>Arabidopsis</i> and <i>soybean KIN</i> gene families showed a non-uniform distribution of <i>PsKIN</i> genes across subfamilies. Homology analysis revealed that the <i>PsKIN</i> family has undergone segmental duplication and is under negative selection pressures, with conserved genes on chromosomes Ps5, Ps6, and Ps7 playing a significant role in pea evolution. Transcriptomics revealed 38 <i>PsKIN</i> genes with distinct tissue-specific expression, with <i>PsKIN76</i>, <i>PsKIN96</i>, <i>PsKIN82</i>, and <i>PsKIN103</i> showing significant levels in roots, lateral roots, stems, petals, and seeds, respectively. Differential expression under drought and saline stress was observed, with <i>PsKIN8</i>, <i>PsKIN11</i>, <i>PsKIN54</i> upregulated under drought, and <i>PsKIN47</i> and <i>PsKIN51</i> under saline stress. These genes are potential candidates for improving plant stress tolerance. This study offers insights into the pea <i>KIN</i> gene family, highlighting their potential in enhancing plant stress tolerance and setting a stage for future research.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1510864"},"PeriodicalIF":2.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11689205/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of hub programmed cell death-related genes and immune infiltration in Crohn's disease using bioinformatics.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2024-12-18 eCollection Date: 2024-01-01 DOI: 10.3389/fgene.2024.1425062
Biyao Wang, Hailing Liu, Qin Guo, Xiang Gao, Kang Chao, Qingfan Yang
{"title":"Identification of hub programmed cell death-related genes and immune infiltration in Crohn's disease using bioinformatics.","authors":"Biyao Wang, Hailing Liu, Qin Guo, Xiang Gao, Kang Chao, Qingfan Yang","doi":"10.3389/fgene.2024.1425062","DOIUrl":"https://doi.org/10.3389/fgene.2024.1425062","url":null,"abstract":"<p><strong>Background: </strong>Crohn's disease (CD) is an immune-mediated disorder characterized by immune cell infiltration that induces persistent chronic inflammation of the gastrointestinal tract. Programmed cell death (PCD) plays a critical role in the pathogenesis of CD. This study identified vital PCD-related genes in CD based on immune infiltration using bioinformatic analysis.</p><p><strong>Methods: </strong>We obtained two CD datasets from the Gene Expression Omnibus (GEO) database and examined immune cell infiltration to investigate immune cell dysregulation in CD. PCD-related genes were retrieved from the GeneCards database. Based on the differentially expressed genes (DEGs) and PCD gene sets, PCD-related DEGs were identified. Candidate hub genes were identified using a protein-protein interaction (PPI) network, and their diagnostic effectiveness was predicted using receiver operating characteristic (ROC) curve analysis. Functional enrichment and immune infiltration analyses were used to assess the distinct roles of the hub genes. Finally, the miRWalk and ENCORI databases were used to predict which microRNAs (miRNAs) regulated the hub genes and to verify gene expression in CD colonic tissues via transcriptome sequencing.</p><p><strong>Results: </strong>A total of 335 PCD-related DEGs and 3 hub genes (<i>MMP1</i>, <i>SAA1</i>, and <i>PLAU</i>) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses indicated the enrichment of these genes in the immune response. Infiltration analysis of immune cells showed abundant endothelial cells, plasma cells, dendritic cells, and monocytes in the CD samples. Based on the correlation analysis, the three hub genes were positively correlated with monocytes and negatively correlated with CD8 naïve T-cells. <i>MMP1, SAA1</i>, and <i>PLAU</i> correlated with the pathogenicity of CD and had good diagnostic value for CD. The three hub genes were highly expressed in the CD tissues, as confirmed using transcriptome sequencing.</p><p><strong>Conclusion: </strong>This study identified <i>MMP1</i>, <i>SAA1</i>, and <i>PLAU</i> as hub genes involved in PCD in patients with CD. These genes regulate immune cell function and their expression levels are closely related to immune cell infiltration. These findings provide novel insights into the mechanisms underlying CD pathogenesis. The identified PCD genes and regulatory miRNAs are potential biomarkers and therapeutic targets for CD.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1425062"},"PeriodicalIF":2.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11688285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Assessing the causal relationships between circulating metabolic biomarkers and breast cancer by using mendelian randomization.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2024-12-18 eCollection Date: 2024-01-01 DOI: 10.3389/fgene.2024.1448748
Bowen Wang, Yue Ling, Hui Zhang, Ming Yang
{"title":"Assessing the causal relationships between circulating metabolic biomarkers and breast cancer by using mendelian randomization.","authors":"Bowen Wang, Yue Ling, Hui Zhang, Ming Yang","doi":"10.3389/fgene.2024.1448748","DOIUrl":"https://doi.org/10.3389/fgene.2024.1448748","url":null,"abstract":"<p><strong>Objective: </strong>Previous studies have established a causal relationship between metabolites and breast cancer (BC), but the underlying mechanisms remain unclear. Thus, we aimed to investigate the genetic relationship between metabolites and BC, including its subtypes, using Mendelian randomization (MR) analysis.</p><p><strong>Methods: </strong>Utilizing the latest and most comprehensive summary statistics from genome-wide association studies we conducted an Mendelian randomization study. Data on 233 metabolites, used as exposure variables, were obtained from a study involving 136,016 participants. BC data, used as outcome variables, were sourced from a study comprising 122,977 cases and 105,974 controls. We used the inverse-variance weighted method as the primary approach, along with three supplementary methods, to assess the causal relationship. We also used Cochran's Q test to detect heterogeneity and MR-Egger regression to examine the presence of horizontal pleiotropy.</p><p><strong>Results: </strong>Upon analyzing 233 metabolites across 11 classes in relation to BC, we found six classes of metabolites (fatty acids glycerides and phospholipids, lipoprotein subclasses, lipids, apolipoproteins, and lipoprotein particle size) associated with overall BC. Five classes of metabolites (fatty acids glycerides and phospholipids, lipoprotein subclasses, lipids, and lipoprotein particle size) were related to estrogen receptor (ER) + BC, and eight classes of metabolites (fatty acids, amino acids, glycerides and phospholipids, lipoprotein subclasses, lipids, apolipoproteins, glycolysis-related metabolites, and lipoprotein particle size) were linked to ER- BC.</p><p><strong>Conclusion: </strong>Our study demonstrates a genetic causal relationship between most metabolites and BC, confirming the link between these factors. This research provides a significant foundation for the prevention and treatment of BC.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1448748"},"PeriodicalIF":2.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11688392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification and validation the predictive biomarkers based on risk-adjusted control chart in gemcitabine with or without erlotinib for pancreatic cancer therapy.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2024-12-17 eCollection Date: 2024-01-01 DOI: 10.3389/fgene.2024.1497254
Aijun Zhao, Dongsheng Tu, Ye He, Liu Liu, Bin Wu, Yixing Ren
{"title":"Identification and validation the predictive biomarkers based on risk-adjusted control chart in gemcitabine with or without erlotinib for pancreatic cancer therapy.","authors":"Aijun Zhao, Dongsheng Tu, Ye He, Liu Liu, Bin Wu, Yixing Ren","doi":"10.3389/fgene.2024.1497254","DOIUrl":"https://doi.org/10.3389/fgene.2024.1497254","url":null,"abstract":"<p><strong>Background: </strong>In a randomized clinical controlled trial (PA.3) conducted by the Canadian Cancer Trials Group, the effects of gemcitabine combined with the targeted drug erlotinib (GEM-E) <i>versus</i> gemcitabine alone (GEM) on patients with unresectable, locally advanced, or metastatic pancreatic cancer were studied. This trial statistically demonstrated that the GEM-E combination therapy moderately improves overall survival (OS) of patients. However, real-world analysis suggested that GEM-E for pancreatic cancer was not more effective than GEM. The heterogeneity in outcomes or treatment effect exist. Thus, we tried to find predictive biomarkers to identifying the heterogeneous patients.</p><p><strong>Methods: </strong>Of the 569 eligible patients, 480 patients had plasma samples. Univariate and multivariate Cox proportional hazards model were used to identify baseline characteristics related to OS, and a risk adjusted Exponentially Weighted Moving Average (EWMA) control chart based on a weighted score test from the Cox model was constructed to monitor patients' survival risk. Maximally selected rank statistics were constructed to identifying the predictive biomarkers, in addition, a risk adjusted control chart based on a weighted score test from the Cox model was constructed to validating the predictive biomarkers, discover the patients who sensitive to the GEM-E or GEM.</p><p><strong>Results: </strong>Three baseline characteristics (ECOG performance status, extent of disease, and pain intensity) were identified related to prognosis. A risk-adjusted EWMA control chart was constructed and showed that GEM-E did improve OS in a few patients. Three biomarkers (BMP2, CXCL6, and HER2) were identified as predictive biomarkers based on maximum selected rank test, and using the risk-adjusted EWMA control chart to validate the reality and discover some patients who are sensitive to the GEM-E therapy.</p><p><strong>Conclusion: </strong>In reality, GEM-E has not shown a significant advantage over GEM in the treatment of pancreatic cancer. However, we discovered some patients who are sensitive to the GEM-E therapy based on the predictive biomarkers, which suggest that the predictive biomarkers provide ideas for personalized medicine in pancreatic cancer.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1497254"},"PeriodicalIF":2.8,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11685217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
miR-210 loss leads to widespread phenotypic and gene expression changes in human 293T cells.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2024-12-16 eCollection Date: 2024-01-01 DOI: 10.3389/fgene.2024.1486252
Xiaoxiao Zhang, Zhen Meng, Chengyong Yang, Chenghao Wang, Kexin Zhang, Anxin Shi, Jingjing Guo, Yong Feng, Yan Zeng
{"title":"miR-210 loss leads to widespread phenotypic and gene expression changes in human 293T cells.","authors":"Xiaoxiao Zhang, Zhen Meng, Chengyong Yang, Chenghao Wang, Kexin Zhang, Anxin Shi, Jingjing Guo, Yong Feng, Yan Zeng","doi":"10.3389/fgene.2024.1486252","DOIUrl":"https://doi.org/10.3389/fgene.2024.1486252","url":null,"abstract":"<p><strong>Introduction: </strong>Hypoxia responses are critical for myriad physiological and pathological processes, such as development, tissue repair, would healing, and tumorigenesis. microRNAs (miRNAs) are a class of small non-coding RNAs that exert their functions by inhibiting the expression of their target genes, and miR-210 is the miRNA universally and most conspicuously upregulated by hypoxia in mammalian systems. For its relationship to hypoxia, miR-210 has been studied extensively, yet no consensus exists on the roles and mechanisms of miR-210 in human physiological processes or diseases, and we know little about genuine miR-210 target genes in humans.</p><p><strong>Methods: </strong>To better investigate the functions and mechanisms of human miR-210, therefore, we derived the human <i>miR-210</i> gene knockout (KO) 293T cell lines using the CRISPR/Cas9 technology. We then examined the cellular phenotypes and gene expression profiles of 293T cells under normoxia and hypoxia conditions.</p><p><strong>Results and discussion: </strong>We found that the loss of miR-210 altered a variety of cellular phenotypes including proliferation and apoptosis. Subsequent global gene expression analyses identified plausible mechanisms underlying these phenotypic changes in 293T cells. In particular, we showed that miR-210 might target the expression of BNIP3L as a potential mechanism to suppress apoptosis. Surprisingly, the mRNA levels of most previously reported miR-210 target genes were not induced upon <i>miR-210</i> KO, suggesting a need to reexamining and studying human miR-210 functions directly and comprehensively. Thus, our work established a human cellular system and opportunity to unravel the complexity of the regulatory networks by miR-210.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1486252"},"PeriodicalIF":2.8,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Localization is the key to action: regulatory peculiarities of lncRNAs.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2024-12-16 eCollection Date: 2024-01-01 DOI: 10.3389/fgene.2024.1478352
Joice de Faria Poloni, Fábio Henrique Schuster de Oliveira, Bruno César Feltes
{"title":"Localization is the key to action: regulatory peculiarities of lncRNAs.","authors":"Joice de Faria Poloni, Fábio Henrique Schuster de Oliveira, Bruno César Feltes","doi":"10.3389/fgene.2024.1478352","DOIUrl":"https://doi.org/10.3389/fgene.2024.1478352","url":null,"abstract":"<p><p>To understand the transcriptomic profile of an individual cell in a multicellular organism, we must comprehend its surrounding environment and the cellular space where distinct molecular stimuli responses are located. Contradicting the initial perception that RNAs were nonfunctional and that only a few could act in chromatin remodeling, over the last few decades, research has revealed that they are multifaceted, versatile regulators of most cellular processes. Among the various RNAs, long non-coding RNAs (LncRNAs) regulate multiple biological processes and can even impact cell fate. In this sense, the subcellular localization of lncRNAs is the primary determinant of their functions. It affects their behavior by limiting their potential molecular partner and which process it can affect. The fine-tuned activity of lncRNAs is also tissue-specific and modulated by their <i>cis</i> and <i>trans</i> regulation. Hence, the spatial context of lncRNAs is crucial for understanding the regulatory networks by which they influence and are influenced. Therefore, predicting a lncRNA's correct location is not just a technical challenge but a critical step in understanding the biological meaning of its activity. Hence, examining these peculiarities is crucial to researching and discussing lncRNAs. In this review, we debate the spatial regulation of lncRNAs and their tissue-specific roles and regulatory mechanisms. We also briefly highlight how bioinformatic tools can aid research in the area.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1478352"},"PeriodicalIF":2.8,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142907018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SiMul-db: a database of single and multi-target Cas9 guides for hazelnut editing.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2024-12-16 eCollection Date: 2024-01-01 DOI: 10.3389/fgene.2024.1467316
Ciro Gianmaria Amoroso, Giuseppe Andolfo
{"title":"SiMul-db: a database of single and multi-target Cas9 guides for hazelnut editing.","authors":"Ciro Gianmaria Amoroso, Giuseppe Andolfo","doi":"10.3389/fgene.2024.1467316","DOIUrl":"https://doi.org/10.3389/fgene.2024.1467316","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1467316"},"PeriodicalIF":2.8,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142907063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Novel variant alters splicing of TGFB2 in family with features of Loeys-Dietz syndrome.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2024-12-16 eCollection Date: 2024-01-01 DOI: 10.3389/fgene.2024.1435734
Emily R Gordon, Stephanie A Felker, Tanner F Coleman, Nadiya Sosonkina, Jada Pugh, Meagan E Cochran, Anna C E Hurst, Sara J Cooper
{"title":"Novel variant alters splicing of <i>TGFB2</i> in family with features of Loeys-Dietz syndrome.","authors":"Emily R Gordon, Stephanie A Felker, Tanner F Coleman, Nadiya Sosonkina, Jada Pugh, Meagan E Cochran, Anna C E Hurst, Sara J Cooper","doi":"10.3389/fgene.2024.1435734","DOIUrl":"https://doi.org/10.3389/fgene.2024.1435734","url":null,"abstract":"<p><p>Loeys-Dietz syndrome (LDS) is a connective tissue disorder representing a wide spectrum of phenotypes, ranging from isolated thoracic aortic aneurysm or dissection to a more severe syndromic presentation with multisystemic involvement. Significant clinical variability has been noted for both related and unrelated individuals with the same pathogenic variant. We report a family of five affected individuals with notable phenotypic variability who appear to have two distinct molecular causes of LDS, one attributable to a missense variant in <i>TGFBR2</i> and the other an intronic variant 6 bp upstream from a splice junction in <i>TGFB2</i>. We tested the functional impacts of the variant identified in the proband alongside other variants in the region reported in ClinVar using a splice reporter system, which resulted in non-canonical splicing products for several variants including the proband. Molecular validation of the splicing products suggests that the <i>TGFB2</i> variants tested impact splicing by reducing efficiency of the canonical acceptor in favor of an alternate acceptor within the exon. These data combined with clinical phenotypes and segregation of the variant with disease support the conclusion that this intronic <i>TGFB2</i> variant may cause LDS in this patient and her mother. These analyses demonstrate that underappreciated intronic variants that alter splicing can be relevant for clinical phenotypes of connective tissue disease. This case highlights the importance of prompt familial cascade testing, clinical evaluation with detailed dysmorphology exam, comprehensive genetic testing, and collaboration between clinicians and scientists to characterize variants of uncertain significance to properly assess risk in LDS patients.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1435734"},"PeriodicalIF":2.8,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Editorial: Genetics, evolution, and utilization of germplasm in crop improvement.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2024-12-16 eCollection Date: 2024-01-01 DOI: 10.3389/fgene.2024.1527639
Yang Zhu, Zhong-Hua Chen, Maximiller Dal-Biaco, Shuijin Hua
{"title":"Editorial: Genetics, evolution, and utilization of germplasm in crop improvement.","authors":"Yang Zhu, Zhong-Hua Chen, Maximiller Dal-Biaco, Shuijin Hua","doi":"10.3389/fgene.2024.1527639","DOIUrl":"https://doi.org/10.3389/fgene.2024.1527639","url":null,"abstract":"","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"15 ","pages":"1527639"},"PeriodicalIF":2.8,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142907009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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