Genomics最新文献

{"title":"Integrated analysis of genomics and transcriptomics revealed the genetic basis for goaty flavor formation in goat milk","authors":"Fuhong Zhang ,&nbsp;Chenbo Shi ,&nbsp;Qiuya He ,&nbsp;Lu Zhu ,&nbsp;Jianqing Zhao ,&nbsp;Weiwei Yao ,&nbsp;Juan J. Loor ,&nbsp;Jun Luo","doi":"10.1016/j.ygeno.2024.110873","DOIUrl":"10.1016/j.ygeno.2024.110873","url":null,"abstract":"<div><p>Goat milk exhibits a robust and distinctive “goaty” flavor. However, the underlying genetic basis of goaty flavor remains elusive and requires further elucidation at the genomic level. Through comparative genomics analysis, we identified divergent signatures of certain proteins in goat, sheep, and cow. MMUT has undergone a goat-specific mutation in the B12 binding domain. We observed the goat FASN exhibits nonsynonymous mutations in the acyltransferase domain. Structural variations in these key proteins may enhance the capacity for synthesizing goaty flavor compounds in goat. Integrated omics analysis revealed the catabolism of branched-chain amino acids contributed to the goat milk flavor. Furthermore, we uncovered a regulatory mechanism in which the transcription factor ZNF281 suppresses the expression of the <em>ECHDC1</em> gene may play a pivotal role in the accumulation of flavor substances in goat milk. These findings provide insights into the genetic basis underlying the formation of goaty flavor in goat milk.</p></div><div><h3>Statement of significance</h3><p>Branched-chain fatty acids (BCFAs) play a crucial role in generating the distinctive “goaty” flavor of goat milk. Whether there is an underlying genetic basis associated with goaty flavor is unknown. To begin deciphering mechanisms of goat milk flavor development, we collected transcriptomic data from mammary tissue of goat, sheep, cow, and buffalo at peak lactation for cross-species transcriptome analysis and downloaded nine publicly available genomes for comparative genomic analysis. Our data indicate that the catabolic pathway of branched-chain amino acids (BCAAs) is under positive selection in the goat genome, and most genes involved in this pathway exhibit significantly higher expression levels in goat mammary tissue compared to other species, which contributes to the development of flavor in goat milk. Furthermore, we have elucidated the regulatory mechanism by which the transcription factor ZNF281 suppresses <em>ECHDC1</em> gene expression, thereby exerting an important influence on the accumulation of flavor compounds in goat milk. These findings provide insights into the genetic mechanisms underlying flavor formation in goat milk and suggest further research to manipulate the flavor of animal products.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000946/pdfft?md5=6816c16362c39809dff22288df385927&pid=1-s2.0-S0888754324000946-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141186334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell analysis of CD4+ tissue residency memory cells (TRMs) in adult atopic dermatitis: A new potential mechanism","authors":"Wenxuan Bai ,&nbsp;Le Yang ,&nbsp;Jing Qiu ,&nbsp;Zihan Zhu ,&nbsp;Shuxing Wang ,&nbsp;Peidi Li ,&nbsp;Dawei Zhou ,&nbsp;Hongyi Wang ,&nbsp;Yuxuan Liao ,&nbsp;Yao Yu ,&nbsp;Zijiang Yang ,&nbsp;Puqiao Wen ,&nbsp;Di Zhang","doi":"10.1016/j.ygeno.2024.110870","DOIUrl":"10.1016/j.ygeno.2024.110870","url":null,"abstract":"<div><p>The pathophysiology of atopic dermatitis (AD) is complex. CD4⁺ T cells play an essential role in the development of lesions in AD. However, the underlying mechanism remains unclear. In the present study, we investigated the differentially expressed genes (DEGs) between adult AD lesioned and non-lesioned skin using two datasets from the Gene Expression Omnibus (GEO) database. 62 DEGs were shown to be related to cytokine response. Compared to non-lesioned skin, lesioned skin showed immune infiltration with increased numbers of activated natural killer (NK) cells and CD4⁺ T memory cells (<em>p</em> &lt; 0.01). We then identified 13 hub genes with a strong association with CD4⁺ T cells using weighted correlation network analysis. Single-cell analysis of AD detected a novel CD4⁺ T subcluster, CD4⁺ tissue residency memory cells (TRMs), which were verified through immunohistochemistry (IHC) to be increased in the dermal area of AD. The significant relationship between CD4⁺ TRM and AD was assessed through further analyses. FOXO1 and SBNO2, two of the 13 hub genes, were characteristically expressed in the CD4⁺ TRM, but down-regulated in IFN-γ/TNF-α-induced HaCaT cells, as shown using quantitative polymerase chain reaction (qPCR). Moreover, SBNO2 expression was associated with increased Th1 infiltration in AD (<em>p</em> &lt; 0.05). In addition, genes filtered using Mendelian randomization were positively correlated with CD4⁺ TRM and were highly expressed in IFN-γ/TNF-α-induced HaCaT cells, as determined using qPCR and western blotting. Collectively, our results revealed that the newly identified CD4⁺ TRM may be involved in the pathogenesis of adult AD.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000910/pdfft?md5=8c01709a6dbe732533a5bd68d7a74b2c&pid=1-s2.0-S0888754324000910-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141184063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic DNA methylation modifications in the cold stress response of cassava","authors":"Guangrun Yu ,&nbsp;Baowang Zhang ,&nbsp;Qi Chen ,&nbsp;Zequan Huang ,&nbsp;Baohong Zhang ,&nbsp;Kai Wang ,&nbsp;Jinlei Han","doi":"10.1016/j.ygeno.2024.110871","DOIUrl":"10.1016/j.ygeno.2024.110871","url":null,"abstract":"<div><p>Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000922/pdfft?md5=e262674eac04fa817b70bd6048696df7&pid=1-s2.0-S0888754324000922-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141161324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide sequence divergence of satellite DNA could underlie meiotic failure in male hybrids of bighead catfish and North African catfish (Clarias, Clariidae)","authors":"Artem Lisachov ,&nbsp;Thitipong Panthum ,&nbsp;Dmitrij Dedukh ,&nbsp;Worapong Singchat ,&nbsp;Syed Farhan Ahmad ,&nbsp;Pish Wattanadilokcahtkun ,&nbsp;Thanyapat Thong ,&nbsp;Phanitada Srikampa ,&nbsp;Kantika Noito ,&nbsp;Ryan Rasoarahona ,&nbsp;Ekaphan Kraichak ,&nbsp;Narongrit Muangmai ,&nbsp;Satid Chatchaiphan ,&nbsp;Kednapat Sriphairoj ,&nbsp;Sittichai Hatachote ,&nbsp;Aingorn Chaiyes ,&nbsp;Chatchawan Jantasuriyarat ,&nbsp;Sahabhop Dokkaew ,&nbsp;Visarut Chailertlit ,&nbsp;Warong Suksavate ,&nbsp;Kornsorn Srikulnath","doi":"10.1016/j.ygeno.2024.110868","DOIUrl":"10.1016/j.ygeno.2024.110868","url":null,"abstract":"<div><p>Hybrid sterility, a hallmark of postzygotic isolation, arises from parental genome divergence disrupting meiosis. While chromosomal incompatibility is often implicated, the underlying mechanisms remain unclear. This study investigated meiotic behavior and genome-wide divergence in bighead catfish (<em>C. macrocephalus</em>), North African catfish (<em>C. gariepinus</em>), and their sterile male hybrids (important in aquaculture). Repetitive DNA analysis using bioinformatics and cytogenetics revealed significant divergence in satellite DNA (satDNA) families between parental species. Notably, one hybrid exhibited successful meiosis and spermatozoa production, suggesting potential variation in sterility expression. Our findings suggest that genome-wide satDNA divergence, rather than chromosome number differences, likely contributes to meiotic failure and male sterility in these catfish hybrids.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000892/pdfft?md5=9af6a1a88e19670acb22df3c2087af98&pid=1-s2.0-S0888754324000892-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141131369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative transcriptome analysis of Fusarium graminearum challenged with distinct fungicides and functional analysis of FgICL gene","authors":"Xuhao Guo ,&nbsp;Kai He ,&nbsp;Mengyu Li ,&nbsp;Yuan Zhang ,&nbsp;Jia Jiang ,&nbsp;Le Qian ,&nbsp;Xuheng Gao ,&nbsp;Chengqi Zhang ,&nbsp;Shengming Liu","doi":"10.1016/j.ygeno.2024.110869","DOIUrl":"10.1016/j.ygeno.2024.110869","url":null,"abstract":"<div><p><em>Fusarium graminearum</em> is an economically important phytopathogenic fungus. Chemical control remains the dominant approach to managing this plant pathogen. In the present study, we performed a comparative transcriptome analysis to understand the effects of four commercially used fungicides on <em>F. graminearum</em>. The results revealed a significant number of differentially expressed genes related to carbohydrate, amino acid, and lipid metabolism, particularly in the carbendazim and phenamacril groups. Central carbon pathways, including the TCA and glyoxylate cycles, were found to play crucial roles across all treatments except tebuconazole. Weighted gene co-expression network analysis reinforced the pivotal role of central carbon pathways based on identified hub genes. Additionally, critical candidates associated with ATP-binding cassette transporters, heat shock proteins, and chitin synthases were identified. The crucial functions of the isocitrate lyase in <em>F. graminearum</em> were also validated. Overall, the study provided comprehensive insights into the mechanisms of how <em>F. graminearum</em> responds to fungicide stress.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000909/pdfft?md5=0767a0a961a795ed30b9376a27af1a5e&pid=1-s2.0-S0888754324000909-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141139871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of walnut (Juglans regia) PME gene family members and expression analysis during infection with Cryptosphaeria pullmanensis pathogens","authors":"Ze Qin ,&nbsp;Chengcai Yan ,&nbsp;Kaiying Yang,&nbsp;Qinpeng Wang,&nbsp;Zhe Wang,&nbsp;Changqing Gou,&nbsp;Hongzu Feng,&nbsp;Qiming Jin,&nbsp;Xianxing Dai,&nbsp;Zulihumar Maitikadir,&nbsp;Haiting Hao,&nbsp;Lan Wang","doi":"10.1016/j.ygeno.2024.110860","DOIUrl":"10.1016/j.ygeno.2024.110860","url":null,"abstract":"<div><p>Walnuts exhibit a higher resistance to diseases, though they are not completely immune. This study focuses on the <em>Pectin methylesterase</em> (<em>PME</em>) gene family to investigate whether it is involved in disease resistance in walnuts. These 21 genes are distributed across 12 chromosomes, with four pairs demonstrating homology. Variations in conserved motifs and gene structures suggest diverse functions within the gene family. Phylogenetic and collinear gene pairs of the <em>PME</em> family indicate that the gene family has evolved in a relatively stable way. The <em>cis</em>-acting elements and gene ontology enrichment of these genes, underscores their potential role in bolstering walnuts' defense mechanisms. Transcriptomic analyses were conducted under conditions of <em>Cryptosphaeria pullmanensis</em> infestation and verified by RT-qPCR. The results showed that certain <em>JrPME</em> family genes were activated in response, leading to the hypothesis that some members may confer resistance to the disease.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000818/pdfft?md5=a808c52f4398e9152e76a48dd0fe8d38&pid=1-s2.0-S0888754324000818-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141081178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cactus: A user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis","authors":"Jérôme Salignon ,&nbsp;Lluís Millan-Ariño ,&nbsp;Maxime U. Garcia ,&nbsp;Christian G. Riedel","doi":"10.1016/j.ygeno.2024.110858","DOIUrl":"10.1016/j.ygeno.2024.110858","url":null,"abstract":"<div><p>The ever decreasing cost of Next-Generation Sequencing coupled with the emergence of efficient and reproducible analysis pipelines has rendered genomic methods more accessible. However, downstream analyses are basic or missing in most workflows, creating a significant barrier for non-bioinformaticians. To help close this gap, we developed Cactus, an end-to-end pipeline for analyzing ATAC-Seq and mRNA-Seq data, either separately or jointly. Its Nextflow-, container-, and virtual environment-based architecture ensures efficient and reproducible analyses. Cactus preprocesses raw reads, conducts differential analyses between conditions, and performs enrichment analyses in various databases, including DNA-binding motifs, ChIP-Seq binding sites, chromatin states, and ontologies. We demonstrate the utility of Cactus in a multi-modal and multi-species case study as well as by showcasing its unique capabilities as compared to other ATAC-Seq pipelines. In conclusion, Cactus can assist researchers in gaining comprehensive insights from chromatin accessibility and gene expression data in a quick, user-friendly, and reproducible manner.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S088875432400079X/pdfft?md5=5940e619de02ee861593f3fd7f961e88&pid=1-s2.0-S088875432400079X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140911609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 conjoint analysis of renal structure and omics characteristics reveal new insight to yak high-altitude hypoxia adaptation","authors":"Yuan Ding,&nbsp;Fangfang Zhao,&nbsp;Jiang Hu,&nbsp;Zhidong Zhao,&nbsp;Bingang Shi,&nbsp;Shaobin Li","doi":"10.1016/j.ygeno.2024.110857","DOIUrl":"10.1016/j.ygeno.2024.110857","url":null,"abstract":"<div><h3>Background</h3><p>Yaks have unique adaptive mechanisms to the hypoxic environment, in which the kidney plays an important role. The aim of this study was to explore the histological changes of yak kidney at different altitudes and the metabolites and genes associated with adaptation to the hypoxic environment.</p></div><div><h3>Methods</h3><p>We analyzed the tissue structure and transcriptomic metabolomic data of yak kidney tissue at two altitudes, 2600 and 4400 m. We compared and identified the morphological adaptations of the kidney and the metabolites and genes associated with hypoxia adaptation in yaks. Changes in renal morphological adaptations, differential metabolites and genes were compared and identified, combining the two in a joint analysis.</p></div><div><h3>Results</h3><p>High-altitude yak kidneys showed significant adaptive changes: increased mitochondria, increased glomerular thylakoid area, and decreased localized ribosomes. Transcriptomics and metabolomics identified 69 DAMs (Differential metabolites) and 594 DEGs (differential genes). Functional enrichment analysis showed that the DAMs were associated with protein digestion and absorption, ABC transporter, and MTOR signaling pathway; the DEGs were significantly enriched in Cholesterol metabolism and P53 signaling pathway. The joint analysis indicated that metabolites such as lysine and arginine, as well as key genes such as <em>ABCB5</em> and <em>COL1A2</em>, were particularly affected under hypoxic conditions, whereas changes in mitochondria in the tissue structure may be related to the expression of <em>MFN1</em> and <em>OPA1</em>, and changes in glomerular thylakoid membranes are related to <em>VEGFA</em> and <em>TGFB3</em>.</p></div><div><h3>Conclusion</h3><p>The kidney regulates metabolites and gene expression related to hormone synthesis, protein metabolism, and angiogenesis by adjusting the mitochondrial and glomerular thylakoid membrane structure to support the survival of yaks in high-altitude environments.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000788/pdfft?md5=2535fa4836db0caa1da52a5868b7e5a2&pid=1-s2.0-S0888754324000788-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140904462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Melatonin promotes proliferation of Inner Mongolia cashmere goat hair follicle papilla cells through Wnt10b","authors":"Wendian Gong ,&nbsp;Junyang Liu ,&nbsp;Qing Mu ,&nbsp;Tergel Chahaer ,&nbsp;Jiasen Liu ,&nbsp;Wenqi Ding ,&nbsp;Tugeqin Bou ,&nbsp;Zixian Wu ,&nbsp;Yanhong Zhao","doi":"10.1016/j.ygeno.2024.110844","DOIUrl":"10.1016/j.ygeno.2024.110844","url":null,"abstract":"<div><p>The study demonstrated that melatonin (MT) can induce the development of secondary hair follicles in Inner Mongolian cashmere goats through the Wnt10b gene, leading to secondary dehairing. However, the mechanisms underlying the expression and molecular function of Wnt10b in dermal papilla cells (DPC) remain unknown. This research aimed to investigate the impact of MT on DPC and the regulation of Wnt10b expression, function, and molecular mechanisms in DPC. The findings revealed that MT promotes DPC proliferation and enhances DPC activity. Co-culturing DPC with overexpressed Wnt10b and MT showed a significant growth promotion. Subsequent RNA sequencing (RNA-seq) of overexpressed Wnt10b and control groups unveiled the regulatory role of Wnt10b in DPC. Numerous genes and pathways, including developmental pathways such as Wnt and MAPK, as well as processes like hair follicle morphogenesis and hair cycle, were identified. These results suggest that Wnt10b promotes the growth of secondary hair follicles in Inner Mongolian cashmere goats by regulating crucial factors and pathways in DPC proliferation.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S088875432400065X/pdfft?md5=4dadf74faca0ff78fc362a9f87d40d05&pid=1-s2.0-S088875432400065X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140776282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of autophagy-related genes in liver cancer prognosis","authors":"Yuling Zhou ,&nbsp;Rong Shan ,&nbsp;Wangti Xie,&nbsp;Qiang Zhou,&nbsp;Qinghua Yin,&nbsp;Yuqi Su,&nbsp;Jia Xiao,&nbsp;Pan Luo,&nbsp;Xiang Yao,&nbsp;Jianlong Fang,&nbsp;Fang Wen,&nbsp;Erdong Shen,&nbsp;Jie Weng","doi":"10.1016/j.ygeno.2024.110852","DOIUrl":"10.1016/j.ygeno.2024.110852","url":null,"abstract":"<div><p>Autophagy, a highly conserved process of protein and organelle degradation, has emerged as a critical regulator in various diseases, including cancer progression. In the context of liver cancer, the predictive value of autophagy-related genes remains ambiguous. Leveraging chip datasets from the TCGA and GTEx databases, we identified 23 differentially expressed autophagy-related genes in liver cancer. Notably, five key autophagy genes, PRKAA2, BIRC5, MAPT, IGF1, and SPNS1, were highlighted as potential prognostic markers, with MAPT showing significant overexpression in clinical samples. In vitro cellular assays further demonstrated that MAPT promotes liver cancer cell proliferation, migration, and invasion by inhibiting autophagy and suppressing apoptosis. Subsequent in vivo studies further corroborated the pro-tumorigenic role of MAPT by suppressing autophagy. Collectively, our model based on the five key genes provides a promising tool for predicting liver cancer prognosis, with MAPT emerging as a pivotal factor in tumor progression through autophagy modulation.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000739/pdfft?md5=0831a478e474cbdf8e994def7bc9851b&pid=1-s2.0-S0888754324000739-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140855254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}