Genomics最新文献

{"title":"Complex chromosomal 6q rearrangements revealed by combined long-molecule genomics technologies","authors":"Sachiko Ohori ,&nbsp;Hironao Numabe ,&nbsp;Satomi Mitsuhashi ,&nbsp;Naomi Tsuchida ,&nbsp;Yuri Uchiyama ,&nbsp;Eriko Koshimizu ,&nbsp;Kohei Hamanaka ,&nbsp;Kazuharu Misawa ,&nbsp;Satoko Miyatake ,&nbsp;Takeshi Mizuguchi ,&nbsp;Atsushi Fujita ,&nbsp;Naomichi Matsumoto","doi":"10.1016/j.ygeno.2024.110894","DOIUrl":"10.1016/j.ygeno.2024.110894","url":null,"abstract":"<div><p>Technologies for detecting structural variation (SV) have advanced with the advent of long-read sequencing, which enables the validation of SV at a nucleotide level. Optical genome mapping (OGM), a technology based on physical mapping, can also provide comprehensive SVs analysis. We applied long-read whole genome sequencing (LRWGS) to accurately reconstruct breakpoint (BP) segments in a patient with complex chromosome 6q rearrangements that remained elusive by conventional karyotyping. Although all BPs were precisely identified by LRWGS, there were two possible ways to construct the BP segments in terms of their orders and orientations. Thus, we also used OGM analysis. Notably, OGM recognized entire inversions exceeding 500 kb in size, which LRWGS could not characterize. Consequently, here we successfully unveil the full genomic structure of this complex chromosomal 6q rearrangement and cryptic SVs through combined long-molecule genomic analyses, showcasing how LRWGS and OGM can complement each other in SV analysis.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001150/pdfft?md5=7b1d2689c4656d8f47c738a43098330e&pid=1-s2.0-S0888754324001150-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141633149","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":"Unraveling the signaling pathways of phytohormones underlying salt tolerance in Elymus sibiricus: A transcriptomic and metabolomic approach","authors":"Ying De,&nbsp;Weihong Yan,&nbsp;Fengqin Gao,&nbsp;Huaibin Mu","doi":"10.1016/j.ygeno.2024.110893","DOIUrl":"10.1016/j.ygeno.2024.110893","url":null,"abstract":"<div><p>Understanding phytohormonal signaling is crucial for elucidating plant defense mechanisms against environmental stressors. However, knowledge regarding phytohormone-mediated tolerance pathways under salt stress in <em>Elymus sibiricus</em>, an important species for forage and ecological restoration, remains limited. In this study, transcriptomic and metabolomic approaches uncover the dynamics of phytohormonal signaling in <em>Elymus sibiricus</em> under salt stress. Notably, four hours after exposure to salt, significant activity was observed in the ABA, JA, IAA, and CTK pathways, with ABA, JA, JA-L-Ile, and IAA identified as key mediators in the response of <em>Elymus sibiricus</em>' to salinity. Moreover, SAPK3, Os04g0167900-like, CAT1, MKK2, and MPK12 were identified as potential central regulators within these pathways. The complex interactions between phytohormones and DEGs are crucial for facilitating the adaptation of <em>Elymus sibiricus</em> to saline environments. These findings enhance our understanding of the salt tolerance mechanisms in <em>Elymus sibiricus</em> and provide a foundation for breeding salt-resistant varieties.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001149/pdfft?md5=deff24d321fb2fa39c0599eb1753062c&pid=1-s2.0-S0888754324001149-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141467376","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":"FOXCUT regulates the malignant phenotype of triple-negative breast Cancer via the miR-337-3p/ANP32E Axis","authors":"Lei Shi,&nbsp;Ziwen Zhang,&nbsp;Yuan Huang,&nbsp;Yabing Zheng","doi":"10.1016/j.ygeno.2024.110892","DOIUrl":"10.1016/j.ygeno.2024.110892","url":null,"abstract":"<div><h3>Background</h3><p>The lack of specific molecular targets and the rapid spread lead to a worse prognosis of triple-negative breast cancer (TNBC). Therefore, identifying new therapeutic and prognostic biomarkers helps to develop effective treatment strategies for TNBC.</p></div><div><h3>Methods</h3><p>Through preliminary bioinformatics analysis, FOXCUT was found to be significantly overexpressed in breast cancer, especially in TNBC. Tissue samples were collected from 15 TNBC patients, and qRT-PCR was employed to validate the expression of FOXCUT in both TNBC patient tissues and TNBC cell lines. We also carried out the GSEA analysis and KEGG enrichment analysis of FOXCUT. Additionally, the effects of FOXCUT knockdown on TNBC cell malignant behaviors, and aerobic glycolysis were assessed by methods including CCK-8, Transwell, western blot, and Seahorse XF 96 analyses. Moreover, utilizing databases predicting interactions between ceRNAs, corresponding lncRNA-miRNA binding relationships, and miRNA-mRNA interactions were predicted. These predictions were subsequently validated through RNA immunoprecipitation and dual-luciferase reporter assays.</p></div><div><h3>Results</h3><p>FOXCUT exhibited high expression in both TNBC tissues and cell lines, fostering cell malignant behaviors and glycolysis. FOXCUT was found to sponge miR-337-3p, while miR-337-3p negatively regulated the expression of ANP32E. Consequently, FOXCUT ultimately facilitated the malignant phenotype of TNBC by upregulating ANP32E expression.</p></div><div><h3>Conclusion</h3><p>This study elucidated the role of FOXCUT in elevating aerobic glycolysis levels in TNBC and driving malignant cancer cell development via the miR-337-3p/ANP32E regulatory axis.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001137/pdfft?md5=f6b04dfe47c32ddb895f237ec04491a6&pid=1-s2.0-S0888754324001137-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141467375","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":"Whole-genome sequencing of two captive black soldier fly populations: Implications for commercial production","authors":"Zexi Cai ,&nbsp;Laura Skrubbeltrang Hansen ,&nbsp;Stine Frey Laursen ,&nbsp;Hanne Marie Nielsen ,&nbsp;Simon Bahrndorff ,&nbsp;Jeffery K. Tomberlin ,&nbsp;Torsten Nygaard Kristensen ,&nbsp;Jesper Givskov Sørensen ,&nbsp;Goutam Sahana","doi":"10.1016/j.ygeno.2024.110891","DOIUrl":"10.1016/j.ygeno.2024.110891","url":null,"abstract":"<div><p>Black soldier fly (BSF; <em>Hermetia illucens</em>) is a promising insect species for food and feed production as its larvae can convert different organic waste to high-value protein. Selective breeding is one way to optimize production, but the potential of breeding is only starting to be explored and not yet utilized for BSF. To assist in monitoring a captive population and implementing a breeding program, genomics tools are imperative. We conducted whole genome sequencing of two captive populations separated by geographical distance - Denmark (DK) and Texas, USA (TX). Various population genetics analyses revealed a moderate genetic differentiation between two populations. Moreover, we observed higher inbreeding in the DK population, and the detection of a subpopulation within DK population aligned well with the recent foundation of the DK population from two captive populations. Additionally, we generated gene ontology annotation and variants annotation for wider potential applications. Our findings establish a robust marker set for research in population genetics, facilitating the monitoring of inbreeding and laying the groundwork for practical breeding programs for BSF.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001125/pdfft?md5=95c13dd07dc4a0f5c048a3436b3dca14&pid=1-s2.0-S0888754324001125-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141442427","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":"Differential gene expression and gut microbiota composition in low-altitude and high-altitude goats","authors":"Zhenzhen Zhang ,&nbsp;Xin Zhang ,&nbsp;Tingting Zhang ,&nbsp;Jingjing Li ,&nbsp;Cuomu Renqing ,&nbsp;Zhaxi Baijiu ,&nbsp;Sangzhu Baima ,&nbsp;Wangjie Zhaxi ,&nbsp;Yuzhen Nima ,&nbsp;Wangsheng Zhao ,&nbsp;Tianzeng Song","doi":"10.1016/j.ygeno.2024.110890","DOIUrl":"10.1016/j.ygeno.2024.110890","url":null,"abstract":"<div><p>Previous studies have presented evidence suggesting that altitude exerts detrimental effects on reproductive processes, yet the underlying mechanism remains elusive. Our study employed two distinct goat breeds inhabiting low and high altitudes, and conducted a comparative analysis of mRNA profiles in testis tissues and the composition of gut microbiota. The results revealed a reduced testis size in high-altitude goats. RNA-seq analysis identified the presence of 214 differentially expressed genes (DEGs) in the testis. These DEGs resulted in a weakened immunosuppressive effect, ultimately impairing spermatogenesis in high-altitude goats. Additionally, 16S rDNA amplicon sequencing recognized statistically significant variations in the abundance of the genera <em>Treponema</em>, <em>unidentified_Oscillospiraceae</em>, <em>Desulfovibrio</em>, <em>Butyricicoccus</em>, <em>Dorea</em>, <em>Parabacteroides</em> between the two groups. The collective evidence demonstrated the gut and testis played a synergistic role in causing decreased fertility at high altitudes. Our research provides a theoretical basis for future investigations into the reproductive fitness of male goats.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001113/pdfft?md5=ab74fc1e5cddecd42bf3124ac17d4442&pid=1-s2.0-S0888754324001113-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141442426","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":"Deep integration of metabolome and transcriptome characterizes alkaloid metabolism in Houttuynia cordata","authors":"Xue Jiang ,&nbsp;Qian Wang ,&nbsp;Jingtian Yang ,&nbsp;Baoguo Du ,&nbsp;Zhaodi Yuan ,&nbsp;Hongyi Liu ,&nbsp;Jiayi Yuan ,&nbsp;Yang Zhang ,&nbsp;Liao Chen ,&nbsp;Lei Liu","doi":"10.1016/j.ygeno.2024.110881","DOIUrl":"10.1016/j.ygeno.2024.110881","url":null,"abstract":"<div><p>Alkaloids are the main medicinal components in <em>Houttuynia cordata</em>. In this study, two accessions 6# and 7# of <em>H. cordata</em> underwent thorough metabolomic analyses to identify and quantify alkaloid phytometabolites. It turned out that the alkaloid types were largely similar between 6# and 7#, and the identified 81 alkaloids could be divided into nine structural classes. However, the content of alkaloids in the two accessions was quite different. According to transcriptome data, a total of 114 differentially expressed genes related to alkaloid metabolism were screened. The alkaloid synthesis pathway of the two varieties was mainly different in the isoquinoline alkaloid biosynthesis and indole alkaloid biosynthesis; four genes <em>A22110063c_transcript_59323</em>, <em>A22110063c_transcript_60118</em>, <em>A22110063c_transcript_51672</em> and <em>A22110063c_transcript_48784</em> were highly expressed in 7#, which could be key candidate genes of alkaloid metabolism and warrant further analysis. These results provide a reference for the medicinal application of <em>H. cordata</em> and breeding alkaloid rich varieties.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001022/pdfft?md5=2c0c4cfd0f21ee18fc9de41ea9cca06c&pid=1-s2.0-S0888754324001022-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141436719","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":"Identification of prognostic biomarkers for cholangiocarcinoma by combined analysis of molecular characteristics of clinical MVI subtypes and molecular subtypes","authors":"Ming-Yue Li ,&nbsp;Ya-Hui Liu ,&nbsp;Feng Wei ,&nbsp;Ping Zhang ,&nbsp;Xiao-Dong Sun ,&nbsp;Meng Wang ,&nbsp;Xiao-Hong Du ,&nbsp;Jun-Feng Ye ,&nbsp;Wei Qiu ,&nbsp;Xiao-Ju Shi ,&nbsp;Bai Ji ,&nbsp;Ying-Chao Wang ,&nbsp;Chao Jiang ,&nbsp;Wen-Gang Chai ,&nbsp;Bo Huang ,&nbsp;Xing-Kai Liu ,&nbsp;Qing-Min Chen ,&nbsp;Yu Fu ,&nbsp;Xin-Tong Hu ,&nbsp;Li-Guo Chen ,&nbsp;Guo-Yue Lv","doi":"10.1016/j.ygeno.2024.110889","DOIUrl":"10.1016/j.ygeno.2024.110889","url":null,"abstract":"<div><p>Cholangiocarcinoma (CCA) is widely noted for its high degree of malignancy, rapid progression, and limited therapeutic options. This study was carried out on transcriptome data of 417 CCA samples from different anatomical locations. The effects of lipid metabolism related genes and immune related genes as CCA classifiers were compared. Key genes were derived from MVI subtypes and better molecular subtypes. Pathways such as epithelial mesenchymal transition (EMT) and cell cycle were significantly activated in MVI-positive group. CCA patients were classified into three (four) subtypes based on lipid metabolism (immune) related genes, with better prognosis observed in lipid metabolism-C1, immune-C2, and immune-C4. IPTW analysis found that the prognosis of lipid metabolism-C1 was significantly better than that of lipid metabolism-C2 + C3 before and after correction. KRT16 was finally selected as the key gene. And knockdown of KRT16 inhibited proliferation, migration and invasion of CCA cells.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001101/pdfft?md5=0d22e1e7daf8eb22ab3a8d218c0688f9&pid=1-s2.0-S0888754324001101-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141431732","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":"Key genes and metabolites that regulate wool fibre diameter identified by combined transcriptome and metabolome analysis","authors":"Lin Yue ,&nbsp;Zengkui Lu ,&nbsp;Tingting Guo ,&nbsp;Jianbin Liu ,&nbsp;Bohui Yang ,&nbsp;Chao Yuan","doi":"10.1016/j.ygeno.2024.110886","DOIUrl":"10.1016/j.ygeno.2024.110886","url":null,"abstract":"<div><h3>Background</h3><p>Fibre diameter is an important economic trait of wool fibre. As the fibre diameter decreases, the economic value of wool increases. Therefore, understanding the mechanism of wool fibre diameter regulation is important in improving the value of wool.</p></div><div><h3>Results</h3><p>In this study, we used non-targeted metabolome and reference transcriptome data to detect differences in metabolites and genes in groups of Alpine Merino sheep with different wool fibre diameter gradients, and integrated metabolome and transcriptome data to identify key genes and metabolites that regulate wool fibre diameter. We found 464 differentially abundant metabolites (DAMs) and 901 differentially expressed genes (DEGs) in four comparisons of groups with different wool fibre diameters. Approximately 25% of the differentially abundant metabolites were lipid and lipid-like molecules. These molecules were predicted to be associated with skin development and keratin filament by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses. Key genes, including <em>COL5A2</em>, <em>COL5A3</em>, <em>CREB3L4</em>, <em>COL1A1</em>, and <em>SFRP4</em>, were identified by gene set enrichment analysis.</p></div><div><h3>Conclusions</h3><p>Key genes regulating wool fibre diameter were identified, the effects of lipid molecules on wool performance were investigated, and potential synergies between genes and metabolites were postulated, providing a theoretical framework for fine wool sheep breeding.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001071/pdfft?md5=8fe9cf7927ff09beab88c3383371f85c&pid=1-s2.0-S0888754324001071-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141330709","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":"Transcriptome and metabolome analysis of the developmental changes in Cynanchum thesioides anther","authors":"Xiaoyao Chang ,&nbsp;Xiaoyan Zhang ,&nbsp;Xiumei Huang ,&nbsp;Zhongren Yang ,&nbsp;Fenglan Zhang","doi":"10.1016/j.ygeno.2024.110884","DOIUrl":"10.1016/j.ygeno.2024.110884","url":null,"abstract":"<div><p><em>Cynanchum thesioides</em>, a xerophytic species utilized both as a medicinal herb and a food source, plays a significant role in arid and desert ecosystem management. Its inflorescence is an umbellate cyme, each carrying nearly a thousand flowers; however, its fruiting rate remains remarkably low. The normal development of the anther is a necessary prerequisite for plants to produce seeds. However, our understanding of the anther development process in <em>Cynanchum thesioides</em> remains limited. To better understand the pollen development process in <em>Cynanchum thesioides</em>, the stages of pollen development were determined through paraffin sectioning, and observations were made on the distribution characteristics of polysaccharides and lipid droplets in the pollen development of <em>Cynanchum thesioides</em> using Periodic Acid-Schiff stain (PAS) and 0.5% Sudan Black B tissue staining. Concurrently, the gene expression patterns and metabolite profiles were delineated across various developmental stages of <em>Cynanchum thesioides</em> anthers (T1: microspore stage, T2: tetrad stage, T3: mononuclear stage, and T4: maturation stage). The findings revealed that <em>Cynanchum thesioides</em> pollen is in an aggregate form. Polysaccharides gradually accumulate during maturation and lipid droplets form a surrounding membrane, thereby preventing pollen dispersion. Furthermore, transcriptomic and metabolomic analyses across distinct developmental phases uncovered a plethora of differentially expressed genes and metabolites associated with the flavonoid biosynthesis pathway. Flavonoid levels exhibited dynamic changes concurrent with anther development, aligning with the gene regulatory patterns of the corresponding biosynthetic pathways. The study identified 63 differentially accumulated flavonoid compounds and 21 differentially expressed genes associated with flavonoid biosynthesis. Weighted gene co-expression network analysis revealed six MYB and ten bHLH transcription factors as key candidates involved in flavonoid biosynthesis, with <em>Ct</em>bHLH (Cluster-6587.1050) and <em>Ct</em>MYB (Cluster-6587.31743) specifically regulating structural genes within the pathway. These findings underscore the pivotal role of flavonoid biosynthesis in anther development of <em>Cynanchum thesioides</em>. In conclusion, this research offers a comprehensive insight into the anther development process in <em>Cynanchum thesioides</em>.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001058/pdfft?md5=f2a3fe88ced43380953765a9b7a08f63&pid=1-s2.0-S0888754324001058-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141327340","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":"Effects of spinal cord injury associated exosomes delivered tRF-41 on the progression of spinal cord injury progression","authors":"Hongfei Cai,&nbsp;Yan Zhang,&nbsp;Fanyu Meng,&nbsp;Yang Li","doi":"10.1016/j.ygeno.2024.110885","DOIUrl":"10.1016/j.ygeno.2024.110885","url":null,"abstract":"<div><h3>Background</h3><p>Spinal cord injury (SCI) is a devastating neurological and pathological condition. Exosomal tsRNAs have reported to be promising biomarkers for cancer diagnosis and therapy. This study aimed to investigate the roles of SCI-associated exosomes, and related tsRNA mechanisms in SCI.</p></div><div><h3>Methods</h3><p>The serum of healthy controls and SCI patients at the acute stage were collected for exosomes isolation, and the two different exosomes were used to treat human astrocytes (HA). The cell viability, apoptosis, and cycle were determined, and the expression of the related proteins were detected by western blot. Then, the two different exosomes were sent for tsRNA sequencing, and four significant known differentially expressed tsRNAs (DE-tsRNAs) were selected for RT-qPCR validation. Finally, tRT-41 was chosen to further explore its roles and related mechanisms in SCI.</p></div><div><h3>Results</h3><p>After sequencing, 21 DE-tsRNAs were identified, which were significantly enriched in pathways of Apelin, AMPK, Hippo, MAPK, Ras, calcium, PI3K-Akt, and Rap1. RT-qPCR showed that tRF-41 had higher levels in the SCI-associated exosomes. Compared with the control HA, healthy exosomes did not significantly affect the growth of HA cells, but SCI-associated exosomes inhibited viability of HA cells, while promoted their apoptosis and increased the HA cells in G2/M phase; but tRF-41 inhibitor reversed the actions of SCI-associated exosomes. Additionally, SCI-associated exosomes, similar with tRF-41 mimics, down-regulated IGF-1, NGF, Wnt3a, and β-catenin, while up-regulated IL-1β and IL-6; but tRF-41 inhibitor had the opposite actions, and reversed the effects induced by SCI-associated exosomes.</p></div><div><h3>Conclusions</h3><p>SCI-associated exosomes delivered tRF-41 may inhibit the growth of HA through regulating Wnt/ β-catenin pathway and inflammation response, thereby facilitating the progression of SCI.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S088875432400106X/pdfft?md5=406db73f55e3927714f593d1e8dacb37&pid=1-s2.0-S088875432400106X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141310447","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}