基于纳米孔的全长转录组测序用于了解糖尿病肾病快速和缓慢进展的潜在分子机制。

IF 2.1 4区 医学 Q3 GENETICS & HEREDITY
Jing E, Shun-Yao Liu, Dan-Na Ma, Guo-Qing Zhang, Shi-Lu Cao, Bo Li, Xiao-Hua Lu, Hong-Yan Luo, Li Bao, Xiao-Mei Lan, Rong-Guo Fu, Ya-Li Zheng
{"title":"基于纳米孔的全长转录组测序用于了解糖尿病肾病快速和缓慢进展的潜在分子机制。","authors":"Jing E, Shun-Yao Liu, Dan-Na Ma, Guo-Qing Zhang, Shi-Lu Cao, Bo Li, Xiao-Hua Lu, Hong-Yan Luo, Li Bao, Xiao-Mei Lan, Rong-Guo Fu, Ya-Li Zheng","doi":"10.1186/s12920-024-02006-2","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Diabetic nephropathy (DN) has been a major factor in the outbreak of end-stage renal disease for decades. As the underlying mechanisms of DN development remains unclear, there is no ideal methods for the diagnosis and therapy.</p><p><strong>Objective: </strong>We aimed to explore the key genes and pathways that affect the rate progression of DN.</p><p><strong>Methods: </strong>Nanopore-based full-length transcriptome sequencing was performed with serum samples from DN patients with slow progression (DNSP, n = 5) and rapid progression (DNRP, n = 6).</p><p><strong>Results: </strong>Here, transcriptome proclaimed 22,682 novel transcripts and obtained 45,808 simple sequence repeats, 1,815 transcription factors, 5,993 complete open reading frames, and 1,050 novel lncRNA from the novel transcripts. Moreover, a total of 341 differentially expressed transcripts (DETs) and 456 differentially expressed genes (DEGs) between the DNSP and DNRP groups were identified. Functional analyses showed that DETs mainly involved in ferroptosis-related pathways such as oxidative phosphorylation, iron ion binding, and mitophagy. Moreover, Functional analyses revealed that DEGs mainly involved in oxidative phosphorylation, lipid metabolism, ferroptosis, autophagy/mitophagy, apoptosis/necroptosis pathway.</p><p><strong>Conclusion: </strong>Collectively, our study provided a full-length transcriptome data source for the future DN research, and facilitate a deeper understanding of the molecular mechanisms underlying the differences in fast and slow progression of DN.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"17 1","pages":"246"},"PeriodicalIF":2.1000,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11463056/pdf/","citationCount":"0","resultStr":"{\"title\":\"Nanopore-based full-length transcriptome sequencing for understanding the underlying molecular mechanisms of rapid and slow progression of diabetes nephropathy.\",\"authors\":\"Jing E, Shun-Yao Liu, Dan-Na Ma, Guo-Qing Zhang, Shi-Lu Cao, Bo Li, Xiao-Hua Lu, Hong-Yan Luo, Li Bao, Xiao-Mei Lan, Rong-Guo Fu, Ya-Li Zheng\",\"doi\":\"10.1186/s12920-024-02006-2\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Diabetic nephropathy (DN) has been a major factor in the outbreak of end-stage renal disease for decades. As the underlying mechanisms of DN development remains unclear, there is no ideal methods for the diagnosis and therapy.</p><p><strong>Objective: </strong>We aimed to explore the key genes and pathways that affect the rate progression of DN.</p><p><strong>Methods: </strong>Nanopore-based full-length transcriptome sequencing was performed with serum samples from DN patients with slow progression (DNSP, n = 5) and rapid progression (DNRP, n = 6).</p><p><strong>Results: </strong>Here, transcriptome proclaimed 22,682 novel transcripts and obtained 45,808 simple sequence repeats, 1,815 transcription factors, 5,993 complete open reading frames, and 1,050 novel lncRNA from the novel transcripts. Moreover, a total of 341 differentially expressed transcripts (DETs) and 456 differentially expressed genes (DEGs) between the DNSP and DNRP groups were identified. Functional analyses showed that DETs mainly involved in ferroptosis-related pathways such as oxidative phosphorylation, iron ion binding, and mitophagy. Moreover, Functional analyses revealed that DEGs mainly involved in oxidative phosphorylation, lipid metabolism, ferroptosis, autophagy/mitophagy, apoptosis/necroptosis pathway.</p><p><strong>Conclusion: </strong>Collectively, our study provided a full-length transcriptome data source for the future DN research, and facilitate a deeper understanding of the molecular mechanisms underlying the differences in fast and slow progression of DN.</p>\",\"PeriodicalId\":8915,\"journal\":{\"name\":\"BMC Medical Genomics\",\"volume\":\"17 1\",\"pages\":\"246\"},\"PeriodicalIF\":2.1000,\"publicationDate\":\"2024-10-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11463056/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"BMC Medical Genomics\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1186/s12920-024-02006-2\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Medical Genomics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1186/s12920-024-02006-2","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0

摘要

背景:几十年来,糖尿病肾病(DN)一直是终末期肾病爆发的主要因素。由于糖尿病肾病的发病机制尚不清楚,目前还没有理想的诊断和治疗方法:我们旨在探索影响 DN 进展速度的关键基因和通路:方法:对进展缓慢(DNSP,n = 5)和进展迅速(DNRP,n = 6)的 DN 患者血清样本进行基于纳米孔的全长转录组测序:结果:转录组宣布了 22,682 个新转录本,并从新转录本中获得了 45,808 个简单序列重复序列、1,815 个转录因子、5,993 个完整开放阅读框和 1,050 个新 lncRNA。此外,还发现了 DNSP 组和 DNRP 组之间共有 341 个差异表达转录本(DETs)和 456 个差异表达基因(DEGs)。功能分析显示,DETs 主要参与氧化磷酸化、铁离子结合和有丝分裂等铁突变相关途径。此外,功能分析显示,DEGs 主要参与氧化磷酸化、脂质代谢、铁突变、自噬/嗜微粒、凋亡/嗜神经通路:总之,我们的研究为未来的 DN 研究提供了全长转录组数据源,有助于深入了解 DN 快速进展和缓慢进展差异的分子机制。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Nanopore-based full-length transcriptome sequencing for understanding the underlying molecular mechanisms of rapid and slow progression of diabetes nephropathy.

Background: Diabetic nephropathy (DN) has been a major factor in the outbreak of end-stage renal disease for decades. As the underlying mechanisms of DN development remains unclear, there is no ideal methods for the diagnosis and therapy.

Objective: We aimed to explore the key genes and pathways that affect the rate progression of DN.

Methods: Nanopore-based full-length transcriptome sequencing was performed with serum samples from DN patients with slow progression (DNSP, n = 5) and rapid progression (DNRP, n = 6).

Results: Here, transcriptome proclaimed 22,682 novel transcripts and obtained 45,808 simple sequence repeats, 1,815 transcription factors, 5,993 complete open reading frames, and 1,050 novel lncRNA from the novel transcripts. Moreover, a total of 341 differentially expressed transcripts (DETs) and 456 differentially expressed genes (DEGs) between the DNSP and DNRP groups were identified. Functional analyses showed that DETs mainly involved in ferroptosis-related pathways such as oxidative phosphorylation, iron ion binding, and mitophagy. Moreover, Functional analyses revealed that DEGs mainly involved in oxidative phosphorylation, lipid metabolism, ferroptosis, autophagy/mitophagy, apoptosis/necroptosis pathway.

Conclusion: Collectively, our study provided a full-length transcriptome data source for the future DN research, and facilitate a deeper understanding of the molecular mechanisms underlying the differences in fast and slow progression of DN.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
BMC Medical Genomics
BMC Medical Genomics 医学-遗传学
CiteScore
3.90
自引率
0.00%
发文量
243
审稿时长
3.5 months
期刊介绍: BMC Medical Genomics is an open access journal publishing original peer-reviewed research articles in all aspects of functional genomics, genome structure, genome-scale population genetics, epigenomics, proteomics, systems analysis, and pharmacogenomics in relation to human health and disease.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信