单细胞 RNA 测序在肾脏病研究中的应用前景。
The promise of single-cell RNA sequencing for kidney disease investigation.
机构信息
Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
出版信息
Kidney Int. 2017 Dec;92(6):1334-1342. doi: 10.1016/j.kint.2017.06.033. Epub 2017 Oct 12.
Abstract
Recent techniques for single-cell RNA sequencing (scRNA-seq) at high throughput are leading to profound new discoveries in biology. The ability to generate vast amounts of transcriptomic data at cellular resolution represents a transformative advance, allowing the identification of novel cell types, states, and dynamics. In this review, we summarize the development of scRNA-seq methodologies and highlight their advantages and drawbacks. We discuss available software tools for analyzing scRNA-Seq data and summarize current computational challenges. Finally, we outline ways in which this powerful technology might be applied to discovery research in kidney development and disease.
摘要
近年来，高通量单细胞 RNA 测序（scRNA-seq）技术正在引领生物学领域的重大新发现。能够以细胞分辨率生成大量转录组数据代表了一项变革性的进展，使人们能够识别新型细胞类型、状态和动态。在这篇综述中，我们总结了 scRNA-seq 方法的发展，并强调了它们的优缺点。我们讨论了用于分析 scRNA-Seq 数据的可用软件工具，并总结了当前的计算挑战。最后，我们概述了这项强大技术如何应用于肾脏发育和疾病的发现研究。
相似文献
1
The promise of single-cell RNA sequencing for kidney disease investigation.单细胞 RNA 测序在肾脏病研究中的应用前景。
Kidney Int. 2017 Dec;92(6):1334-1342. doi: 10.1016/j.kint.2017.06.033. Epub 2017 Oct 12.
2
Data Analysis in Single-Cell Transcriptome Sequencing.单细胞转录组测序中的数据分析
Methods Mol Biol. 2018;1754:311-326. doi: 10.1007/978-1-4939-7717-8_18.
3
An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data.一个用于分析和探索单细胞转录组数据的可访问的交互式基因模式笔记本。
F1000Res. 2018 Aug 16;7:1306. doi: 10.12688/f1000research.15830.2. eCollection 2018.
4
SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis.SINCERA：一种用于单细胞RNA测序分析的流程
PLoS Comput Biol. 2015 Nov 24;11(11):e1004575. doi: 10.1371/journal.pcbi.1004575. eCollection 2015 Nov.
5
Single-Cell Transcriptomics of Immune Cells: Cell Isolation and cDNA Library Generation for scRNA-Seq.单细胞转录组学分析免疫细胞：单细胞 RNA 测序的免疫细胞分离和 cDNA 文库构建。
Methods Mol Biol. 2020;2184:1-18. doi: 10.1007/978-1-0716-0802-9_1.
6
Single-cell and spatial transcriptomics approaches of cardiovascular development and disease.单细胞和空间转录组学方法在心血管发育和疾病中的应用。
BMB Rep. 2020 Aug;53(8):393-399. doi: 10.5483/BMBRep.2020.53.8.130.
7
Pseudotime Reconstruction Using TSCAN.使用TSCAN进行伪时间重建
Methods Mol Biol. 2019;1935:115-124. doi: 10.1007/978-1-4939-9057-3_8.
8
Rare Cell Type Detection.罕见细胞类型检测
Methods Mol Biol. 2019;1935:79-89. doi: 10.1007/978-1-4939-9057-3_5.
9
Identification of Cell Types from Single-Cell Transcriptomic Data.从单细胞转录组数据中识别细胞类型。
Methods Mol Biol. 2019;1935:45-77. doi: 10.1007/978-1-4939-9057-3_4.
10
Bias, robustness and scalability in single-cell differential expression analysis.单细胞差异表达分析中的偏差、稳健性和可扩展性。
Nat Methods. 2018 Apr;15(4):255-261. doi: 10.1038/nmeth.4612. Epub 2018 Feb 26.
引用本文的文献
1
Identification of podocyte molecular markers in diabetic kidney disease via single-cell RNA sequencing and machine learning.通过单细胞RNA测序和机器学习鉴定糖尿病肾病中的足细胞分子标志物
PLoS One. 2025 Jul 21;20(7):e0328352. doi: 10.1371/journal.pone.0328352. eCollection 2025.
2
Inflammatory Cell Interactions in the Rotator Cuff Microenvironment: Insights From Single-Cell Sequencing.肩袖微环境中的炎症细胞相互作用：单细胞测序的见解
Int J Genomics. 2025 Apr 15;2025:6175946. doi: 10.1155/ijog/6175946. eCollection 2025.
3
Single-Cell Analysis of Endothelial Cell Injury in IgA Nephropathy.IgA肾病中内皮细胞损伤的单细胞分析
Immun Inflamm Dis. 2025 Feb;13(2):e70149. doi: 10.1002/iid3.70149.
4
The advance of single cell transcriptome to study kidney immune cells in diabetic kidney disease.单细胞转录组学在研究糖尿病肾病中肾脏免疫细胞的进展。
BMC Nephrol. 2024 Nov 16;25(1):412. doi: 10.1186/s12882-024-03853-y.
5
Proximal tubule cells in blood and urine as potential biomarkers for kidney disease biopsy.血液和尿液中的近端肾小管细胞作为肾脏疾病活检的潜在生物标志物。
PeerJ. 2023 Dec 6;11:e16499. doi: 10.7717/peerj.16499. eCollection 2023.
6
Single-cell RNA sequencing in juvenile idiopathic arthritis.青少年特发性关节炎中的单细胞RNA测序
Genes Dis. 2023 May 24;11(2):633-644. doi: 10.1016/j.gendis.2023.04.014. eCollection 2024 Mar.
7
Single-cell transcriptomic profiles in the pathophysiology within the microenvironment of early diabetic kidney disease.单细胞转录组谱在早期糖尿病肾病微环境病理生理学中的作用。
Cell Death Dis. 2023 Jul 17;14(7):442. doi: 10.1038/s41419-023-05947-1.
8
Single-cell RNA sequencing for the study of kidney disease.单细胞 RNA 测序在肾脏疾病研究中的应用。
Mol Med. 2023 Jul 3;29(1):85. doi: 10.1186/s10020-023-00693-8.
9
Single-cell RNA and transcriptome sequencing profiles identify immune-associated key genes in the development of diabetic kidney disease.单细胞 RNA 和转录组测序谱鉴定出糖尿病肾病发展过程中的免疫相关关键基因。
Front Immunol. 2023 Mar 29;14:1030198. doi: 10.3389/fimmu.2023.1030198. eCollection 2023.
10
Deconvolution of Focal Segmental Glomerulosclerosis Pathophysiology Using Transcriptomics Techniques.运用转录组学技术对局灶节段性肾小球硬化病理生理学进行反卷积分析。
Glomerular Dis. 2021 Jul 14;1(4):265-276. doi: 10.1159/000518404. eCollection 2021 Oct.
本文引用的文献
1
Mouse embryonic stem cells can differentiate via multiple paths to the same state.小鼠胚胎干细胞可以通过多种途径分化为相同的状态。
Elife. 2017 Oct 9;6:e26945. doi: 10.7554/eLife.26945.
2
Massively parallel single-nucleus RNA-seq with DroNc-seq.采用DroNc-seq技术的大规模平行单核RNA测序
Nat Methods. 2017 Oct;14(10):955-958. doi: 10.1038/nmeth.4407. Epub 2017 Aug 28.
3
Cell fixation and preservation for droplet-based single-cell transcriptomics.用于基于微滴的单细胞转录组学的细胞固定和保存
BMC Biol. 2017 May 19;15(1):44. doi: 10.1186/s12915-017-0383-5.
4
Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis.单细胞RNA测序剖析狼疮性肾炎的分子异质性。
JCI Insight. 2017 May 4;2(9). doi: 10.1172/jci.insight.93009.
5
Cell diversity and network dynamics in photosensitive human brain organoids.光敏性人脑类器官中的细胞多样性与网络动力学
Nature. 2017 May 4;545(7652):48-53. doi: 10.1038/nature22047. Epub 2017 Apr 26.
6
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.单细胞RNA测序揭示了人类血液中新型树突状细胞、单核细胞和祖细胞。
Science. 2017 Apr 21;356(6335). doi: 10.1126/science.aah4573.
7
Single-cell RNA-sequence analysis of mouse glomerular mesangial cells uncovers mesangial cell essential genes.单细胞 RNA 测序分析揭示了小鼠肾小球系膜细胞中的系膜细胞必需基因。
Kidney Int. 2017 Aug;92(2):504-513. doi: 10.1016/j.kint.2017.01.016. Epub 2017 Mar 18.
8
Comparative Analysis of Single-Cell RNA Sequencing Methods.单细胞 RNA 测序方法的比较分析。
Mol Cell. 2017 Feb 16;65(4):631-643.e4. doi: 10.1016/j.molcel.2017.01.023.
9
Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.Seq-Well：高通量、便携式、低成本的单细胞 RNA 测序。
Nat Methods. 2017 Apr;14(4):395-398. doi: 10.1038/nmeth.4179. Epub 2017 Feb 13.
10
Massively parallel digital transcriptional profiling of single cells.大规模平行数字化单细胞转录组分析。
Nat Commun. 2017 Jan 16;8:14049. doi: 10.1038/ncomms14049.
Zotero 插件