Literature DB >> 31492507

Understanding the kidney one cell at a time.

Jihwan Park1, Chang Linda Liu1, Junhyong Kim2, Katalin Susztak3.   

Abstract

A revolution in cellular measurement technology is underway. Whereas prior studies have been able to analyze only the averaged outputs from renal tissue, we now can accurately monitor genome-wide gene expression, regulation, function, cellular history, and cellular interactions in thousands of individual cells in a single experiment. These methods are key drivers in changing our previous morphotype-based organ and disease descriptions to unbiased genomic definitions and therefore improving our understanding of kidney development, homeostasis, and disease.
Copyright © 2019 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

Entities:  

Keywords:  RNA-seq; epigenome; kidney disease; single cell

Mesh：

Substances：

Year:  2019        PMID： 31492507      PMCID： PMC6777841          DOI： 10.1016/j.kint.2019.03.035

Source DB:  PubMed          Journal:  Kidney Int        ISSN： 0085-2538            Impact factor:   10.612


  58 in total

1.  Full-length RNA-seq from single cells using Smart-seq2.

Authors:  Simone Picelli; Omid R Faridani; Asa K Björklund; Gösta Winberg; Sven Sagasser; Rickard Sandberg
Journal:  Nat Protoc       Date:  2014-01-02       Impact factor: 13.491

2.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Authors:  Evan Z Macosko; Anindita Basu; Rahul Satija; James Nemesh; Karthik Shekhar; Melissa Goldman; Itay Tirosh; Allison R Bialas; Nolan Kamitaki; Emily M Martersteck; John J Trombetta; David A Weitz; Joshua R Sanes; Alex K Shalek; Aviv Regev; Steven A McCarroll
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

3.  Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.

Authors:  Saiful Islam; Una Kjällquist; Annalena Moliner; Pawel Zajac; Jian-Bing Fan; Peter Lönnerberg; Sten Linnarsson
Journal:  Genome Res       Date:  2011-05-04       Impact factor: 9.043

4.  Diffusion maps for high-dimensional single-cell analysis of differentiation data.

Authors:  Laleh Haghverdi; Florian Buettner; Fabian J Theis
Journal:  Bioinformatics       Date:  2015-05-21       Impact factor: 6.937

5.  CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.

Authors:  Tamar Hashimshony; Florian Wagner; Noa Sher; Itai Yanai
Journal:  Cell Rep       Date:  2012-08-30       Impact factor: 9.423

6.  Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

Authors:  Patrik L Ståhl; Fredrik Salmén; Sanja Vickovic; Anna Lundmark; José Fernández Navarro; Jens Magnusson; Stefania Giacomello; Michaela Asp; Jakub O Westholm; Mikael Huss; Annelie Mollbrink; Sten Linnarsson; Simone Codeluppi; Åke Borg; Fredrik Pontén; Paul Igor Costea; Pelin Sahlén; Jan Mulder; Olaf Bergmann; Joakim Lundeberg; Jonas Frisén
Journal:  Science       Date:  2016-07-01       Impact factor: 47.728

7.  RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.

Authors:  Kok Hao Chen; Alistair N Boettiger; Jeffrey R Moffitt; Siyuan Wang; Xiaowei Zhuang
Journal:  Science       Date:  2015-04-09       Impact factor: 47.728

8.  Conserved and Divergent Features of Mesenchymal Progenitor Cell Types within the Cortical Nephrogenic Niche of the Human and Mouse Kidney.

Authors:  Nils O Lindström; Jinjin Guo; Albert D Kim; Tracy Tran; Qiuyu Guo; Guilherme De Sena Brandine; Andrew Ransick; Riana K Parvez; Matthew E Thornton; Laurence Baskin; Brendan Grubbs; Jill A McMahon; Andrew D Smith; Andrew P McMahon
Journal:  J Am Soc Nephrol       Date:  2018-02-15       Impact factor: 10.121

9.  Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas.

Authors:  Yu Hou; Huahu Guo; Chen Cao; Xianlong Li; Boqiang Hu; Ping Zhu; Xinglong Wu; Lu Wen; Fuchou Tang; Yanyi Huang; Jirun Peng
Journal:  Cell Res       Date:  2016-02-23       Impact factor: 25.617

10.  3D structures of individual mammalian genomes studied by single-cell Hi-C.

Authors:  Tim J Stevens; David Lando; Srinjan Basu; Liam P Atkinson; Yang Cao; Steven F Lee; Martin Leeb; Kai J Wohlfahrt; Wayne Boucher; Aoife O'Shaughnessy-Kirwan; Julie Cramard; Andre J Faure; Meryem Ralser; Enrique Blanco; Lluis Morey; Miriam Sansó; Matthieu G S Palayret; Ben Lehner; Luciano Di Croce; Anton Wutz; Brian Hendrich; Dave Klenerman; Ernest D Laue
Journal:  Nature       Date:  2017-03-13       Impact factor: 49.962
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  26 in total

1.  Single-cell RNA profiling of glomerular cells in diabetic kidney: a step forward for understanding diabetic nephropathy.

Authors:  María José Soler; Daniel Batlle
Journal:  Ann Transl Med       Date:  2019-12

2.  Kidney cell type-specific changes in the chromatin and transcriptome landscapes following epithelial Hdac1 and Hdac2 knockdown.

Authors:  Kelly A Hyndman; David K Crossman
Journal:  Physiol Genomics       Date:  2021-12-10       Impact factor: 3.107

Review 3.  Myeloid Heterogeneity in Kidney Disease as Revealed through Single-Cell RNA Sequencing.

Authors:  Rachel M B Bell; Laura Denby
Journal:  Kidney360       Date:  2021-09-02

4.  Time to Abandon Kidney Biopsy to Diagnose Membranous Nephropathy?

Authors:  Pierre Ronco; Emmanuelle Plaisier
Journal:  Clin J Am Soc Nephrol       Date:  2021-11-15       Impact factor: 8.237

5.  Integration of GWAS Summary Statistics and Gene Expression Reveals Target Cell Types Underlying Kidney Function Traits.

Authors:  Yong Li; Stefan Haug; Pascal Schlosser; Alexander Teumer; Adrienne Tin; Cristian Pattaro; Anna Köttgen; Matthias Wuttke
Journal:  J Am Soc Nephrol       Date:  2020-08-06       Impact factor: 10.121

Review 6.  Clinical Integration of Genome Diagnostics for Congenital Anomalies of the Kidney and Urinary Tract.

Authors:  Rik Westland; Kirsten Y Renkema; Nine V A M Knoers
Journal:  Clin J Am Soc Nephrol       Date:  2020-04-20       Impact factor: 8.237

7.  Urinary Single-Cell Profiling Captures the Cellular Diversity of the Kidney.

Authors:  Amin Abedini; Yuan O Zhu; Shatakshee Chatterjee; Gabor Halasz; Kishor Devalaraja-Narashimha; Rojesh Shrestha; Michael S Balzer; Jihwan Park; Tong Zhou; Ziyuan Ma; Katie Marie Sullivan; Hailong Hu; Xin Sheng; Hongbo Liu; Yi Wei; Carine M Boustany-Kari; Uptal Patel; Salem Almaani; Matthew Palmer; Raymond Townsend; Shira Blady; Jonathan Hogan; Lori Morton; Katalin Susztak
Journal:  J Am Soc Nephrol       Date:  2021-02-02       Impact factor: 10.121

8.  Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline.

Authors:  Michael J Ferkowicz; Seth Winfree; Angela R Sabo; Malgorzata M Kamocka; Suraj Khochare; Daria Barwinska; Michael T Eadon; Ying-Hua Cheng; Carrie L Phillips; Timothy A Sutton; Katherine J Kelly; Pierre C Dagher; Tarek M El-Achkar; Kenneth W Dunn
Journal:  Lab Invest       Date:  2021-01-06       Impact factor: 5.662

Review 9.  The study of single cells in diabetic kidney disease.

Authors:  Harmandeep Kaur; Andrew Advani
Journal:  J Nephrol       Date:  2021-01-21       Impact factor: 3.902

Review 10.  Gaining insight into metabolic diseases from human genetic discoveries.

Authors:  Melina Claussnitzer; Katalin Susztak
Journal:  Trends Genet       Date:  2021-07-24       Impact factor: 11.639
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