Literature DB >> 32740968

The Power of Single-Cell Analysis for the Study of Liver Pathobiology.

Angela L Chu1, Joel D Schilling2, Kevin R King3, Ariel E Feldstein1.   

Abstract

Single cell transcriptomics has emerged as a powerful lens through which to study the molecular diversity of complex tissues such as the liver, during health and disease, both in animal models and in humans. The earliest gene expression methods measured bulk tissue RNA, but the results were often confusing because they derived from the combined transcriptomes of many different cell types in unknown proportions. To better delineate cell-type-specific expression, investigators developed cell isolation, purification, and sorting protocols, yet still, the RNA derived from ensembles of cells obscured recognition of cellular heterogeneity. Profiling transcriptomes at the single-cell level has opened the door to analyses that were not possible in the past. In this review, we discuss the evolution of single cell transcriptomics and how it has been applied for the study of liver physiology and pathobiology to date.
© 2020 American Association for the Study of Liver Diseases.

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Year:  2021        PMID: 32740968      PMCID: PMC7854989          DOI: 10.1002/hep.31485

Source DB:  PubMed          Journal:  Hepatology        ISSN: 0270-9139            Impact factor:   17.425


  44 in total

1.  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

Review 2.  The origin of fibrogenic myofibroblasts in fibrotic liver.

Authors:  Tatiana Kisseleva
Journal:  Hepatology       Date:  2017-01-11       Impact factor: 17.425

3.  Myeloid cells in liver and bone marrow acquire a functionally distinct inflammatory phenotype during obesity-related steatohepatitis.

Authors:  Oliver Krenkel; Jana Hundertmark; Ali T Abdallah; Marlene Kohlhepp; Tobias Puengel; Tilmann Roth; Diogo Philippini Pontual Branco; Jana C Mossanen; Tom Luedde; Christian Trautwein; Ivan G Costa; Frank Tacke
Journal:  Gut       Date:  2019-05-10       Impact factor: 23.059

4.  Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.

Authors:  Alexander B Rosenberg; Charles M Roco; Richard A Muscat; Anna Kuchina; Paul Sample; Zizhen Yao; Lucas T Graybuck; David J Peeler; Sumit Mukherjee; Wei Chen; Suzie H Pun; Drew L Sellers; Bosiljka Tasic; Georg Seelig
Journal:  Science       Date:  2018-03-15       Impact factor: 47.728

Review 5.  Global epidemiology of nonalcoholic fatty liver disease-Meta-analytic assessment of prevalence, incidence, and outcomes.

Authors:  Zobair M Younossi; Aaron B Koenig; Dinan Abdelatif; Yousef Fazel; Linda Henry; Mark Wymer
Journal:  Hepatology       Date:  2016-02-22       Impact factor: 17.425

6.  Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

Authors:  Junyue Cao; Darren A Cusanovich; Vijay Ramani; Delasa Aghamirzaie; Hannah A Pliner; Andrew J Hill; Riza M Daza; Jose L McFaline-Figueroa; Jonathan S Packer; Lena Christiansen; Frank J Steemers; Andrew C Adey; Cole Trapnell; Jay Shendure
Journal:  Science       Date:  2018-08-30       Impact factor: 47.728

7.  Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue.

Authors:  Ditte Lovatt; Brittani K Ruble; Jaehee Lee; Hannah Dueck; Tae Kyung Kim; Stephen Fisher; Chantal Francis; Jennifer M Spaethling; John A Wolf; M Sean Grady; Alexandra V Ulyanova; Sean B Yeldell; Julianne C Griepenburg; Peter T Buckley; Junhyong Kim; Jai-Yoon Sul; Ivan J Dmochowski; James Eberwine
Journal:  Nat Methods       Date:  2014-01-12       Impact factor: 28.547

8.  The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Authors:  Cole Trapnell; Davide Cacchiarelli; Jonna Grimsby; Prapti Pokharel; Shuqiang Li; Michael Morse; Niall J Lennon; Kenneth J Livak; Tarjei S Mikkelsen; John L Rinn
Journal:  Nat Biotechnol       Date:  2014-03-23       Impact factor: 54.908

9.  Single-Cell RNA Sequencing of Visceral Adipose Tissue Leukocytes Reveals that Caloric Restriction Following Obesity Promotes the Accumulation of a Distinct Macrophage Population with Features of Phagocytic Cells.

Authors:  Ada Weinstock; Emily J Brown; Michela L Garabedian; Stephanie Pena; Monika Sharma; Juan Lafaille; Kathryn J Moore; Edward A Fisher
Journal:  Immunometabolism       Date:  2019-07-19

10.  Reversed graph embedding resolves complex single-cell trajectories.

Authors:  Xiaojie Qiu; Qi Mao; Ying Tang; Li Wang; Raghav Chawla; Hannah A Pliner; Cole Trapnell
Journal:  Nat Methods       Date:  2017-08-21       Impact factor: 47.990

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  2 in total

Review 1.  Cell-Type Resolved Insights into the Cis-Regulatory Genome of NAFLD.

Authors:  Trine V Dam; Nicolaj I Toft; Lars Grøntved
Journal:  Cells       Date:  2022-03-03       Impact factor: 6.600

2.  Spatial transcriptomics identifies enriched gene expression and cell types in human liver fibrosis.

Authors:  Brian K Chung; Jonas Øgaard; Henrik Mikael Reims; Tom H Karlsen; Espen Melum
Journal:  Hepatol Commun       Date:  2022-06-20
  2 in total

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