Literature DB >> 29960011

Single-cell epigenetics - Chromatin modification atlas unveiled by mass cytometry.

Peggie Cheung1, Francesco Vallania2, Mai Dvorak1, Sarah E Chang1, Steven Schaffert2, Michele Donato2, Aditya M Rao2, Rong Mao1, Paul J Utz3, Purvesh Khatri4, Alex J Kuo5.   

Abstract

Modifications of histone proteins are fundamental to the regulation of epigenetic phenotypes. Dysregulations of histone modifications have been linked to the pathogenesis of diverse human diseases. However, identifying differential histone modifications in patients with immune-mediated diseases has been challenging, in part due to the lack of a powerful analytic platform to study histone modifications in the complex human immune system. We recently developed a highly multiplexed platform, Epigenetic landscape profiling using cytometry by Time-Of-Flight (EpiTOF), to analyze the global levels of a broad array of histone modifications in single cells using mass cytometry. In this review, we summarize the development of EpiTOF and discuss its potential applications in biomedical research. We anticipate that this platform will provide new insights into the roles of epigenetic regulation in hematopoiesis, immune cell functions, and immune system aging, and reveal aberrant epigenetic patterns associated with immune-mediated diseases.
Copyright © 2018. Published by Elsevier Inc.

Entities:  

Keywords:  Chromatin; EpiTOF; Epigenetics; Histone post-translational modifications; Immune system; Mass cytometry

Mesh：

Substances：

Year:  2018        PMID： 29960011      PMCID： PMC6422338          DOI： 10.1016/j.clim.2018.06.009

Source DB:  PubMed          Journal:  Clin Immunol        ISSN： 1521-6616            Impact factor:   3.969


  53 in total

Review 1.  Methyl-CpG-binding domain proteins: readers of the epigenome.

Authors:  Qian Du; Phuc-Loi Luu; Clare Stirzaker; Susan J Clark
Journal:  Epigenomics       Date:  2015-04-30       Impact factor: 4.778

2.  Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4.

Authors:  R E Sobel; R G Cook; C A Perry; A T Annunziato; C D Allis
Journal:  Proc Natl Acad Sci U S A       Date:  1995-02-14       Impact factor: 11.205

3.  USP49 deubiquitinates histone H2B and regulates cotranscriptional pre-mRNA splicing.

Authors:  Zhuo Zhang; Amanda Jones; Heui-Yun Joo; Dewang Zhou; Ying Cao; Shaoxia Chen; Hediye Erdjument-Bromage; Matthew Renfrow; Hang He; Paul Tempst; Tim M Townes; Keith E Giles; Ligeng Ma; Hengbin Wang
Journal:  Genes Dev       Date:  2013-07-03       Impact factor: 11.361

Review 4.  Readout of epigenetic modifications.

Authors:  Dinshaw J Patel; Zhanxin Wang
Journal:  Annu Rev Biochem       Date:  2013       Impact factor: 23.643

5.  A platinum-based covalent viability reagent for single-cell mass cytometry.

Authors:  Harris G Fienberg; Erin F Simonds; Wendy J Fantl; Garry P Nolan; Bernd Bodenmiller
Journal:  Cytometry A       Date:  2012-05-10       Impact factor: 4.355

6.  The sequence of the human genome.

Authors:  J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal:  Science       Date:  2001-02-16       Impact factor: 47.728

7.  Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.

Authors:  Hongshan Guo; Ping Zhu; Xinglong Wu; Xianlong Li; Lu Wen; Fuchou Tang
Journal:  Genome Res       Date:  2013-10-31       Impact factor: 9.043

8.  Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses.

Authors:  Marta Andres-Terre; Helen M McGuire; Yannick Pouliot; Erika Bongen; Timothy E Sweeney; Cristina M Tato; Purvesh Khatri
Journal:  Immunity       Date:  2015-12-15       Impact factor: 31.745

Review 9.  The molecular hallmarks of epigenetic control.

Authors:  C David Allis; Thomas Jenuwein
Journal:  Nat Rev Genet       Date:  2016-06-27       Impact factor: 53.242

Review 10.  Epigenetic regulation of asthma and allergic disease.

Authors:  Philippe Bégin; Kari C Nadeau
Journal:  Allergy Asthma Clin Immunol       Date:  2014-05-28       Impact factor: 3.406
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  6 in total

Review 1.  Single cell immune profiling in transplantation research.

Authors:  Lauren E Higdon; Steven Schaffert; Purvesh Khatri; Jonathan S Maltzman
Journal:  Am J Transplant       Date:  2019-03-20       Impact factor: 8.086

2.  Combining Isoprenoid Probes with Antibody Markers for Mass Cytometric Analysis of Prenylation in Single Cells.

Authors:  Zoë A Maxwell; Kiall F Suazo; Heather M G Brown; Mark D Distefano; Edgar A Arriaga
Journal:  Anal Chem       Date:  2022-08-11       Impact factor: 8.008

Review 3.  Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts.

Authors:  Reema Baskar; Sam C Kimmey; Sean C Bendall
Journal:  Trends Cell Biol       Date:  2022-02-16       Impact factor: 21.167

Review 4.  Single-cell technologies - studying rheumatic diseases one cell at a time.

Authors:  Peggie Cheung; Purvesh Khatri; Paul J Utz; Alex J Kuo
Journal:  Nat Rev Rheumatol       Date:  2019-06       Impact factor: 20.543

5.  Repression of CTSG, ELANE and PRTN3-mediated histone H3 proteolytic cleavage promotes monocyte-to-macrophage differentiation.

Authors:  Peggie Cheung; Steven Schaffert; Sarah E Chang; Mai Dvorak; Michele Donato; Claudia Macaubas; Mariko H Foecke; Tie-Mei Li; Lichao Zhang; John P Coan; Grant S Schulert; Alexei A Grom; Lauren A Henderson; Peter A Nigrovic; Joshua E Elias; Or Gozani; Elizabeth D Mellins; Purvesh Khatri; Paul J Utz; Alex J Kuo
Journal:  Nat Immunol       Date:  2021-05-20       Impact factor: 25.606

Review 6.  Applications of Single-Cell Omics in Tumor Immunology.

Authors:  Junwei Liu; Saisi Qu; Tongtong Zhang; Yufei Gao; Hongyu Shi; Kaichen Song; Wei Chen; Weiwei Yin
Journal:  Front Immunol       Date:  2021-06-09       Impact factor: 7.561
  6 in total

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