Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels.
CAR-T cell
epigenetics
lentiviral integration site
single-cell genomics
Journal
Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
Titre abrégé: Proc Natl Acad Sci U S A
Pays: United States
ID NLM: 7505876
Informations de publication
Date de publication:
10 03 2020
10 03 2020
Historique:
pubmed:
26
2
2020
medline:
14
7
2020
entrez:
26
2
2020
Statut:
ppublish
Résumé
Chimeric antigen receptor (CAR)-T immunotherapy has yielded impressive results in several B cell malignancies, establishing itself as a powerful means to redirect the natural properties of T lymphocytes. In this strategy, the T cell genome is modified by the integration of lentiviral vectors encoding CAR that direct tumor cell killing. However, this therapeutic approach is often limited by the extent of CAR-T cell expansion in vivo. A major outstanding question is whether or not CAR-T integration itself enhances the proliferative competence of individual T cells by rewiring their regulatory landscape. To address this question, it is critical to define the identity of an individual CAR-T cell and simultaneously chart where the CAR-T vector integrates into the genome. Here, we report the development of a method called EpiVIA (https://github.com/VahediLab/epiVIA) for the joint profiling of the chromatin accessibility and lentiviral integration site analysis at the population and single-cell levels. We validate our technique in clonal cells with previously defined integration sites and further demonstrate the ability to measure lentiviral integration sites and chromatin accessibility of host and viral genomes at the single-cell resolution in CAR-T cells. We anticipate that EpiVIA will enable the single-cell deconstruction of gene regulation during CAR-T therapy, leading to the discovery of cellular factors associated with durable treatment.
Identifiants
pubmed: 32094195
pii: 1919259117
doi: 10.1073/pnas.1919259117
pmc: PMC7071901
doi:
Substances chimiques
Chromatin
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5442-5452Informations de copyright
Copyright © 2020 the Author(s). Published by PNAS.
Déclaration de conflit d'intérêts
The authors declare no competing interest.
Références
Mol Cell. 2018 Sep 6;71(5):858-871.e8
pubmed: 30078726
Cell. 2002 Aug 23;110(4):521-9
pubmed: 12202041
J Biol Chem. 1994 Oct 7;269(40):25031-41
pubmed: 7929189
Adv Immunol. 2016;129:277-314
pubmed: 26791862
Nature. 2018 Jun;558(7709):307-312
pubmed: 29849141
Genome Res. 2019 Feb;29(2):236-249
pubmed: 30655336
Mol Ther Methods Clin Dev. 2016 Dec 18;4:39-49
pubmed: 28344990
Cell Host Microbe. 2016 Dec 14;20(6):798-809
pubmed: 27866901
J Infect Dis. 2007 Mar 1;195(5):716-25
pubmed: 17262715
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):5913-7
pubmed: 8016088
Retrovirology. 2017 Jul 28;14(1):39
pubmed: 28754126
Nat Commun. 2019 Sep 6;10(1):4059
pubmed: 31492853
Cell. 2015 Jan 29;160(3):420-32
pubmed: 25635456
EMBO J. 1994 Oct 3;13(19):4704-14
pubmed: 7925312
Retrovirology. 2016 Jul 04;13(1):47
pubmed: 27377064
Nucleic Acids Res. 2014 Apr;42(7):4257-69
pubmed: 24464997
J Clin Invest. 2018 Aug 31;128(9):4074-4085
pubmed: 30024859
Cell Host Microbe. 2016 May 11;19(5):588-98
pubmed: 27173927
Cell Stem Cell. 2018 Jul 05;23(1):132-146.e9
pubmed: 29979988
J Virol. 2004 Jun;78(12):6122-33
pubmed: 15163705
Viruses. 2014 Oct 31;6(11):4140-64
pubmed: 25365582
Retrovirology. 2013 Aug 16;10:90
pubmed: 23953889
Nat Methods. 2007 Dec;4(12):1051-7
pubmed: 18049469
Nat Immunol. 2014 Apr;15(4):373-83
pubmed: 24584090
Cell. 2018 Aug 23;174(5):1309-1324.e18
pubmed: 30078704
Genome Res. 2015 Nov;25(11):1757-70
pubmed: 26314830
Mol Ther Methods Clin Dev. 2017 Oct 05;8:31-41
pubmed: 29159201
Nat Biotechnol. 2019 Aug;37(8):925-936
pubmed: 31375813
Nature. 2015 Feb 19;518(7539):317-30
pubmed: 25693563
Nat Biotechnol. 2018 Dec 03;:
pubmed: 30531897
Science. 1989 Nov 10;246(4931):780-6
pubmed: 2814500
Cell. 1992 Oct 2;71(1):11-22
pubmed: 1394427
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Nat Methods. 2017 Oct;14(10):975-978
pubmed: 28825706
Nature. 2015 Jul 16;523(7560):366-9
pubmed: 26061770
Front Genet. 2018 Aug 15;9:319
pubmed: 30158954
Nat Rev Microbiol. 2017 Feb;15(2):69-82
pubmed: 27941817
Nat Rev Genet. 2019 Apr;20(4):207-220
pubmed: 30675018
J Virol. 2016 Apr 14;90(9):4511-4519
pubmed: 26912621
Science. 2014 Jul 11;345(6193):179-83
pubmed: 24968937
Genes Dev. 2015 Nov 1;29(21):2287-97
pubmed: 26545813
Science. 2014 Aug 1;345(6196):570-3
pubmed: 25011556
Nature. 2015 May 14;521(7551):227-31
pubmed: 25731161
Nat Commun. 2019 Feb 4;10(1):575
pubmed: 30718508
J Acquir Immune Defic Syndr. 2003 Jul 1;33(3):308-20
pubmed: 12843741
Immunity. 2018 Feb 20;48(2):243-257.e10
pubmed: 29466756
Methods Mol Biol. 2016;1418:335-51
pubmed: 27008022
Nat Commun. 2016 May 06;7:11485
pubmed: 27151365