Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
22 02 2023
22 02 2023
Historique:
received:
17
06
2021
accepted:
20
01
2023
entrez:
22
2
2023
pubmed:
23
2
2023
medline:
25
2
2023
Statut:
epublish
Résumé
Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer's proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer.
Identifiants
pubmed: 36813776
doi: 10.1038/s41467-023-36202-y
pii: 10.1038/s41467-023-36202-y
pmc: PMC9946941
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
982Informations de copyright
© 2023. The Author(s).
Références
Nat Protoc. 2009;4(8):1184-91
pubmed: 19617889
Cancer Cell. 2015 Jan 12;27(1):15-26
pubmed: 25584892
Genomics Proteomics Bioinformatics. 2021 Apr;19(2):253-266
pubmed: 33662621
Genome Biol. 2015 Feb 13;16:35
pubmed: 25786235
Genome Res. 2014 Nov;24(11):1881-93
pubmed: 25060187
Bioinformatics. 2011 Jun 15;27(12):1739-40
pubmed: 21546393
Nucleic Acids Res. 2015 Apr 20;43(7):e47
pubmed: 25605792
Nat Methods. 2014 Apr;11(4):396-8
pubmed: 24633410
Cell. 2019 Nov 14;179(5):1207-1221.e22
pubmed: 31730858
Annu Rev Med. 2016;67:11-28
pubmed: 26473415
Nat Commun. 2018 Jan 18;9(1):284
pubmed: 29348443
Nat Biotechnol. 2021 May;39(5):599-608
pubmed: 33462507
Genome Res. 2017 Mar;27(3):491-499
pubmed: 28100584
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Genome Res. 2018 Aug;28(8):1217-1227
pubmed: 29898899
BMC Genomics. 2018 Jun 19;19(1):477
pubmed: 29914354
Nucleic Acids Res. 2012 May;40(10):4288-97
pubmed: 22287627
Nat Rev Genet. 2017 Apr;18(4):213-229
pubmed: 28190876
Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5
pubmed: 20837533
R J. 2016 Aug;8(1):289-317
pubmed: 27818791
N Engl J Med. 2012 Mar 8;366(10):883-892
pubmed: 22397650
Nature. 2019 Jan;565(7738):251-254
pubmed: 30602787
Nat Biotechnol. 2022 Oct;40(10):1452-1457
pubmed: 35637418
Bioinformatics. 2012 Feb 1;28(3):423-5
pubmed: 22155870
Genome Biol. 2015 Feb 13;16:36
pubmed: 25786108
Nucleic Acids Res. 2015 Feb 27;43(4):e23
pubmed: 25477383
Genome Biol. 2020 Jan 14;21(1):10
pubmed: 31937348
Nat Methods. 2020 Apr;17(4):414-421
pubmed: 32203388
BMC Bioinformatics. 2014 Feb 01;15:35
pubmed: 24484323
Biochim Biophys Acta Rev Cancer. 2017 Apr;1867(2):127-138
pubmed: 28193548
Nat Methods. 2020 Feb;17(2):137-145
pubmed: 31792435
Genome Biol. 2016 May 05;17:86
pubmed: 27149953
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
PLoS Biol. 2011 Jul;9(7):e1001091
pubmed: 21750661
Nucleic Acids Res. 2019 May 7;47(8):e47
pubmed: 30783653
Science. 1976 Oct 1;194(4260):23-8
pubmed: 959840
Genome Biol. 2019 Mar 12;20(1):54
pubmed: 30866997
BMC Cancer. 2012 Aug 29;12:379
pubmed: 22931248
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Biochim Biophys Acta Rev Cancer. 2017 Apr;1867(2):151-161
pubmed: 28110020
Nat Biotechnol. 2014 Apr;32(4):381-386
pubmed: 24658644
Exp Mol Med. 2020 Sep;52(9):1452-1465
pubmed: 32929226
Nat Biotechnol. 2020 Jun;38(6):708-714
pubmed: 32518404
Genome Biol. 2017 Mar 1;18(1):44
pubmed: 28249593
Nat Methods. 2017 Feb;14(2):167-173
pubmed: 28068316
Cold Spring Harb Perspect Med. 2017 Aug 1;7(8):
pubmed: 28270531
Nat Commun. 2019 Jun 21;10(1):2750
pubmed: 31227714
Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):E5528-37
pubmed: 27573852
Genome Biol. 2022 Jan 21;23(1):31
pubmed: 35063006
Bioinformatics. 2012 Jul 15;28(14):1811-7
pubmed: 22581179
Nat Commun. 2017 Jan 16;8:14049
pubmed: 28091601
Genome Biol. 2017 Apr 26;18(1):74
pubmed: 28446220
Cell. 2012 May 25;149(5):994-1007
pubmed: 22608083
Mol Ecol Resour. 2017 Jan;17(1):44-53
pubmed: 27401132
Nat Methods. 2016 Jul;13(7):573-6
pubmed: 27183439
Nature. 2012 Jan 11;481(7382):506-10
pubmed: 22237025
Nucleic Acids Res. 2012 Sep 1;40(17):e133
pubmed: 22638577
Genome Biol. 2016 Apr 15;17:69
pubmed: 27083415