Proteogenomic Characterization of Endometrial Carcinoma.
Acetylation
Animals
Antigens, Neoplasm
/ genetics
Carcinoma
/ genetics
Endometrial Neoplasms
/ genetics
Epithelial-Mesenchymal Transition
/ genetics
Feedback, Physiological
Female
Gene Expression Regulation, Neoplastic
Genomic Instability
Humans
Mice
MicroRNAs
/ genetics
Microsatellite Repeats
Phosphorylation
Protein Processing, Post-Translational
Proteome
/ genetics
Signal Transduction
Transcriptome
CTNNB1
TP53
acetylation
circular RNA
endometrial cancer
endometrioid endometrial cancer
immune evasion
proteogenomics
proteomics
serous endometrial cancer
Journal
Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066
Informations de publication
Date de publication:
20 02 2020
20 02 2020
Historique:
received:
29
05
2019
revised:
11
11
2019
accepted:
16
01
2020
pubmed:
16
2
2020
medline:
25
8
2020
entrez:
16
2
2020
Statut:
ppublish
Résumé
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences of perturbations to the p53 and Wnt/β-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways. An extensive genome-wide acetylation survey yielded insights into regulatory mechanisms linking Wnt signaling and histone acetylation. We also characterized aspects of the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, identify new molecular associations of potential mechanistic significance in the development of endometrial cancers, and suggest novel approaches for identifying potential therapeutic targets.
Identifiants
pubmed: 32059776
pii: S0092-8674(20)30107-0
doi: 10.1016/j.cell.2020.01.026
pmc: PMC7233456
mid: NIHMS1566438
pii:
doi:
Substances chimiques
Antigens, Neoplasm
0
MicroRNAs
0
Proteome
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
729-748.e26Subventions
Organisme : NCI NIH HHS
ID : U24 CA210954
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210985
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210967
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210986
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210972
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210993
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210979
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA214125
Pays : United States
Organisme : NCI NIH HHS
ID : UG1 CA233339
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210955
Pays : United States
Organisme : NIGMS NIH HHS
ID : P20 GM130423
Pays : United States
Investigateurs
Anupriya Agarwal
(A)
Meenakshi Anurag
(M)
Dmitry Avtonomov
(D)
Chet Birger
(C)
Michael J Birrer
(MJ)
Simina M Boca
(SM)
William E Bocik
(WE)
Uma Borate
(U)
Melissa Borucki
(M)
Meghan C Burke
(MC)
Shuang Cai
(S)
Anna Calinawan
(A)
Steven A Carr
(SA)
Sonya Carter
(S)
Patricia Castro
(P)
Sandra Cerda
(S)
Michelle Chaikin
(M)
Daniel W Chan
(DW)
Doug Chan
(D)
Alyssa Charamut
(A)
Feng Chen
(F)
Jin Chen
(J)
Lijun Chen
(L)
Lin S Chen
(LS)
David Chesla
(D)
Milan G Chheda
(MG)
Arul M Chinnaiyan
(AM)
Shrabanti Chowdhury
(S)
Marcin P Cieslik
(MP)
David J Clark
(DJ)
Sandra Cottingham
(S)
Houston Culpepper
(H)
Jacob Day
(J)
Stephanie De Young
(S)
Emek Demir
(E)
Saravana Mohan Dhanasekaran
(SM)
Rajiv Dhir
(R)
Marcin J Domagalski
(MJ)
Peter Dottino
(P)
Brian Druker
(B)
Elizabeth Duffy
(E)
Maureen Dyer
(M)
Nathan J Edwards
(NJ)
Robert Edwards
(R)
Kim Elburn
(K)
Jayson B Field
(JB)
Alicia Francis
(A)
Stacey Gabriel
(S)
Yifat Geffen
(Y)
Daniel Geiszler
(D)
Michael A Gillette
(MA)
Andrew K Godwin
(AK)
Pamela Grady
(P)
Linda Hannick
(L)
Pushpa Hariharan
(P)
Sue Hilsenbeck
(S)
Barbara Hindenach
(B)
Katherine A Hoadley
(KA)
Runyu Hong
(R)
Galen Hostetter
(G)
James J Hsieh
(JJ)
Yingwei Hu
(Y)
Michael M Ittmann
(MM)
Eric Jaehnig
(E)
Scott D Jewell
(SD)
Jiayi Ji
(J)
Corbin D Jones
(CD)
Renee Karabon
(R)
Karen A Ketchum
(KA)
Munziba Khan
(M)
Beom-Jun Kim
(BJ)
Azra Krek
(A)
Tanya Krubit
(T)
Chandan Kumar-Sinha
(C)
Felipe D Leprevost
(FD)
Michael Lewis
(M)
Qing Kay Li
(QK)
Yize Li
(Y)
Hongwei Liu
(H)
Jan Lubinski
(J)
Weiping Ma
(W)
Rashna Madan
(R)
Ewa Malc
(E)
Anna Malovannaya
(A)
Sailaja Mareedu
(S)
Sanford P Markey
(SP)
Annette Marrero-Oliveras
(A)
John Martignetti
(J)
Jason McDermott
(J)
Peter B McGarvey
(PB)
John McGee
(J)
Piotr Mieczkowski
(P)
Francesmary Modugno
(F)
Rebecca Montgomery
(R)
Chelsea J Newton
(CJ)
Gilbert S Omenn
(GS)
Amanda G Paulovich
(AG)
Amy M Perou
(AM)
Francesca Petralia
(F)
Paul Piehowski
(P)
Larisa Polonskaya
(L)
Liqun Qi
(L)
Shannon Richey
(S)
Karna Robinson
(K)
Nancy Roche
(N)
Daniel C Rohrer
(DC)
Eric E Schadt
(EE)
Michael Schnaubelt
(M)
Yan Shi
(Y)
Tara Skelly
(T)
Lori J Sokoll
(LJ)
Xiaoyu Song
(X)
Stephen E Stein
(SE)
James Suh
(J)
Donghui Tan
(D)
Darlene Tansil
(D)
Guo Ci Teo
(GC)
Ratna R Thangudu
(RR)
Cristina Tognon
(C)
Elie Traer
(E)
Jeffrey Tyner
(J)
Ki Sung Um
(KS)
Dana R Valley
(DR)
Negin Vatanian
(N)
Pankaj Vats
(P)
Uma Velvulou
(U)
Michael Vernon
(M)
Liang-Bo Wang
(LB)
Ying Wang
(Y)
Alex Webster
(A)
Thomas Westbrook
(T)
David Wheeler
(D)
Jeffrey R Whiteaker
(JR)
George D Wilson
(GD)
Yuriy Zakhartsev
(Y)
Robert Zelt
(R)
Hui Zhang
(H)
Yuping Zhang
(Y)
Zhen Zhang
(Z)
Grace Zhao
(G)
Informations de copyright
Copyright © 2020 Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration Of Interests The authors declare no competing interests.
Références
Clin Cancer Res. 2016 Feb 1;22(3):609-20
pubmed: 26420858
Genome Res. 2019 Mar;29(3):485-493
pubmed: 30610011
J Biol Chem. 2000 Jun 16;275(24):18424-31
pubmed: 10747992
Gynecol Oncol. 2002 Jul;86(1):62-8
pubmed: 12079302
Nat Rev Mol Cell Biol. 2014 Aug;15(8):536-50
pubmed: 25053359
Cell Rep. 2018 Apr 3;23(1):227-238.e3
pubmed: 29617662
Front Oncol. 2015 Nov 11;5:249
pubmed: 26618142
Hum Mol Genet. 1999 Apr;8(4):661-6
pubmed: 10072435
Front Oncol. 2018 May 28;8:179
pubmed: 29911069
Cancer. 2017 Mar 1;123(5):802-813
pubmed: 28061006
J Oncol. 2015;2015:865816
pubmed: 25883654
Oncotarget. 2015 Sep 29;6(29):28440-52
pubmed: 26308378
N Engl J Med. 2016 Sep 22;375(12):1109-12
pubmed: 27653561
Genome Res. 2016 Jan;26(1):108-18
pubmed: 26556708
J Proteome Res. 2016 Mar 4;15(3):691-706
pubmed: 26653538
J Mol Biol. 2009 Jan 9;385(1):249-65
pubmed: 18996393
Nucleic Acids Res. 2015 Jan;43(Database issue):D531-5
pubmed: 25332398
Oncogene. 2016 Jul 7;35(27):3514-23
pubmed: 26522722
Science. 2007 May 25;316(5828):1160-6
pubmed: 17525332
Cell. 2018 Apr 5;173(2):371-385.e18
pubmed: 29625053
Nat Biotechnol. 2012 May;30(5):413-21
pubmed: 22544022
Nucleic Acids Res. 2016 Jan 4;44(D1):D548-54
pubmed: 26467481
Nature. 2016 May 25;534(7605):55-62
pubmed: 27251275
Nucleic Acids Res. 2016 Jul 27;44(13):6274-86
pubmed: 27260798
Nat Biotechnol. 2013 Mar;31(3):213-9
pubmed: 23396013
Nat Commun. 2014 Oct 31;5:5277
pubmed: 25358478
Bioinformatics. 2019 Apr 1;35(7):1249-1251
pubmed: 30169737
J Proteome Res. 2008 Aug;7(8):3354-63
pubmed: 18597511
Bioinformatics. 2017 Jul 15;33(14):2131-2139
pubmed: 28334396
Mol Cell Biol. 2004 Apr;24(8):3404-14
pubmed: 15060161
Bioinformatics. 2010 Mar 1;26(5):589-95
pubmed: 20080505
Nucleic Acids Res. 2019 Jul 2;47(W1):W199-W205
pubmed: 31114916
Hum Pathol. 2002 Feb;33(2):206-12
pubmed: 11957146
J Biomed Inform. 2011 Oct;44(5):839-47
pubmed: 21605702
Epigenetics. 2010 Aug 16;5(6):491-8
pubmed: 20543579
Nat Rev Cancer. 2018 Jan;18(1):51-63
pubmed: 29192214
Exp Ther Med. 2018 Jul;16(1):133-140
pubmed: 29896233
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nat Commun. 2016 Apr 06;7:11215
pubmed: 27050392
Nat Commun. 2017 Mar 28;8:14864
pubmed: 28348404
Cancer Res. 2013 Sep 15;73(18):5609-12
pubmed: 24014594
CA Cancer J Clin. 2018 Jan;68(1):7-30
pubmed: 29313949
Nucleic Acids Res. 2018 Jan 4;46(D1):D1068-D1073
pubmed: 29156001
Cell Rep. 2013 Sep 26;4(6):1116-30
pubmed: 24055055
Genes Dev. 2000 Jun 15;14(12):1448-59
pubmed: 10859164
Cold Spring Harb Perspect Med. 2016 Nov 1;6(11):
pubmed: 27503997
Mod Pathol. 2015 Jun;28(6):836-44
pubmed: 25720322
Cell. 2019 Feb 7;176(4):831-843.e22
pubmed: 30735634
J Biol Chem. 2002 Jul 12;277(28):25562-7
pubmed: 11973335
CA Cancer J Clin. 2019 Jan;69(1):7-34
pubmed: 30620402
Mol Cell Biol. 2002 Dec;22(24):8612-25
pubmed: 12446780
Cancer Sci. 2009 Aug;100(8):1502-9
pubmed: 19459850
Oncogene. 2018 Feb 1;37(5):555-565
pubmed: 28991235
Dev Cell. 2018 Jun 4;45(5):637-650.e7
pubmed: 29870721
J Biol Chem. 2007 Jul 13;282(28):20059-63
pubmed: 17502367
Cell. 2016 Jul 28;166(3):755-765
pubmed: 27372738
Science. 2009 Aug 14;325(5942):834-40
pubmed: 19608861
Nucleic Acids Res. 2018 Jan 4;46(D1):D296-D302
pubmed: 29126174
Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1914-8
pubmed: 9050879
Cancer Sci. 2007 Nov;98(11):1803-8
pubmed: 17784873
Cell. 2015 Mar 12;160(6):1125-34
pubmed: 25768908
J Natl Cancer Inst. 2014 Sep 10;106(9):
pubmed: 25214561
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
Gynecol Oncol. 2014 Aug;134(2):426-7
pubmed: 24952365
Mol Cell. 2009 Mar 13;33(5):591-601
pubmed: 19285943
Nat Cell Biol. 2017 May;19(5):518-529
pubmed: 28414315
J Clin Oncol. 2009 Nov 10;27(32):5331-6
pubmed: 19805679
Semin Cancer Biol. 2012 Oct;22(5-6):417-27
pubmed: 22548723
Science. 1998 Dec 4;282(5395):1893-7
pubmed: 9836640
Nat Rev Mol Cell Biol. 2014 Mar;15(3):178-96
pubmed: 24556840
Cell Rep. 2016 Nov 15;17(8):2075-2086
pubmed: 27851969
Cancer Discov. 2017 Feb;7(2):188-201
pubmed: 27903500
Cell. 2019 Feb 7;176(4):869-881.e13
pubmed: 30735636
Cancer Res. 2018 May 15;78(10):2732-2746
pubmed: 29472518
Histol Histopathol. 2011 Jul;26(7):941-51
pubmed: 21630223
Dis Markers. 2018 Dec 17;2018:3810108
pubmed: 30647797
Cancer Res. 2014 Jan 1;74(1):287-97
pubmed: 24240700
BMC Bioinformatics. 2011 Aug 04;12:323
pubmed: 21816040
BMC Cancer. 2017 Oct 23;17(1):696
pubmed: 29061125
Nature. 2008 Sep 4;455(7209):119-23
pubmed: 18615013
BMC Bioinformatics. 2017 Mar 21;18(1):183
pubmed: 28327092
Mol Cell Proteomics. 2016 Mar;15(3):1060-71
pubmed: 26631509
DNA Repair (Amst). 2008 Jan 1;7(1):48-56
pubmed: 17827074
Cell Cycle. 2015;14(4):481-7
pubmed: 25607528
Comput Biol Chem. 2008 Jun;32(3):215-7
pubmed: 18440872
Trends Cancer. 2017 Aug;3(8):583-592
pubmed: 28780935
Nature. 2009 Nov 5;462(7269):108-12
pubmed: 19847166
Bioinformatics. 2015 Dec 1;31(23):3838-40
pubmed: 26243018
Cell Biol Int. 2017 Sep;41(9):1056-1064
pubmed: 28707774
Trends Biotechnol. 2014 Sep;32(9):456-65
pubmed: 24998519
Nature. 2013 Mar 21;495(7441):333-8
pubmed: 23446348
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Nat Genet. 2016 Aug;48(8):827-37
pubmed: 27294619
IEEE Trans Pattern Anal Mach Intell. 2013 Jul;35(7):1592-605
pubmed: 23681989
J Natl Cancer Inst. 2018 Mar 1;110(3):
pubmed: 28903484
J Proteome Res. 2015 Jun 5;14(6):2707-13
pubmed: 25873244
Exp Cell Res. 2015 Jun 10;334(2):350-8
pubmed: 25842165
Nat Commun. 2018 Jan 2;9(1):20
pubmed: 29295995
Elife. 2017 Oct 20;6:
pubmed: 29052541
Nucleic Acids Res. 2016 Jan 8;44(1):e3
pubmed: 26271990
Cell Rep. 2017 Jan 3;18(1):248-262
pubmed: 28052254
Cancer Biol Ther. 2013 Jan;14(1):13-9
pubmed: 23114646
Cell. 2005 Jan 14;120(1):15-20
pubmed: 15652477
Clin Cancer Res. 2017 Dec 1;23(23):7232-7241
pubmed: 28939739
Cell. 2013 Nov 7;155(4):858-68
pubmed: 24209623
Nat Cell Biol. 2016 Jun 28;18(7):711-7
pubmed: 27350441
Nucleic Acids Res. 2016 Apr 7;44(6):2859-72
pubmed: 26837576
Mol Cancer Res. 2017 Aug;15(8):1051-1062
pubmed: 28483946
Nucleic Acids Res. 2009 Jan;37(Database issue):D816-9
pubmed: 18838390
Nucleic Acids Res. 2011 Jan;39(Database issue):D163-9
pubmed: 21071411
Genome Biol. 2015 Jan 13;16:4
pubmed: 25583365
BMC Bioinformatics. 2013 Jan 16;14:7
pubmed: 23323831
Nat Biotechnol. 2006 Oct;24(10):1285-92
pubmed: 16964243
Cell Res. 2011 Feb;21(2):316-26
pubmed: 20820189
Bioinformatics. 2009 Nov 1;25(21):2865-71
pubmed: 19561018
J Immunol. 2017 Nov 1;199(9):3360-3368
pubmed: 28978689
DNA Repair (Amst). 2019 Jan;73:34-48
pubmed: 30448208
Oncogene. 2017 Jul 6;36(27):3925-3933
pubmed: 28319071
J Biol Chem. 2014 Oct 3;289(40):27386-99
pubmed: 25143390
Clin Cancer Res. 2016 Jun 15;22(12):2865-73
pubmed: 26763250
Oncotarget. 2016 Jun 28;7(26):39885-39893
pubmed: 27213585
Nat Commun. 2018 Aug 1;9(1):3012
pubmed: 30069007
Nucleic Acids Res. 2008 Jan;36(Database issue):D646-50
pubmed: 17965090
PLoS One. 2010 Feb 02;5(2):e9001
pubmed: 20126405
N Engl J Med. 2017 Oct 12;377(15):1409-1412
pubmed: 29020592
Mod Pathol. 2017 Jul;30(7):1032-1041
pubmed: 28281553
Cell. 2004 Dec 17;119(6):861-72
pubmed: 15607981
Genome Biol. 2011;12(1):R1
pubmed: 21205303
Genome Biol. 2014 Dec 03;15(12):503
pubmed: 25599564
Nature. 2013 Aug 22;500(7463):415-21
pubmed: 23945592
Cancers (Basel). 2017 Oct 24;9(10):
pubmed: 29064439
Cell. 2017 Jul 27;170(3):577-592.e10
pubmed: 28753431
Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655
pubmed: 29145629
Am J Clin Pathol. 2010 Jun;133(6):899-908
pubmed: 20472848
Am J Pathol. 2002 Feb;160(2):389-401
pubmed: 11839557
PLoS One. 2014 May 29;9(5):e98438
pubmed: 24875183
PLoS Biol. 2010 Jan 26;8(1):e1000287
pubmed: 20126263
Chromosoma. 2012 Dec;121(6):565-72
pubmed: 22566210
Nature. 2014 Sep 18;513(7518):382-7
pubmed: 25043054
Cell. 2019 Sep 19;179(1):236-250.e18
pubmed: 31495571
Cell. 2019 May 2;177(4):1035-1049.e19
pubmed: 31031003
Genome Res. 2012 Mar;22(3):568-76
pubmed: 22300766
Am J Surg Pathol. 2008 Feb;32(2):304-15
pubmed: 18223334
CA Cancer J Clin. 2018 Nov;68(6):394-424
pubmed: 30207593
Mol Cancer Ther. 2009 May;8(5):1055-66
pubmed: 19435871
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Genes Dev. 2015 Sep 1;29(17):1850-62
pubmed: 26341558
Crit Rev Oncol Hematol. 2019 Mar;135:21-29
pubmed: 30819443
Cell. 2016 Jun 30;166(1):21-45
pubmed: 27368099
Bioinformatics. 2012 Jul 15;28(14):1811-7
pubmed: 22581179
Oncotarget. 2017 Jul 31;8(40):68530-68541
pubmed: 28978135
Cell. 2018 Apr 5;173(2):321-337.e10
pubmed: 29625050
Immunotherapy. 2019 Feb;11(2):69-74
pubmed: 30727800
J Proteome Res. 2012 Feb 3;11(2):1009-17
pubmed: 22103967
Nature. 2013 May 2;497(7447):67-73
pubmed: 23636398
Genome Res. 2012 Aug;22(8):1589-98
pubmed: 22759861
Oncotarget. 2017 Nov 24;9(4):5492-5508
pubmed: 29435196
Bioinformatics. 2014 Apr 1;30(7):1015-6
pubmed: 24371154
EMBO J. 2018 Jul 2;37(13):
pubmed: 29871889
Nucleic Acids Res. 2018 Jan 4;46(D1):D956-D963
pubmed: 29136207
Mol Cancer Ther. 2017 Nov;16(11):2598-2608
pubmed: 28835386
Int J Oncol. 2015 Apr;46(4):1498-506
pubmed: 25625960
Annu Rev Biochem. 2004;73:39-85
pubmed: 15189136
Cell. 2006 Sep 22;126(6):1203-17
pubmed: 16990141
Nat Genet. 2019 Feb;51(2):202-206
pubmed: 30643254
Nat Methods. 2016 Nov 29;13(12):966-967
pubmed: 27898060
Cell Death Differ. 2013 Jul;20(7):855-7
pubmed: 23749181
Science. 2002 May 31;296(5573):1653-5
pubmed: 12040185
Cell Death Differ. 2012 Dec;19(12):1992-2002
pubmed: 22790872
J Cell Sci. 2017 May 1;130(9):1532-1544
pubmed: 28289266
Bioinformatics. 2012 Dec 15;28(24):3232-9
pubmed: 23093608
Nucleic Acids Res. 2014 Jan;42(Database issue):D975-9
pubmed: 24297256
Bioinformatics. 2014 Dec 1;30(23):3310-6
pubmed: 25143287
Nat Biotechnol. 2017 Oct;35(10):951-959
pubmed: 28892075
Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2651-6
pubmed: 12601173
Lancet. 2005 Aug 6-12;366(9484):491-505
pubmed: 16084259