Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

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dc.contributor Sistema FMUSP-HC: Faculdade de Medicina da Universidade de São Paulo (FMUSP) e Hospital das Clínicas da FMUSP
dc.contributor.author CAMPBELL, Joshua D.
YAU, Christina
BOWLBY, Reanne
LIU, Yuexin
BRENNAN, Kevin
FAN, Huihui
TAYLOR, Alison M.
WANG, Chen
WALTER, Vonn
AKBANI, Rehan
BYERS, Lauren Averett
CREIGHTON, Chad J.
COARFA, Cristian
SHIH, Juliann
CHERNIACK, Andrew D.
GEVAERT, Olivier
PRUNELLO, Marcos
SHEN, Hui
ANUR, Pavana
CHEN, Jianhong
CHENG, Hui
HAYES, D. Neil
BULLMAN, Susan
PEDAMALLU, Chandra Sekhar
OJESINA, Akinyemi I.
SADEGHI, Sara
MUNGALL, Karen L.
ROBERTSON, A. Gordon
BENZ, Christopher
SCHULTZ, Andre
KANCHI, Rupa S.
GAY, Carl M.
HEGDE, Apurva
DIAO, Lixia
WANG, Jing
MA, Wencai
SUMAZIN, Pavel
CHIU, Hua-Sheng
CHEN, Ting-Wen
GUNARATNE, Preethi
DONEHOWER, Larry
RADER, Janet S.
ZUNA, Rosemary
AL-AHMADIE, Hikmat
LAZAR, Alexander J.
FLORES, Elsa R.
TSAI, Kenneth Y.
ZHOU, Jane H.
RUSTGI, Anil K.
DRILL, Esther
SHEN, Ronglei
WONG, Christopher K.
STUART, Joshua M.
LAIRD, Peter W.
HOADLEY, Katherine A.
WEINSTEIN, John N.
PETO, Myron
PICKERING, Curtis R.
CHEN, Zhong
WAES, Carter Van
dc.date.issued 2018
dc.identifier.citation CELL REPORTS, v.23, n.1, p.194-212.e6, 2018
dc.identifier.issn 2211-1247
dc.identifier.uri http://observatorio.fm.usp.br/handle/OPI/30112
dc.description.abstract This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the Delta Np63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.
dc.description.sponsorship · NIH [U54 HG003273, U54 HG003067, U54 HG003079, U24 CA143799, U24 CA143835, U24 CA143840, U24 CA143843, U24 CA143845, U24 CA143848, U24 CA143858, U24 CA143866, U24 CA143867, U24 CA143882, U24 CA143883, U24 CA144025, P30 CA016672]
· NIDCD [ZIA-DC-000074]
dc.language.iso eng
dc.publisher CELL PRESS
dc.relation.ispartof Cell Reports
dc.rights openAccess
dc.subject.other cell carcinoma; fanconi-anemia; neck-cancer; human-papillomavirus; antitumor-activity; tumor types; stem-cells; human head; inhibitor; expression
dc.title Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
dc.type article
dc.rights.holder Copyright CELL PRESS
dc.contributor.groupauthor Canc Genome Atlas Res Network
LONGATTO-FILHO, Adhemar FMUSP-HC
dc.description.group LIM/14
dc.identifier.doi 10.1016/j.celrep.2018.03.063
dc.identifier.pmid 29617660
dc.type.category original article
dc.type.version publishedVersion
hcfmusp.author LONGATTO-FILHO, Adhemar:FM:
hcfmusp.author.external · CAMPBELL, Joshua D.:Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02215 USA; MIT, Eli & Edythe L Broad Inst, Cambridge, MA 02142 USA; Harvard Univ, Cambridge, MA 02142 USA; Boston Univ, Sch Med, Boston, MA 02118 USA
· YAU, Christina:Univ Calif San Francisco, Dept Surg, San Francisco, CA 94115 USA
· BOWLBY, Reanne:Buck Inst Res Aging, 8001 Redwood Blvd, Novato, CA 94945 USA
· LIU, Yuexin:BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada
· BRENNAN, Kevin:Univ Texas MD Anderson Canc Ctr, Dept Bioinformat & Computat Biol, Houston, TX 77030 USA
· FAN, Huihui:Stanford Univ, Dept Med Biomed Informat Res, Stanford, CA 94305 USA
· TAYLOR, Alison M.:Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02215 USA; MIT, Eli & Edythe L Broad Inst, Cambridge, MA 02142 USA; Harvard Univ, Cambridge, MA 02142 USA
· WANG, Chen:Van Andel Res Inst, Ctr Epigenet, Grand Rapids, MI 49503 USA
· WALTER, Vonn:Mayo Clin, Dept Hlth Sci Res, Div Biomed Stat & Informat, Rochester, MN 55905 USA; Penn State Milton Hershey Med Ctr, Dept Publ Hlth Sci, Hershey, PA 17033 USA
· AKBANI, Rehan:BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada
· BYERS, Lauren Averett:BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada; Univ N Carolina, Lineberger Comprehens Canc Ctr, Chapel Hill, NC 27599 USA
· CREIGHTON, Chad J.:BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada; Univ Texas MD Anderson Canc Ctr, Dept Thorac Head & Neck Med Oncol, Houston, TX 77030 USA; Baylor Coll Med, Dept Med, Houston, TX 77030 USA
· COARFA, Cristian:Baylor Coll Med, Dan L Duncan Comprehens Canc Ctr, Div Biostat, Houston, TX 77030 USA
· SHIH, Juliann:Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02215 USA; MIT, Eli & Edythe L Broad Inst, Cambridge, MA 02142 USA; Harvard Univ, Cambridge, MA 02142 USA
· CHERNIACK, Andrew D.:Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02215 USA; MIT, Eli & Edythe L Broad Inst, Cambridge, MA 02142 USA; Harvard Univ, Cambridge, MA 02142 USA
· GEVAERT, Olivier:Univ Texas MD Anderson Canc Ctr, Dept Bioinformat & Computat Biol, Houston, TX 77030 USA
· PRUNELLO, Marcos:Univ Texas MD Anderson Canc Ctr, Dept Bioinformat & Computat Biol, Houston, TX 77030 USA
· SHEN, Hui:Stanford Univ, Dept Med Biomed Informat Res, Stanford, CA 94305 USA
· ANUR, Pavana:Baylor Coll Med, Dept Mol & Cell Biol, Houston, TX 77030 USA
· CHEN, Jianhong:Oregon Hlth & Sci Univ, Dept Mol & Med Genet, Portland, OR 97201 USA
· CHENG, Hui:Oregon Hlth & Sci Univ, Dept Mol & Med Genet, Portland, OR 97201 USA
· HAYES, D. Neil:Penn State Milton Hershey Med Ctr, Dept Publ Hlth Sci, Hershey, PA 17033 USA
· BULLMAN, Susan:Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02215 USA; MIT, Eli & Edythe L Broad Inst, Cambridge, MA 02142 USA; Harvard Univ, Cambridge, MA 02142 USA
· PEDAMALLU, Chandra Sekhar:Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02215 USA; MIT, Eli & Edythe L Broad Inst, Cambridge, MA 02142 USA; Harvard Univ, Cambridge, MA 02142 USA
· OJESINA, Akinyemi I.:NIH, Natl Inst Deafness & Other Commun Disorders, Head & Neck Surg Branch, Bethesda, MD 20892 USA; Univ Alabama Birmingham, Dept Epidemiol, Birmingham, AL 35294 USA
· SADEGHI, Sara:Buck Inst Res Aging, 8001 Redwood Blvd, Novato, CA 94945 USA
· MUNGALL, Karen L.:Buck Inst Res Aging, 8001 Redwood Blvd, Novato, CA 94945 USA
· ROBERTSON, A. Gordon:Buck Inst Res Aging, 8001 Redwood Blvd, Novato, CA 94945 USA
· BENZ, Christopher:Univ Calif San Francisco, Dept Surg, San Francisco, CA 94115 USA
· SCHULTZ, Andre:BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada
· KANCHI, Rupa S.:BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada
· GAY, Carl M.:Univ N Carolina, Lineberger Comprehens Canc Ctr, Chapel Hill, NC 27599 USA
· HEGDE, Apurva:BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada
· DIAO, Lixia:BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada
· WANG, Jing:BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada
· MA, Wencai:BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada
· SUMAZIN, Pavel:Hudson Alpha Inst Biotechnol, Huntsville, AL 35806 USA
· CHIU, Hua-Sheng:Hudson Alpha Inst Biotechnol, Huntsville, AL 35806 USA
· CHEN, Ting-Wen:Hudson Alpha Inst Biotechnol, Huntsville, AL 35806 USA
· GUNARATNE, Preethi:Baylor Coll Med, Texas Childrens Canc Ctr, Dept Med Pediat, Houston, TX 77030 USA; Univ Houston, UH SeqNEdit Core, Dept Biol & Biochem, Houston, TX 77204 USA
· DONEHOWER, Larry:Baylor Coll Med, Human Genome Sequencing Ctr, Houston, TX 77030 USA
· RADER, Janet S.:Baylor Coll Med, Ctr Comparat Med, Houston, TX 77030 USA
· ZUNA, Rosemary:Med Coll Wisconsin, Dept Obstet & Gynecol, Milwaukee, WI 53226 USA
· AL-AHMADIE, Hikmat:Univ Oklahoma, Hlth Sci Ctr, Dept Pathol, Oklahoma City, OK 73104 USA
· LAZAR, Alexander J.:Mem Sloan Kettering Canc Ctr, Dept Pathol, New York, NY 10065 USA; Univ Texas MD Anderson Canc Ctr, Dept Pathol, Houston, TX 77401 USA; Univ Texas MD Anderson Canc Ctr, Dept Genom Med, Houston, TX 77401 USA; Univ Texas MD Anderson Canc Ctr, Dept Dermatol, Houston, TX 77401 USA
· FLORES, Elsa R.:Univ Texas MD Anderson Canc Ctr, Dept Translat Mol Pathol, Houston, TX 77401 USA
· TSAI, Kenneth Y.:H Lee Moffitt Canc Ctr & Res Inst, Mol Oncol, Tampa, FL 33612 USA; H Lee Moffitt Canc Ctr & Res Inst, Dept Anat Pathol, Tampa, FL 33612 USA
· ZHOU, Jane H.:H Lee Moffitt Canc Ctr & Res Inst, Dept Tumor Biol, Tampa, FL 33612 USA
· RUSTGI, Anil K.:Roswell Pk Comprehens Canc Ctr, Dept Pathol, Buffalo, NY 14263 USA; Univ Penn, Perelman Sch Med, Abramson Canc Ctr, Div Gastroenterol,Dept Med, Philadelphia, PA 19104 USA
· DRILL, Esther:Univ Penn, Perelman Sch Med, Abramson Canc Ctr, Dept Genet, Philadelphia, PA 19104 USA
· SHEN, Ronglei:Univ Penn, Perelman Sch Med, Abramson Canc Ctr, Dept Genet, Philadelphia, PA 19104 USA
· WONG, Christopher K.:Mem Sloan Kettering Canc Ctr, Dept Epidemiol & Biostat, New York, NY 10065 USA
· STUART, Joshua M.:Mem Sloan Kettering Canc Ctr, Dept Epidemiol & Biostat, New York, NY 10065 USA
· LAIRD, Peter W.:Stanford Univ, Dept Med Biomed Informat Res, Stanford, CA 94305 USA
· HOADLEY, Katherine A.:Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Dept Biomol Engn, Santa Cruz, CA 95064 USA
· WEINSTEIN, John N.:BC Canc Agcy, Canadas Michael Smith Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada
· PETO, Myron:Baylor Coll Med, Dept Mol & Cell Biol, Houston, TX 77030 USA
· PICKERING, Curtis R.:Univ N Carolina, Dept Genet, Chapel Hill, NC 27599 USA
· CHEN, Zhong:Oregon Hlth & Sci Univ, Dept Mol & Med Genet, Portland, OR 97201 USA
· WAES, Carter Van:Oregon Hlth & Sci Univ, Dept Mol & Med Genet, Portland, OR 97201 USA
hcfmusp.origem.id WOS:000429092900018
hcfmusp.origem.id 2-s2.0-85044610513
hcfmusp.publisher.city CAMBRIDGE
hcfmusp.publisher.country USA
hcfmusp.relation.reference · Aarts M, 2015, MOL CANCER THER, V14, P865, DOI 10.1158/1535-7163.MCT-14-0845
· Alter BP, 2013, INT J CANCER, V133, P1513, DOI 10.1002/ijc.28157
· Banerjee R, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms5527
· Barbieri CE, 2003, J BIOL CHEM, V278, P51408, DOI 10.1074/jbc.M309943200
· Broom BM, 2017, CANCER RES, V77, pE23, DOI 10.1158/0008-5472.CAN-17-0318
· Budach S, 2016, GENETICS, V203, P1629, DOI 10.1534/genetics.116.187153
· Burk RD, 2017, NATURE, V543, P378, DOI 10.1038/nature21386
· Campbell JD, 2016, NAT GENET, V48, P607, DOI 10.1038/ng.3564
· Ceccaldi R, 2016, NAT REV MOL CELL BIO, V17, P337, DOI 10.1038/nrm.2016.48
· Charoentong P, 2017, CELL REP, V18, P248, DOI 10.1016/j.celrep.2016.12.019
· Chen FJ, 2016, CELL REP, V14, P2476, DOI 10.1016/j.celrep.2016.02.024
· Chen JY, 2017, ONCOGENESIS, V6, DOI 10.1038/oncsis.2017.71
· Chou CH, 2016, NUCLEIC ACIDS RES, V44, pD239, DOI 10.1093/nar/gkv1258
· Davis RJ, 2016, ORAL ONCOL, V58, P59, DOI 10.1016/j.oraloncology.2016.05.002
· Derakhshan A, 2017, CLIN CANCER RES, V23, P1379, DOI 10.1158/1078-0432.CCR-16-2172
· Dibble CC, 2009, MOL CELL BIOL, V29, P5657, DOI 10.1128/MCB.00735-09
· Doecke JD, 2016, CANCER GENET-NY, V209, P463, DOI 10.1016/j.cancergen.2016.09.001
· Dotto GP, 2016, CANCER CELL, V29, P622, DOI 10.1016/j.ccell.2016.04.004
· Ehsanian R, 2010, ONCOGENE, V29, P6160, DOI 10.1038/onc.2010.339
· Eytan DF, 2016, CANCER RES, V76, P5442, DOI 10.1158/0008-5472.CAN-15-3317
· Fisher ML, 2017, ONCOTARGET, V8, P73407, DOI 10.18632/oncotarget.20562
· Friedman JA, 2013, TRANSL ONCOL, V6, P429, DOI 10.1593/tlo.13292
· Gao YB, 2014, NAT GENET, V46, P1097, DOI 10.1038/ng.3076
· Gentles AJ, 2015, NAT MED, V21, P938, DOI 10.1038/nm.3909
· Gevaert O, 2015, BIOINFORMATICS, V31, P1839, DOI 10.1093/bioinformatics/btv020
· Gonzalez-Angulo Ana M, 2011, Clin Proteomics, V8, P11, DOI 10.1186/1559-0275-8-11
· Grilley-Olson JE, 2016, INVEST NEW DRUG, V34, P740, DOI 10.1007/s10637-016-0377-0
· Hajek M, 2017, CANCER-AM CANCER SOC, V123, P1778, DOI 10.1002/cncr.30570
· Hammerman PS, 2012, NATURE, V489, P519, DOI 10.1038/nature11404
· Haraguchi K, 2008, ONCOGENE, V27, P274, DOI 10.1038/sj.onc.1210644
· He Q, 2016, SCI REP-UK, V6, DOI 10.1038/srep23216
· Hennessy BT, 2007, CLIN CANCER RES, V13, P7421, DOI 10.1158/1078-0432.CCR-07-0760
· Hennessy Bryan T, 2010, Clin Proteomics, V6, P129, DOI 10.1007/s12014-010-9055-y
· Herzog A, 2013, CLIN CANCER RES, V19, P3808, DOI 10.1158/1078-0432.CCR-12-2716
· Hoadley KA, 2014, CELL, V158, P929, DOI 10.1016/j.cell.2014.06.049
· Hou MM, 2014, ONCOTARGET, V5, P11168, DOI 10.18632/oncotarget.2584
· Hu J, 2007, BIOINFORMATICS, V23, P1986, DOI 10.1093/bioinformatics/btm283
· Hu LH, 2016, OR SURG OR MED OR PA, V122, P460, DOI 10.1016/j.oooo.2016.05.018
· Huang DW, 2009, NAT PROTOC, V4, P44, DOI 10.1038/nprot.2008.211
· Huang HY, 2017, CANCER RES, V77, P5769, DOI 10.1158/0008-5472.CAN-17-0449
· Kaisari S, 2017, P NATL ACAD SCI USA, V114, P956, DOI 10.1073/pnas.1620451114
· Kao M, 2017, JAMA OTOLARYNGOL, V143, P631, DOI 10.1001/jamaoto.2016.4563
· Kim BR, 2017, MOL CELL PROTEOMICS, V16, P1864, DOI 10.1074/mcp.M116.064451
· Kim J, 2017, NATURE, V541, P169, DOI 10.1038/nature20805
· Kostic AD, 2011, NAT BIOTECHNOL, V29, P393, DOI 10.1038/nbt.1868
· Lau LF, 2016, J CELL COMMUN SIGNAL, V10, P121, DOI 10.1007/s12079-016-0324-z
· Lawrence MS, 2015, NATURE, V517, P576, DOI 10.1038/nature14129
· Lawrence MS, 2014, NATURE, V505, P495, DOI 10.1038/nature12912
· Leiker AJ, 2015, CLIN CANCER RES, V21, P2792, DOI 10.1158/1078-0432.CCR-14-3279
· Li L, 2016, SCI REP, V6, P1, DOI 10.1038/SREP26591
· Liang JY, 2007, NAT CELL BIOL, V9, P218, DOI 10.1038/ncb1537
· Lund TC, 1999, CELL SIGNAL, V11, P789, DOI 10.1016/S0898-6568(99)00045-5
· Ma J, 2015, ONCOTARGET, V6, P43881, DOI 10.18632/oncotarget.6316
· Macrae M, 2005, CANCER CELL, V8, P111, DOI 10.1016/j.ccr.2005.07.005
· Marsico A, 2013, GENOME BIOL, V14, DOI 10.1186/gb-2013-14-8-r84
· Mazumdar T, 2014, MOL CANCER THER, V13, P2738, DOI 10.1158/1535-7163.MCT-13-1090
· McCormick DL, 2015, PLOS ONE, V10, DOI 10.1371/journal.pone.0141849
· Mermel CH, 2011, GENOME BIOL, V12, DOI 10.1186/gb-2011-12-4-r41
· Mohan S, 2015, CLIN CANCER RES, V21, P3946, DOI 10.1158/1078-0432.CCR-14-3377
· Neeley ES, 2009, BIOINFORMATICS, V25, P1384, DOI 10.1093/bioinformatics/btp174
· Newton Y, 2017, CANCER RES, V77, pE111, DOI 10.1158/0008-5472.CAN-17-0580
· Okuyama R, 2007, ONCOGENE, V26, P4478, DOI 10.1038/sj.onc.1210235
· Papillon-Cavanagh S, 2017, NAT GENET, V49, P180, DOI 10.1038/ng.3757
· Park BJ, 2000, CANCER RES, V60, P3370
· Rajadurai CV, 2016, J CELL BIOL, V214, P719, DOI 10.1083/jcb.201501003
· Sadelain M, 2012, NAT REV CANCER, V12, P51, DOI 10.1038/nrc3179
· Saladi SV, 2017, CANCER CELL, V31, P35, DOI 10.1016/j.ccell.2016.12.001
· Saloura V, 2017, SCI REP-UK, V7, DOI 10.1038/srep40664
· Saloura V, 2016, ONCOTARGET, V7, P42527, DOI 10.18632/oncotarget.9897
· Sen GL, 2012, DEV CELL, V22, P669, DOI 10.1016/j.devcel.2011.12.001
· Sen M, 2015, NEOPLASIA, V17, P256, DOI 10.1016/j.neo.2015.01.003
· Shen RL, 2009, BIOINFORMATICS, V25, P2906, DOI 10.1093/bioinformatics/btp543
· Simarro M, 2010, BIOCHEM BIOPH RES CO, V401, P440, DOI 10.1016/j.bbrc.2010.09.075
· Subramanian U, 2016, PHYSIOL GENOMICS, V48, P477, DOI 10.1152/physiolgenomics.00073.2015
· Thakur R, 2016, PHARMACOL THERAPEUT, V168, P61, DOI 10.1016/j.pharmthera.2016.09.002
· Tibes R, 2006, MOL CANCER THER, V5, P2512, DOI 10.1158/1535-7163.MCT-06-0334
· Vaske CJ, 2010, BIOINFORMATICS, V26, pi237, DOI 10.1093/bioinformatics/btq182
· Weinstein JN, 2014, NATURE, V507, P315, DOI 10.1038/nature12965
· Wilkerson MD, 2010, BIOINFORMATICS, V26, P1572, DOI 10.1093/bioinformatics/btq170
· Yeger H, 2016, J CELL COMMUN SIGNAL, V10, P229, DOI 10.1007/s12079-016-0346-6
dc.description.index MEDLINE
hcfmusp.citation.scopus 29
hcfmusp.citation.wos 28
hcfmusp.affiliation.country Brasil
hcfmusp.affiliation.country Canadá
hcfmusp.affiliation.country Estados Unidos


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