Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling
Breast cancers (BCs) of the luminal B subtype are estrogen receptor-positive (ER+), highly proliferative, resistant to standard therapies and have a poor prognosis. To better understand this subtype we compared DNA copy number aberrations (CNAs), DNA promoter methylation, gene expression profiles, a...
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| Veröffentlicht in: | PloS one 2014-01, Vol.9 (1), p.e81843-e81843 |
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| creator | Cornen, Stéphanie Guille, Arnaud Adélaïde, José Addou-Klouche, Lynda Finetti, Pascal Saade, Marie-Rose Manai, Marwa Carbuccia, Nadine Bekhouche, Ismahane Letessier, Anne Raynaud, Stéphane Charafe-Jauffret, Emmanuelle Jacquemier, Jocelyne Spicuglia, Salvatore de The, Hugues Viens, Patrice Bertucci, François Birnbaum, Daniel Chaffanet, Max |
| description | Breast cancers (BCs) of the luminal B subtype are estrogen receptor-positive (ER+), highly proliferative, resistant to standard therapies and have a poor prognosis. To better understand this subtype we compared DNA copy number aberrations (CNAs), DNA promoter methylation, gene expression profiles, and somatic mutations in nine selected genes, in 32 luminal B tumors with those observed in 156 BCs of the other molecular subtypes. Frequent CNAs included 8p11-p12 and 11q13.1-q13.2 amplifications, 7q11.22-q34, 8q21.12-q24.23, 12p12.3-p13.1, 12q13.11-q24.11, 14q21.1-q23.1, 17q11.1-q25.1, 20q11.23-q13.33 gains and 6q14.1-q24.2, 9p21.3-p24,3, 9q21.2, 18p11.31-p11.32 losses. A total of 237 and 101 luminal B-specific candidate oncogenes and tumor suppressor genes (TSGs) presented a deregulated expression in relation with their CNAs, including 11 genes previously reported associated with endocrine resistance. Interestingly, 88% of the potential TSGs are located within chromosome arm 6q, and seven candidate oncogenes are potential therapeutic targets. A total of 100 candidate oncogenes were validated in a public series of 5,765 BCs and the overexpression of 67 of these was associated with poor survival in luminal tumors. Twenty-four genes presented a deregulated expression in relation with a high DNA methylation level. FOXO3, PIK3CA and TP53 were the most frequent mutated genes among the nine tested. In a meta-analysis of next-generation sequencing data in 875 BCs, KCNB2 mutations were associated with luminal B cases while candidate TSGs MDN1 (6q15) and UTRN (6q24), were mutated in this subtype. In conclusion, we have reported luminal B candidate genes that may play a role in the development and/or hormone resistance of this aggressive subtype. |
| doi_str_mv | 10.1371/journal.pone.0081843 |
| format | Article |
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To better understand this subtype we compared DNA copy number aberrations (CNAs), DNA promoter methylation, gene expression profiles, and somatic mutations in nine selected genes, in 32 luminal B tumors with those observed in 156 BCs of the other molecular subtypes. Frequent CNAs included 8p11-p12 and 11q13.1-q13.2 amplifications, 7q11.22-q34, 8q21.12-q24.23, 12p12.3-p13.1, 12q13.11-q24.11, 14q21.1-q23.1, 17q11.1-q25.1, 20q11.23-q13.33 gains and 6q14.1-q24.2, 9p21.3-p24,3, 9q21.2, 18p11.31-p11.32 losses. A total of 237 and 101 luminal B-specific candidate oncogenes and tumor suppressor genes (TSGs) presented a deregulated expression in relation with their CNAs, including 11 genes previously reported associated with endocrine resistance. Interestingly, 88% of the potential TSGs are located within chromosome arm 6q, and seven candidate oncogenes are potential therapeutic targets. A total of 100 candidate oncogenes were validated in a public series of 5,765 BCs and the overexpression of 67 of these was associated with poor survival in luminal tumors. Twenty-four genes presented a deregulated expression in relation with a high DNA methylation level. FOXO3, PIK3CA and TP53 were the most frequent mutated genes among the nine tested. In a meta-analysis of next-generation sequencing data in 875 BCs, KCNB2 mutations were associated with luminal B cases while candidate TSGs MDN1 (6q15) and UTRN (6q24), were mutated in this subtype. In conclusion, we have reported luminal B candidate genes that may play a role in the development and/or hormone resistance of this aggressive subtype.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0081843</identifier><identifier>PMID: 24416132</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Aberration ; Analysis ; Biology ; Breast cancer ; Breast Neoplasms - genetics ; Breast Neoplasms - pathology ; Cancer ; Cancer genetics ; Cancer therapies ; Chromosomes, Human, Pair 6 - genetics ; Copy number ; Deoxyribonucleic acid ; Deregulation ; Development and progression ; Divisions ; DNA ; DNA Copy Number Variations - genetics ; DNA fingerprinting ; DNA methylation ; DNA Methylation - genetics ; Estrogen receptors ; Estrogens ; Female ; FOXO3 protein ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene mutation ; Gene sequencing ; Genes ; Genes, Neoplasm - genetics ; Genetic aspects ; Genetic Association Studies ; Genome, Human - genetics ; Genomes ; Genomics ; Health aspects ; High-Throughput Nucleotide Sequencing ; Humans ; Kaplan-Meier Estimate ; Life Sciences ; Medical research ; Medicine ; Meta-analysis ; Meta-Analysis as Topic ; Methylation ; MicroRNAs ; Multivariate Analysis ; Mutation ; Mutation - genetics ; Oncology ; p53 Protein ; Prognosis ; Promoter Regions, Genetic - genetics ; RecQ Helicases - genetics ; RecQ Helicases - metabolism ; Reproducibility of Results ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; Studies ; Tracking stock ; Tumor proteins ; Tumor suppressor genes ; Tumorigenesis ; Tumors ; Utrophin</subject><ispartof>PloS one, 2014-01, Vol.9 (1), p.e81843-e81843</ispartof><rights>COPYRIGHT 2014 Public Library of Science</rights><rights>2014 Cornen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Attribution</rights><rights>2014 Cornen et al 2014 Cornen et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c726t-389760042c28c3ab8870c09da48595996fb205d951a019bb92f27906ae04e57d3</citedby><cites>FETCH-LOGICAL-c726t-389760042c28c3ab8870c09da48595996fb205d951a019bb92f27906ae04e57d3</cites><orcidid>0000-0002-2674-3123 ; 0000-0002-0157-0959 ; 0000-0002-0286-1299 ; 0000-0002-8101-7108 ; 0000-0002-2344-1488</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886975/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886975/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23865,27923,27924,53790,53792,79371,79372</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24416132$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://amu.hal.science/hal-01614950$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Creighton, Chad</contributor><creatorcontrib>Cornen, Stéphanie</creatorcontrib><creatorcontrib>Guille, Arnaud</creatorcontrib><creatorcontrib>Adélaïde, José</creatorcontrib><creatorcontrib>Addou-Klouche, Lynda</creatorcontrib><creatorcontrib>Finetti, Pascal</creatorcontrib><creatorcontrib>Saade, Marie-Rose</creatorcontrib><creatorcontrib>Manai, Marwa</creatorcontrib><creatorcontrib>Carbuccia, Nadine</creatorcontrib><creatorcontrib>Bekhouche, Ismahane</creatorcontrib><creatorcontrib>Letessier, Anne</creatorcontrib><creatorcontrib>Raynaud, Stéphane</creatorcontrib><creatorcontrib>Charafe-Jauffret, Emmanuelle</creatorcontrib><creatorcontrib>Jacquemier, Jocelyne</creatorcontrib><creatorcontrib>Spicuglia, Salvatore</creatorcontrib><creatorcontrib>de The, Hugues</creatorcontrib><creatorcontrib>Viens, Patrice</creatorcontrib><creatorcontrib>Bertucci, François</creatorcontrib><creatorcontrib>Birnbaum, Daniel</creatorcontrib><creatorcontrib>Chaffanet, Max</creatorcontrib><title>Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Breast cancers (BCs) of the luminal B subtype are estrogen receptor-positive (ER+), highly proliferative, resistant to standard therapies and have a poor prognosis. To better understand this subtype we compared DNA copy number aberrations (CNAs), DNA promoter methylation, gene expression profiles, and somatic mutations in nine selected genes, in 32 luminal B tumors with those observed in 156 BCs of the other molecular subtypes. Frequent CNAs included 8p11-p12 and 11q13.1-q13.2 amplifications, 7q11.22-q34, 8q21.12-q24.23, 12p12.3-p13.1, 12q13.11-q24.11, 14q21.1-q23.1, 17q11.1-q25.1, 20q11.23-q13.33 gains and 6q14.1-q24.2, 9p21.3-p24,3, 9q21.2, 18p11.31-p11.32 losses. A total of 237 and 101 luminal B-specific candidate oncogenes and tumor suppressor genes (TSGs) presented a deregulated expression in relation with their CNAs, including 11 genes previously reported associated with endocrine resistance. Interestingly, 88% of the potential TSGs are located within chromosome arm 6q, and seven candidate oncogenes are potential therapeutic targets. A total of 100 candidate oncogenes were validated in a public series of 5,765 BCs and the overexpression of 67 of these was associated with poor survival in luminal tumors. Twenty-four genes presented a deregulated expression in relation with a high DNA methylation level. FOXO3, PIK3CA and TP53 were the most frequent mutated genes among the nine tested. In a meta-analysis of next-generation sequencing data in 875 BCs, KCNB2 mutations were associated with luminal B cases while candidate TSGs MDN1 (6q15) and UTRN (6q24), were mutated in this subtype. In conclusion, we have reported luminal B candidate genes that may play a role in the development and/or hormone resistance of this aggressive subtype.</description><subject>Aberration</subject><subject>Analysis</subject><subject>Biology</subject><subject>Breast cancer</subject><subject>Breast Neoplasms - genetics</subject><subject>Breast Neoplasms - pathology</subject><subject>Cancer</subject><subject>Cancer genetics</subject><subject>Cancer therapies</subject><subject>Chromosomes, Human, Pair 6 - genetics</subject><subject>Copy number</subject><subject>Deoxyribonucleic acid</subject><subject>Deregulation</subject><subject>Development and progression</subject><subject>Divisions</subject><subject>DNA</subject><subject>DNA Copy Number Variations - genetics</subject><subject>DNA fingerprinting</subject><subject>DNA methylation</subject><subject>DNA Methylation - genetics</subject><subject>Estrogen receptors</subject><subject>Estrogens</subject><subject>Female</subject><subject>FOXO3 protein</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>Gene mutation</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genes, Neoplasm - genetics</subject><subject>Genetic aspects</subject><subject>Genetic Association Studies</subject><subject>Genome, Human - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Health aspects</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Humans</subject><subject>Kaplan-Meier Estimate</subject><subject>Life Sciences</subject><subject>Medical research</subject><subject>Medicine</subject><subject>Meta-analysis</subject><subject>Meta-Analysis as Topic</subject><subject>Methylation</subject><subject>MicroRNAs</subject><subject>Multivariate Analysis</subject><subject>Mutation</subject><subject>Mutation - genetics</subject><subject>Oncology</subject><subject>p53 Protein</subject><subject>Prognosis</subject><subject>Promoter Regions, Genetic - genetics</subject><subject>RecQ Helicases - genetics</subject><subject>RecQ Helicases - metabolism</subject><subject>Reproducibility of Results</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>Studies</subject><subject>Tracking stock</subject><subject>Tumor proteins</subject><subject>Tumor suppressor genes</subject><subject>Tumorigenesis</subject><subject>Tumors</subject><subject>Utrophin</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk11r2zAUhs3YWLtu_2BshsJYYckkS5atm0GWfTRQVtjXrZClY0eZbWWSXZp_P7lxS1x6MXxhc_S8r6z36ETRS4zmmGT4_cb2rpX1fGtbmCOU45ySR9Ex5iSZsQSRxwffR9Ez7zcIpSRn7Gl0lFCKGSbJcfRnKVtttOwgrvvGBMP4Y1w4kL6LlWwVuLiCFnxsNLSdKQ3ouNgNNdvAu5u1GK63Drw3to2DWfzp2yJuoFvvatkNta2zpalNWz2PnpSy9vBifJ9Ev758_rk8n11cfl0tFxczlSWsm5GcZwwhmqgkV0QWeZ4hhbiWNE95yjkriwSlmqdYIsyLgidlknHEJCAKaabJSfR677utrRdjTl5gmrEkxymmgVjtCW3lRmydaaTbCSuNuClYVwnpOqNqEFpnGlhRMJ2VlBFSFHmaMoZKzUGDSoPXh3G3vmhAqxCTk_XEdLrSmrWo7JUgec54Nhic7Q3W92Tniwsx1FDoFeUpusKBfTtu5uzfHnwnGuMV1LVswfbDGTnKGE0ZD-jpPfThJEaqkuGwpi1t-Ec1mIoFzUL0mGMSqPkDVHg0NEaFCxgaDFPB2UQQmA6uu0r23ovVj-__z17-nrJvDtg1yLpbe1v3w0XzU5DuQeWs9w7Ku2QxEsP83KYhhvkR4_wE2avDZt6JbgeG_AOKiRQM</recordid><startdate>20140109</startdate><enddate>20140109</enddate><creator>Cornen, 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luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling</title><author>Cornen, Stéphanie ; Guille, Arnaud ; Adélaïde, José ; Addou-Klouche, Lynda ; Finetti, Pascal ; Saade, Marie-Rose ; Manai, Marwa ; Carbuccia, Nadine ; Bekhouche, Ismahane ; Letessier, Anne ; Raynaud, Stéphane ; Charafe-Jauffret, Emmanuelle ; Jacquemier, Jocelyne ; Spicuglia, Salvatore ; de The, Hugues ; Viens, Patrice ; Bertucci, François ; Birnbaum, Daniel ; Chaffanet, Max</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c726t-389760042c28c3ab8870c09da48595996fb205d951a019bb92f27906ae04e57d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Aberration</topic><topic>Analysis</topic><topic>Biology</topic><topic>Breast cancer</topic><topic>Breast Neoplasms - genetics</topic><topic>Breast Neoplasms - pathology</topic><topic>Cancer</topic><topic>Cancer 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Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Cornen, Stéphanie</au><au>Guille, Arnaud</au><au>Adélaïde, José</au><au>Addou-Klouche, Lynda</au><au>Finetti, Pascal</au><au>Saade, Marie-Rose</au><au>Manai, Marwa</au><au>Carbuccia, Nadine</au><au>Bekhouche, Ismahane</au><au>Letessier, Anne</au><au>Raynaud, Stéphane</au><au>Charafe-Jauffret, Emmanuelle</au><au>Jacquemier, Jocelyne</au><au>Spicuglia, Salvatore</au><au>de The, Hugues</au><au>Viens, Patrice</au><au>Bertucci, François</au><au>Birnbaum, Daniel</au><au>Chaffanet, Max</au><au>Creighton, Chad</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2014-01-09</date><risdate>2014</risdate><volume>9</volume><issue>1</issue><spage>e81843</spage><epage>e81843</epage><pages>e81843-e81843</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Breast cancers (BCs) of the luminal B subtype are estrogen receptor-positive (ER+), highly proliferative, resistant to standard therapies and have a poor prognosis. To better understand this subtype we compared DNA copy number aberrations (CNAs), DNA promoter methylation, gene expression profiles, and somatic mutations in nine selected genes, in 32 luminal B tumors with those observed in 156 BCs of the other molecular subtypes. Frequent CNAs included 8p11-p12 and 11q13.1-q13.2 amplifications, 7q11.22-q34, 8q21.12-q24.23, 12p12.3-p13.1, 12q13.11-q24.11, 14q21.1-q23.1, 17q11.1-q25.1, 20q11.23-q13.33 gains and 6q14.1-q24.2, 9p21.3-p24,3, 9q21.2, 18p11.31-p11.32 losses. A total of 237 and 101 luminal B-specific candidate oncogenes and tumor suppressor genes (TSGs) presented a deregulated expression in relation with their CNAs, including 11 genes previously reported associated with endocrine resistance. Interestingly, 88% of the potential TSGs are located within chromosome arm 6q, and seven candidate oncogenes are potential therapeutic targets. A total of 100 candidate oncogenes were validated in a public series of 5,765 BCs and the overexpression of 67 of these was associated with poor survival in luminal tumors. Twenty-four genes presented a deregulated expression in relation with a high DNA methylation level. FOXO3, PIK3CA and TP53 were the most frequent mutated genes among the nine tested. In a meta-analysis of next-generation sequencing data in 875 BCs, KCNB2 mutations were associated with luminal B cases while candidate TSGs MDN1 (6q15) and UTRN (6q24), were mutated in this subtype. In conclusion, we have reported luminal B candidate genes that may play a role in the development and/or hormone resistance of this aggressive subtype.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24416132</pmid><doi>10.1371/journal.pone.0081843</doi><tpages>e81843</tpages><orcidid>https://orcid.org/0000-0002-2674-3123</orcidid><orcidid>https://orcid.org/0000-0002-0157-0959</orcidid><orcidid>https://orcid.org/0000-0002-0286-1299</orcidid><orcidid>https://orcid.org/0000-0002-8101-7108</orcidid><orcidid>https://orcid.org/0000-0002-2344-1488</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2014-01, Vol.9 (1), p.e81843-e81843 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1476281514 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Aberration Analysis Biology Breast cancer Breast Neoplasms - genetics Breast Neoplasms - pathology Cancer Cancer genetics Cancer therapies Chromosomes, Human, Pair 6 - genetics Copy number Deoxyribonucleic acid Deregulation Development and progression Divisions DNA DNA Copy Number Variations - genetics DNA fingerprinting DNA methylation DNA Methylation - genetics Estrogen receptors Estrogens Female FOXO3 protein Gene expression Gene Expression Profiling Gene Expression Regulation, Neoplastic Gene mutation Gene sequencing Genes Genes, Neoplasm - genetics Genetic aspects Genetic Association Studies Genome, Human - genetics Genomes Genomics Health aspects High-Throughput Nucleotide Sequencing Humans Kaplan-Meier Estimate Life Sciences Medical research Medicine Meta-analysis Meta-Analysis as Topic Methylation MicroRNAs Multivariate Analysis Mutation Mutation - genetics Oncology p53 Protein Prognosis Promoter Regions, Genetic - genetics RecQ Helicases - genetics RecQ Helicases - metabolism Reproducibility of Results RNA, Messenger - genetics RNA, Messenger - metabolism Studies Tracking stock Tumor proteins Tumor suppressor genes Tumorigenesis Tumors Utrophin |
| title | Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling |
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