Transcriptional Profiling by Sequencing of Oropharyngeal Cancer
Abstract Objective To compare full transcriptome expression levels of matched tumor and normal samples from patients with oropharyngeal carcinoma stratified by known tumor etiologic factors. Patients and Methods Full transcriptome sequencing was analyzed for 10 matched tumor and normal tissue sample...
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| Veröffentlicht in: | Mayo Clinic proceedings 2012-03, Vol.87 (3), p.226-232 |
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| creator | Laborde, Rebecca R., PhD Wang, Vivian W., MD, PhD Smith, Todd M., PhD Olson, N. Eric, PhD Olsen, Steven M., MD García, Joaquín J., MD Olsen, Kerry D., MD Moore, Eric J., MD Kasperbauer, Jan L., MD Tombers, Nicole M Smith, David I., PhD |
| description | Abstract Objective To compare full transcriptome expression levels of matched tumor and normal samples from patients with oropharyngeal carcinoma stratified by known tumor etiologic factors. Patients and Methods Full transcriptome sequencing was analyzed for 10 matched tumor and normal tissue samples from patients with previously untreated oropharyngeal carcinoma. Transcriptomes were analyzed using massively parallel messenger RNA sequencing and validated using the NanoString nCounter system. Global gene expression levels were compared in samples grouped by smoking status and human papillomavirus status. This study was completed between June 10, 2010, and June 30, 2011. Results Global gene expression analysis indicated tumor tissue from former smokers grouped more closely to the never smokers than the current smokers. Pathway analysis revealed alterations in the expression of genes involved in the p53 DNA damage-repair pathway, including CHEK2 and ATR , which display patterns of increased expression that is associated with human papillomavirus–negative current smokers rather than former or never smokers. Conclusion These findings support the application of messenger RNA sequencing technology as an important clinical tool for more accurately stratifying patients based on individual tumor biology with the goal of improving our understanding of tumor prognosis and treatment response, ultimately leading to individualized patient care strategies. |
| doi_str_mv | 10.1016/j.mayocp.2011.10.008 |
| format | Article |
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Eric, PhD ; Olsen, Steven M., MD ; García, Joaquín J., MD ; Olsen, Kerry D., MD ; Moore, Eric J., MD ; Kasperbauer, Jan L., MD ; Tombers, Nicole M ; Smith, David I., PhD</creator><creatorcontrib>Laborde, Rebecca R., PhD ; Wang, Vivian W., MD, PhD ; Smith, Todd M., PhD ; Olson, N. Eric, PhD ; Olsen, Steven M., MD ; García, Joaquín J., MD ; Olsen, Kerry D., MD ; Moore, Eric J., MD ; Kasperbauer, Jan L., MD ; Tombers, Nicole M ; Smith, David I., PhD</creatorcontrib><description>Abstract Objective To compare full transcriptome expression levels of matched tumor and normal samples from patients with oropharyngeal carcinoma stratified by known tumor etiologic factors. Patients and Methods Full transcriptome sequencing was analyzed for 10 matched tumor and normal tissue samples from patients with previously untreated oropharyngeal carcinoma. Transcriptomes were analyzed using massively parallel messenger RNA sequencing and validated using the NanoString nCounter system. Global gene expression levels were compared in samples grouped by smoking status and human papillomavirus status. This study was completed between June 10, 2010, and June 30, 2011. Results Global gene expression analysis indicated tumor tissue from former smokers grouped more closely to the never smokers than the current smokers. Pathway analysis revealed alterations in the expression of genes involved in the p53 DNA damage-repair pathway, including CHEK2 and ATR , which display patterns of increased expression that is associated with human papillomavirus–negative current smokers rather than former or never smokers. Conclusion These findings support the application of messenger RNA sequencing technology as an important clinical tool for more accurately stratifying patients based on individual tumor biology with the goal of improving our understanding of tumor prognosis and treatment response, ultimately leading to individualized patient care strategies.</description><identifier>ISSN: 0025-6196</identifier><identifier>EISSN: 1942-5546</identifier><identifier>DOI: 10.1016/j.mayocp.2011.10.008</identifier><identifier>PMID: 22386177</identifier><identifier>CODEN: MACPAJ</identifier><language>eng</language><publisher>Rochester, MN: Elsevier Inc</publisher><subject>Aged ; Ataxia Telangiectasia Mutated Proteins ; Biological and medical sciences ; Care and treatment ; Cell Cycle Proteins - genetics ; Checkpoint Kinase 2 ; Development and progression ; DNA Damage - genetics ; DNA Repair - genetics ; Female ; Gene Expression Profiling ; General aspects ; Genes, p53 - genetics ; Genetic aspects ; Genetic transcription ; Humans ; Internal Medicine ; Male ; Medical sciences ; Messenger RNA ; Middle Aged ; Original ; Oropharyngeal Neoplasms - etiology ; Oropharyngeal Neoplasms - genetics ; Otorhinolaryngology. Stomatology ; Papillomavirus Infections - complications ; Physiological aspects ; Protein-Serine-Threonine Kinases - genetics ; RNA, Neoplasm - genetics ; Signal Transduction - genetics ; Smoking - adverse effects ; Throat cancer ; Tumors ; Upper respiratory tract, upper alimentary tract, paranasal sinuses, salivary glands: diseases, semeiology</subject><ispartof>Mayo Clinic proceedings, 2012-03, Vol.87 (3), p.226-232</ispartof><rights>Mayo Foundation for Medical Education and Research</rights><rights>2012 Mayo Foundation for Medical Education and Research</rights><rights>2015 INIST-CNRS</rights><rights>Copyright © 2012 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.</rights><rights>COPYRIGHT 2012 Elsevier, Inc.</rights><rights>Copyright Mayo Foundation for Medical Education and Research Mar 2012</rights><rights>2012 Published by Elsevier Inc. on behalf of Mayo Foundation for Medical Education and Research. 2012 Mayo Foundation for Medical Education and Research</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c644t-3a2eb14cf990aee0145ca9f69049688a48d24638a3be42da77b703bfdaf67ae73</citedby><cites>FETCH-LOGICAL-c644t-3a2eb14cf990aee0145ca9f69049688a48d24638a3be42da77b703bfdaf67ae73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538409/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538409/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=25619373$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22386177$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Laborde, Rebecca R., PhD</creatorcontrib><creatorcontrib>Wang, Vivian W., MD, PhD</creatorcontrib><creatorcontrib>Smith, Todd M., PhD</creatorcontrib><creatorcontrib>Olson, N. Eric, PhD</creatorcontrib><creatorcontrib>Olsen, Steven M., MD</creatorcontrib><creatorcontrib>García, Joaquín J., MD</creatorcontrib><creatorcontrib>Olsen, Kerry D., MD</creatorcontrib><creatorcontrib>Moore, Eric J., MD</creatorcontrib><creatorcontrib>Kasperbauer, Jan L., MD</creatorcontrib><creatorcontrib>Tombers, Nicole M</creatorcontrib><creatorcontrib>Smith, David I., PhD</creatorcontrib><title>Transcriptional Profiling by Sequencing of Oropharyngeal Cancer</title><title>Mayo Clinic proceedings</title><addtitle>Mayo Clin Proc</addtitle><description>Abstract Objective To compare full transcriptome expression levels of matched tumor and normal samples from patients with oropharyngeal carcinoma stratified by known tumor etiologic factors. Patients and Methods Full transcriptome sequencing was analyzed for 10 matched tumor and normal tissue samples from patients with previously untreated oropharyngeal carcinoma. Transcriptomes were analyzed using massively parallel messenger RNA sequencing and validated using the NanoString nCounter system. Global gene expression levels were compared in samples grouped by smoking status and human papillomavirus status. This study was completed between June 10, 2010, and June 30, 2011. Results Global gene expression analysis indicated tumor tissue from former smokers grouped more closely to the never smokers than the current smokers. Pathway analysis revealed alterations in the expression of genes involved in the p53 DNA damage-repair pathway, including CHEK2 and ATR , which display patterns of increased expression that is associated with human papillomavirus–negative current smokers rather than former or never smokers. Conclusion These findings support the application of messenger RNA sequencing technology as an important clinical tool for more accurately stratifying patients based on individual tumor biology with the goal of improving our understanding of tumor prognosis and treatment response, ultimately leading to individualized patient care strategies.</description><subject>Aged</subject><subject>Ataxia Telangiectasia Mutated Proteins</subject><subject>Biological and medical sciences</subject><subject>Care and treatment</subject><subject>Cell Cycle Proteins - genetics</subject><subject>Checkpoint Kinase 2</subject><subject>Development and progression</subject><subject>DNA Damage - genetics</subject><subject>DNA Repair - genetics</subject><subject>Female</subject><subject>Gene Expression Profiling</subject><subject>General aspects</subject><subject>Genes, p53 - genetics</subject><subject>Genetic aspects</subject><subject>Genetic transcription</subject><subject>Humans</subject><subject>Internal Medicine</subject><subject>Male</subject><subject>Medical sciences</subject><subject>Messenger RNA</subject><subject>Middle Aged</subject><subject>Original</subject><subject>Oropharyngeal Neoplasms - etiology</subject><subject>Oropharyngeal Neoplasms - genetics</subject><subject>Otorhinolaryngology. Stomatology</subject><subject>Papillomavirus Infections - complications</subject><subject>Physiological aspects</subject><subject>Protein-Serine-Threonine Kinases - genetics</subject><subject>RNA, Neoplasm - genetics</subject><subject>Signal Transduction - genetics</subject><subject>Smoking - adverse effects</subject><subject>Throat cancer</subject><subject>Tumors</subject><subject>Upper respiratory tract, upper alimentary tract, paranasal sinuses, salivary glands: diseases, semeiology</subject><issn>0025-6196</issn><issn>1942-5546</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BEC</sourceid><sourceid>BENPR</sourceid><recordid>eNqFkktv1DAUhSMEotPCP0BohERZJfgVO96AqhEvqVKRWtaW49zMeEjs1E4qzb_HYYbpY4OysGJ_9_j6nJtlbzAqMML847bo9c6boSAI47RVIFQ9yxZYMpKXJePPswVCpMw5lvwkO41xixASUrKX2QkhtOJYiEX2-SZoF02ww2i9093yZ_Ct7axbL-vd8hpuJ3Bm_vPt8ir4YaPDzq0hgSvtDIRX2YtWdxFeH9az7NfXLzer7_nl1bcfq4vL3HDGxpxqAjVmppUSaQCEWWm0bLlETPKq0qxqCOO00rQGRhotRC0QrdtGt1xoEPQs-7TXHaa6h8aAG4Pu1BBsnzpSXlv1-MTZjVr7O0VLWjEkk8CHg0Dw6VFxVL2NBrpOO_BTVJLwEokKl4l894Tc-ikkb2ZIYFIRNvdT7KG17kBZ1_p0q0lfA7013kEyEdQFqVjJS_pX9fxBwSY5OG6i76bZ9vgYZHvQBB9jgPb4SIzUnLzaqn3yak5-3k3Jp7K3Dw06Fv2LOgHvD4CORndtyt3YeM-VaVCooPdOQ4rzzkJQ0dg0BNDYAGZUjbf_6-SpgEnzZNOdv2EH8WgmVpEopK7nKZ2HFBOEMGGU_gGEpuJV</recordid><startdate>20120301</startdate><enddate>20120301</enddate><creator>Laborde, Rebecca R., PhD</creator><creator>Wang, Vivian W., MD, PhD</creator><creator>Smith, Todd M., PhD</creator><creator>Olson, N. 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Eric, PhD ; Olsen, Steven M., MD ; García, Joaquín J., MD ; Olsen, Kerry D., MD ; Moore, Eric J., MD ; Kasperbauer, Jan L., MD ; Tombers, Nicole M ; Smith, David I., PhD</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c644t-3a2eb14cf990aee0145ca9f69049688a48d24638a3be42da77b703bfdaf67ae73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Aged</topic><topic>Ataxia Telangiectasia Mutated Proteins</topic><topic>Biological and medical sciences</topic><topic>Care and treatment</topic><topic>Cell Cycle Proteins - genetics</topic><topic>Checkpoint Kinase 2</topic><topic>Development and progression</topic><topic>DNA Damage - genetics</topic><topic>DNA Repair - genetics</topic><topic>Female</topic><topic>Gene Expression Profiling</topic><topic>General aspects</topic><topic>Genes, p53 - genetics</topic><topic>Genetic aspects</topic><topic>Genetic transcription</topic><topic>Humans</topic><topic>Internal Medicine</topic><topic>Male</topic><topic>Medical sciences</topic><topic>Messenger RNA</topic><topic>Middle Aged</topic><topic>Original</topic><topic>Oropharyngeal Neoplasms - etiology</topic><topic>Oropharyngeal Neoplasms - genetics</topic><topic>Otorhinolaryngology. Stomatology</topic><topic>Papillomavirus Infections - complications</topic><topic>Physiological aspects</topic><topic>Protein-Serine-Threonine Kinases - genetics</topic><topic>RNA, Neoplasm - genetics</topic><topic>Signal Transduction - genetics</topic><topic>Smoking - adverse effects</topic><topic>Throat cancer</topic><topic>Tumors</topic><topic>Upper respiratory tract, upper alimentary tract, paranasal sinuses, salivary glands: diseases, semeiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Laborde, Rebecca R., PhD</creatorcontrib><creatorcontrib>Wang, Vivian W., MD, PhD</creatorcontrib><creatorcontrib>Smith, Todd M., PhD</creatorcontrib><creatorcontrib>Olson, N. 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Eric, PhD</au><au>Olsen, Steven M., MD</au><au>García, Joaquín J., MD</au><au>Olsen, Kerry D., MD</au><au>Moore, Eric J., MD</au><au>Kasperbauer, Jan L., MD</au><au>Tombers, Nicole M</au><au>Smith, David I., PhD</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Transcriptional Profiling by Sequencing of Oropharyngeal Cancer</atitle><jtitle>Mayo Clinic proceedings</jtitle><addtitle>Mayo Clin Proc</addtitle><date>2012-03-01</date><risdate>2012</risdate><volume>87</volume><issue>3</issue><spage>226</spage><epage>232</epage><pages>226-232</pages><issn>0025-6196</issn><eissn>1942-5546</eissn><coden>MACPAJ</coden><abstract>Abstract Objective To compare full transcriptome expression levels of matched tumor and normal samples from patients with oropharyngeal carcinoma stratified by known tumor etiologic factors. Patients and Methods Full transcriptome sequencing was analyzed for 10 matched tumor and normal tissue samples from patients with previously untreated oropharyngeal carcinoma. Transcriptomes were analyzed using massively parallel messenger RNA sequencing and validated using the NanoString nCounter system. Global gene expression levels were compared in samples grouped by smoking status and human papillomavirus status. This study was completed between June 10, 2010, and June 30, 2011. Results Global gene expression analysis indicated tumor tissue from former smokers grouped more closely to the never smokers than the current smokers. Pathway analysis revealed alterations in the expression of genes involved in the p53 DNA damage-repair pathway, including CHEK2 and ATR , which display patterns of increased expression that is associated with human papillomavirus–negative current smokers rather than former or never smokers. Conclusion These findings support the application of messenger RNA sequencing technology as an important clinical tool for more accurately stratifying patients based on individual tumor biology with the goal of improving our understanding of tumor prognosis and treatment response, ultimately leading to individualized patient care strategies.</abstract><cop>Rochester, MN</cop><pub>Elsevier Inc</pub><pmid>22386177</pmid><doi>10.1016/j.mayocp.2011.10.008</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Aged Ataxia Telangiectasia Mutated Proteins Biological and medical sciences Care and treatment Cell Cycle Proteins - genetics Checkpoint Kinase 2 Development and progression DNA Damage - genetics DNA Repair - genetics Female Gene Expression Profiling General aspects Genes, p53 - genetics Genetic aspects Genetic transcription Humans Internal Medicine Male Medical sciences Messenger RNA Middle Aged Original Oropharyngeal Neoplasms - etiology Oropharyngeal Neoplasms - genetics Otorhinolaryngology. Stomatology Papillomavirus Infections - complications Physiological aspects Protein-Serine-Threonine Kinases - genetics RNA, Neoplasm - genetics Signal Transduction - genetics Smoking - adverse effects Throat cancer Tumors Upper respiratory tract, upper alimentary tract, paranasal sinuses, salivary glands: diseases, semeiology |
| title | Transcriptional Profiling by Sequencing of Oropharyngeal Cancer |
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