ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP Were Identified as Reference Genes in Neuroendocrine Lung Cancer via the nCounter Technology
Neuroendocrine lung cancer (NELC) represents 25% of all lung cancer cases and large patient collectives exist as formalin-fixed, paraffin-embedded (FFPE) tissue only. FFPE is controversially discussed as source for molecular biological analyses and reference genes for NELC are poorly establishes. Fo...
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| description | Neuroendocrine lung cancer (NELC) represents 25% of all lung cancer cases and large patient collectives exist as formalin-fixed, paraffin-embedded (FFPE) tissue only. FFPE is controversially discussed as source for molecular biological analyses and reference genes for NELC are poorly establishes.
Forty-three representative FFPE-specimens were used for mRNA expression analysis using the digital nCounter technology (NanoString). Based on recent literature, a total of 91 mRNA targets were investigated as potential tumor markers or reference genes. The geNorm, NormFinder algorithms and coefficient of correlation were used to identify the most stable reference genes. Statistical analysis was performed by using the R programming environment (version 3.1.1).
RNA integrity (RIN) ranged from 1.8 to 2.6 and concentrations from 34 to 2,109 ng/μl. However, the nCounter technology gave evaluable results for all samples tested. ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP were identified as constantly expressed genes with high stability (M-)values according to geNorm, NormFinder and coefficients of correlation.
FFPE-derived mRNA is suitable for molecular biological investigations via the nCounter technology, although it is highly degraded. ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP are potent reference genes in neuroendocrine tumors of the lung. |
| doi_str_mv | 10.1371/journal.pone.0165181 |
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Forty-three representative FFPE-specimens were used for mRNA expression analysis using the digital nCounter technology (NanoString). Based on recent literature, a total of 91 mRNA targets were investigated as potential tumor markers or reference genes. The geNorm, NormFinder algorithms and coefficient of correlation were used to identify the most stable reference genes. Statistical analysis was performed by using the R programming environment (version 3.1.1).
RNA integrity (RIN) ranged from 1.8 to 2.6 and concentrations from 34 to 2,109 ng/μl. However, the nCounter technology gave evaluable results for all samples tested. ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP were identified as constantly expressed genes with high stability (M-)values according to geNorm, NormFinder and coefficients of correlation.
FFPE-derived mRNA is suitable for molecular biological investigations via the nCounter technology, although it is highly degraded. ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP are potent reference genes in neuroendocrine tumors of the lung.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0165181</identifier><identifier>PMID: 27802291</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acids ; Algorithms ; Analysis ; Biology and Life Sciences ; Cancer ; Cancer genetics ; Cell cycle ; Classification ; Correlation ; Cyclin-Dependent Kinase Inhibitor p27 - genetics ; Engineering and Technology ; Formaldehyde ; Gene expression ; Gene Expression - genetics ; Gene Expression Regulation, Neoplastic - genetics ; Genes ; Genetic research ; Glyceraldehyde-3-phosphate dehydrogenase ; Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - genetics ; GRB2 Adaptor Protein - genetics ; Grb2 protein ; Humans ; Lung cancer ; Lung diseases ; Lung Neoplasms - genetics ; Medical research ; Medicine and Health Sciences ; Methods ; Neuroendocrine tumors ; Neuroendocrine Tumors - genetics ; Paraffin ; Paraffin Embedding - methods ; Pathology ; Physical Sciences ; Research and Analysis Methods ; rhoA GTP-Binding Protein - genetics ; RhoA protein ; Ribonucleic acid ; RNA ; RNA, Messenger - genetics ; Statistical analysis ; Statistical methods ; Syntenins - genetics ; Technology ; Technology application ; Tissue Fixation - methods ; Tumor markers ; Tumors</subject><ispartof>PloS one, 2016-11, Vol.11 (11), p.e0165181-e0165181</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Walter 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>2016 Walter et al 2016 Walter et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c795t-f32e78fea4b85f5c8494e10a73b85a1af85ba443574b0abbcfd86abcd5e2c9013</citedby><cites>FETCH-LOGICAL-c795t-f32e78fea4b85f5c8494e10a73b85a1af85ba443574b0abbcfd86abcd5e2c9013</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/PMC5089548/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5089548/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27802291$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Walter, Robert Fred Henry</creatorcontrib><creatorcontrib>Werner, Robert</creatorcontrib><creatorcontrib>Vollbrecht, Claudia</creatorcontrib><creatorcontrib>Hager, Thomas</creatorcontrib><creatorcontrib>Flom, Elena</creatorcontrib><creatorcontrib>Christoph, Daniel Christian</creatorcontrib><creatorcontrib>Schmeller, Jan</creatorcontrib><creatorcontrib>Schmid, Kurt Werner</creatorcontrib><creatorcontrib>Wohlschlaeger, Jeremias</creatorcontrib><creatorcontrib>Mairinger, Fabian Dominik</creatorcontrib><title>ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP Were Identified as Reference Genes in Neuroendocrine Lung Cancer via the nCounter Technology</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Neuroendocrine lung cancer (NELC) represents 25% of all lung cancer cases and large patient collectives exist as formalin-fixed, paraffin-embedded (FFPE) tissue only. FFPE is controversially discussed as source for molecular biological analyses and reference genes for NELC are poorly establishes.
Forty-three representative FFPE-specimens were used for mRNA expression analysis using the digital nCounter technology (NanoString). Based on recent literature, a total of 91 mRNA targets were investigated as potential tumor markers or reference genes. The geNorm, NormFinder algorithms and coefficient of correlation were used to identify the most stable reference genes. Statistical analysis was performed by using the R programming environment (version 3.1.1).
RNA integrity (RIN) ranged from 1.8 to 2.6 and concentrations from 34 to 2,109 ng/μl. However, the nCounter technology gave evaluable results for all samples tested. ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP were identified as constantly expressed genes with high stability (M-)values according to geNorm, NormFinder and coefficients of correlation.
FFPE-derived mRNA is suitable for molecular biological investigations via the nCounter technology, although it is highly degraded. ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP are potent reference genes in neuroendocrine tumors of the lung.</description><subject>Acids</subject><subject>Algorithms</subject><subject>Analysis</subject><subject>Biology and Life Sciences</subject><subject>Cancer</subject><subject>Cancer genetics</subject><subject>Cell cycle</subject><subject>Classification</subject><subject>Correlation</subject><subject>Cyclin-Dependent Kinase Inhibitor p27 - genetics</subject><subject>Engineering and Technology</subject><subject>Formaldehyde</subject><subject>Gene expression</subject><subject>Gene Expression - genetics</subject><subject>Gene Expression Regulation, Neoplastic - genetics</subject><subject>Genes</subject><subject>Genetic research</subject><subject>Glyceraldehyde-3-phosphate dehydrogenase</subject><subject>Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - genetics</subject><subject>GRB2 Adaptor Protein - genetics</subject><subject>Grb2 protein</subject><subject>Humans</subject><subject>Lung cancer</subject><subject>Lung diseases</subject><subject>Lung Neoplasms - genetics</subject><subject>Medical research</subject><subject>Medicine and Health Sciences</subject><subject>Methods</subject><subject>Neuroendocrine tumors</subject><subject>Neuroendocrine Tumors - genetics</subject><subject>Paraffin</subject><subject>Paraffin Embedding - methods</subject><subject>Pathology</subject><subject>Physical Sciences</subject><subject>Research and Analysis Methods</subject><subject>rhoA GTP-Binding Protein - genetics</subject><subject>RhoA protein</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Messenger - genetics</subject><subject>Statistical analysis</subject><subject>Statistical methods</subject><subject>Syntenins - genetics</subject><subject>Technology</subject><subject>Technology application</subject><subject>Tissue Fixation - methods</subject><subject>Tumor markers</subject><subject>Tumors</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk2Fv0zAQhiMEYmPwDxBYQkIgrSWOncT-gtRlsFVM29QN-Gg5zrl1ldrFTib2B_jduKybFjQJFEWXXJ57z3ntS5KXOB1jUuIPS9d7K9vx2lkYp7jIMcOPkl3MSTYqspQ8vve8kzwLYZmmOWFF8TTZyUqWZhnHu8mvSXV5sI-qwy-nOMajyfnhcQyzg2wfzY7PJkjaBl0cVgfn6Dt4QNMGbGe0gQbJgGagY9IqQEdgISBj0Sn03oFtnPLGAjrp7RxVMiIeXRmJugUgW7nedjFxCWphXevm18-TJ1q2AV5s417y9fOny-p4dHJ2NK0mJyNV8rwbaZJByTRIWrNc54pRTgGnsiTxXWKpWV5LSkle0jqVda10wwpZqyaHTPEUk73k9Y3uunVBbC0MAjNCWbwzEonpDdE4uRRrb1bSXwsnjfiTcH4upO-MakHwUhGiZUaj-5RyYEWDJdega1JkJd1ofdx26-sVNCpa52U7EB1-sWYh5u5K5CnjOWVR4N1WwLsfPYROrExQ0LbSgus366YFTSmJzf6NEso5p2UW0Td_oQ8bsaXmMv6rsdrFJaqNqJjQEpc8Nt0YOn6AilcDK6Pi0dQm5gcF7wcFkengZzeXfQhiejH7f_bs25B9e49dgGy7RXBt3xlnwxCkN6DyLgQP-m4_cCo2k3XrhthMlthOVix7dX8v74puR4n8BqShGeI</recordid><startdate>20161101</startdate><enddate>20161101</enddate><creator>Walter, Robert Fred Henry</creator><creator>Werner, Robert</creator><creator>Vollbrecht, Claudia</creator><creator>Hager, Thomas</creator><creator>Flom, Elena</creator><creator>Christoph, Daniel Christian</creator><creator>Schmeller, Jan</creator><creator>Schmid, Kurt Werner</creator><creator>Wohlschlaeger, Jeremias</creator><creator>Mairinger, Fabian Dominik</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20161101</creationdate><title>ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP Were Identified as Reference Genes in Neuroendocrine Lung Cancer via the nCounter Technology</title><author>Walter, Robert Fred Henry ; Werner, Robert ; Vollbrecht, Claudia ; Hager, Thomas ; Flom, Elena ; Christoph, Daniel Christian ; Schmeller, Jan ; Schmid, Kurt Werner ; Wohlschlaeger, Jeremias ; Mairinger, Fabian Dominik</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c795t-f32e78fea4b85f5c8494e10a73b85a1af85ba443574b0abbcfd86abcd5e2c9013</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Acids</topic><topic>Algorithms</topic><topic>Analysis</topic><topic>Biology and Life Sciences</topic><topic>Cancer</topic><topic>Cancer genetics</topic><topic>Cell cycle</topic><topic>Classification</topic><topic>Correlation</topic><topic>Cyclin-Dependent Kinase Inhibitor p27 - genetics</topic><topic>Engineering and Technology</topic><topic>Formaldehyde</topic><topic>Gene expression</topic><topic>Gene Expression - genetics</topic><topic>Gene Expression Regulation, Neoplastic - genetics</topic><topic>Genes</topic><topic>Genetic research</topic><topic>Glyceraldehyde-3-phosphate dehydrogenase</topic><topic>Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - genetics</topic><topic>GRB2 Adaptor Protein - genetics</topic><topic>Grb2 protein</topic><topic>Humans</topic><topic>Lung cancer</topic><topic>Lung diseases</topic><topic>Lung Neoplasms - genetics</topic><topic>Medical research</topic><topic>Medicine and Health Sciences</topic><topic>Methods</topic><topic>Neuroendocrine tumors</topic><topic>Neuroendocrine Tumors - genetics</topic><topic>Paraffin</topic><topic>Paraffin Embedding - methods</topic><topic>Pathology</topic><topic>Physical Sciences</topic><topic>Research and Analysis Methods</topic><topic>rhoA GTP-Binding Protein - genetics</topic><topic>RhoA protein</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA, Messenger - 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Academic</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>Walter, Robert Fred Henry</au><au>Werner, Robert</au><au>Vollbrecht, Claudia</au><au>Hager, Thomas</au><au>Flom, Elena</au><au>Christoph, Daniel Christian</au><au>Schmeller, Jan</au><au>Schmid, Kurt Werner</au><au>Wohlschlaeger, Jeremias</au><au>Mairinger, Fabian Dominik</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP Were Identified as Reference Genes in Neuroendocrine Lung Cancer via the nCounter Technology</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2016-11-01</date><risdate>2016</risdate><volume>11</volume><issue>11</issue><spage>e0165181</spage><epage>e0165181</epage><pages>e0165181-e0165181</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Neuroendocrine lung cancer (NELC) represents 25% of all lung cancer cases and large patient collectives exist as formalin-fixed, paraffin-embedded (FFPE) tissue only. FFPE is controversially discussed as source for molecular biological analyses and reference genes for NELC are poorly establishes.
Forty-three representative FFPE-specimens were used for mRNA expression analysis using the digital nCounter technology (NanoString). Based on recent literature, a total of 91 mRNA targets were investigated as potential tumor markers or reference genes. The geNorm, NormFinder algorithms and coefficient of correlation were used to identify the most stable reference genes. Statistical analysis was performed by using the R programming environment (version 3.1.1).
RNA integrity (RIN) ranged from 1.8 to 2.6 and concentrations from 34 to 2,109 ng/μl. However, the nCounter technology gave evaluable results for all samples tested. ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP were identified as constantly expressed genes with high stability (M-)values according to geNorm, NormFinder and coefficients of correlation.
FFPE-derived mRNA is suitable for molecular biological investigations via the nCounter technology, although it is highly degraded. ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP are potent reference genes in neuroendocrine tumors of the lung.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>27802291</pmid><doi>10.1371/journal.pone.0165181</doi><tpages>e0165181</tpages><oa>free_for_read</oa></addata></record> |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Acids Algorithms Analysis Biology and Life Sciences Cancer Cancer genetics Cell cycle Classification Correlation Cyclin-Dependent Kinase Inhibitor p27 - genetics Engineering and Technology Formaldehyde Gene expression Gene Expression - genetics Gene Expression Regulation, Neoplastic - genetics Genes Genetic research Glyceraldehyde-3-phosphate dehydrogenase Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - genetics GRB2 Adaptor Protein - genetics Grb2 protein Humans Lung cancer Lung diseases Lung Neoplasms - genetics Medical research Medicine and Health Sciences Methods Neuroendocrine tumors Neuroendocrine Tumors - genetics Paraffin Paraffin Embedding - methods Pathology Physical Sciences Research and Analysis Methods rhoA GTP-Binding Protein - genetics RhoA protein Ribonucleic acid RNA RNA, Messenger - genetics Statistical analysis Statistical methods Syntenins - genetics Technology Technology application Tissue Fixation - methods Tumor markers Tumors |
| title | ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP Were Identified as Reference Genes in Neuroendocrine Lung Cancer via the nCounter Technology |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-08T04%3A12%3A51IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=ACTB,%20CDKN1B,%20GAPDH,%20GRB2,%20RHOA%20and%20SDCBP%20Were%20Identified%20as%20Reference%20Genes%20in%20Neuroendocrine%20Lung%20Cancer%20via%20the%20nCounter%20Technology&rft.jtitle=PloS%20one&rft.au=Walter,%20Robert%20Fred%20Henry&rft.date=2016-11-01&rft.volume=11&rft.issue=11&rft.spage=e0165181&rft.epage=e0165181&rft.pages=e0165181-e0165181&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0165181&rft_dat=%3Cgale_plos_%3EA471797431%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1834883423&rft_id=info:pmid/27802291&rft_galeid=A471797431&rft_doaj_id=oai_doaj_org_article_97c33fa24016449e86d1a9fefb362743&rfr_iscdi=true |