Comparative Membranome expression analysis in primary tumors and derived cell lines.

Despite the wide use of cell lines in cancer research, the extent to which their surface properties correspond to those of primary tumors is poorly characterized. The present study addresses this problem from a transcriptional standpoint, analyzing the expression of membrane protein genes--the Membr...

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Autores principales:	Paolo Uva, Armin Lahm, Andrea Sbardellati, Anita Grigoriadis, Andrew Tutt, Emanuele de Rinaldis
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b0633bf307544eceb7890b32b9747282
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spelling	oai:doaj.org-article:b0633bf307544eceb7890b32b97472822021-12-02T20:19:48ZComparative Membranome expression analysis in primary tumors and derived cell lines.1932-620310.1371/journal.pone.0011742https://doaj.org/article/b0633bf307544eceb7890b32b97472822010-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20668533/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Despite the wide use of cell lines in cancer research, the extent to which their surface properties correspond to those of primary tumors is poorly characterized. The present study addresses this problem from a transcriptional standpoint, analyzing the expression of membrane protein genes--the Membranome--in primary tumors and immortalized in-vitro cultured tumor cells. 409 human samples, deriving from ten independent studies, were analyzed. These comprise normal tissues, primary tumors and tumor derived cell lines deriving from eight different tissues: brain, breast, colon, kidney, leukemia, lung, melanoma, and ovary. We demonstrated that the Membranome has greater power than the remainder of the transcriptome when used as input for the automatic classification of tumor samples. This feature is maintained in tumor derived cell lines. In most cases primary tumors show maximal similarity in Membranome expression with cell lines of same tissue origin. Differences in Membranome expression between tumors and cell lines were analyzed also at the pathway level and biological themes were identified that were differentially regulated in the two settings. Moreover, by including normal samples in the analysis, we quantified the degree to which cell lines retain the Membranome up- and down-regulations observed in primary tumors with respect to their normal counterparts. We showed that most of the Membranome up-regulations observed in primary tumors are lost in the in-vitro cultured cells. Conversely, the majority of Membranome genes down-regulated upon tumor transformation maintain lower expression levels also in the cell lines. This study points towards a central role of Membranome genes in the definition of the tumor phenotype. The comparative analysis of primary tumors and cell lines identifies the limits of cell lines as a model for the study of cancer-related processes mediated by the cell surface. Results presented allow for a more rational use of the cell lines as a model of cancer.Paolo UvaArmin LahmAndrea SbardellatiAnita GrigoriadisAndrew TuttEmanuele de RinaldisPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 7, p e11742 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Paolo Uva Armin Lahm Andrea Sbardellati Anita Grigoriadis Andrew Tutt Emanuele de Rinaldis Comparative Membranome expression analysis in primary tumors and derived cell lines.
description	Despite the wide use of cell lines in cancer research, the extent to which their surface properties correspond to those of primary tumors is poorly characterized. The present study addresses this problem from a transcriptional standpoint, analyzing the expression of membrane protein genes--the Membranome--in primary tumors and immortalized in-vitro cultured tumor cells. 409 human samples, deriving from ten independent studies, were analyzed. These comprise normal tissues, primary tumors and tumor derived cell lines deriving from eight different tissues: brain, breast, colon, kidney, leukemia, lung, melanoma, and ovary. We demonstrated that the Membranome has greater power than the remainder of the transcriptome when used as input for the automatic classification of tumor samples. This feature is maintained in tumor derived cell lines. In most cases primary tumors show maximal similarity in Membranome expression with cell lines of same tissue origin. Differences in Membranome expression between tumors and cell lines were analyzed also at the pathway level and biological themes were identified that were differentially regulated in the two settings. Moreover, by including normal samples in the analysis, we quantified the degree to which cell lines retain the Membranome up- and down-regulations observed in primary tumors with respect to their normal counterparts. We showed that most of the Membranome up-regulations observed in primary tumors are lost in the in-vitro cultured cells. Conversely, the majority of Membranome genes down-regulated upon tumor transformation maintain lower expression levels also in the cell lines. This study points towards a central role of Membranome genes in the definition of the tumor phenotype. The comparative analysis of primary tumors and cell lines identifies the limits of cell lines as a model for the study of cancer-related processes mediated by the cell surface. Results presented allow for a more rational use of the cell lines as a model of cancer.
format	article
author	Paolo Uva Armin Lahm Andrea Sbardellati Anita Grigoriadis Andrew Tutt Emanuele de Rinaldis
author_facet	Paolo Uva Armin Lahm Andrea Sbardellati Anita Grigoriadis Andrew Tutt Emanuele de Rinaldis
author_sort	Paolo Uva
title	Comparative Membranome expression analysis in primary tumors and derived cell lines.
title_short	Comparative Membranome expression analysis in primary tumors and derived cell lines.
title_full	Comparative Membranome expression analysis in primary tumors and derived cell lines.
title_fullStr	Comparative Membranome expression analysis in primary tumors and derived cell lines.
title_full_unstemmed	Comparative Membranome expression analysis in primary tumors and derived cell lines.
title_sort	comparative membranome expression analysis in primary tumors and derived cell lines.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/b0633bf307544eceb7890b32b9747282
work_keys_str_mv	AT paolouva comparativemembranomeexpressionanalysisinprimarytumorsandderivedcelllines AT arminlahm comparativemembranomeexpressionanalysisinprimarytumorsandderivedcelllines AT andreasbardellati comparativemembranomeexpressionanalysisinprimarytumorsandderivedcelllines AT anitagrigoriadis comparativemembranomeexpressionanalysisinprimarytumorsandderivedcelllines AT andrewtutt comparativemembranomeexpressionanalysisinprimarytumorsandderivedcelllines AT emanuelederinaldis comparativemembranomeexpressionanalysisinprimarytumorsandderivedcelllines
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Comparative Membranome expression analysis in primary tumors and derived cell lines.

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