TP53 isoform junction reads based analysis in malignant and normal contexts

Abstract TP53 is one of the most frequently altered genes in cancer; it can be inactivated by a number of different mechanisms. NM_000546.6 (ENST00000269305.9) is by far the predominant TP53 isoform, however a few other alternative isoforms have been described to be expressed at much lower levels. T...

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Autores principales:	Suleyman Vural, Lun-Ching Chang, Laura M. Yee, Dmitriy Sonkin
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8e296f6de39e4f9788c5d915b7962f4c
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spelling	oai:doaj.org-article:8e296f6de39e4f9788c5d915b7962f4c2021-12-02T16:34:58ZTP53 isoform junction reads based analysis in malignant and normal contexts10.1038/s41598-021-96700-12045-2322https://doaj.org/article/8e296f6de39e4f9788c5d915b7962f4c2021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-96700-1https://doaj.org/toc/2045-2322Abstract TP53 is one of the most frequently altered genes in cancer; it can be inactivated by a number of different mechanisms. NM_000546.6 (ENST00000269305.9) is by far the predominant TP53 isoform, however a few other alternative isoforms have been described to be expressed at much lower levels. To better understand patterns of TP53 alternative isoforms expression in cancer and normal samples we performed exon-exon junction reads based analysis of TP53 isoforms using RNA-seq data from The Cancer Genome Atlas (TCGA), Cancer Cell Line Encyclopedia (CCLE), and Genotype-Tissue Expression (GTEx) project. TP53 C-terminal alternative isoforms have abolished or severely decreased tumor suppressor activity, and therefore, an increase in fraction of TP53 C-terminal alternative isoforms may be expected in tumors with wild type TP53. Despite our expectation that there would be increase of fraction of TP53 C-terminal alternative isoforms, we observed no substantial increase in fraction of TP53 C-terminal alternative isoforms in TCGA tumors and CCLE cancer cell lines with wild type TP53, likely indicating that TP53 C-terminal alternative isoforms expression cannot be reliably selected for during tumor progression.Suleyman VuralLun-Ching ChangLaura M. YeeDmitriy SonkinNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-7 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Suleyman Vural Lun-Ching Chang Laura M. Yee Dmitriy Sonkin TP53 isoform junction reads based analysis in malignant and normal contexts
description	Abstract TP53 is one of the most frequently altered genes in cancer; it can be inactivated by a number of different mechanisms. NM_000546.6 (ENST00000269305.9) is by far the predominant TP53 isoform, however a few other alternative isoforms have been described to be expressed at much lower levels. To better understand patterns of TP53 alternative isoforms expression in cancer and normal samples we performed exon-exon junction reads based analysis of TP53 isoforms using RNA-seq data from The Cancer Genome Atlas (TCGA), Cancer Cell Line Encyclopedia (CCLE), and Genotype-Tissue Expression (GTEx) project. TP53 C-terminal alternative isoforms have abolished or severely decreased tumor suppressor activity, and therefore, an increase in fraction of TP53 C-terminal alternative isoforms may be expected in tumors with wild type TP53. Despite our expectation that there would be increase of fraction of TP53 C-terminal alternative isoforms, we observed no substantial increase in fraction of TP53 C-terminal alternative isoforms in TCGA tumors and CCLE cancer cell lines with wild type TP53, likely indicating that TP53 C-terminal alternative isoforms expression cannot be reliably selected for during tumor progression.
format	article
author	Suleyman Vural Lun-Ching Chang Laura M. Yee Dmitriy Sonkin
author_facet	Suleyman Vural Lun-Ching Chang Laura M. Yee Dmitriy Sonkin
author_sort	Suleyman Vural
title	TP53 isoform junction reads based analysis in malignant and normal contexts
title_short	TP53 isoform junction reads based analysis in malignant and normal contexts
title_full	TP53 isoform junction reads based analysis in malignant and normal contexts
title_fullStr	TP53 isoform junction reads based analysis in malignant and normal contexts
title_full_unstemmed	TP53 isoform junction reads based analysis in malignant and normal contexts
title_sort	tp53 isoform junction reads based analysis in malignant and normal contexts
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8e296f6de39e4f9788c5d915b7962f4c
work_keys_str_mv	AT suleymanvural tp53isoformjunctionreadsbasedanalysisinmalignantandnormalcontexts AT lunchingchang tp53isoformjunctionreadsbasedanalysisinmalignantandnormalcontexts AT lauramyee tp53isoformjunctionreadsbasedanalysisinmalignantandnormalcontexts AT dmitriysonkin tp53isoformjunctionreadsbasedanalysisinmalignantandnormalcontexts
_version_	1718383768574623744

TP53 isoform junction reads based analysis in malignant and normal contexts

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