Prognostic nomogram of hypoxia-related genes predicting overall survival of colorectal cancer–Analysis of TCGA database

Joon Hyop Lee, Sohee Jung, Won Seo Park, Eun Kyung Choe, Eunyoung Kim, Ru Mi Shin, Suung Chul Heo, Jae Hyun Lee, Kwangsoo Kim, Young Jun Chai

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Hypoxia-related gene (HRG) expression is associated with survival outcomes of colorectal cancer (CRC). Our aim was developing a nomogram predicting CRC overall survival (OS) with HRGs and clinicopathological factors. The Cancer Genome Atlas (TCGA) database was used as discovery cohort and two Gene Expression Omnibus databases (GSE39582 and GSE41258) served as validation cohorts. A genetic risk score model prognosticating OS was developed using mRNA expression level of HRGs. Nomogram predicting OS was developed using genetic risk score model and clinicopathological variables. The genetic risk score model included four HRGs (HSPA1L, PUM1, UBE2D2, and HSP27) and successfully prognosticated OS of discovery and two validation cohorts (p < 0.001 for TCGA discovery set, p < 0.003 for the GSE39582 and p = 0.042 for the GSE41258 datasets). Nomogram included genetic risk score, age, and TNM stage. Harrell’s concordance indexes of the nomogram were higher than those of TNM stage alone in the discovery set (0.77 vs. 0.69, p < 0.001), GSE39582 (0.65 vs. 0.63, p < 0.001), and GSE41258 datasets (0.78 vs. 0.77, p < 0.001). Our nomogram successfully predicted OS of CRC patients. The mRNA expression level of the HRGs might be useful as an ancillary marker for prognosticating CRC outcome.

Original languageEnglish
Article number1803
Pages (from-to)1803
JournalScientific Reports
Volume9
Issue number1
DOIs
StatePublished - 12 Feb 2019

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Nomograms
Atlases
Genome
Databases
Survival
Colorectal Neoplasms
Genes
Neoplasms
Gene Expression
Messenger RNA
Hypoxia
histidine-rich proteins

Cite this

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title = "Prognostic nomogram of hypoxia-related genes predicting overall survival of colorectal cancer–Analysis of TCGA database",
abstract = "Hypoxia-related gene (HRG) expression is associated with survival outcomes of colorectal cancer (CRC). Our aim was developing a nomogram predicting CRC overall survival (OS) with HRGs and clinicopathological factors. The Cancer Genome Atlas (TCGA) database was used as discovery cohort and two Gene Expression Omnibus databases (GSE39582 and GSE41258) served as validation cohorts. A genetic risk score model prognosticating OS was developed using mRNA expression level of HRGs. Nomogram predicting OS was developed using genetic risk score model and clinicopathological variables. The genetic risk score model included four HRGs (HSPA1L, PUM1, UBE2D2, and HSP27) and successfully prognosticated OS of discovery and two validation cohorts (p < 0.001 for TCGA discovery set, p < 0.003 for the GSE39582 and p = 0.042 for the GSE41258 datasets). Nomogram included genetic risk score, age, and TNM stage. Harrell’s concordance indexes of the nomogram were higher than those of TNM stage alone in the discovery set (0.77 vs. 0.69, p < 0.001), GSE39582 (0.65 vs. 0.63, p < 0.001), and GSE41258 datasets (0.78 vs. 0.77, p < 0.001). Our nomogram successfully predicted OS of CRC patients. The mRNA expression level of the HRGs might be useful as an ancillary marker for prognosticating CRC outcome.",
author = "Lee, {Joon Hyop} and Sohee Jung and Park, {Won Seo} and Choe, {Eun Kyung} and Eunyoung Kim and Shin, {Ru Mi} and Heo, {Suung Chul} and Lee, {Jae Hyun} and Kwangsoo Kim and Chai, {Young Jun}",
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Prognostic nomogram of hypoxia-related genes predicting overall survival of colorectal cancer–Analysis of TCGA database. / Lee, Joon Hyop; Jung, Sohee; Park, Won Seo; Choe, Eun Kyung; Kim, Eunyoung; Shin, Ru Mi; Heo, Suung Chul; Lee, Jae Hyun; Kim, Kwangsoo; Chai, Young Jun.

In: Scientific Reports, Vol. 9, No. 1, 1803, 12.02.2019, p. 1803.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Lee, Joon Hyop

AU - Jung, Sohee

AU - Park, Won Seo

AU - Choe, Eun Kyung

AU - Kim, Eunyoung

AU - Shin, Ru Mi

AU - Heo, Suung Chul

AU - Lee, Jae Hyun

AU - Kim, Kwangsoo

AU - Chai, Young Jun

PY - 2019/2/12

Y1 - 2019/2/12

N2 - Hypoxia-related gene (HRG) expression is associated with survival outcomes of colorectal cancer (CRC). Our aim was developing a nomogram predicting CRC overall survival (OS) with HRGs and clinicopathological factors. The Cancer Genome Atlas (TCGA) database was used as discovery cohort and two Gene Expression Omnibus databases (GSE39582 and GSE41258) served as validation cohorts. A genetic risk score model prognosticating OS was developed using mRNA expression level of HRGs. Nomogram predicting OS was developed using genetic risk score model and clinicopathological variables. The genetic risk score model included four HRGs (HSPA1L, PUM1, UBE2D2, and HSP27) and successfully prognosticated OS of discovery and two validation cohorts (p < 0.001 for TCGA discovery set, p < 0.003 for the GSE39582 and p = 0.042 for the GSE41258 datasets). Nomogram included genetic risk score, age, and TNM stage. Harrell’s concordance indexes of the nomogram were higher than those of TNM stage alone in the discovery set (0.77 vs. 0.69, p < 0.001), GSE39582 (0.65 vs. 0.63, p < 0.001), and GSE41258 datasets (0.78 vs. 0.77, p < 0.001). Our nomogram successfully predicted OS of CRC patients. The mRNA expression level of the HRGs might be useful as an ancillary marker for prognosticating CRC outcome.

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SN - 2045-2322

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