Cargando…

The Dysregulation of SOX Family Correlates with DNA Methylation and Immune Microenvironment Characteristics to Predict Prognosis in Hepatocellular Carcinoma

BACKGROUND: Due to the molecular heterogeneity of hepatocellular carcinoma (HCC), majority of patients respond poorly among various of therapy. This study is aimed at conducting a comprehensive analysis about roles of SOX family in HCC for obtaining more therapeutic targets and biomarkers which may...

Descripción completa

Detalles Bibliográficos
Autores principales: Qin, Sha, Liu, Gaoming, Jin, Haoer, Chen, Xue, He, Jiang, Xiao, Juxiong, Qin, Yan, Mao, Yitao, Zhao, Luqing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9020970/
https://www.ncbi.nlm.nih.gov/pubmed/35465267
http://dx.doi.org/10.1155/2022/2676114
_version_ 1784689690262110208
author Qin, Sha
Liu, Gaoming
Jin, Haoer
Chen, Xue
He, Jiang
Xiao, Juxiong
Qin, Yan
Mao, Yitao
Zhao, Luqing
author_facet Qin, Sha
Liu, Gaoming
Jin, Haoer
Chen, Xue
He, Jiang
Xiao, Juxiong
Qin, Yan
Mao, Yitao
Zhao, Luqing
author_sort Qin, Sha
collection PubMed
description BACKGROUND: Due to the molecular heterogeneity of hepatocellular carcinoma (HCC), majority of patients respond poorly among various of therapy. This study is aimed at conducting a comprehensive analysis about roles of SOX family in HCC for obtaining more therapeutic targets and biomarkers which may bring new ideas for the treatment of HCC. METHODS: UALCAN, Kaplan Meier plotter, cBioPortal, STRING, WebGestalt, Metascape, TIMER 2.0, DiseaseMeth, MethSurv, HPA, CCLE database, and Cytoscape software were used to comprehensively analyze the bioinformatic data. RESULTS: SOX2, SOX4, SOX8, SOX10, SOX11, SOX12, SOX17, and SOX18 were significantly differentially expressed in HCC and normal tissues and were valuable for the grade and survival of HCC patients. In addition, the gene alterations of SOX family happened frequently, and SOX4 and SOX17 had the highest mutation rate. The function of SOX family on HCC may be closely correlated with the regulation of angiogenesis-related signaling pathways. Moreover, SOX4, SOX8, SOX11, SOX12, SOX17, and SOX18 were correlation with 8 types of immune cells (including CD8+ T cell, CD4+ T cell, B cell, Tregs, neutrophil, macrophage, myeloid DC, and NK cell), and we found that most types of immune cells had a positive correlation with SOX family. Notably, CD4+ T cell and macrophage were positively related with all these SOX family. NK cells were negatively related with most SOX family genes. DNA methylation levels in promoter area of SOX2, SOX4, and SOX10 were lower in HCC than normal tissues, while SOX8, SOX11, SOX17, and SOX18 had higher DNA methylation levels than normal tissues. Moreover, higher DNA methylation level of SOX12 and SOX18 demonstrated worse survival rates in patients with HCC. CONCLUSION: SOX family genes could predict the prognosis of HCC. In addition, the regulation of angiogenesis-related signaling pathways may participate in the development of HCC. DNA methylation level and immune microenvironment characteristics (especially CD4+ T cell and macrophage immune cell infiltration) could be a novel insight for predicting prognosis in HCC.
format Online
Article
Text
id pubmed-9020970
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Hindawi
record_format MEDLINE/PubMed
spelling pubmed-90209702022-04-21 The Dysregulation of SOX Family Correlates with DNA Methylation and Immune Microenvironment Characteristics to Predict Prognosis in Hepatocellular Carcinoma Qin, Sha Liu, Gaoming Jin, Haoer Chen, Xue He, Jiang Xiao, Juxiong Qin, Yan Mao, Yitao Zhao, Luqing Dis Markers Research Article BACKGROUND: Due to the molecular heterogeneity of hepatocellular carcinoma (HCC), majority of patients respond poorly among various of therapy. This study is aimed at conducting a comprehensive analysis about roles of SOX family in HCC for obtaining more therapeutic targets and biomarkers which may bring new ideas for the treatment of HCC. METHODS: UALCAN, Kaplan Meier plotter, cBioPortal, STRING, WebGestalt, Metascape, TIMER 2.0, DiseaseMeth, MethSurv, HPA, CCLE database, and Cytoscape software were used to comprehensively analyze the bioinformatic data. RESULTS: SOX2, SOX4, SOX8, SOX10, SOX11, SOX12, SOX17, and SOX18 were significantly differentially expressed in HCC and normal tissues and were valuable for the grade and survival of HCC patients. In addition, the gene alterations of SOX family happened frequently, and SOX4 and SOX17 had the highest mutation rate. The function of SOX family on HCC may be closely correlated with the regulation of angiogenesis-related signaling pathways. Moreover, SOX4, SOX8, SOX11, SOX12, SOX17, and SOX18 were correlation with 8 types of immune cells (including CD8+ T cell, CD4+ T cell, B cell, Tregs, neutrophil, macrophage, myeloid DC, and NK cell), and we found that most types of immune cells had a positive correlation with SOX family. Notably, CD4+ T cell and macrophage were positively related with all these SOX family. NK cells were negatively related with most SOX family genes. DNA methylation levels in promoter area of SOX2, SOX4, and SOX10 were lower in HCC than normal tissues, while SOX8, SOX11, SOX17, and SOX18 had higher DNA methylation levels than normal tissues. Moreover, higher DNA methylation level of SOX12 and SOX18 demonstrated worse survival rates in patients with HCC. CONCLUSION: SOX family genes could predict the prognosis of HCC. In addition, the regulation of angiogenesis-related signaling pathways may participate in the development of HCC. DNA methylation level and immune microenvironment characteristics (especially CD4+ T cell and macrophage immune cell infiltration) could be a novel insight for predicting prognosis in HCC. Hindawi 2022-04-13 /pmc/articles/PMC9020970/ /pubmed/35465267 http://dx.doi.org/10.1155/2022/2676114 Text en Copyright © 2022 Sha Qin et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Qin, Sha
Liu, Gaoming
Jin, Haoer
Chen, Xue
He, Jiang
Xiao, Juxiong
Qin, Yan
Mao, Yitao
Zhao, Luqing
The Dysregulation of SOX Family Correlates with DNA Methylation and Immune Microenvironment Characteristics to Predict Prognosis in Hepatocellular Carcinoma
title The Dysregulation of SOX Family Correlates with DNA Methylation and Immune Microenvironment Characteristics to Predict Prognosis in Hepatocellular Carcinoma
title_full The Dysregulation of SOX Family Correlates with DNA Methylation and Immune Microenvironment Characteristics to Predict Prognosis in Hepatocellular Carcinoma
title_fullStr The Dysregulation of SOX Family Correlates with DNA Methylation and Immune Microenvironment Characteristics to Predict Prognosis in Hepatocellular Carcinoma
title_full_unstemmed The Dysregulation of SOX Family Correlates with DNA Methylation and Immune Microenvironment Characteristics to Predict Prognosis in Hepatocellular Carcinoma
title_short The Dysregulation of SOX Family Correlates with DNA Methylation and Immune Microenvironment Characteristics to Predict Prognosis in Hepatocellular Carcinoma
title_sort dysregulation of sox family correlates with dna methylation and immune microenvironment characteristics to predict prognosis in hepatocellular carcinoma
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9020970/
https://www.ncbi.nlm.nih.gov/pubmed/35465267
http://dx.doi.org/10.1155/2022/2676114
work_keys_str_mv AT qinsha thedysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT liugaoming thedysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT jinhaoer thedysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT chenxue thedysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT hejiang thedysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT xiaojuxiong thedysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT qinyan thedysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT maoyitao thedysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT zhaoluqing thedysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT qinsha dysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT liugaoming dysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT jinhaoer dysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT chenxue dysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT hejiang dysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT xiaojuxiong dysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT qinyan dysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT maoyitao dysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma
AT zhaoluqing dysregulationofsoxfamilycorrelateswithdnamethylationandimmunemicroenvironmentcharacteristicstopredictprognosisinhepatocellularcarcinoma