Construction of m6A-based prognosis signature and prediction for immune and anti-angiogenic response
Background: Increasing evidence illustrated that m6A regulator-mediated modification plays a crucial role in regulating tumor immune and angiogenesis microenvironment. And the combination of immune checkpoint inhibitor and anti-angiogenic therapy has been approved as new first-line therapy for advan...
Main Authors: | , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2022-10-01
|
Series: | Frontiers in Molecular Biosciences |
Subjects: | |
Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2022.1034928/full |
_version_ | 1811344523704401920 |
---|---|
author | Xiang-Xu Wang Li-Hong Wu Qiong-Yi Dou Liping Ai Yajie Lu Shi-Zhou Deng Qing-Qing Liu Hongchen Ji Hong-Mei Zhang |
author_facet | Xiang-Xu Wang Li-Hong Wu Qiong-Yi Dou Liping Ai Yajie Lu Shi-Zhou Deng Qing-Qing Liu Hongchen Ji Hong-Mei Zhang |
author_sort | Xiang-Xu Wang |
collection | DOAJ |
description | Background: Increasing evidence illustrated that m6A regulator-mediated modification plays a crucial role in regulating tumor immune and angiogenesis microenvironment. And the combination of immune checkpoint inhibitor and anti-angiogenic therapy has been approved as new first-line therapy for advanced HCC. This study constructed a novel prognosis signature base on m6A-mediated modification and explored the related mechanism in predicting immune and anti-angiogenic responses.Methods: Gene expression profiles and clinical information were collected from TCGA and GEO. The ssGSEA, MCPCOUNT, and TIMER 2.0 algorithm was used to Estimation of immune cell infiltration. The IC50 of anti-angiogenic drugs in GDSC was calculated by the “pRRophetic” package. IMvigor210 cohort and Liu et al. cohort were used to validate the capability of immunotherapy response. Hepatocellular carcinoma single immune cells sequencing datasets GSE140228 were collected to present the expression landscapes of 5 hub genes in different sites and immune cell subpopulations of HCC patients.Results: Three m6A clusters with distinct immune and angiogenesis microenvironments were identified by consistent cluster analysis based on the expression of m6A regulators. We further constructed a 5-gene prognosis signature (termed as m6Asig-Score) which could predict both immune and anti-angiogenic responses. We illustrated that high m6Asig-Score is associated with poor prognosis, advanced TNM stage, and high TP53 mutation frequency. Besides, the m6Asig-Score was negatively associated with immune checkpoint inhibitors and anti-angiogenic drug response. We further found that two of the five m6Asig-Score inner genes, B2M and SMOX, were associated with immune cell infiltration, immune response, and the sensitivity to sorafenib, which were validated in two independent immunotherapy cohorts and the Genomics of Drug Sensitivity in Cancer (GDSC) database.Conclusion: We constructed a novel prognosis signature and identified B2M and SMOX for predicting immune and anti-angiogenic efficacy in HCC, which may guide the combined treatment strategies of immunotherapy and anti-angiogenic therapy in HCC. |
first_indexed | 2024-04-13T19:48:32Z |
format | Article |
id | doaj.art-bbb4fea760e24c8887759dc9b4693de7 |
institution | Directory Open Access Journal |
issn | 2296-889X |
language | English |
last_indexed | 2024-04-13T19:48:32Z |
publishDate | 2022-10-01 |
publisher | Frontiers Media S.A. |
record_format | Article |
series | Frontiers in Molecular Biosciences |
spelling | doaj.art-bbb4fea760e24c8887759dc9b4693de72022-12-22T02:32:38ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2022-10-01910.3389/fmolb.2022.10349281034928Construction of m6A-based prognosis signature and prediction for immune and anti-angiogenic responseXiang-Xu Wang0Li-Hong Wu1Qiong-Yi Dou2Liping Ai3Yajie Lu4Shi-Zhou Deng5Qing-Qing Liu6Hongchen Ji7Hong-Mei Zhang8Department of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, ChinaXijing 986 Hospital Department, Fourth Military Medical University, Xi’an, Shaanxi, ChinaDepartment of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, ChinaDepartment of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, ChinaDepartment of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, ChinaDepartment of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, ChinaDepartment of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, ChinaDepartment of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, ChinaDepartment of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, ChinaBackground: Increasing evidence illustrated that m6A regulator-mediated modification plays a crucial role in regulating tumor immune and angiogenesis microenvironment. And the combination of immune checkpoint inhibitor and anti-angiogenic therapy has been approved as new first-line therapy for advanced HCC. This study constructed a novel prognosis signature base on m6A-mediated modification and explored the related mechanism in predicting immune and anti-angiogenic responses.Methods: Gene expression profiles and clinical information were collected from TCGA and GEO. The ssGSEA, MCPCOUNT, and TIMER 2.0 algorithm was used to Estimation of immune cell infiltration. The IC50 of anti-angiogenic drugs in GDSC was calculated by the “pRRophetic” package. IMvigor210 cohort and Liu et al. cohort were used to validate the capability of immunotherapy response. Hepatocellular carcinoma single immune cells sequencing datasets GSE140228 were collected to present the expression landscapes of 5 hub genes in different sites and immune cell subpopulations of HCC patients.Results: Three m6A clusters with distinct immune and angiogenesis microenvironments were identified by consistent cluster analysis based on the expression of m6A regulators. We further constructed a 5-gene prognosis signature (termed as m6Asig-Score) which could predict both immune and anti-angiogenic responses. We illustrated that high m6Asig-Score is associated with poor prognosis, advanced TNM stage, and high TP53 mutation frequency. Besides, the m6Asig-Score was negatively associated with immune checkpoint inhibitors and anti-angiogenic drug response. We further found that two of the five m6Asig-Score inner genes, B2M and SMOX, were associated with immune cell infiltration, immune response, and the sensitivity to sorafenib, which were validated in two independent immunotherapy cohorts and the Genomics of Drug Sensitivity in Cancer (GDSC) database.Conclusion: We constructed a novel prognosis signature and identified B2M and SMOX for predicting immune and anti-angiogenic efficacy in HCC, which may guide the combined treatment strategies of immunotherapy and anti-angiogenic therapy in HCC.https://www.frontiersin.org/articles/10.3389/fmolb.2022.1034928/fullhepatocellular carcinomam6A modificationtumor microenvironmentprognostic signatureimmunotherapy |
spellingShingle | Xiang-Xu Wang Li-Hong Wu Qiong-Yi Dou Liping Ai Yajie Lu Shi-Zhou Deng Qing-Qing Liu Hongchen Ji Hong-Mei Zhang Construction of m6A-based prognosis signature and prediction for immune and anti-angiogenic response Frontiers in Molecular Biosciences hepatocellular carcinoma m6A modification tumor microenvironment prognostic signature immunotherapy |
title | Construction of m6A-based prognosis signature and prediction for immune and anti-angiogenic response |
title_full | Construction of m6A-based prognosis signature and prediction for immune and anti-angiogenic response |
title_fullStr | Construction of m6A-based prognosis signature and prediction for immune and anti-angiogenic response |
title_full_unstemmed | Construction of m6A-based prognosis signature and prediction for immune and anti-angiogenic response |
title_short | Construction of m6A-based prognosis signature and prediction for immune and anti-angiogenic response |
title_sort | construction of m6a based prognosis signature and prediction for immune and anti angiogenic response |
topic | hepatocellular carcinoma m6A modification tumor microenvironment prognostic signature immunotherapy |
url | https://www.frontiersin.org/articles/10.3389/fmolb.2022.1034928/full |
work_keys_str_mv | AT xiangxuwang constructionofm6abasedprognosissignatureandpredictionforimmuneandantiangiogenicresponse AT lihongwu constructionofm6abasedprognosissignatureandpredictionforimmuneandantiangiogenicresponse AT qiongyidou constructionofm6abasedprognosissignatureandpredictionforimmuneandantiangiogenicresponse AT lipingai constructionofm6abasedprognosissignatureandpredictionforimmuneandantiangiogenicresponse AT yajielu constructionofm6abasedprognosissignatureandpredictionforimmuneandantiangiogenicresponse AT shizhoudeng constructionofm6abasedprognosissignatureandpredictionforimmuneandantiangiogenicresponse AT qingqingliu constructionofm6abasedprognosissignatureandpredictionforimmuneandantiangiogenicresponse AT hongchenji constructionofm6abasedprognosissignatureandpredictionforimmuneandantiangiogenicresponse AT hongmeizhang constructionofm6abasedprognosissignatureandpredictionforimmuneandantiangiogenicresponse |