Potential Immune Biomarker Candidates and Immune Subtypes of Lung Adenocarcinoma for Developing mRNA Vaccines

mRNA vaccines against cancer have advantages in safety, improved therapeutic efficacy, and large-scale production. Therefore, our purpose is to identify immune biomarkers and to analyze immune status for developing mRNA vaccines and selecting appropriate patients for vaccination. We downloaded clini...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Yang Wang, Huaicheng Tan, Ting Yu, Xiaoxuan Chen, Fangqi Jing, Huashan Shi
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	mRNA vaccine lung adenocarcinoma immune subtype tumor mutation burden immune landscape immunogenic cell death Immunologic diseases. Allergy RC581-607
Acceso en línea:	https://doaj.org/article/1d7571e2ea164be0afb1a0198899abe0
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:1d7571e2ea164be0afb1a0198899abe0
record_format	dspace
spelling	oai:doaj.org-article:1d7571e2ea164be0afb1a0198899abe02021-12-01T19:37:31ZPotential Immune Biomarker Candidates and Immune Subtypes of Lung Adenocarcinoma for Developing mRNA Vaccines1664-322410.3389/fimmu.2021.755401https://doaj.org/article/1d7571e2ea164be0afb1a0198899abe02021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fimmu.2021.755401/fullhttps://doaj.org/toc/1664-3224mRNA vaccines against cancer have advantages in safety, improved therapeutic efficacy, and large-scale production. Therefore, our purpose is to identify immune biomarkers and to analyze immune status for developing mRNA vaccines and selecting appropriate patients for vaccination. We downloaded clinical information and RNA-seq data of 494 LUAD patients from TCGA. LUAD mutational information was hierarchically clustered by NMF package (Version 0.23.0). DeconstructSigs package (Version 1.8.0) and NMF consistency clustering were used to identify mutation signatures. Maftools package (Version 2.6.05) was used to select LUAD-related immune biomarkers. TIMER was used to discuss the correlation between genetic mutations and cellular components. Unsupervised clustering Pam method was used to identify LUAD immune subtypes. Log-rank test and univariate/multivariate cox regression were used to predict the prognosis of immune subtypes. Dimensionality reduction analysis was dedicated to the description of LUAD immune landscape. LUAD patients are classified into four signatures: T >C, APOBEC mutation, age, and tobacco. Then, GPRIN1, MYRF, PLXNB2, SLC9A4, TRIM29, UBA6, and XDH are potential LUAD-related immune biomarker candidates to activate the immune response. Next, we clustered five LUAD-related immune subtypes (IS1–IS5) by prognostic prediction. IS3 showed prolonged survival. The reliability of our five immune subtypes was validated by Thorsson’s results. IS2 and IS4 patients had high tumor mutation burden and large number of somatic mutations. Besides, we identified that immune subtypes of cold immunity (patients with IS2 and IS4) are ideal mRNA vaccination recipients. Finally, LUAD immune landscape revealed immune cells and prognostic conditions, which provides important information to select patients for vaccination. GPRIN1, MYRF, PLXNB2, SLC9A4, TRIM29, UBA6, and XDH are potential LUAD-related immune biomarker candidates to activate the immune response. Patients with IS2 and IS4 might potentially be immunization-sensitive patients for vaccination.Yang WangYang WangHuaicheng TanTing YuXiaoxuan ChenFangqi JingHuashan ShiHuashan ShiFrontiers Media S.A.articlemRNA vaccinelung adenocarcinomaimmune subtypetumor mutation burdenimmune landscapeimmunogenic cell deathImmunologic diseases. AllergyRC581-607ENFrontiers in Immunology, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	mRNA vaccine lung adenocarcinoma immune subtype tumor mutation burden immune landscape immunogenic cell death Immunologic diseases. Allergy RC581-607
spellingShingle	mRNA vaccine lung adenocarcinoma immune subtype tumor mutation burden immune landscape immunogenic cell death Immunologic diseases. Allergy RC581-607 Yang Wang Yang Wang Huaicheng Tan Ting Yu Xiaoxuan Chen Fangqi Jing Huashan Shi Huashan Shi Potential Immune Biomarker Candidates and Immune Subtypes of Lung Adenocarcinoma for Developing mRNA Vaccines
description	mRNA vaccines against cancer have advantages in safety, improved therapeutic efficacy, and large-scale production. Therefore, our purpose is to identify immune biomarkers and to analyze immune status for developing mRNA vaccines and selecting appropriate patients for vaccination. We downloaded clinical information and RNA-seq data of 494 LUAD patients from TCGA. LUAD mutational information was hierarchically clustered by NMF package (Version 0.23.0). DeconstructSigs package (Version 1.8.0) and NMF consistency clustering were used to identify mutation signatures. Maftools package (Version 2.6.05) was used to select LUAD-related immune biomarkers. TIMER was used to discuss the correlation between genetic mutations and cellular components. Unsupervised clustering Pam method was used to identify LUAD immune subtypes. Log-rank test and univariate/multivariate cox regression were used to predict the prognosis of immune subtypes. Dimensionality reduction analysis was dedicated to the description of LUAD immune landscape. LUAD patients are classified into four signatures: T >C, APOBEC mutation, age, and tobacco. Then, GPRIN1, MYRF, PLXNB2, SLC9A4, TRIM29, UBA6, and XDH are potential LUAD-related immune biomarker candidates to activate the immune response. Next, we clustered five LUAD-related immune subtypes (IS1–IS5) by prognostic prediction. IS3 showed prolonged survival. The reliability of our five immune subtypes was validated by Thorsson’s results. IS2 and IS4 patients had high tumor mutation burden and large number of somatic mutations. Besides, we identified that immune subtypes of cold immunity (patients with IS2 and IS4) are ideal mRNA vaccination recipients. Finally, LUAD immune landscape revealed immune cells and prognostic conditions, which provides important information to select patients for vaccination. GPRIN1, MYRF, PLXNB2, SLC9A4, TRIM29, UBA6, and XDH are potential LUAD-related immune biomarker candidates to activate the immune response. Patients with IS2 and IS4 might potentially be immunization-sensitive patients for vaccination.
format	article
author	Yang Wang Yang Wang Huaicheng Tan Ting Yu Xiaoxuan Chen Fangqi Jing Huashan Shi Huashan Shi
author_facet	Yang Wang Yang Wang Huaicheng Tan Ting Yu Xiaoxuan Chen Fangqi Jing Huashan Shi Huashan Shi
author_sort	Yang Wang
title	Potential Immune Biomarker Candidates and Immune Subtypes of Lung Adenocarcinoma for Developing mRNA Vaccines
title_short	Potential Immune Biomarker Candidates and Immune Subtypes of Lung Adenocarcinoma for Developing mRNA Vaccines
title_full	Potential Immune Biomarker Candidates and Immune Subtypes of Lung Adenocarcinoma for Developing mRNA Vaccines
title_fullStr	Potential Immune Biomarker Candidates and Immune Subtypes of Lung Adenocarcinoma for Developing mRNA Vaccines
title_full_unstemmed	Potential Immune Biomarker Candidates and Immune Subtypes of Lung Adenocarcinoma for Developing mRNA Vaccines
title_sort	potential immune biomarker candidates and immune subtypes of lung adenocarcinoma for developing mrna vaccines
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/1d7571e2ea164be0afb1a0198899abe0
work_keys_str_mv	AT yangwang potentialimmunebiomarkercandidatesandimmunesubtypesoflungadenocarcinomafordevelopingmrnavaccines AT yangwang potentialimmunebiomarkercandidatesandimmunesubtypesoflungadenocarcinomafordevelopingmrnavaccines AT huaichengtan potentialimmunebiomarkercandidatesandimmunesubtypesoflungadenocarcinomafordevelopingmrnavaccines AT tingyu potentialimmunebiomarkercandidatesandimmunesubtypesoflungadenocarcinomafordevelopingmrnavaccines AT xiaoxuanchen potentialimmunebiomarkercandidatesandimmunesubtypesoflungadenocarcinomafordevelopingmrnavaccines AT fangqijing potentialimmunebiomarkercandidatesandimmunesubtypesoflungadenocarcinomafordevelopingmrnavaccines AT huashanshi potentialimmunebiomarkercandidatesandimmunesubtypesoflungadenocarcinomafordevelopingmrnavaccines AT huashanshi potentialimmunebiomarkercandidatesandimmunesubtypesoflungadenocarcinomafordevelopingmrnavaccines
_version_	1718404618969415680

Potential Immune Biomarker Candidates and Immune Subtypes of Lung Adenocarcinoma for Developing mRNA Vaccines

Ejemplares similares