Dataset Information

Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma.

ABSTRACT:

Background

There are currently no treatments targeting the immune microenvironment (TME) as an extension of immunotherapy. Our research aims to provide guidance for the development of immune-related mRNA vaccines and the identification of immune subtypes for vaccine treatment in lung adenocarcinoma (LUAD).

Methods

HTRNA-Seq and single cell RNA-seq data were obtained from The Cancer Genome Atlas (TCGA) and Gene-Expression Omnibus (GEO, GSE87340, GSE140343, GSE148071) databases. Immune checkpoints (ICP) were used as criteria to differentiate immune subtypes and immune resistance score (IRS) system is constructed by ssGSEA to judge the immune microenvironment status of patients.

Results

Two overexpressed tumor-specific antigens, including ZC3H12D and TXNDC5, were found to be associated with both disease-free survival (DFS) and overall survival (OS). In addition, the expression of two genes correlated with antigen-presenting cell (APC) infiltration and tumor purity. Subsequently, the immune subtype of the patient was defined by constructing an IRS scoring system. The lower the IRS, the stronger the immune response in the TME. This result was verified in external datasets and at the single-cell level.

Conclusions

ZC3H12D and TXNDC5 are potential tumor-specific antigens for developing mRNA vaccines in LUAD. Importantly, patients with low IRS are more suitable for the use of immunotherapy and vaccines. Our research enhances understanding of TME features and guides more effective immunotherapy strategies.

SUBMITTER: Zhao D

PROVIDER: S-EPMC9483806 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Publications

Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma.

Zhao Deze D Liu Xianyu X Shan Yunhan Y Li JiaJia J Cui Weifang W Wang Jun J Jiang Junjie J Xie Qun Q Zhang Chunfang C Duan Chaojun C

Computational and structural biotechnology journal 20220905

<h4>Background</h4>There are currently no treatments targeting the immune microenvironment (TME) as an extension of immunotherapy. Our research aims to provide guidance for the development of immune-related mRNA vaccines and the identification of immune subtypes for vaccine treatment in lung adenocarcinoma (LUAD).<h4>Methods</h4>HTRNA-Seq and single cell RNA-seq data were obtained from The Cancer Genome Atlas (TCGA) and Gene-Expression Omnibus (GEO, GSE87340, GSE140343, GSE148071) databases. Imm ...[more]

PMID: 36187916

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Project description:BackgroundAlthough mRNA vaccines have been efficient for combating a variety of tumors, their effectiveness against glioma remains unclear. There is growing evidence that immunophenotyping can reflect the comprehensive immune status and microenvironment of the tumor, which correlates closely with treatment response and vaccination potency. The purpose of this research was to screen for effective antigens in glioma that could be used for developing mRNA vaccines and to further differentiate the immune subtypes of glioma to create an selection criteria for suitable patients for vaccination.MethodsGene expression profiles and clinical data of 698 glioma samples were extracted from The Cancer Genome Atlas, and RNA_seq data of 1018 glioma samples was gathered from Chinese Glioma Genome Atlas. Gene Expression Profiling Interactive Analysis was used to determine differential expression genes and prognostic markers, cBioPortal software was used to verify gene alterations, and Tumor Immune Estimation Resource was used to investigate the relationships among genes and immune infiltrating cells. Consistency clustering was applied for consistent matrix construction and data aggregation, Gene oncology enrichment was performed for functional annotation, and a graph learning-based dimensionality reduction method was applied to describe the subtypes of immunity.ResultsFour overexpressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in glioma, including TP53, IDH1, C3, and TCF12. Besides, four immune subtypes of glioma (IS1-IS4) and 10 immune gene modules were identified consistently in the TCGA data. The immune subtypes had diverse molecular, cellular, and clinical features. IS1 and IS4 displayed an immune-activating phenotype and were associated with worse survival than the other two subtypes, while IS2 and IS3 had lower levels of tumor immune infiltration. Immunogenic cell death regulators and immune checkpoints were also diversely expressed in the four immune subtypes.ConclusionTP53, IDH1, C3, and TCF12 are effective antigens for the development of anti-glioma mRNA vaccines. We found four stable and repeatable immune subtypes of human glioma, the classification of the immune subtypes of glioma may play a crucial role in the predicting mRNA vaccine outcome.

Project description:BackgroundNowadays, researchers are leveraging the mRNA-based vaccine technology used to develop personalized immunotherapy for cancer. However, its application against glioma is still in its infancy. In this study, the applicable candidates were excavated for mRNA vaccine treatment in the perspective of immune regulation, and suitable glioma recipients with corresponding immune subtypes were further investigated.MethodsThe RNA-seq data and clinical information of 702 and 325 patients were recruited from TCGA and CGGA, separately. The genetic alteration profile was visualized and compared by cBioPortal. Then, we explored prognostic outcomes and immune correlations of the selected antigens to validate their clinical relevance. The prognostic index was measured via GEPIA2, and infiltration of antigen-presenting cells (APCs) was calculated and visualized by TIMER. Based on immune-related gene expression, immune subtypes of glioma were identified using consensus clustering analysis. Moreover, the immune landscape was visualized by graph learning-based dimensionality reduction analysis.ResultsFour glioma antigens, namely ANXA5, FKBP10, MSN, and PYGL, associated with superior prognoses and infiltration of APCs were selected. Three immune subtypes IS1-IS3 were identified, which fundamentally differed in molecular, cellular, and clinical signatures. Patients in subtypes IS2 and IS3 carried immunologically cold phenotypes, whereas those in IS1 carried immunologically hot phenotype. Particularly, patients in subtypes IS3 and IS2 demonstrated better outcomes than that in IS1. Expression profiles of immune checkpoints and immunogenic cell death (ICD) modulators showed a difference among IS1-IS3 tumors. Ultimately, the immune landscape of glioma elucidated considerable heterogeneity not only between individual patients but also within the same immune subtype.ConclusionsANXA5, FKBP10, MSN, and PYGL are identified as potential antigens for anti-glioma mRNA vaccine production, specifically for patients in immune subtypes 2 and 3. In summary, this study may shed new light on the promising approaches of immunotherapy, such as devising mRNA vaccination tailored to applicable glioma recipients.

Dataset Information

Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma.

Background

Methods

Results

Conclusions

Publications

Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma.

Similar Datasets

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