Metatranscriptomic Analysis of Human Lung Metagenomes from Patients with Lung Cancer

• Published in: Genes Vol. 12; no. 9; p. 1458
• Main Authors: Chang, Ya-Sian, Hsu, Ming-Hung, Tu, Siang-Jyun, Yen, Ju-Chen, Lee, Ya-Ting, Fang, Hsin-Yuan, Chang, Jan-Gowth
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 21.09.2021; MDPI
• Subjects: Adenocarcinoma of Lung - genetics; Adenocarcinoma of Lung - immunology; Adenocarcinoma of Lung - microbiology; Bacterial infections; Carcinoma, Non-Small-Cell Lung - genetics; Carcinoma, Non-Small-Cell Lung - immunology; Carcinoma, Non-Small-Cell Lung - microbiology; Carcinoma, Non-Small-Cell Lung - mortality; Carcinoma, Squamous Cell - genetics; Carcinoma, Squamous Cell - immunology; Carcinoma, Squamous Cell - microbiology; CD4 antigen; CD8 antigen; CD8-positive T-lymphocytes; computer software; Dendritic cells; Disease; Epidermal growth factor; epidermal growth factor receptors; Gene Expression Profiling; genes; Genomes; Humans; immunologic receptors; Immunological memory; landscapes; Lavage; Lung cancer; lung neoplasms; Lung Neoplasms - genetics; Lung Neoplasms - immunology; Lung Neoplasms - microbiology; Lung Neoplasms - mortality; lungs; Lymphocytes B; Lymphocytes T; Medical prognosis; memory; Memory cells; Metagenome; metagenomics; microbiome; Microbiomes; Microbiota; Microenvironments; Microorganisms; Mutation; Pilot Projects; Prognosis; Pseudomonas; Receptors, Antigen, B-Cell - immunology; Receptors, Antigen, T-Cell - immunology; RNA, Ribosomal, 16S; rRNA 16S; sequence analysis; Sequence Analysis, RNA; Software; Survival analysis; T cell receptors; Taxonomy; transcriptomics; Tumor Microenvironment - immunology; Tumors; United States > US; China; lung cancer; T cell receptor repertoires; metatranscriptomic; B cell receptor repertoires; microenvironments
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes12091458

This study was designed to characterize the microbiomes of the lung tissues of lung cancer patients. RNA-sequencing was performed on lung tumor samples from 49 patients with lung cancer. Metatranscriptomics data were analyzed using SAMSA2 and Kraken2 software. 16S rRNA sequencing was also performed. The heterogeneous cellular landscape and immune repertoires of the lung samples were examined using xCell and TRUST4, respectively. We found that nine bacteria were significantly enriched in the lung tissues of cancer patients, and associated with reduced overall survival (OS). We also found that subjects with mutations in the epidermal growth factor receptor gene were less likely to experience the presence of Pseudomonas. aeruginosa. We found that the presence of CD8+ T-cells, CD4+ naive T-cells, dendritic cells, and CD4+ central memory T cells were associated with a good prognosis, while the presence of pro B-cells was associated with a poor prognosis. Furthermore, high clone numbers were associated with a high ImmuneScore for all immune receptor repertoires. Clone numbers and diversity were significantly higher in unpresented subjects compared to presented subjects. Our results provide insight into the microbiota of human lung cancer, and how its composition is linked to the tumor immune microenvironment, immune receptor repertoires, and OS.