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Volume 12
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10.3390/genes12091458
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Article

Metatranscriptomic Analysis of Human Lung Metagenomes from Patients with Lung Cancer

by
Ya-Sian Chang
1,2,3,
Ming-Hung Hsu
2,
Siang-Jyun Tu
2,
Ju-Chen Yen
1,
Ya-Ting Lee
1,
Hsin-Yuan Fang
4 and
Jan-Gowth Chang
1,2,3,5,*
1
Epigenome Research Center, China Medical University Hospital, Taichung 404, Taiwan
2
Center for Precision Medicine, China Medical University Hospital, Taichung 404, Taiwan
3
School of Medicine, China Medical University, Taichung 404, Taiwan
4
Department of Thoracic Surgery, China Medical University Hospital, Taichung 404, Taiwan
5
Department of Bioinformatics and Medical Engineering, Asia University, Taichung 413, Taiwan
*
Author to whom correspondence should be addressed.
Genes 2021, 12(9), 1458; https://doi.org/10.3390/genes12091458
Submission received: 30 July 2021 / Revised: 15 September 2021 / Accepted: 16 September 2021 / Published: 21 September 2021
(This article belongs to the Section Human Genomics and Genetic Diseases)
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Abstract

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.
Keywords: metatranscriptomic; lung cancer; microenvironments; T cell receptor repertoires; B cell receptor repertoires metatranscriptomic; lung cancer; microenvironments; T cell receptor repertoires; B cell receptor repertoires

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MDPI and ACS Style

Chang, Y.-S.; Hsu, M.-H.; Tu, S.-J.; Yen, J.-C.; Lee, Y.-T.; Fang, H.-Y.; Chang, J.-G. Metatranscriptomic Analysis of Human Lung Metagenomes from Patients with Lung Cancer. Genes 2021, 12, 1458. https://doi.org/10.3390/genes12091458

AMA Style

Chang Y-S, Hsu M-H, Tu S-J, Yen J-C, Lee Y-T, Fang H-Y, Chang J-G. Metatranscriptomic Analysis of Human Lung Metagenomes from Patients with Lung Cancer. Genes. 2021; 12(9):1458. https://doi.org/10.3390/genes12091458

Chicago/Turabian Style

Chang, Ya-Sian, Ming-Hung Hsu, Siang-Jyun Tu, Ju-Chen Yen, Ya-Ting Lee, Hsin-Yuan Fang, and Jan-Gowth Chang. 2021. "Metatranscriptomic Analysis of Human Lung Metagenomes from Patients with Lung Cancer" Genes 12, no. 9: 1458. https://doi.org/10.3390/genes12091458

APA Style

Chang, Y.-S., Hsu, M.-H., Tu, S.-J., Yen, J.-C., Lee, Y.-T., Fang, H.-Y., & Chang, J.-G. (2021). Metatranscriptomic Analysis of Human Lung Metagenomes from Patients with Lung Cancer. Genes, 12(9), 1458. https://doi.org/10.3390/genes12091458

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