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Yoneshima Y, Iwama E, Matsumoto S, Matsubara T, Tagawa T, Ota K, Tanaka K, Takenoyama M, Okamoto T, Goto K, Mori M, Okamoto I. Paired analysis of tumor mutation burden for lung adenocarcinoma and associated idiopathic pulmonary fibrosis. Sci Rep 2021; 11:12732. [PMID: 34140559 PMCID: PMC8211684 DOI: 10.1038/s41598-021-92098-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Genetic alterations underlying the development of lung cancer in individuals with idiopathic pulmonary fibrosis (IPF) have remained unclear. To explore whether genetic alterations in IPF tissue contribute to the development of IPF-associated lung cancer, we here evaluated tumor mutation burden (TMB) and somatic variants in 14 paired IPF and tumor samples from patients with IPF-associated lung adenocarcinoma. We also determined TMB for 22 samples of lung adenocarcinoma from patients without IPF. TMB for IPF-associated lung adenocarcinoma was significantly higher than that for matched IPF tissue (median of 2.94 vs. 1.26 mutations/Mb, P = 0.002). Three and 102 somatic variants were detected in IPF and matched lung adenocarcinoma samples, respectively, with only one pair of specimens sharing one somatic variant. TMB for IPF-associated lung adenocarcinoma was similar to that for lung adenocarcinoma samples with driver mutations (median of 2.94 vs. 2.51 mutations/Mb) and lower than that for lung adenocarcinoma samples without known driver mutations (median of 2.94 vs. 5.03 mutations/Mb, P = 0.130) from patients without IPF. Our findings suggest that not only the accumulation of somatic mutations but other factors such as inflammation and oxidative stress might contribute to the development and progression of lung cancer in patients with IPF.
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Affiliation(s)
- Yasuto Yoneshima
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Eiji Iwama
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Shingo Matsumoto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Taichi Matsubara
- Department of Thoracic Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Testuzo Tagawa
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiichi Ota
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kentaro Tanaka
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Mitsuhiro Takenoyama
- Department of Thoracic Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Tatsuro Okamoto
- Department of Thoracic Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Masaki Mori
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Isamu Okamoto
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
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Liu X, Zhang Y. Bioinformatics Analysis of Dysregulated MicroRNA-Messenger RNA Networks in Small Cell Lung Cancer. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The present study aimed to identify a key module of differentially expressed miRNAs (DE-miRNAs) together with the corresponding differentially expressed mRNAs (DE-mRNAs) within small cell lung cancer (SCLC). Linear models were applied to ascertain the DE-miRNAs and DE-mRNAs in SCLC
versus matched non-carcinoma samples obtained from the RNA expression datasets of GSE19945, GSE74190 and GSE6044. The common DE-miRNAs were identified using the Venn plot. Then, 3 databases were used to retrieve the DE-miRNAs target genes, and the intersection was taken for validating the
shared target genes. Besides, Cytoscape was utilized for constructing the miRNAmRNA network for SCLC. Finally, a key module of five DE-miRNAs and four hub genes was determined based on the degree. In addition, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses
were conducted for exploring those hub genes in terms of their functions along with the involved signal transduction pathways. Altogether 106 shared DE-miRNAs were identified, which were used to predict 63 common target genes. In addition, a key module of five DE-miRNAs (hsa-miR-17-5p, hsa-miR-20a-5p,
hsa-miR-20b-5p, hsa-miR-93-5p and hsa-miR- 106b-5p) and four hub genes (SOX4, DPYSL2, TGFBR2 and F3) were extracted from the miRNAmRNA network according to their degree. Finally, the hub genes were subjected to GO as well as KEGG analysis, which revealed that cell cycle G1/S phase transition,
the extracellular matrix, and cellular senescence signaling pathways exerted vial parts during SCLC progression. A key module of five DE-miRNAs and four hub genes may be potentially used as clinical biomarkers to predict SCLC.
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Affiliation(s)
- Xingsheng Liu
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Yi Zhang
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
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Kobayashi H, Serizawa M, Naito T, Konno H, Kojima H, Mizuno T, Isaka M, Endo M, Nagashima T, Kusuhara M, Urakami K, Ohshima K, Yamaguchi K, Ohde Y, Takahashi T. Characterization of tumour mutation burden in patients with non-small cell lung cancer and interstitial lung disease. Respirology 2020; 25:850-854. [PMID: 31694070 PMCID: PMC7496253 DOI: 10.1111/resp.13726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/03/2019] [Accepted: 10/22/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND AND OBJECTIVE The efficacy expectation of immune checkpoint inhibitors against NSCLC in patients with ILD seems to be high because these populations are supposed to have high TMB. However, information about the characterization of TMB in patients with NSCLC and ILD is limited. Therefore, this study aimed to evaluate TMB in samples of NSCLC with ILD and clarify factors that influence TMB values. METHODS The medical records of patients with NSCLC who underwent thoracic surgery at our institution between January 2014 and January 2017 were retrospectively reviewed. Whole-exome sequencing with an Ion Proton system and gene expression profiling of fresh surgical specimens were performed. RESULTS Among 367 patients with NSCLC, 62 (16.9%) were diagnosed with ILD. All samples were collected from primary tumours with a median TMB of approximately 2.1 (range: 0.1-64.4) mutation/Mb. Among 81 squamous cell carcinomas, we compared 27 tumours with concomitant ILD and 54 tumours without ILD. Univariate analyses revealed that tumours with concomitant ILD showed lower TMB values than those without ILD. Multivariate analysis revealed that concomitant ILD was significantly associated with low TMB values. Conversely, no difference was noted in the TMB value of adenocarcinoma between patients with and without ILD. CONCLUSION Squamous cell carcinoma and adenocarcinoma with ILD do not have high TMB values. Therefore, considering the risk of severe pneumonitis, immune checkpoint inhibitors should not be used routinely against patients with NSCLC and ILD based on the expectation of high TMB values.
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Affiliation(s)
- Haruki Kobayashi
- Division of Thoracic OncologyShizuoka Cancer CenterShizuokaJapan
| | - Masakuni Serizawa
- Drug Discovery and Development DivisionShizuoka Cancer Center Research InstituteShizuokaJapan
| | - Tateaki Naito
- Division of Thoracic OncologyShizuoka Cancer CenterShizuokaJapan
| | - Hayato Konno
- Division of Thoracic SurgeryShizuoka Cancer CenterShizuokaJapan
| | - Hideaki Kojima
- Division of Thoracic SurgeryShizuoka Cancer CenterShizuokaJapan
| | - Tetsuya Mizuno
- Division of Thoracic SurgeryShizuoka Cancer CenterShizuokaJapan
| | - Mitsuhiro Isaka
- Division of Thoracic SurgeryShizuoka Cancer CenterShizuokaJapan
| | - Masahiro Endo
- Division of Diagnostic RadiologyShizuoka Cancer CenterShizuokaJapan
| | | | - Masatoshi Kusuhara
- Region Resources DivisionShizuoka Cancer Center Research InstituteShizuokaJapan
| | - Kenichi Urakami
- Cancer Diagnostics DivisionShizuoka Cancer Center Research InstituteShizuokaJapan
| | - Keiichi Ohshima
- Medical Genetics DivisionShizuoka Cancer Center Research InstituteShizuokaJapan
| | | | - Yasuhisa Ohde
- Division of Thoracic SurgeryShizuoka Cancer CenterShizuokaJapan
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Liam CK. Tumour mutation burden of non-small cell lung cancer with pre-existing ILD. Respirology 2019; 25:784-786. [PMID: 31805607 DOI: 10.1111/resp.13750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 11/09/2019] [Accepted: 11/21/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Chong-Kin Liam
- Division of Respiratory Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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