Comprehensive analyses of genomic features and mutational signatures in adenosquamous carcinoma of the lung

Hongbiao Wang; Jun Liu; Sujuan Zhu; Kun Miao; Zhifeng Li; Xiaofang Qi; Lujia Huang; Lijie Guo; Yan Wang; Yuyin Cai; Yingcheng Lin

doi:10.3389/fonc.2022.945843

Comprehensive analyses of genomic features and mutational signatures in adenosquamous carcinoma of the lung

Front Oncol. 2022 Sep 14:12:945843. doi: 10.3389/fonc.2022.945843. eCollection 2022.

Authors

Hongbiao Wang¹, Jun Liu², Sujuan Zhu¹, Kun Miao³, Zhifeng Li¹, Xiaofang Qi⁴, Lujia Huang⁴, Lijie Guo⁴, Yan Wang⁴, Yuyin Cai⁵, Yingcheng Lin¹

Affiliations

¹ Medical Oncology Session No.1, Cancer Hospital of Shantou University Medical College, Shantou, China.
² Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, China.
³ Department of Medical Oncology, The First People's Hospital of Yunnan Province, Kunming, China.
⁴ Medical Department, OrigiMed Co., Ltd, Shanghai, China.
⁵ Department of Thoracic Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China.

Abstract

Adenosquamous carcinoma (ASC) of the lung is a relatively rare tumor with strong aggressiveness and poor prognosis. The analysis of mutational signatures is becoming routine in cancer genomics and has implications for pathogenesis, classification, and prognosis. However, the distribution of mutational signatures in ASC patients has not been evaluated. In this study, we sought to reveal the landscape of genomic mutations and mutational signatures in ASC. Next-generation sequencing (NGS) technology was used to retrieve genomic information for 124 ASC patients. TP53 and EGFR were the most prevalent somatic mutations observed, and were present in 66.9% and 54.8% of patients, respectively. CDKN2A (21%), TERT (21%), and LRP1B (18.5%) mutations were also observed. An analysis of gene fusion/rearrangement characteristics revealed a total of 64 gene fusions. The highest frequency of variants was determined for ALK fusions, with six ALK-EML4 classical and two intergenic ALK fusions, followed by three CD74-ROS1 fusions and one ROS1-SYN3 fusion. EGFR 19del (45.6%), and EGFR L858R (38.2%) and its amplification (29.4%) were the top three EGFR mutations. We extracted mutational signatures from NGS data and then performed a statistical analysis in order to search for genomic and clinical features that could be linked to mutation signatures. Amongst signatures cataloged at COSMIC, the most prevalent, high-frequency base changes were for C > T; and the five most frequent signatures, from highest to lowest, were 2, 3, 1, 30, and 13. Signatures 1 and 6 were determined to be associated with age and tumor stage, respectively, and Signatures 22 and 30 were significantly related to smoking. We additionally evaluated the correlation between tumor mutational burden (TMB) and genomic variations. We found that mutations ARID2, BRCA1, and KEAP1 were associated with high TMB. The homologous recombination repair (HRR) pathway-related gene mutation displayed a slightly higher TMB than those without mutations. Our study is the first to report comprehensive genomic features and mutational signatures in Chinese ASC patients. Results obtained from our study will help the scientific community better understand signature-related mutational processes in ASC.

Keywords: EGFR mutation; TMB; adenosquamous carcinoma of the lung; mutational signature; next-generation sequencing.