Genomic Stability and Non-Exhausted Immune Phenotype in Indolent T4N0M0 (Diameter ≥7 cm) Non-Small Cell Lung Cancers

Background: T4N0M0 (diameter ≥7 cm) non-small cell lung cancers (NSCLCs) constitute a unique tumour type, with a huge tumour size but no regional or distant metastases. However, the genomic features of T4N0M0 NSCLCs have not been elucidated. We systematically investigated intra-tumoural heterogeneity, clonal structure, chromosomal instability (CIN), and immune microenvironment in T4N0M0 (≥7 cm) NSCLCs.Methods: Whole-exome sequencing, RNA sequencing, and multiplex immunohistochemistry (mIHC) were conducted to analyse 24 spatially segregated tumour samples from eight patients who were pathologically diagnosed with T4N0M0 (≥7 cm) stage IIIA NSCLCs. Adjacent normal tissues and peripheral blood served as controls.Findings: In total, 35·2% of mutations and 91·1% of somatic copy number alterations were classified as sub-clonal events, which exhibited widespread genetic intra-tumoural heterogeneity. A low degree of CIN was observed. No patients had genome doubling. The burden of loss of heterozygosity, aneuploidy, and genome instability index of these tumours was significantly lower than that in the TRACERx cohort. Expression profiles revealed significant upregulation of cell division-related signals and the G2/M checkpoint pathway. An imbalance in immune infiltration between the tumour and non-tumour regions was not observed, which is indicative of a non-exhausted immune phenotype.Interpretation: Intra-tumoural heterogeneity and CIN were not observed consistently in these indolent tumours. A low degree of CIN and non-exhausted immune phenotype may contribute to low metastatic capability.Funding Information: Natural Science Foundation of Guangdong Province (2018A030313681, S.D.), Bethune Charitable Foundation (HZB-20190528-15, S.D.), Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer (2017B030314120, Y.L. Wu), Guangdong Provincial People's Hospital Scientific Research Funds for Leading Medical Talents in Guangdong Province (KJ012019426, Y.L. Wu), Guangdong Provincial People's Hospital Young Talent Project (GDPPHYTP201902, W.Z. Zhong).Declaration of Interests: Qing Zhou declares speaker fees from AstraZeneca and Roche. Wen-Zhao Zhong declares speaker fees from AstraZeneca and Roche. Yi-Long Wu declares speaker fees from AstraZeneca, Eli Lilly, Pfizer, Roche, and Sanofi. None of the other authors have any conflicts of interest to declare. Ethics Approval Statement: This study was approved by the Institutional Review Board of the Guangdong Provincial People’s Hospital (Approval No. GDREC2019523H). Written informed consent was obtained from all patients.