Tobacco smoking related mutational signatures (MS) in classifying smoking and non-smoking associated metastatic non-small cell lung cancer (mNSCLC)

Patient-reported smoking history is frequently used as stratification factor or for subgroup analyses in NSCLC directed clinical research, even though this classification does not fully reflect the mutational processes in a tumour. Additionally, the label ‘smoker’ can add to the lung cancer stigma. Next generation sequencing can be used to identify MS associated with tobacco smoking, such as the single base MS (SBS) 4 and indel based MS (ID) 3. This provides an opportunity to redefine the classification of smoking and non-smoking associated NSCLC based on individual genomic tumour characteristics. Whole genome sequencing and clinical data was obtained from 3 prospective cohorts of mNSCLC. MS analysis was performed based on the MS of the COSMIC catalog (cancer.sanger.ac.uk/signatures/). We calculated the proportion of the relative contribution (RC) of SBS4 compared to the summed RCs of SBS1 (age), SBS4 and SBS5 (age), and the proportion of ID3 compared to the summed RCs of ID1 (mismatch repair deficiency (MMRd)/age), ID2 (MMRd/age) and ID3. These proportions and the absolute counts of SBS4 and ID3 were used to divide the cohort into smoking associated (SH) and non-smoking associated (SL) clusters (k-means; k = 2). 316 tumour samples were analysed, 169 were clustered as SH, 147 as SL. The clusters differed significantly in tumour mutational burden, MS contribution and gene enrichment. The clusters and smoking history overlapped considerably. However, 26% of samples from patients with an active smoking history were included in SL, of which 52% harboured an EGFR/ALK/RET/ROS1 alteration, and 4% from patients without smoking history were included in SH. The discordant samples were genomically similar to the rest of their respective cluster. A subset of mNSCLC is classified differently into smoking and non-smoking associated tumours based on SBS4 and ID3 contribution than based on smoking history. The MS classification seems more accurate in grouping genomically similar tumours together and should therefore be considered as stratification factor in future clinical research. Replacing smoking history could also help reduce the lung cancer stigma.