Deciphering the clonal evolution of non-small cell lung cancer

Abstract

Lung cancer is the most common and deadliest malignancy worldwide and the emergence of metastases is the main cause of lethality. One reason for this high mortality is intratumoral heterogeneity (ITH). This is the presence of multiple subclones with genetic heterogeneity as a consequence of cancer evolution, which means that tumor cells undergo molecular and phenotypic changes. Therefore, resistant or metastatic subclones can survive unnoticed for a long time and often remain undiscovered at the time of diagnosis. The aim of this work was to shed light on the tumor evolution of three subtypes of non-small cell lung cancer (NSCLC), the most common form of lung cancer. First, the clonal relationship of primary lung adenocarcinomas (LUAD) and their matched metastases was deciphered by studying copy number variations (CNVs) and somatic mutations (SNVs) in a unique cohort of 16 patients. Lung squamous cell carcinomas (LUSC) were genomically characterized in a second cohort consisting of six patients with matched, clonally related metastases using a similar approach. And third, genomic alterations of adenosquamous carcinoma (ASC), which is a tumor entity with a mixture of LUAD and LUSC components, were investigated in three cases. Tumor purity is a major constraint in genomic analyses. To overcome this limitation, we refined and validated a flow-sorting approach to increase the availability of tumor material with high tumor purity. This strategy increased tumor purity from 54% to 92% in LUAD and from 33% to 70% in LUSC. Using this approach, we found that more than 88% of CNVs and 80% of SNVs are shared between primary tumors and metastases in LUAD. Similarly, more than 76% of CNVs and 64% of SNVs were common between primary LUSC and the matched metastases. Both studies therefore demonstrated a close genomic relationship between primary tumors and metastases with only a limited number of subclonal genetic alterations. In addition, tumor ploidy remained stable over time, regardless if tumors were diploid or aneuploid. Together, this suggests an early accumulation of CNVs and SNVs, often before metastatic spread, with limited chromosomal instability over the disease course of both tumor entities, at least from the time the primary tumors are established. We also found high concordance of CNVs and SNVs in the LUAD and LUSC components of all three ASCs. This unequivocally confirmed a monoclonal origin of the two distinct components in ASC. Strikingly, we found LUAD-specific mutations that are rarely observed in LUSC, which suggests a LUAD-like common ancestor cell as the cell of origin for ASC. Our findings shed light on the genomic evolution of LUAD and LUSC and suggest that most genetic alterations can be detected in the primary tumors, thereby ITH is unlikely to significantly alter the landscape of targetable alterations due to sampling. In addition, our work is the study on the genomic landscape of ASC, a rare and highly aggressive form of NSCLC, in a comprehensive manner. Although further studies in larger cohorts are needed to confirm our findings, our studies will serve as a basis for future explorations and eventually help patients in dire need.