Multiregion Whole-Exome Sequencing Uncovers the Genetic Evolution and Mutational Heterogeneity of Early-Stage Metastatic Melanoma

Abstract

Cancer genome sequencing has shed light on the underlying genetic aberrations that drive tumorigenesis. However, current sequencing-based strategies, which focus on a single tumor biopsy, fail to take into account intratumoral heterogeneity. To address this challenge and elucidate the evolutionary history of melanoma, we performed whole-exome and transcriptome sequencing of 41 multiple melanoma biopsies from eight individual tumors. This approach revealed heterogeneous somatic mutations in the range of 3%-38% in individual tumors. Known mutations in melanoma drivers BRAF and NRAS were always ubiquitous events. Using RNA sequencing, we found that the majority of mutations were not expressed or were expressed at very low levels, and preferential expression of a particular mutated allele did not occur frequently. In addition, we found that the proportion of ultraviolet B (UVB) radiation-induced C>T transitions differed significantly (P < 0.001) between early and late mutation acquisition, suggesting that different mutational processes operate during the evolution of metastatic melanoma. Finally, clinical history reports revealed that patients harboring a high degree of mutational heterogeneity were associated with more aggressive disease progression. In conclusion, our multiregion tumor-sequencing approach highlights the genetic evolution and non-UVB mutational signatures associated with melanoma development and progression, and may provide a more comprehensive perspective of patient outcome.

The PI3K Pathway in Human Disease

“…These same two genes appear to be particularly prone to heterogeneous mutation patterns in primary tumor tissues. Subclonal mutations in PIK3CA were reported in several cancer subtypes, including NSCLC, colorectal cancer, breast cancer, and others (Harbst et al, 2016; de Bruin et al, 2014; McGranahan and Swanton, 2017; Uchi et al, 2016; Yates et al, 2015). Consistent with these findings, a study spanning nine cancer subtypes demonstrated that subclonal mutations in the PI3K-AKT-mTOR pathway were considerably more frequent than subclonal mutations in the RAS-MAPK pathway, which tended to be ubiquitously expressed in all subclones in the tumor (McGranahan et al, 2015).…”

Cancer evolution and heterogeneity

“…Somatic mutations are present in all cells and they are the consequence of multiple mutational processes, including the intrinsic slight infidelity of the DNA replication machinery, exogenous or endogenous mutagen exposures, and enzymatic modification of DNA and, at present, they have been classified into 30 signatures 35, 36, 37, 38. The nucleotide substitutions in those tumors were characterized as C>T from ultraviolet light (signature 7)23 and C>A from smoking (signature 4) 19, 20. Both substitutions were observed as founder events.…”

“…1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 This multiregional analysis (MRA) sequencing approach enabled us not only to observe spatial heterogeneity, but also to calculate temporal alterations and eventually disclose the evolution of tumors. There are two types of somatic aberration in a tumor: ubiquitous aberrations (founder mutations, trunk mutations, or clonal mutations) and scattered aberrations (progressor mutations, branch/leaf mutations, or subclonal mutations).…”

Contemporary and potential future molecular diagnosis of melanoma

“…Recently, Harbst and colleagues [53] performed whole-exome and transcriptome sequencing of 41 multiple melanoma biopsies from 8 tumors. The Authors found that heterogeneous somatic mutations occurred in the range of 3-38% in individual tumors, and that the proportion of UVR signature differed significantly between early and late mutation acquisition, suggesting that different mutational processes operate during the evolution of metastatic melanoma.…”

“…The Authors found that heterogeneous somatic mutations occurred in the range of 3-38% in individual tumors, and that the proportion of UVR signature differed significantly between early and late mutation acquisition, suggesting that different mutational processes operate during the evolution of metastatic melanoma. Moreover, a high degree of melanoma mutational heterogeneity was associated with a more aggressive disease progression [53].…”