The genetic evolution of acral melanoma

Abstract

Acral melanoma is an aggressive type of melanoma with unknown origins. It is the most common type of melanoma in individuals with dark skin and is notoriously challenging to treat. We examine exome sequencing data of 139 tissue samples, spanning different progression stages, from 37 patients. We find that 78.4% of the melanomas display clustered copy number transitions with focal amplifications, recurring predominantly on chromosomes 5, 11, 12, and 22. These complex genomic aberrations are typically shared across all progression stages of individual patients. TERT activating alterations also arise early, whereas MAP-kinase pathway mutations appear later, an inverted order compared to the canonical evolution. The punctuated formation of complex aberrations and early TERT activation suggest a unique mutational mechanism that initiates acral melanoma. The marked intratumoral heterogeneity, especially concerning MAP-kinase pathway mutations, may partly explain the limited success of therapies for this melanoma subtype.

Fig. 1. Clusters of copy number transitions (hailstorms) are common in acral melanomas and arise early in their evolution.

a A melanoma (case 101) with hailstorms on chromosome 5p and 12q (upper panel) defined as genomic regions with high-level amplifications and high density of copy number transitions (CNT) (lower panel). The higher resolution panels underneath show the location of putative driver genes within the amplicons and reveal foci of kataegis on 12q. b Hailstorms in acral melanoma are distributed non-randomly, and preferentially involve chromosomes 5, 11, 12, and 22. c Most hailstorms are shared across all samples of a given patient, placing them on the trunk of the respective phylogenetic tree. d An example case (case 110) with hailstorms on 5p, 11q, and 19q shared across the melanoma in situ (MIS) and two separate invasive areas (Inv 1 and Inv 2) of the primary melanoma. The copy number profiles of all three tumor areas show identical hailstorms on three chromosomal arms with congruent copy number transitions. The coding regions of amplified oncogenes are highlighted in pink. Source data are provided as a Source Data file.

Fig. 2. TERT alterations arise during the earliest progression stages.

a Amplifications, upstream structural rearrangements, and promoter mutations of TERT all occurred on the trunk of phylogenetic trees and invariably were identifiable in the earliest progression stage of melanomas that carried these alterations. The relative frequency of the different types of TERT alterations are shown. b An example case with structural rearrangement immediately upstream of TERT (left) shared across all three tumor areas from two different progression stages. The corresponding phylogenetic tree is shown (right). Source data are provided as a Source Data file.

Fig. 3. Two acral melanomas with UV signature mutations accumulating after tumor initiation.

For both cases, the highest percentages of [C/T]C > T or CC > TT substitutions were observed in the MIS areas, which in case 48 (left panel) had an elevated mutation burden (5.7 vs. 1.1–1.3 mutations/megabase). The fractions were lower on the evolutionary trunks of both melanomas, suggesting limited or no exposure to UV radiation in the most recent common ancestors of both tumors. Source data are provided as a Source Data file.

Fig. 4. Intratumoral heterogeneity of genetic alterations exemplified by case 62.

a Hematoxylin and eosin-stained sections of the primary tumor on the thumb and corresponding lymph node metastases. The in situ, and invasive areas of the primary and three areas of the corresponding metastases were microdissected as indicated by the dashed white lines. Scale bar: 5 mm. b The cancer cell fraction (CCF) of pathogenic or likely pathogenic mutations shows notable differences among different tumor areas. c The invasive area A (Inv A) that lacks the BRAF V600E mutation shows amplification of RAF1, whereas invasive area B (Inv B) shows amplification of YAP1, which can be traced back to the melanoma in situ (MIS) area (not shown). d The immunohistochemistry for YAP1 visualizes the striking heterogeneity within the primary tumor. One tissue section from each of the primary tumor and the metastases was used. Scale bar: 5 mm. Complex copy number alterations on chromosome 22 (e) and structural rearrangement immediately upstream of TERT (f) are shared across all progression stages of the tumor with congruent copy number transitions. g The relevant genetic alterations shown in an inferred phylogenetic tree. See Figshare for more detailed analyses. Source data are provided as a Source Data file.

Fig. 5. MAP-kinase pathway driver mutations tend to arise after tumor initiation.

NRAS mutations (a), NF1 mutations (b), CIC homozygous deletion (c), PTPN11 mutation (d), and KIT mutations (e) arose after tumor initiation in multiple acral melanomas, placing them on the respective branches of the corresponding phylogenetic trees.

Fig. 6. Genetic differences of metastases and primary melanoma indicate early dissemination of metastatic clones.

a Evolutionary trees for three cases, one with a cutaneous metastasis and two with lymph node metastases showing comparatively early branching of the metastatic lineages from the corresponding primary melanomas. In two other melanomas multiple metastases were analyzed (b, c). The lineages of the brain metastases diverge early from the primary in both patients. The in situ portion of case 102 was computationally inferred to contain two different subclones. b, c Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en).

Fig. 7. A model of the genomic evolution of acral melanoma.

The progression cascade begins with field cells, i.e., histopathologically normal acral melanocytes distributed along the basilar epidermis at normal density but already harboring hailstorms as demonstrated by prior FISH studies^,. As cell density increases, the nascent tumor becomes histopathological and clinically manifest as melanoma in situ, which later develops foci of dermal invasion with genetically heterogeneous subclones that can seed metastases. Activation of TERT arises before canonical driver mutations of melanoma, which activate the MAP-kinase pathway, override the G1/S checkpoint, and further disrupt other pathways.