Targeted next-generation sequencing reveals high frequency of mutations in epigenetic regulators across treatment-naïve patient melanomas

Abstract

Background: Recent developments in genomic sequencing have advanced our understanding of the mutations underlying human malignancy. Melanoma is a prototype of an aggressive, genetically heterogeneous cancer notorious for its biologic plasticity and predilection towards developing resistance to targeted therapies. Evidence is rapidly accumulating that dysregulated epigenetic mechanisms (DNA methylation/demethylation, histone modification, non-coding RNAs) may play a central role in the pathogenesis of melanoma. Therefore, we sought to characterize the frequency and nature of mutations in epigenetic regulators in clinical, treatment-naïve, patient melanoma specimens obtained from one academic institution.

Results: Targeted next-generation sequencing for 275 known and investigative cancer genes (of which 41 genes, or 14.9 %, encoded an epigenetic regulator) of 38 treatment-naïve patient melanoma samples revealed that 22.3 % (165 of 740) of all non-silent mutations affected an epigenetic regulator. The most frequently mutated genes were BRAF, MECOM, NRAS, TP53, MLL2, and CDKN2A. Of the 40 most commonly mutated genes, 12 (30.0 %) encoded epigenetic regulators, including genes encoding enzymes involved in histone modification (MECOM, MLL2, SETD2), chromatin remodeling (ARID1B, ARID2), and DNA methylation and demethylation (TET2, IDH1). Among the 38 patient melanoma samples, 35 (92.1 %) harbored at least one mutation in an epigenetic regulator. The genes with the highest number of total UVB-signature mutations encoded epigenetic regulators, including MLL2 (100 %, 16 of 16) and MECOM (82.6 %, 19 of 23). Moreover, on average, epigenetic genes harbored a significantly greater number of UVB-signature mutations per gene than non-epigenetic genes (3.7 versus 2.4, respectively; p = 0.01). Bioinformatics analysis of The Cancer Genome Atlas (TCGA) melanoma mutation dataset also revealed a frequency of mutations in the 41 epigenetic genes comparable to that found within our cohort of patient melanoma samples.

Conclusions: Our study identified a high prevalence of somatic mutations in genes encoding epigenetic regulators, including those involved in DNA demethylation, histone modification, chromatin remodeling, and microRNA processing. Moreover, UVB-signature mutations were found more commonly among epigenetic genes than in non-epigenetic genes. Taken together, these findings further implicate epigenetic mechanisms, particularly those involving the chromatin-remodeling enzyme MECOM/EVI1 and histone-modifying enzyme MLL2, in the pathobiology of melanoma.

Keywords: 5-hydroxymethylcytosine; DNA demethylation; Epigenetics; Isocitrate dehydrogenase 2 (IDH2); MECOM (MDS1 and EV1 complex locus); MLL2; Melanoma; Next-generation sequencing (NGS); Ten-eleven translocation (TET).

Fig. 1

Bar graph summarizing distribution of mutation types in our 38 patient melanoma samples

Fig. 2

Chart summarizing the top 40 most frequently mutated genes. *Epigenetic gene

Fig. 3

Frequency of mutated epigenetic genes organized by functional epigenetic category

Fig. 4

Presence of mutations in epigenetic regulators, organized by patient melanoma sample and key primary cutaneous melanoma histopathologic parameters

Fig. 5

Ingenuity Pathway Analysis® of the 41 epigenetic regulators sequenced by our targeted next-generation sequencing platform (Oncopanel, BWH/DFCI). Unique shape indicates key epigenetic function while the color reflects the prevalence of mutations in that gene

Fig. 6

Spectrum of UV-signature mutations among non-epigenetic genes. Note the low frequency of UVB-signature mutations in BRAF

Fig. 7

Spectrum of UV-signature mutations among epigenetic genes. Note the high frequency (100 %) of UVB-signature mutations among the gene encoding histone lysine methyltransferase, MLL2 (KMT2D)

Fig. 8

Distribution of UVB-signature mutations among non-epigenetic genes and epigenetic genes. Collectively, epigenetic genes harbored a significantly greater number of mean UVB-signature mutations than non-epigenetic genes. Turquoise bar reflects the median among both distributions

Fig. 9

Distribution of mutations in our “Top 40” genes among TCGA cutaneous melanomas (n = 278) (data publicly accessible via http://www.cbioportal.org)

Fig. 10

Distribution of mutations in our “Top 40” genes among the Broad Institute cutaneous melanoma samples (n = 121) (data publicly accessible via http://www.cbioportal.org)

Fig. 11

Mutational spectrum among epigenetic genes tested in “Oncopanel” within TCGA cutaneous melanomas (n = 278) (data publicly accessible via http://www.cbioportal.org)

Fig. 12

Distribution of mutations in epigenetic genes tested in “Oncopanel” within Broad Institute cutaneous melanomas (n = 121) (data publicly accessible via http://www.cbioportal.org)