title: 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.
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA.
authors.forename: Jonathan J
authors.initials: JJ
authors.lastname: Lee
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA.
authors.forename: Lynette M
authors.initials: LM
authors.lastname: Sholl
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA.
authors.forename: Neal I
authors.initials: NI
authors.lastname: Lindeman
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA.
authors.forename: Scott R
authors.initials: SR
authors.lastname: Granter
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA.
authors.forename: Alvaro C
authors.initials: AC
authors.lastname: Laga
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA.
authors.forename: Priyanka
authors.initials: P
authors.lastname: Shivdasani
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA.
authors.forename: Gary
authors.initials: G
authors.lastname: Chin
authors.affiliation: Melanoma Center, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA.
authors.forename: Jason J
authors.initials: JJ
authors.lastname: Luke
authors.affiliation: Melanoma Center, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA.
authors.forename: Patrick A
authors.initials: PA
authors.lastname: Ott
authors.affiliation: Melanoma Center, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA.
authors.forename: F Stephen
authors.initials: FS
authors.lastname: Hodi
authors.affiliation: Melanoma Center, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA.
authors.forename: Martin C
authors.initials: MC
authors.lastname: Mihm
authors.affiliation: Melanoma Center, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA.
authors.forename: Jennifer Y
authors.initials: JY
authors.lastname: Lin
authors.affiliation: Melanoma Center, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Werchniak
authors.affiliation: Melanoma Center, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA.
authors.forename: Harley A
authors.initials: HA
authors.lastname: Haynes
authors.affiliation: Melanoma Center, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02215-5450 USA.
authors.forename: Nancy
authors.initials: N
authors.lastname: Bailey
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Liu
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA.
authors.forename: George F
authors.initials: GF
authors.lastname: Murphy
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston, MA 02115 USA.
authors.forename: Christine G
authors.initials: CG
authors.lastname: Lian
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)