Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation
Brateil Badal, Alexander Solovyov, Serena Di Cecilia, Joseph Minhow Chan, Li-Wei Chang, Ramiz Iqbal, Iraz T. Aydin, Geena S. Rajan, Chen Chen, Franco Abbate, Kshitij S. Arora, Antoine Tanne, Stephen B. Gruber, Timothy M. Johnson, Douglas R. Fullen, Leon Raskin, Robert Phelps, Nina Bhardwaj, Emily Bernstein, David T. Ting, Georg Brunner, Eric E. Schadt, Benjamin D. Greenbaum, Julide Tok Celebi
Brateil Badal, Alexander Solovyov, Serena Di Cecilia, Joseph Minhow Chan, Li-Wei Chang, Ramiz Iqbal, Iraz T. Aydin, Geena S. Rajan, Chen Chen, Franco Abbate, Kshitij S. Arora, Antoine Tanne, Stephen B. Gruber, Timothy M. Johnson, Douglas R. Fullen, Leon Raskin, Robert Phelps, Nina Bhardwaj, Emily Bernstein, David T. Ting, Georg Brunner, Eric E. Schadt, Benjamin D. Greenbaum, Julide Tok Celebi
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Clinical Research and Public Health Dermatology Oncology

Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation

Abstract

BACKGROUND. Melanoma is a heterogeneous malignancy. We set out to identify the molecular underpinnings of high-risk melanomas, those that are likely to progress rapidly, metastasize, and result in poor outcomes.

METHODS. We examined transcriptome changes from benign states to early-, intermediate-, and late-stage tumors using a set of 78 treatment-naive melanocytic tumors consisting of primary melanomas of the skin and benign melanocytic lesions. We utilized a next-generation sequencing platform that enabled a comprehensive analysis of protein-coding and -noncoding RNA transcripts.

RESULTS. Gene expression changes unequivocally discriminated between benign and malignant states, and a dual epigenetic and immune signature emerged defining this transition. To our knowledge, we discovered previously unrecognized melanoma subtypes. A high-risk primary melanoma subset was distinguished by a 122-epigenetic gene signature (“epigenetic” cluster) and TP53 family gene deregulation (TP53, TP63, and TP73). This subtype associated with poor overall survival and showed enrichment of cell cycle genes. Noncoding repetitive element transcripts (LINEs, SINEs, and ERVs) that can result in immunostimulatory signals recapitulating a state of “viral mimicry” were significantly repressed. The high-risk subtype and its poor predictive characteristics were validated in several independent cohorts. Additionally, primary melanomas distinguished by specific immune signatures (“immune” clusters) were identified.

CONCLUSION. The TP53 family of genes and genes regulating the epigenetic machinery demonstrate strong prognostic and biological relevance during progression of early disease. Gene expression profiling of protein-coding and -noncoding RNA transcripts may be a better predictor for disease course in melanoma. This study outlines the transcriptional interplay of the cancer cell’s epigenome with the immune milieu with potential for future therapeutic targeting.

FUNDING. National Institutes of Health (CA154683, CA158557, CA177940, CA087497-13), Tisch Cancer Institute, Melanoma Research Foundation, the Dow Family Charitable Foundation, and the Icahn School of Medicine at Mount Sinai.

Authors

Brateil Badal, Alexander Solovyov, Serena Di Cecilia, Joseph Minhow Chan, Li-Wei Chang, Ramiz Iqbal, Iraz T. Aydin, Geena S. Rajan, Chen Chen, Franco Abbate, Kshitij S. Arora, Antoine Tanne, Stephen B. Gruber, Timothy M. Johnson, Douglas R. Fullen, Leon Raskin, Robert Phelps, Nina Bhardwaj, Emily Bernstein, David T. Ting, Georg Brunner, Eric E. Schadt, Benjamin D. Greenbaum, Julide Tok Celebi

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Figure 4

Noncoding repetitive element transcripts are repressed in high-risk melanomas.

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Noncoding repetitive element transcripts are repressed in high-risk mela...
(A) Heatmaps indicating differentially expressed protein-coding transcripts involved in epigenetic regulation and immune response between the Epgn1 and Epgn3 subtypes as well as noncoding repetitive element transcripts (retrotransposons). Tumors are ordered based on the clusters identified and shown in Figure 3B (x axis, Epgn1 and Epgn3), and genes are ordered according to functional categories or sequence homology in accordance with retrotransposon classification (y axis). ERV, endogenous retrovirus; SINE, short-interspersed nuclear element; LINE, long-interspersed nuclear element. (B) Box plots represent expression of TP53 family genes and LINE1 between the Epgn1 and Epgn3 groups (2-tailed Mann-Whitney test). (C) TIL scores on H&E examination of Epgn1 versus Epgn3 clusters (statistically not significant, 2-tailed Fisher’s exact test). N.A., not available. (D and E) Melanoma tissue arrays (n = 116) and those limited to primary cutaneous melanomas (n = 54) were assayed for p53 and p73 protein expression by immunohistochemistry and for LINE1 and 18S rRNA (housekeeping gene) transcripts by RNA in situ hybridization. Representative examples are depicted. Scale bar: 25 μm. Inset: 18 μm x 18 μm. Graphs show correlation coefficient and relative risk values for p53 versus LINE1 or p73 versus LINE1 expression (Spearman correlation). (F) Melanoma cell lines established from primary melanoma tumors (WM35, stage I and WM1552C, stage III) were obtained. TP53 and TP73 transcripts were examined by qPCR. Normal human primary melanocytes (MC) are shown as a reference (1-tailed Student’s t test). (G) Cell pellets were formalin-fixed and paraffin-embedded and assayed for endogenous elements (LINE1) by RNA in situ hybridization. 18S rRNA was employed as a housekeeping transcript. Representative examples are shown. Scale bar: 25 μm. (H) Gene expression classifier distinguishing low-risk Epgn1 and high-risk Epgn3 groups based on repetitive element expression.