Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma

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Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma. / Mitra, Shamik; Lauss, Martin; Cabrita, Rita; Choi, Jiyeon; Zhang, Tongwu; Isaksson, Karolin; Olsson, Håkan; Ingvar, Christian; Carneiro, Ana; Staaf, Johan; Ringnér, Markus; Nielsen, Kari; Brown, Kevin M; Jönsson, Göran.

I: Molecular Oncology, Vol. 14, Nr. 5, 05.2020, s. 933-950.

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T1 - Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma

AU - Mitra, Shamik

AU - Lauss, Martin

AU - Cabrita, Rita

AU - Choi, Jiyeon

AU - Zhang, Tongwu

AU - Isaksson, Karolin

AU - Olsson, Håkan

AU - Ingvar, Christian

AU - Carneiro, Ana

AU - Staaf, Johan

AU - Ringnér, Markus

AU - Nielsen, Kari

AU - Brown, Kevin M

AU - Jönsson, Göran

N1 - This article is protected by copyright. All rights reserved.

PY - 2020/5

Y1 - 2020/5

N2 - The presence of immune cells in the tumor microenvironment has been associated with response to immunotherapies across several cancer types, including melanoma. Despite its therapeutic relevance, characterization of the melanoma immune microenvironments remains insufficiently explored. To distinguish the immune microenvironment in a cohort of 180 metastatic melanoma clinical specimens, we developed a method using promoter CpG methylation of immune cell type-specific genes extracted from genome-wide methylation arrays. Unsupervised clustering identified three immune-methylation clusters with varying levels of immune CpG methylation that are related to patient survival. Matching protein and gene expression data further corroborated the identified epigenetic characterization. Exploration of the possible immune exclusion mechanisms at play revealed likely dependency on MITF protein level and PTEN loss-of-function events for melanomas unresponsive to immunotherapies (immune-low). To understand if melanoma tumors resemble other solid tumors in terms of immune-methylation characteristics, we explored 15 different solid tumor cohorts from TCGA. Low-dimensional projection based on immune cell type-specific methylation revealed grouping of the solid tumors in line with melanoma immune-methylation clusters rather than tumor types. Association of survival outcome with immune cell type-specific methylation differed across tumor and cell types. However, in melanomas immune-cell type-specific methylation was associated with inferior patient survival. Exploration of the immune-methylation patterns in a pan-cancer context suggested that specific immune-microenvironments might occur across the cancer spectrum. Together, our findings underscore the existence of diverse immune microenvironments, which may be informative for future immunotherapeutic applications.

AB - The presence of immune cells in the tumor microenvironment has been associated with response to immunotherapies across several cancer types, including melanoma. Despite its therapeutic relevance, characterization of the melanoma immune microenvironments remains insufficiently explored. To distinguish the immune microenvironment in a cohort of 180 metastatic melanoma clinical specimens, we developed a method using promoter CpG methylation of immune cell type-specific genes extracted from genome-wide methylation arrays. Unsupervised clustering identified three immune-methylation clusters with varying levels of immune CpG methylation that are related to patient survival. Matching protein and gene expression data further corroborated the identified epigenetic characterization. Exploration of the possible immune exclusion mechanisms at play revealed likely dependency on MITF protein level and PTEN loss-of-function events for melanomas unresponsive to immunotherapies (immune-low). To understand if melanoma tumors resemble other solid tumors in terms of immune-methylation characteristics, we explored 15 different solid tumor cohorts from TCGA. Low-dimensional projection based on immune cell type-specific methylation revealed grouping of the solid tumors in line with melanoma immune-methylation clusters rather than tumor types. Association of survival outcome with immune cell type-specific methylation differed across tumor and cell types. However, in melanomas immune-cell type-specific methylation was associated with inferior patient survival. Exploration of the immune-methylation patterns in a pan-cancer context suggested that specific immune-microenvironments might occur across the cancer spectrum. Together, our findings underscore the existence of diverse immune microenvironments, which may be informative for future immunotherapeutic applications.

U2 - 10.1002/1878-0261.12663

DO - 10.1002/1878-0261.12663

M3 - Article

C2 - 32147909

VL - 14

SP - 933

EP - 950

JO - Molecular Oncology

JF - Molecular Oncology

SN - 1574-7891

IS - 5

ER -