DNA methylation intratumor heterogeneity in localized lung adenocarcinomas

// Kelly Quek 1, 2, * , Jun Li 2, * , Marcos Estecio 3 , Jiexin Zhang 4 , Junya Fujimoto 5 , Emily Roarty 2 , Latasha Little 2 , Chi-Wan Chow 5 , Xingzhi Song 2 , Carmen Behrens 5 , Taiping Chen 4 , William N. William 1 , Stephen Swisher 6 , John Heymach 1, 7 , Ignacio Wistuba 5 , Jianhua Zhang 2 , Andrew Futreal 2 , Jianjun Zhang 1, 2 1 Department of Thoracic/Head and Neck Medical Oncology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA 2 Department of Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA 3 Department of Epigenetics and Molecular Carcinogenesis, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA 4 Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA 5 Department of Translational Molecular Pathology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA 6 Department of Thoracic Surgery, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA 7 Department of Cancer Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA * Co-first authors Correspondence to: Jianjun Zhang, email: JZhang20@mdanderson.org Andrew Futreal, email: AFutreal@mdanderson.org Jianhua Zhang, email: JZhang22@mdanderson.org Keywords: intra-tumor heterogeneity, non-small cell lung cancer, DNA methylation Received: November 30, 2016 Accepted: January 27, 2017 Published: February 28, 2017 ABSTRACT Cancers are composed of cells with distinct molecular and phenotypic features within a given tumor, a phenomenon termed intratumor heterogeneity (ITH). Previously, we have demonstrated genomic ITH in localized lung adenocarcinomas; however, the nature of methylation ITH in lung cancers has not been well investigated. In this study, we generated methylation profiles of 48 spatially separated tumor regions from 11 localized lung adenocarcinomas and their matched normal lung tissues using Illumina Infinium Human Methylation 450K BeadChip array. We observed methylation ITH within the same tumors, but to a much less extent compared to inter-individual heterogeneity. On average, 25% of all differentially methylated probes compared to matched normal lung tissues were shared by all regions from the same tumors. This is in contrast to somatic mutations, of which approximately 77% were shared events amongst all regions of individual tumors, suggesting that while the majority of somatic mutations were early clonal events, the tumor-specific DNA methylation might be associated with later branched evolution of these 11 tumors. Furthermore, our data showed that a higher extent of DNA methylation ITH was associated with larger tumor size (average Euclidean distance of 35.64 (> 3cm, median size) versus 27.24 (<= 3cm), p = 0.014), advanced age (average Euclidean distance of 34.95 (above 65) verse 28.06 (below 65), p = 0.046) and increased risk of postsurgical recurrence (average Euclidean distance of 35.65 (relapsed patients) versus 29.03 (patients without relapsed), p = 0.039).