Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas

Xin Hu,Jianjun Zhang,Alexandre Reuben,Myrna C.b Godoy ,Linghua Wang,Mara B Antonoff,Carmen Behrens,Junya Fukuoka,Jean–Pierre J Issa ,Hoa H.n Pham ,Brett W Carter,Ara A Vaporciyan,John Lee ,Ying Liu ,Dan Su,Humam Kadara,Paul Scheet,Junya Fujimoto,Runzhe Chen,Marcos R.h Estécio ,Harvey I Pass,Andrew Futreal ,Yao Lu ,Ignacio I Wistuba,Chi-Wan Chow,Nicholas Mcgranahan,John V Heymach,Boris Sepesi,Jianhua Zhang,Jian Carrot‐Zhang

doi:10.1038/s41467-021-20907-z

Abstract

The evolution of DNA methylome and methylation intra-tumor heterogeneity (ITH) during early carcinogenesis of lung adenocarcinoma has not been systematically studied. We perform reduced representation bisulfite sequencing of invasive lung adenocarcinoma and its precursors, atypical adenomatous hyperplasia, adenocarcinoma in situ and minimally invasive adenocarcinoma. We observe gradual increase of methylation aberrations and significantly higher level of methylation ITH in later-stage lesions. The phylogenetic patterns inferred from methylation aberrations resemble those based on somatic mutations suggesting parallel methylation and genetic evolution. De-convolution reveal higher ratio of T regulatory cells (Tregs) versus CD8 + T cells in later-stage diseases, implying progressive immunosuppression with neoplastic progression. Furthermore, increased global hypomethylation is associated with higher mutation burden, copy number variation burden and AI burden as well as higher Treg/CD8 ratio, highlighting the potential impact of methylation on chromosomal instability, mutagenesis and tumor immune microenvironment during early carcinogenesis of lung adenocarcinomas.

Highlights

1234567890():,; The evolution of DNA methylome and methylation intra-tumor heterogeneity (ITH) during early carcinogenesis of lung adenocarcinoma has not been systematically studied
It has been proposed that invasive lung ADC evolves from atypical adenomatous hyperplasia (AAH), the only recognized precancer for lung ADC, which could progress to ADC in situ (AIS), a preinvasive lung cancer, to minimally invasive ADC (MIA), and eventually frankly invasive ADC3
In this study, using a unique cohort of resected indeterminate pulmonary nodules (IPNs) of different histologic stages, we delineate the evolution of the methylation landscape and reveal increased methylation ITH in lung ADC than its precursors of early stages, as well as global hypomethylation correlates with immune infiltration, mutational burden, and copy number alterations

Summary

Introduction

1234567890():,; The evolution of DNA methylome and methylation intra-tumor heterogeneity (ITH) during early carcinogenesis of lung adenocarcinoma has not been systematically studied. We initiated an international collaboration for the collection and characterization of these lung precancers, preinvasive, and early invasive ADC presenting as IPNs. We recently reported the genomic landscape, including the genomic intra-tumor heterogeneity (ITH), and revealed evidence of progressive evolution from AAH to AIS, MIA, and ADC5. Methylation aberrations have been reported in AAH lesions and tumor-adjacent lung tissues, suggesting that methylation changes may be early molecular events[9,10] These pioneer studies only analyzed small numbers of genes implicated in lung carcinogenesis. In this study, using a unique cohort of resected IPNs of different histologic stages, we delineate the evolution of the methylation landscape and reveal increased methylation ITH in lung ADC than its precursors of early stages, as well as global hypomethylation correlates with immune infiltration, mutational burden, and copy number alterations

Methods

Results

Conclusion