Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions

Nat Med. 2019 Mar;25(3):517-525. doi: 10.1038/s41591-018-0323-0. Epub 2019 Jan 21.

Abstract

The molecular alterations that occur in cells before cancer is manifest are largely uncharted. Lung carcinoma in situ (CIS) lesions are the pre-invasive precursor to squamous cell carcinoma. Although microscopically identical, their future is in equipoise, with half progressing to invasive cancer and half regressing or remaining static. The cellular basis of this clinical observation is unknown. Here, we profile the genomic, transcriptomic, and epigenomic landscape of CIS in a unique patient cohort with longitudinally monitored pre-invasive disease. Predictive modeling identifies which lesions will progress with remarkable accuracy. We identify progression-specific methylation changes on a background of widespread heterogeneity, alongside a strong chromosomal instability signature. We observed mutations and copy number changes characteristic of cancer and chart their emergence, offering a window into early carcinogenesis. We anticipate that this new understanding of cancer precursor biology will improve early detection, reduce overtreatment, and foster preventative therapies targeting early clonal events in lung cancer.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Carcinogenesis / genetics
  • Carcinoma in Situ / genetics*
  • Carcinoma, Squamous Cell / genetics*
  • Chromosomal Instability / genetics
  • Cohort Studies
  • DNA Copy Number Variations
  • DNA Methylation / genetics
  • Disease Progression
  • Epigenomics
  • Female
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic*
  • Genomics
  • Humans
  • Longitudinal Studies
  • Lung Neoplasms / genetics*
  • Male
  • Middle Aged
  • Mutation