DNA methylation-based immune response signature improves patient diagnosis in multiple cancers

J Clin Invest. 2017 Aug 1;127(8):3090-3102. doi: 10.1172/JCI91095. Epub 2017 Jul 17.


Background: The tumor immune response is increasingly associated with better clinical outcomes in breast and other cancers. However, the evaluation of tumor-infiltrating lymphocytes (TILs) relies on histopathological measurements with limited accuracy and reproducibility. Here, we profiled DNA methylation markers to identify a methylation of TIL (MeTIL) signature that recapitulates TIL evaluations and their prognostic value for long-term outcomes in breast cancer (BC).

Methods: MeTIL signature scores were correlated with clinical endpoints reflecting overall or disease-free survival and a pathologic complete response to preoperative anthracycline therapy in 3 BC cohorts from the Jules Bordet Institute in Brussels and in other cancer types from The Cancer Genome Atlas.

Results: The MeTIL signature measured TIL distributions in a sensitive manner and predicted survival and response to chemotherapy in BC better than did histopathological assessment of TILs or gene expression-based immune markers, respectively. The MeTIL signature also improved the prediction of survival in other malignancies, including melanoma and lung cancer. Furthermore, the MeTIL signature predicted differences in survival for malignancies in which TILs were not known to have a prognostic value. Finally, we showed that MeTIL markers can be determined by bisulfite pyrosequencing of small amounts of DNA from formalin-fixed, paraffin-embedded tumor tissue, supporting clinical applications for this methodology.

Conclusions: This study highlights the power of DNA methylation to evaluate tumor immune responses and the potential of this approach to improve the diagnosis and treatment of breast and other cancers.

Funding: This work was funded by the Fonds National de la Recherche Scientifique (FNRS) and Télévie, the INNOVIRIS Brussels Region BRUBREAST Project, the IUAP P7/03 program, the Belgian "Foundation against Cancer," the Breast Cancer Research Foundation (BCRF), and the Fonds Gaston Ithier.

MeSH terms

  • Aged
  • Anthracyclines / therapeutic use
  • Breast Neoplasms / diagnosis*
  • Breast Neoplasms / genetics
  • Breast Neoplasms / therapy
  • Cell Line, Tumor
  • Cell Separation
  • Cohort Studies
  • Combined Modality Therapy
  • DNA Methylation*
  • Disease-Free Survival
  • Female
  • Humans
  • Immune System
  • Lung Neoplasms / diagnosis
  • Lung Neoplasms / genetics
  • Lung Neoplasms / therapy
  • Lymphocytes, Tumor-Infiltrating / cytology
  • Male
  • Melanoma / diagnosis
  • Melanoma / genetics
  • Melanoma / therapy
  • Middle Aged
  • Preoperative Period
  • Prognosis
  • Proportional Hazards Models
  • Sequence Analysis, DNA
  • Skin Neoplasms / diagnosis
  • Skin Neoplasms / genetics
  • Skin Neoplasms / therapy
  • Treatment Outcome


  • Anthracyclines