Treatment Response Monitoring in Patients with Advanced Malignancies Using Cell-Free SHOX2 and SEPT9 DNA Methylation in Blood: An Observational Prospective Study

J Mol Diagn. 2020 Jul;22(7):920-933. doi: 10.1016/j.jmoldx.2020.04.205. Epub 2020 Apr 30.


Patients with incurable cancer usually receive palliative treatment with significant toxicity and limited efficacy. Methylation analysis of circulating cell-free DNA (ccfDNA) in blood from cancer patients represents a promising approach for minimally invasive, real-time monitoring of treatment response. Short stature homeobox 2 (SHOX2) and septin 9 (SEPT9) methylation was analyzed in N = 8865 malignant and N = 746 normal adjacent tissues across 33 different malignancies from The Cancer Genome Atlas. Furthermore, we performed quantitative SHOX2 and SEPT9 ccfDNA methylation analysis in plasma obtained before and consecutively during treatment from prospectively enrolled N = 115 patients with various advanced cancers. SHOX2 and/or SEPT9 hypermethylation in malignant tissues is present in various carcinomas, sarcoma, melanoma, brain tumors, mesothelioma, and hematopoietic malignancies. Among the prospectively enrolled cancer patients, 61% (70/115) of patients had a baseline-positive blood cumulative ccfDNA methylation score (CMS) and were eligible for response monitoring. Dynamic changes of CMS during treatment were strongly associated with treatment response. A CMS increase indicated response up to 80 days before conventional monitoring. SHOX2 and SEPT9 ccfDNA methylation represents a pan-cancer biomarker and has the potential to be a powerful tool for monitoring treatment response in patients with solid tumors and lymphomas. The early identification of nonresponders might allow for a timely change of treatment regimen.

Publication types

  • Observational Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biomarkers, Tumor / blood
  • Biomarkers, Tumor / genetics
  • Cell-Free Nucleic Acids / blood*
  • Cell-Free Nucleic Acids / genetics*
  • DNA Methylation*
  • Feasibility Studies
  • Homeodomain Proteins / blood*
  • Homeodomain Proteins / genetics*
  • Humans
  • Neoplasms / blood*
  • Neoplasms / genetics*
  • Prospective Studies
  • Septins / blood*
  • Septins / genetics*


  • Biomarkers, Tumor
  • Cell-Free Nucleic Acids
  • Homeodomain Proteins
  • SHOX2 protein, human
  • SEPTIN9 protein, human
  • Septins