# Circulating DNA methylation biomarkers in micrometastatic breast cancer

> **NIH NIH R01** · UNIVERSITY OF SOUTHERN CALIFORNIA · 2021 · $380,678

## Abstract

Abstract
 Metastatic breast cancer (MBC) is an incurable disease, affecting 10-15% of breast cancer patients,
and is often refractory to therapy. Since tumor tissue is not always available after therapy is complete, there is
a need for biomarkers that can be monitored noninvasively such as from blood to measure risk of recurrence
due to microscopic metastatic residual disease. Numerous studies suggest that DNA methylation could be a
useful biomarker for improving the clinical management of disease. Recently circulating cell-free (cf)DNA has
attracted attention for clinical use in the context of risk prediction, prognostication and prediction of response to
chemotherapy in human cancer and several groups have now reported the detection of tumor-associated DNA
methylation patterns in plasma or serum. We identified by whole genome bisulfite sequencing
hypermethylation of 21 CpG islands (CGI) in plasma of MBC compared with disease free survivors or healthy
cases. Our hypothesis is that a 21-gene DNA hypermethylation signature involving rationally selected hotspots
detectable in circulation can be used to detect micrometastatic disease at the end of therapy in patients with
early stage breast cancer. In Aim 1 we plan to determine the frequency and the sensitivity and specificity of this
DNA methylation signature as a prognostic test in retrospectively collected plasma samples with targeted
bisulfite amplicon sequencing. In Aim 2 we will determine the analytical limit of detection and track how
different degrees of tumor burden impacts the methylation status of the signature in cell-free DNA in preclinical
models of breast cancer metastasis. To clinically validate the biomarker, in Aim 3 we will analyze samples
collected as part of prospective study already initiated where we plan to enroll 100 newly diagnosed high-risk
breast cancer patients. Blood will be collected after neoadjuvant therapy and surgery and CpG4C in cfDNA will
be tested by bAmplicon-seq. We have already collected blood from 20/39 consented patients after their
neoadjuvant therapy and subsequent surgery. We will classify patients as positive or negative for CpG4C at
the end of neo-adjuvant therapy and additionally at the post-operative blood draw based on cut-off criteria
defined in Aim 1 and statistically determine the utility of the marker to prognosticate recurrence. In time such a
blood test would also be advantageous at the time of surgery and/or after the completion of chemotherapy to
predict which patients could benefit from additional and curative therapies.

## Key facts

- **NIH application ID:** 10224828
- **Project number:** 5R01CA201352-05
- **Recipient organization:** UNIVERSITY OF SOUTHERN CALIFORNIA
- **Principal Investigator:** Bodour Salhia
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $380,678
- **Award type:** 5
- **Project period:** 2017-09-15 → 2023-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10224828

## Citation

> US National Institutes of Health, RePORTER application 10224828, Circulating DNA methylation biomarkers in micrometastatic breast cancer (5R01CA201352-05). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10224828. Licensed CC0.

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