# Enhancing Epigenetic Analysis Of Rare Cells With Multi-Phase Microfluidics

> **NIH NIH R01** · UNIVERSITY OF WISCONSIN-MADISON · 2020 · $610,874

## Abstract

PROJECT SUMMARY
While the genomic revolution has identified several important mutations involved in cancer
progression, only a minority of patients benefit from therapies that target these alterations. An
emerging area of interest involves aberrant epigenetic modifications, which have been implicated
in a broad range of solid tumor malignancies. Importantly, specific epigenetic biomarkers have
been identified, often at much higher frequencies than genomic markers (e.g., hypermethylation
of the GSTP1 promoter is found in more than 90% of prostate cancer primary tumors). Thus, there
is a critical need to extend the concepts of precision medicine beyond genomic aberrations to
include epigenomic alterations that drive cancer progression and treatment resistance.
Unfortunately, assays to identify epigenetic biomarkers lack the sensitivity to measure many
clinical samples, which often contain relatively low cell numbers. Much of this insensitivity stems
from the extensive manipulation of DNA/protein complexes required to identify specific epigenetic
markers and the associated inadvertent dissociation of these interactions (resulting in analyte
loss). Therefore, we aim to improve the state-of-the-art of epigenetic analyses via the
implementation of two technologies to preserve molecular interactions: 1) Exclusion-based
Sample Preparation (ESP) and 2) Exclusive Liquid Repellency (ELR). With ESP, analytes are
bound to functionalized paramagnetic particles (PMPs) and magnetically transferred across
phase boundaries (e.g., air/aqueous, oil/aqueous) to isolate the PMP-bound analyte(s). The rapid
and non-dilutive nature of ESP preserves molecular interactions, particularly those that are labile
or short-lived. ELR utilizes aqueous droplets in oil that are “repelled” from a surface (i.e., they
remain suspended and do not contact the surface) to minimize surface-derived analyte loss (e.g.,
adsorption) while also minimizing reaction volumes (mitigating inadvertent dissociation).
Together, the combination of ESP-ELR platform will significantly improve the efficiency of
epigenetic analyses, facilitating epigenetic measurements within small clinical samples (e.g.,
needle biopsies, circulating tumor cells). Specifically, we will develop, optimize, and benchmark
ESP-ELR versions of methylation analysis (where a methylated DNA binding protein (MBD2) is
employed to selectively capture methylated DNA sequences) and chromatin immunoprecipitation
(ChIP; where histone/DNA complexes are isolated in order to interrogate chromatin status).
Lastly, we will automate the platform and use it to perform a prospective biomarker validation
study of GSTP1 paving the way for it’s use in clinical trials. Here we focus on prostate cancer as
a model system, but we expect that an improved platform for epigenetic analysis will have broad
impact across the biomedical sciences.

## Key facts

- **NIH application ID:** 9916997
- **Project number:** 1R01CA247479-01
- **Recipient organization:** UNIVERSITY OF WISCONSIN-MADISON
- **Principal Investigator:** David J Beebe
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $610,874
- **Award type:** 1
- **Project period:** 2020-02-03 → 2025-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9916997

## Citation

> US National Institutes of Health, RePORTER application 9916997, Enhancing Epigenetic Analysis Of Rare Cells With Multi-Phase Microfluidics (1R01CA247479-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9916997. Licensed CC0.

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