Grant Details
Grant Number: |
7R21CA191186-03 Interpret this number |
Primary Investigator: |
Bailey, Ryan |
Organization: |
University Of Michigan At Ann Arbor |
Project Title: |
Droplet Microfluidic Platform for Ultralow Input Epigenetics |
Fiscal Year: |
2016 |
Abstract
DESCRIPTION (provided by applicant): Epigenomic analyses are playing increasingly prominent roles in the development of personalized strategies for treating cancer. However, the translation of fundamental epigenomic insight to the clinic is wrought with challenges. Take for example the study of post-translational histone protein modifications, which can serve to either promote or repress the transcription of pendant DNA sequences. Analyses of these critically important interactions bridge genomics and proteomics and present significant challenges in the clinical setting. Chromatin immunoprecipitation (ChIP) is the method of choice for analyzing protein-DNA interactions and the basic method involves fragmentation of chromatin, separation of modified proteins using antibodies and magnetic beads, and subsequent analysis of the associated DNA by qPCR or sequencing. While sounding simple, a typical ChIP workflow involves ~30 steps, takes 4+ days, and requires 106-107 cells as input. These requirements significantly limit the applicability of ChIP in a clinical setting-particularly when minimal sampl is available, such as in the analysis of tumor biopsies, stem cells, or circulating tumor cells. Microfluidic devices offer many attractive benefits over traditional macro-scale methods including reduced volume requirements, parallelization capability, and automated operation, which make them particularly well- suited to sample-constrained epigenetic analyses. A handful of recent reports suggest a substantial opportunity for microfluidically-enabled ChIP analyses; however, there is still considerable room for further improvement. We propose to develop a powerful and versatile, droplet microfluidics-based, nanoliter-scale Chromatin ImmunoCapture (nChIC) platform suitable for individualized medicine applications. Droplet microfluidics offer several benefits, including rapid, controlled, and efficient fluid handling, and the capacity to handle variable sample sizes, since devices can accommodate larger samples by simply operating for longer periods of time. Our nChIC platform will incorporate every major step in the ChIP workflow into an automated device, including cell lysis, chromatin digestion, immunocapture, and DNA purification. Importantly, these processes will be carried out at the single cell level, which promises to provide unique insights into epigenomic tumor heterogeneity. Beyond single cells, the unprecedented ability to handle samples of variable input will also facilitate robust validation against traditional ChIP assays to demonstrate broad genomic coverage. Taken together, we feel that the nChIC platform will be a powerful new tool that enables the translation of epigenomic insight into individualized cancer treatment at the point of care.
Publications
Plug-in tubes allow tunable oil removal, droplet packing, and reaction incubation for time-controlled droplet-based assays.
Authors: Sun M.
, Maryu G.
, Wang S.
, Yang Q.
, Bailey R.C.
.
Source: Biomicrofluidics, 2021 Mar; 15(2), p. 024108.
EPub date: 2021-04-05 00:00:00.0.
PMID: 33841602
Related Citations
Translational Opportunities for Microfluidic Technologies to Enable Precision Epigenomics.
Authors: Xu Y.
, Doonan S.R.
, Ordog T.
, Bailey R.C.
.
Source: Analytical Chemistry, 2020-06-16 00:00:00.0; 92(12), p. 7989-7997.
EPub date: 2020-06-04 00:00:00.0.
PMID: 32496751
Related Citations
Droplet CAR-Wash: continuous picoliter-scale immunocapture and washing.
Authors: Doonan S.R.
, Lin M.
, Bailey R.C.
.
Source: Lab On A Chip, 2019-04-23 00:00:00.0; 19(9), p. 1589-1598.
PMID: 30963149
Related Citations
Ionophore-Based Biphasic Chemical Sensing in Droplet Microfluidics.
Authors: Wang X.
, Sun M.
, Ferguson S.A.
, Hoff J.D.
, Qin Y.
, Bailey R.C.
, Meyerhoff M.E.
.
Source: Angewandte Chemie (international Ed. In English), 2019-04-17 00:00:00.0; , .
EPub date: 2019-04-17 00:00:00.0.
PMID: 30997728
Related Citations
Droplet Microfluidics in Thermoplastics: Device Fabrication, Droplet Generation, and Content Manipulation using Integrated Electric and Magnetic Fields.
Authors: Sahore V.
, Doonan S.R.
, Bailey R.C.
.
Source: Analytical Methods : Advancing Methods And Applications, 2018-09-21 00:00:00.0; 10(35), p. 4264-4274.
EPub date: 2018-08-20 00:00:00.0.
PMID: 30886651
Related Citations
A droplet microfluidic platform for efficient enzymatic chromatin digestion enables robust determination of nucleosome positioning.
Authors: Xu Y.
, Lee J.H.
, Li Z.
, Wang L.
, Ordog T.
, Bailey R.C.
.
Source: Lab On A Chip, 2018-07-26 00:00:00.0; , .
EPub date: 2018-07-26 00:00:00.0.
PMID: 30046796
Related Citations
K-Channel: A Multifunctional Architecture for Dynamically Reconfigurable Sample Processing in Droplet Microfluidics.
Authors: Doonan S.R.
, Bailey R.C.
.
Source: Analytical Chemistry, 2017-04-04 00:00:00.0; 89(7), p. 4091-4099.
EPub date: 2017-03-13 00:00:00.0.
PMID: 28222260
Related Citations
Hedgehog Pathway Dysregulation Contributes To The Pathogenesis Of Human Gastrointestinal Stromal Tumors Via Gli-mediated Activation Of Kit Expression
Authors: Tang C.M.
, Lee T.E.
, Syed S.A.
, Burgoyne A.M.
, Leonard S.Y.
, Gao F.
, Chan J.C.
, Shi E.
, Chmielecki J.
, Morosini D.
, et al.
.
Source: Oncotarget, 2016-10-25 00:00:00.0; , .
PMID: 27793025
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Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies.
Authors: Yan H.
, Tian S.
, Slager S.L.
, Sun Z.
, Ordog T.
.
Source: American Journal Of Epidemiology, 2016-01-15 00:00:00.0; 183(2), p. 96-109.
EPub date: 2016-01-15 00:00:00.0.
PMID: 26721890
Related Citations
The common point for forensic and anthropologic genetics and individualized medicine.
Authors: Kayser M.
, Ordog T.
.
Source: Croatian Medical Journal, 2015 Jun; 56(3), p. 177-8.
PMID: 26088841
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