SINGLE-CELL EPIGENOMIC PROFILING USING DROPLET FLUIDICS AND CHEMICALLY MODIFIED HYDROGELS

SINGLE-CELL EPIGENOMIC PROFILING USING DROPLET FLUIDICS AND CHEMICALLY MODIFIED HYDROGELS

Researchers at UCSF have developed materials and methods for high throughput single cell epigenomic sequencing using a capture/profiling approach with hydrogel scaffolds, thus facilitating a scale and form of epigenomic profiling beyond what has been previously possible.

Traditional sequencing methods work with samples of many cells, thereby providing cell signal averages and are unable to resolve cellular heterogeneity. Although many single-cell sequencing methods are now available, there remain several limitations. For example, microfluidics-based approaches are technologically challenging for biologists to perform. Well plate methods lack sufficient throughput. Finally, most single cell methods are targeted for transcriptome sequencing, while single-cell genome sequencing and other multi-omic approaches are not well established. There exists a need in the state of the art for high-throughput single cell epigenomic sequencing in a massively parallelized fashion.

Stage of Research

The inventors have developed a suite of methods centered around hydrogel beads that enable the capture, barcoding and processing of nucleic acids or proteins to determine the epigenomic state of single cells. Central to the method is capturing and lysing of individual cells that have been immobilized in a hydrogel matrix that entraps genomic DNA. The hydrogel itself is modified with chemical handles that facilitate the capture of DNA through one of two approaches: 1) the use of biochemical modification of DNA to tag epigenomic modifications and/or 2) the use of affinity reagents that either directly or indirectly bind DNA of interest, akin to the method of chromatin immunoprecipitation.

Applications

Life science research into single-cell epigenetics
Single-cell cancer profiling for treatment or prognosis stratification
Drug efficacy or mechanism screening

Advantages

High throughput, single cell epigenomic sequencing
Capture and profiling using the hydrogel scaffold facilitates a scale and form of epigenomic profiling beyond what has been previously reported
Compatibility with further integration of other microfluidic omic’s approaches

Stage of Development

Research – in vitro

Publications

PCT/US2022/052670