(222c) Profiling Cell-Type-Specific Epigenomic Changes Associated with BRCA1 Mutation in Breast Tissues Using a Low-Input Microfluidic Technology
- Conference: AIChE Annual Meeting
- Year: 2019
- Proceeding: 2019 AIChE Annual Meeting
- Group: Topical Conference: Chemical Engineers in Medicine
- Time: Monday, November 11, 2019 - 4:12pm-4:33pm
Cancer-free BRCA1 mutant (carrier) or normal (non-carrier) breast tissues were obtained from adult female patients who underwent cosmetic reduction of mammoplasty, diagnostic biopsies, or mastectomy. Four different cell types from the same patient were sorted by FACS. The coated beads and sheared chromatin (from 50k cells) were loaded to MOWChIP device for ChIP process. We examined genome-wide H3K4me3 and H3K27ac. After ChIP, DNA was purified, used for library preparation and sequenced by Illumina HiSeq 4000. The digital data were analyzed with Bowtie, MACS, and DiffBind.
Using the MOWChIP device enables us to perform ChIP on rare samples in less time and with improved quality of sequencing data. Stromal cells displayed the most differences in H3K27ac peak signal intensity between carrier and non-carrier groups, with the vast majority of peak regions having higher H3K27ac levels in non-carriers. Similarly, non-carrier mature luminal cells also had increased H3K27ac peak signal intensity, though very few peaks were significantly different between the two groups. In contrast, non-carriers had lower H3K27ac peak signal intensity across thousands of regions in both basal and luminal progenitor cells. These differences support widespread and cell-specific epigenomic changes associated with the BRCA1 mutation. Our work suggests strong genetic and epigenetic interactions due to mutations.