Abstract 3765: Epigenomics at the speed of sound: High throughput epigenomic mapping of low cell input samples using acoustic enhanced immunoprecipitation

Abstract

Abstract Mapping the epigenetic landscape of Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML) is essential for understanding gene regulatory mechanisms during cell fate changes, disease onset, progression, as well as for optimizing therapeutic regime. In addition, these information hold immense potential for accurate identification of disease biomarkers, cell of origin, and targets for epigenetic therapy. However, existing chromatin immunoprecipitation sequencing (ChIP-Seq) workflows require significant cellular material and are very time-consuming, requiring cumbersome optimization. Moreover, cellular heterogeneity can influence the accuracy of results from the perspective of sample preparation efficiency and also population-biased effects. Both normal and malignant bone marrow are heterogeneous in cell type and stage of differentiation that leads to imprecise results with regard to epigenetic determinates.In our study, we implemented Covaris’ Adaptive Focused Acoustics® (AFA®) technology to miniaturize sample volumes for both chromatin shearing and immunoprecipitation in a 96-well format. This approach enables a standardized, robust, automatable, half-day workflow for both ChIP and Hi-ChIP applications. Additionally, we evaluated low input in vitro and in vivo samples, where we utilized a range of epitopes including major histone modifications (H3K27ac) and factors (CTCF). AFA was applied to flow-sorted stem and progenitor populations from individual mice. The low cell input capability permitted deconvolution of dynamic epigenetic changes in protein binding and chromatin structure during normal lineage specification of hematopoietic stem cells. Epigenetic remodeling of these sites were consistent with established gene programs essential for myeloid differentiation. Data were found to be in alignment with standard ChIP-seq and Hi-C datasets generated from similar cell populations.The simplified and significantly shortened (Hi)ChIP-seq processes showcased in this study will be highly beneficial for both research and clinical diagnostic applications owing to their requirements for using 96-well plate format and their ability to become integrated into automated workflows. Taken together, this technology and workflow represent a high throughput epigenetic system for small cell numbers of cells with a multitude of applications enabling laboratories focused on cell biology and translational research. Citation Format: Besmira Alija, Stephanie Braunstein, Jane Xu, Tom O'Hare, Angela Garding, Aaron Viny. Epigenomics at the speed of sound: High throughput epigenomic mapping of low cell input samples using acoustic enhanced immunoprecipitation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3765.