Abstract 207: snNOMeHiC: joint profiling of 3D genome, DNA methylation, and chromatin accessibility from the same nuclei at flash-frozen tissue and primary tumor sample

Abstract Epigenetic marks, including DNA methylation, chromatin accessibility, and three-dimensional (3D) genome organization, play instrumental roles in gene regulation in mammals. Gene activation or repression potential, however, cannot be entirely predicted by looking at a single modality. Accurate predictive models require multiple modalities simultaneously. We previously developed single-cell Methyl-HiC technology to jointly profile DNA methylation and 3D genome from the same cells. Further, we incorporated an additional footprint of GpC methyltransferase activity (i.e., chromatin accessibility) into the assay, named NOMe-HiC, but at the bulk level. Here, we extended NOMe-HiC technology to the single-cell level to enable the joint profiling of the 3D genome, DNA methylation, and chromatin accessibility from the same nuclei. We performed snNOMe-HiC at IMR-90 cell lines and found high concordance across all three modalities with the bulk NOMe-HiC by pooling the single cells. We further prepared a mixture of GM12878 and IMR-90 cells and processed the cell mixture with snNOMe-HiC. snNOMe-HiC can distinguish the two cell types using each of the three epigenetic features, respectively. To benchmark the performance of snNOMe-HiC at flash-frozen heterogeneous tissues, we generated snNOMe-HiC data from ∼2000 nuclei at flash-frozen mice cortex. We identified all the major known cell types in the previous studies across three modalities and showed reproducible results across replicates. Finally, we applied snNOMe-HiC to a primary meningioma sample. We identified previously known copy number alterations in tumor-related cell clusters and found concordant changes of epigenetic heterogeneity across cell populations, which can potentially reveal the crosstalk between genetics and multiple epigenetic marks during the clonal evolution in cancer progression. In summary, snNOMe-HiC is a robust technology that can profile three epigenetic modalities and genetic aberrations in the same nuclei from flash-frozen tissues and primary tumors. Citation Format: Hailu Fu, Jiayan Ma, Eric Tong, Mark Youngblood, Harrshavasan Congivaram, Mateo Gomez, Juan Wang, Feng Yue, Li Wang, Yaping Liu. snNOMeHiC: joint profiling of 3D genome, DNA methylation, and chromatin accessibility from the same nuclei at flash-frozen tissue and primary tumor sample [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 207.