Adding spatial resolution and technical improvements to a novel single-cell DNA methylation sequencing technology

About This Grant

ABSTRACT DNA methylation (DNAme) is a core layer of epigenetic regulation with central roles in the establishment and maintenance of cellular identity. Methods to profile DNAme at single-cell resolution are needed to elucidate epigenetic networks governing cell state in healthy tissues and understand their dysregulation in disease and aging. However, existing methods for single-cell methylome profiling are highly inaccessible, and no methods to experimentally profile both DNAme and spatial location currently exist. I have developed a novel method for single-cell DNAme profiling that leverages the widely available 10x Single Cell Multiome and NEB EM-seq kits, which I have named droplet-implemented single-cell DNA methylation sequencing (discDNAme). Applied to nuclei isolated from mouse brain, discDNAme recovered ~3,000 high-quality methylomes that clustered into clearly separated neuronal and non-neuronal subtypes and displayed stereotyped patterns of CpG dinucleotide methylation around key genomic features. However, these measurements lack spatial information on the native tissue contexts of profiled cells, and the protocol’s per-cell library size is lower than current gold-standard methods for measuring single-cell DNAme. I propose (1) development of a spatially resolved single-cell DNA methylation technology by combining discDNAme with slide-tags, a platform for spatially resolved single-nucleus RNA- and/or ATAC-seq developed by our group. To integrate slide-tags with discDNAme, I will develop a protocol in which the “spatial barcode oligos” we use to position nuclei are physically separated from genomic DNA prior to unmethylated cytosine conversion, benchmark this technology in the mouse hippocampus, and apply it to study glioblastoma multiforme. I further propose (2) experiments to improve and benchmark my discDNAme technology. I will systematically test various independent approaches to increase library complexity at different steps of the discDNAme protocol, combine these optimizations into a second-generation protocol, and benchmark this against our original protocol and other leading methods for single-cell DNAme profiling. Completion of this proposal will result in (1) the first high-resolution method to measure spatially resolved single- cell methylomes—a major advancement in spatial omics technologies—and (2) an accessible yet capable tool for single-cell DNAme profiling that will open single-cell DNAme studies to the broader single-cell community.