Single-Cell Platform for Mapping DNA Damage in Disease and Aging

Background & Unmet Need

• DNA damage is a critical factor in cellular aging and disease, but current technologies can only measure damage across bulk cell populations
• Single-cell approaches have revolutionized our understanding of cell-specific molecular programs but mapping DNA damage at single-cell level has remained challenging
• The stochastic nature of DNA damage formation complicates investigation of its relationship with other cellular functions
• Unmet Need: Methods that can simultaneously map DNA damage and gene expression at single-cell resolution to understand how DNA damage impacts cellular function

Technology Overview

• The Technology: A high-throughput method, termed Paired-Damage-seq, that enables simultaneous mapping of oxidative & ssDNA damage with transcriptomes at single-cell resolution
• The "labeling-by-repair" approach uses DNA repair proteins to remove existing DNA damage sites, followed by incorporation of biotin-modified dUTPs at the damaged sites
• The method combines Paired-Tag RNA sequencing with split-pool barcoding to enable high-throughput analysis of hundreds of thousands to million of cells
• PoC Data: Validated in HeLa cells with strong agreement to existing bulk methods, showing 87% correspondence with RNA-seq and 72% similarity to CLAPS-seq DNA damage profiles
• Successfully applied to mouse brain tissue demonstrating cell-type specific damage patterns
• Demonstrated connection between DNA damage accumulation and epigenetic information loss

Technology Applications

• Screen chemical compounds to identify promising drug candidates
• Identify and validate therapeutic targets to develop cell-specific treatments based on DNA damage patterns
• Facilitate biomarker discovery for diseases associated with DNA damage and repair deficiencies

Technology Advantages

• Simultaneously measures DNA damage and gene expression at single-cell resolution
• High-throughput capability at single-cell resolution
• Seamless integration with existing sequencing workflows and screening platforms

Figure: Schematic of the Paired-Damage-seq workflow with the ‘Labeling-by-repair’ strategy to label damage sites. OG, 8oxoguanine; AP, apyrimidinic site; RT, reverse transcription.