A new industry partnership—between the companies EpiCypher and AtlasXomics—marries one technology that allows for investigation of the epigenome together with a spatial technology that enables analyses of cellular and molecular heterogeneity from intact tissues.

EpiCypher was founded in 2012 in response to the growing demand for reagents to study chromatin regulation and enable epigenetics-focused drug discovery. The company commercialized CUT&Tag (Cleavage Under Targets and Tagmentation) developed by Steven Henikoff, PhD, professor in the basic sciences division at Fred Hutch and an HHMI investigator.

The approach uses a fusion of Tn5 transposase, protein A, and protein G (pAG-Tn5) to cleave and add sequencing adapters at antibody-bound chromatin. EpiCypher’s CUTANA platform allows for ChIC, CUT&RUN, and CUT&Tag profiling assays.

The application of the chromatin mapping assay CUT&Tag to spatial techniques is critical to the study of biological mechanisms in development and disease.

DBiT-seq (Deterministic Barcoding in Tissue for Spatial Omics Sequencing) was originally developed by Rong Fan, PhD, professor of biomedical engineering at Yale University and has been commercialized by AtlasXomics for spatial ATAC-seq assays to map chromatin accessibility.

DBiT-seq utilizes a combination of microfluidics and next-generation sequencing for high-resolution spatial profiling in tissues. AtlasXomics, a 2020 Yale University spin-out located in New Haven, CT, has a platform built on DBiT-seq that can create transformative multi-omics maps (proteomics, transcriptomics, and epigenomics) in tissue at cellular resolution, unlocking information about interactions between cells in localized neighborhoods. AtlasXomics’ spatial omics products start with spatial epigenomics through its spatial CUT&Tag and spatial ATAC-seq assays.

The partnership with EpiCypher will introduce spatial CUT&Tag for profiling chromatin proteins, including histone PTMs and transcription factors. AtlasXomics and EpiCypher have focused initial development efforts on fresh frozen samples. Their long-term goal is to optimize spatial CUT&Tag for formalin-fixed paraffin-embedded (FFPE) samples, thereby greatly enhancing the versatility of these assays for clinical applications.

“By seamlessly integrating molecular biology with histology, the DBiT-seq platform is revolutionizing epigenomics research,” stated Colin Ng, vice president of business development at AtlasXomics. “We have developed robust spatial assays that incorporate EpiCypher’s proprietary pAG-Tn5 enzyme and high-efficiency antibodies to provide the optimal balance of sensitivity and specificity required for in-depth exploration of histone modifications and chromatin-associated proteins. Together, we will bring spatial CUT&Tag assays to market, including an expanded set of validated antibodies to provide customers with immediate access to diverse critical targets.”

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