Background Advances in spatial transcriptomics and proteomics have enabled increasingly complex investigations into gene expression across various cellular subtypes and tissues.^1–3 However, these methods do not explore the epigenome, which regulates gene expression in a cell-specific manner and plays a critical role in human diseases including cancer. A nuanced understanding of epigenetic dysregulation of chromatin structure and regulatory proteins can drive therapeutic development.

Methods To address the need for tools beyond bulk molecular assays for this research, we have enhanced the application of deterministic barcoding in tissue for spatial omics sequencing (DBiT-seq), a technique first published in 2022 by Dr. Rong Fan’s lab at Yale.^{2 3} Our platform extends the assay area and resolution to investigate a 5.5 mm x 5.5 mm region at the single-nucleus level, up to 10µm resolution. This platform enables spatial cleavage under targets and tagmentation (spatial CUT&Tag), allowing for the detection of both histone modifications and chromatin-associated proteins in tissues and revealing complex spatial gene regulation patterns. The platform can also map open chromatin in tissues using spatial ATAC-seq.

Results We demonstrate detection of cellular subtypes and regulatory elements at specific genes important to the tumor microenvironment by spatial chromatin accessibility and activating histone mark profiling in human gastric adenocarcinoma, adjacent normal stomach tissue, and adjacent lymph node. In stomach tissue and lymph node, spatial epigenomic profiles align with the underlying anatomy and we observe large scale epigenomic remodeling in tumor tissue, altering transcription factor binding. We have also developed a fully integrated bioinformatics suite designed to allow non-bioinformatics users to easily explore and identify spatial epigenetic elements.

Conclusions We have created a framework that enables easy integration with existing spatial and single-cell datasets for a unique multi-omics solution necessary for the complexity of the tissue environment in cancer. This innovative platform not only paves the way for unprecedented insights into the epigenetic landscape but also holds the potential to transform our approach to personalized medicine and therapeutic intervention.

References

1. Liu Y, Yang M, Deng Y, Su G, Enninful A, Guo CC, Tebaldi T, Zhang D, Kim D, Bai Z, Norris E, Pan A, Li J, Xiao Y, Halene S, Fan R. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell. 2020;183:1665–1681.

2. Deng Y, Bartosovic M, Kukanja P, Zhang D, Liu Y, Su G, Enninful A, Bai Z, Castelo-Branco G, Fan R. Spatial-CUT&Tag: spatially resolved chromatin modification profiling at the cellular level. Science. 2022;375:681–686.

3. Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature. 2022;609:375–383.

Ethics Approval Zyagen certifies that all tissue samples are received from certified tissue banks in the USA: (1) All the human tissue samples were and will be collected with informed consents from the donors and their relatives, while the documents are not provided to Zyagen; (2) All tissues were and will be donated for only research purposes; (3) The specimens were and will be collected at facilities throughout the United States in compliance with all applicable federal and state laws and regulations and ethical guidelines; (4) All tissues were and will be excised by licensed Medical Doctors; (5) Donors did not receive any payment; and (6) the specimens are tested and negative for virus, HIV, Hepatitis B and Hepatitis C.