Spatial Proteomics and Epigenomics Reveal Cell Morphology and Epigenetic Gene Regulation in Human Hippocampus

Abstract

Abstract We present the first spatial tri-omic (proteomic, transcriptomic, and epigenomic) taxonomy of human hippocampus, addressing two key challenges in single-cell and spatial transcriptomics: visualizing cell morphology and epigenetic gene regulation in situ. By designing and multiplex imaging a novel panel of 25 protein targets, we generated the first large scale spatial proteomics map of the hippocampus at single cell resolution (330 nanometers). Through integrated spatial proteomic and transcriptomic analyses, we identified canonical hippocampal subfields and distinct cell types within the dentate gyrus and cornu Ammonis (CA). RNA synthesis rates were the highest in the CA pyramidal neurons than any other hippocampal subfields. To map gene regulation, we applied state-of-art spatial ATAC-seq to identify open chromatin regions and cis-regulatory elements, revealing how chromatin landscapes differ across hippocampal subfields. These regional differences help explain why certain neurons are more excitable and recruited for circuit formation, as their chromatin is open and responsive to transcription factors. Together, these approaches created the most comprehensive spatial atlas of the human hippocampus to date, consisting of over 1.6 million single cells from 16 individuals. This study demonstrates the use of spatial proteomics and epigenomics to investigate the molecular neuropathology of human brain in both healthy and diseased states.