Histo-LCM-Hi-C Reveals 3D Chromatin Conformations of Spatially Localized Rare Cells in Tissues at High Resolution

Understanding chromatin structure is essential to delineate the mechanisms underlying genomic processes. However, while methods to obtain such information from cells in vitro are widely available, there is presently a significant lack of techniques that can acquire these data from cells in tissue. Such a capability is critical to determine the dependence of the local tissue environment on cell function. Further, this ability is particularly necessary for cells that constitute a significant minority of the total tissue population, as they are often obscured in data dominated by more abundant cell types. Here, we developed a high-throughput chromosome conformation capture (Hi-C)-based method, Histological laser capture microdissection Hi-C (Histo-LCM-Hi-C), to enable the characterization of chromatin architecture of phenotype-defined, spatially localized cells within intact tissue sections from as few as ∼ 300 cells. We demonstrated the effectiveness of this approach by generating the first 3D Hi-C map of liver-resident macrophages, the Kupffer cells (KCs), a minor cell population in the normal liver. As expected, owing to their relative rarity, these KC maps were significantly different from those obtained from the whole liver, revealing distant contacts between putative enhancers and genes involved in key KC functions, as well as significant differences from those of in vitro induced bone marrow-derived macrophages. We anticipate that this method will prove to be an indispensable technique in the growing repertoire of methodologies for characterizing the genomic properties of cells within their native environment.