Fig. 2

Use of single-cell sequencing allows assessment of epigenetic regulation of tumor heterogeneity not accurately assessed by previous bulk methodologies. Due to the complex cellular heterogeneity of many types of tumors, valid information about individual cells is often masked by the average data of bulk sequencing when using bulk sequencing. However, the emergence of single-cell sequencing has enabled the investigation of epigenetic regulation of tumor heterogeneity, including clonal heterogeneity, cellular crosstalk, tumor stem cells, tumor metastasis, circulating tumor cells, treatment resistance, spatial organization, and tumor microenvironment (TME) mechanisms, which was previously unattainable. A Clonal heterogeneity: single-cell sequencing can monitor novel tumor cell subtypes adapted to the tumor microenvironment in the context of epigenetic alterations, revealing the impact of tumor heterogeneity in cancer patients by epigenetic modifications. B Single-cell sequencing can infer cellular interactions by correlating the expression of known ligands and receptors, and unravel the epigenomic alterations regulated by this interaction set that lead to tumor development. C Cancer stem cells: single-cell sequencing can study the epigenetic background of tumor stem cell differentiation trajectory to predict tumor progression and reveal the heterogeneity of tumor cells. D Tumor metastasis: single-cell sequencing can monitor rare cellular mutations that acquire invasiveness, metastasis, immune escape and EMT during tumor development and investigate the mechanisms underlying the epigenetic regulation of this process. E Circulating tumor cells: single-cell sequencing can be used to investigate the epigenetic regulation of metastasis by comparing the expression differences between CTCs in blood with metastatic dissemination of tumors and the primary tumor. F Treatment resistance: single-cell sequencing allows monitoring rare cellular mutations that acquire treatment resistance in tumors (e.g., intrinsic drug resistance and acquired drug resistance) and investigating the mechanisms of epigenetic regulation of this process. G Spatial organization: single-cell sequencing can obtain temporal and spatial information on gene expression, and in situ measurement of the epigenome can better reveal the association between cellular spatial distribution and gene regulation in tumor tissues. H Tumor microenvironment (TME): single-cell sequencing can investigate the phenotypic and functional heterogeneity of various cell types caused by epigenomic alterations in the tumor microenvironment (TME) during tumorigenesis and progression