Spatial Multiomics Analysis Reveals Only Minor Genetic and Epigenetic Changes in Human Liver Cancer Stem-Like Cells Compared With Other Tumor Parenchymal Cells.

Dan Liu,Yixue Li,Mincheng Qu,Hui Dong,Liguang Yang,Yufei He,Hongyang Wang,Lina Chen,Hong Li

doi:10.3389/fcell.2022.810687

Abstract

Cancer stem cells (CSCs) usually account for a very small tumor cell population but play pivotal roles in human cancer development and recurrence. A fundamental question in cancer biology is what genetic and epigenetic changes occur in CSCs. Here we show that the in-situ global levels of DNA cytosine modifications, including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC), are similar between liver cancer stem-like (LCSL) cells and paratumor liver cells of liver cancer patients. We then developed a robust method combining immunohistochemistry, laser capture microdissection and genome sequencing with ultra-low-input cells (CIL-seq) to study the detailed genetic and DNA methylation changes in human LCSL cells. We first used clinical samples of mixed hepatocellular carcinoma-cholangiocarcinoma (HCC-CCA) with stem cell features to investigate human LCSL cells. The CIL-seq analysis of HCC-CCA and HCC patients showed that LCSL cells had strong spatial genetic and epigenetic heterogeneity. More interestingly, although the LCSL cells had some potential key changes in their genome, they had substantially fewer somatic single nucleotide variants (SNVs), copy number alterations (CNAs) and differentially methylated regions than other tumor parenchymal cells. The cluster analysis of SNVs, CNAs, DNA methylation patterns and spatial transcriptomes all clearly showed that the LCSL cells were clustered with the paratumor liver cells. Thus, spatial multiomics analysis showed that LCSL cells had only minor genetic and epigenetic changes compared with other tumor parenchymal cells. Targeting key changes in CSCs, not just changes in bulk tumor cells, should be more effective for human cancer therapy.

Highlights

Human cancer development is a complex evolutionary process (Greaves and Maley, 2012; Black and McGranahan, 2021)
The proportion of Cancer stem cell (CSC) or liver cancer stem-like (LCSL) cells in mixed hepatocellular cholangiocarcinoma (HCC-CCA) is usually much higher than that in other types of tumors. This type of primary liver cancer (PLC) can provide us with a perfect tumor object directly from clinical patients to help investigate human CSCs or LCSL cells and compare the similarities and differences between LCSL cells and HCC or CCA cells within the same liver cancer sample
We found many copy number alteration (CNA) amplification regions in the tumor, but most of them were centralized in HCC and CCA cells, including the amplification of chromosome 8q, which is often detected in liver cancer (Zhai et al, 2017; Cancer Genome Atlas Resea, 2017; Xue et al, 2019), while only very few CNA regions were detected in LCSL cells (Figure 2G and Supplementary Table S4)

Summary

Introduction

Human cancer development is a complex evolutionary process (Greaves and Maley, 2012; Black and McGranahan, 2021). It is universally acknowledged that cancer cells possess many significant genetic and epigenetic changes caused by multiple factors compared with normal cells. Some of these changes are essential for tumor evolution (Black and McGranahan, 2021). Many cancers are thought to originate from cancer stem cells (CSCs), which pose a high risk of therapy resistance and cancer relapse (Greaves and Maley, 2012; Black and McGranahan, 2021). Understanding the genetic and epigenetic changes in human CSCs should shed light on a better understanding of the developmental and evolutionary trajectory of a tumor and the design of better cancer therapeutic approaches. The genetic and epigenetic changes that occur in human CSCs are still poorly understood

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