Transcriptomic profiling disclosed the role of DNA methylation and histone modifications in tumor-infiltrating myeloid-derived suppressor cell subsets in colorectal cancer

Abstract

Background: Increased numbers of myeloid-derived suppressor cells (MDSCs) are positively correlated with poor prognosis and reduced survivals of cancer patients. They play central roles in tumor immune evasion and tumor metastasis. However, limited data are available on phenotypic/transcriptomic characteristics of the different MDSCs subsets in cancer. These cells include immature (I-MDSCs), monocytic (M-MDSCs), and polymorphonuclear/ granulocytic (PMN-MDSCs). Methods: Phenotypic characterization of myeloid subsets from 27 colorectal cancer (CRC) patients was assessed by flow cytometric analyses. RNA-sequencing of sorted I-MDSCs, PMN-MDSCs, and antigen-presenting cells (APCs) was also performed. Results: We found that the levels of I-MDSCs and PMN-MDSCs were increased in tumor tissues (TT), compared with normal tissues (NT) in colorectal cancer. Our functional annotation analyses showed that genes associated with histone deacetylase (HDAC) activation-and DNA methylation-mediated transcriptional silencing were upregulated, and histone acetyl transferase (HAT)-related genes were downregulated in tumorinfiltrating I-MDSCs. Moreover, pathways implicated in cell trafficking and immune suppression, including Wnt, interleukin-6 (IL-6), and mitogen-activated protein kinase (MAPK) signaling, were upregulated in I-MDSCs. Notably, PMN-MDSCs showed downregulation in genes related to DNA methylation and HDAC binding. Using an ex vivo model, we found that inhibition of HDAC activation or neutralization of IL-6 in CRC tumor tissues downregulates the expression of genes associated with immunosuppression and myeloid cell chemotaxis, confirming the importance of HDAC activation and IL-6 signaling pathway in MDSC function and chemotaxis. Conclusions: This study provides novel insights into the epigenetic regulations and other molecular pathways in different myeloid cell subsets within the CRC tumor microenvironment (TME), giving opportunities to potential targets for therapeutic benefits.

Connections between Metabolism and Epigenetic Modification in MDSCs

“…In colorectal cancer patients, genes associated with HDAC activation were up-regulated in tumor-invasive I-MDSCs, while genes associated with HAT were down-regulated. Inhibition of HDAC activation or neutralization of IL-6 in colorectal cancer tissues can down-regulate the expression of immunosuppressant and chemotaxis-related genes in myeloid cells, confirming the importance of HDAC activation and IL-6 signaling pathways in the function and chemotaxis of MDSCs [ 84 ]. Chromatin modified histone deacetylase inhibitors (HDACi) exhibit anti-inflammatory properties, reflecting their ability to inhibit DC function and enhance Tregs.…”

“…PMN-MDSCs showed down-regulation of genes associated with DNA methylation and histone deacetylase (HDAC) binding. This suggests that the regulation of gene expression in these MDSC subpopulations is regulated through different epigenetic mechanisms, and the activation of some cell pathways may be realized through epigenetic modifications [ 84 ].…”

Transcriptomic Analyses of Myeloid-Derived Suppressor Cell Subsets in the Circulation of Colorectal Cancer Patients

“…Isolated PBMCs were stained as previously described ( 17 , 18 ). Briefly, cells were stained with antibodies against CD33–fluorescein isothiocyanate (clone HIM3-4; BD Biosciences, Oxford, UK), HLA DR–phycoerythrin (clone G46-6; BD Biosciences), CD14–phycoerythrin–Cy7 (clone M5E2; BD Biosciences), and CD15–allophycocyanin (clone HI98; BioLegend, San Diego, CA, USA).…”

“…7-AAD viability dye (eBioscience, San Diego, CA, USA) was used to identify live cells. The cells were prepared for analyses and sorting as previously described ( 17 , 18 ) Minimal sorter-induced cell stress was ensured following applicable measures, as previously described ( 19 ). FlowJo V10 software (FlowJo, Ashland, OR, USA) was used to perform data analyses.…”

“…Study design and pipeline for bioinformatics analyses were performed, as we have previously described ( 18 ). Briefly, 1,000 I-MDSCs, M-MDSCs, PMN-MDSCs, and monocytic APCs cells were sorted with high purity from PBMCs of CRC patients.…”