DNA methylation of indoleamine 2,3-dioxygenase 1 (IDO1) in head and neck squamous cell carcinomas correlates with IDO1 expression, HPV status, patients’ survival, immune cell infiltrates, mutational load, and interferon γ signature

Abstract

BackgroundThe immune checkpoint, indoleamine 2,3-dioxygenase 1, is under investigation as target of novel immunotherapies for cancers, including head and neck squamous cell carcinomas (HNSCC). The aim of our study was to analyze DNA methylation of the encoding gene (IDO1) in HNSCC.MethodsMethylation of three CpG sites within the promoter, promoter flank, and gene body was investigated and correlated with mRNA expression, immune cell infiltration, mutational burden, human papillomavirus (HPV)-status, and overall survival in a cohort of N = 528 HNSCC patients obtained from The Cancer Genome Atlas. In addition, IDO1 immunohistochemistry and DNA methylation analysis was performed in an independent cohort of N = 138 HNSCC samples.FindingsSignificant inverse correlations of IDO1 methylation and IDO1 mRNA expression were found in the promoter and promoter flank region (Spearman's ρ = −0.163 and ρ = −0.377, respectively) while a positive correlation was present in the gene body (ρ = 0.502; all P < 0.001). IDO1 DNA methylation significantly correlated with IDO1 protein expressing immune cells as well as tumor cells. IDO1 promoter flank hypermethylation was significantly associated with poor overall survival (P < 0.001). In addition, we discovered significant correlations between IDO1 methylation and expression with RNA signatures of immune cell infiltrates and with HPV-status, mutational load (methylation only), and interferon γ signature.InterpretationOur results suggest IDO1 expression levels are epigenetically regulated by DNA methylation. This study provides rationale to test IDO1 methylation as potential biomarker for prediction of response to IDO1 immune checkpoint inhibitors in HNSCC.

LAG3(LAG-3,CD223) DNA methylation correlates with LAG3 expression by tumor and immune cells, immune cell infiltration, and overall survival in clear cell renal cell carcinoma

“…immunohistochemistry Immunohistochemical staining of CD45, CD8, and CD4 was performed as previously described using the following monoclonal antibodies and dilutions: 26 anti-CD45 clones 2B11+PD7/26 (#M070101, Dako/Agilent Technologies, Santa Clara, California, USA), 1:100; anti-CD8 clone C8/144B (#M710301, Dako/Agilent Technologies), 1:50; anti-CD4 clone SP35, #503-3354 (Zytomed Systems GmbH, Berlin, Germany), 1:20. CD45 + , CD8 + , and CD4 + immune cell infiltrates were evaluated as percentage of positive cells from all cells in the tumor.…”

HPV-Related Oropharyngeal Cancer and Biomarkers Based on Epigenetics and Microbiome Profile

“…In HPV-associated tumors (HNSCC), increased expression of the IDO1 gene was found in conjunction with significantly lower DNA methylation in the promoter flank region. The research results were verified by further investigations of the regulator interferon γ (IFNγ) and the expression levels of all genes involved in the pathway [interferon gamma (IFNG), signal tranducer and activator of transcription (STAT)1, STAT2, Janus kinase (JAK)2, and IFN regulator factor (IRF)9] were positively correlated ( Sailer et al, 2019 ). The sal-like 3 protein (SALL3) binds to DNA methyltransferase 3 alpha (DNMT3A), and the silencing of this gene is involved in the regulation of cell growth ( Shikauchi et al, 2009 ).…”

IL4I1 Is Expressed by Head–Neck Cancer-Derived Mesenchymal Stromal Cells and Contributes to Suppress T Cell Proliferation

“…The finding that IDO1 and IL4I1 are both expressed in cancer cells [ 4 ] and in stromal cells (MSC), further supports this observation. Moreover, IDO1 expression has been proposed as a candidate prognostic factor for clinical outcome in HNSCC patients [ 12 ]. IL4I1 may have a similar prognostic impact, thus future studies investigating this aspect should be considered.…”