DNA methylation-based depiction of the immune microenvironment and immune-associated long non-coding RNAs in oral cavity squamous cell carcinomas

Naiade Calanca; Ana Lucia Noronha Francisco; Daniela Bizinelli; Hellen Kuasne; Mateus Camargo Barros Filho; Bianca Campos Troncarelli Flores; Clóvis Antonio Lopes Pinto; Claudia Aparecida Rainho; Milena Botelho Pereira Soares; Fabio Albuquerque Marchi; Luiz Paulo Kowalski; Silvia Regina Rogatto

doi:10.1016/j.biopha.2023.115559

DNA methylation-based depiction of the immune microenvironment and immune-associated long non-coding RNAs in oral cavity squamous cell carcinomas

Biomed Pharmacother. 2023 Nov:167:115559. doi: 10.1016/j.biopha.2023.115559. Epub 2023 Sep 22.

Affiliations

¹ Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark; Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil.
² Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil.
³ International Research Center (CIPE), A.C.Camargo Cancer Center, São Paulo 01508-010, SP, Brazil.
⁴ Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal H3A1A3, QC, Canada.
⁵ Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark.
⁶ Department of Pathology, A.C.Camargo Cancer Center, São Paulo 01509-010, SP, Brazil.
⁷ Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil.
⁸ Health Technology Institute, SENAI CIMATEC, Salvador 41650-010, BA, Brazil; Gonçalo Moniz Institute, FIOCRUZ, Salvador 40296-710, BA, Brazil.
⁹ Department of Head and Neck Surgery, University of São Paulo Medical School, São Paulo 05402-000, SP, Brazil.
¹⁰ Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil; Department of Head and Neck Surgery, University of São Paulo Medical School, São Paulo 05402-000, SP, Brazil.
¹¹ Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark. Electronic address: silvia.regina.rogatto@rsyd.dk.

PMID: 37742611
DOI: 10.1016/j.biopha.2023.115559

Abstract

Oral cavity squamous cell carcinoma (OSCC) is a complex and dynamic disease characterized by clinicopathological and molecular heterogeneity. Spatial and temporal heterogeneity of cell subpopulations has been associated with cancer progression and implicated in the prognosis and therapy response. Emerging evidence indicates that aberrant epigenetic profiles in OSCC may foster an immunosuppressive tumor microenvironment by modulating the expression of immune-related long non-coding RNAs (lncRNAs). DNA methylation analysis was performed in 46 matched OSCC and normal adjacent tissue samples using a genome-wide platform (Infinium HumanMethylation450 BeadChip). Reference-based computational deconvolution (MethylCIBERSORT) was applied to infer the immune cell composition of the bulk samples. The expression levels of genes encoding immune markers and differentially methylated lncRNAs were investigated using The Cancer Genome Atlas dataset. OSCC specimens presented distinct immune cell composition, including the enrichment of monocyte lineage cells, natural killer cells, cytotoxic T-lymphocytes, regulatory T-lymphocytes, and neutrophils. In contrast, B-lymphocytes, effector T-lymphocytes, and fibroblasts were diminished in tumor samples. The hypomethylation of three immune-associated lncRNAs (MEG3, MIR155HG, and WFDC21P) at individual CpG sites was confirmed by bisulfite-pyrosequencing. Also, the upregulation of a set of immune markers (FOXP3, GZMB, IL10, IL2RA, TGFB, IFNG, TDO2, IDO1, and HIF1A) was detected. The immune cell composition, immune markers alteration, and dysregulation of immune-associated lncRNAs reinforce the impact of the immune microenvironment in OSCC. These concurrent factors contribute to tumor heterogeneity, suggesting that epi-immunotherapy could be an efficient alternative to treat OSCC.

Keywords: DNA methylation; Deconvolution; LncRNAs; Oral cancer; Tumor immune microenvironment.