Tumor immune microenvironment lncRNAs

• Published in: Briefings in bioinformatics Vol. 23; no. 1
• Main Authors: Park, Eun-Gyeong, Pyo, Sung-Jin, Cui, Youxi, Yoon, Sang-Ho, Nam, Jin-Wu
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 17.01.2022; Oxford Publishing Limited (England)
• Subjects: Annotations; Base Sequence; Functionals; Gene expression; Gene sequencing; Humans; Immune response; Immune system; Immunity - genetics; Microenvironments; Neoplasms - genetics; Neoplasms - immunology; Non-coding RNA; Review; Ribonucleic acid; RNA; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; Sequence Analysis, RNA; Tumor Microenvironment - genetics; Tumor Microenvironment - immunology; Tumorigenesis; Tumors; single-cell RNA-sequencing; immune cells; long non-coding RNA; tumor immune microenvironment; cell type-specific expression; bulk RNA-sequencing
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbab504

Abstract Long non-coding ribonucleic acids (RNAs) (lncRNAs) are key players in tumorigenesis and immune responses. The nature of their cell type-specific gene expression and other functional evidence support the idea that lncRNAs have distinct cellular functions in the tumor immune microenvironment (TIME). To date, the majority of lncRNA studies have heavily relied on bulk RNA-sequencing data in which various cell types contribute to an averaged signal, limiting the discovery of cell type-specific lncRNA functions. Single-cell RNA-sequencing (scRNA-seq) is a potential solution for tackling this limitation despite the lack of annotations for low abundance yet cell type-specific lncRNAs. Hence, updated annotations and further understanding of the cellular expression of lncRNAs will be necessary for characterizing cell type-specific functions of lncRNA genes in the TIME. In this review, we discuss lncRNAs that are specifically expressed in tumor and immune cells, summarize the regulatory functions of the lncRNAs at the cell type level and highlight how a scRNA-seq approach can help to study the cell type-specific functions of TIME lncRNAs.