The Global Landscape of Immune-derived LncRNA Signature in Colorectal Cancer

Overview

Journal Heliyon

Specialty Social Sciences

Date 2024 Feb 29

PMID 38420407

Authors

Mengying Zhang

Yifei Wu

Jingyi Mou

Yang Yao

Pengbo Wen

Xin Liu

Shipeng Shang

Xingxing Kang

Jiaqi Tian

Yan Liu

Enhui Lv

Liang Wang

Affiliations

Soon will be listed here.

Abstract

Background: Colorectal cancer (CRC) is a highly heterogeneous cancer. This heterogeneity has an impact on the efficacy of immunotherapy. Long noncoding RNAs (lncRNAs) have been found to play regulatory functions in cancer immunity. However, the global landscape of immune-derived lncRNA signatures has not yet been explored in colorectal cancer.

Methods: In this study, we applied DESeq2 to identify differentially expressed lncRNAs in colon cancer. Next, we performed an integrative analysis to globally identify immune-driven lncRNA markers in CRC, including immune-associated pathways, tumor immunogenomic features, tumor-infiltrating immune cells, immune checkpoints, microsatellite instability (MSI) and tumor mutation burden (TMB).

Results: We also identified dysregulated lncRNAs, such as LINC01354 and LINC02257, and their clinical relevance in CRC. Our findings revealed that the differentially expressed lncRNAs were closely associated with immune pathways. In addition, we found that RP11-354P11.3 and RP11-545G3.1 had the highest association with the immunogenomic signature. As a result, these signatures could serve as markers to assess immunogenomic activity in CRC. Among the immune cells, resting mast cells and M0 macrophages had the highest association with lncRNAs in CRC. The AC006129.2 gene was significantly associated with several immune checkpoints, for example, programmed cell death protein 1 (PD-1) and B and T lymphocyte attenuator (BTLA). Therefore, the AC006129.2 gene could be targeted to regulate the condition of immune cells or immune checkpoints to enhance the efficacy of immunotherapy in CRC patients. Finally, we identified 15 immune-related lncRNA-generated open reading frames (ORFs) corresponding to 15 cancer immune epitopes.

Conclusion: In conclusion, we provided a genome-wide immune-driven lncRNA signature for CRC that might provide new insights into clinical applications and immunotherapy.

Citing Articles

Chen T, Jiang Q, Wang Z, Wang F, Fu Z Transl Cancer Res. 2024; 13(10):5347-5364.

PMID: 39525019 PMC: 11543043. DOI: 10.21037/tcr-24-378.

The roles of lncRNA in clinical implications, immune landscape and carcinogenesis of colorectal cancer.

Chen T, Jiang Q, Wang Z, Zhang H, Fu Z Transl Cancer Res. 2024; 13(7):3465-3481.

PMID: 39145049 PMC: 11319950. DOI: 10.21037/tcr-24-145.

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