N6-methyladenine regulator-mediated RNA methylation modification patterns in immune microenvironment regulation of osteoarthritis

Yong Gu; Zhengming Wang; Rui Wang; Yunshang Yang; Peijian Tong; Shuaijie Lv; Long Xiao; Zhirong Wang

doi:10.3389/fgene.2023.1113515

N6-methyladenine regulator-mediated RNA methylation modification patterns in immune microenvironment regulation of osteoarthritis

Front Genet. 2023 Jan 26:14:1113515. doi: 10.3389/fgene.2023.1113515. eCollection 2023.

Authors

Yong Gu^{1

2}, Zhengming Wang^{3

4}, Rui Wang⁵, Yunshang Yang^{1

2}, Peijian Tong⁵, Shuaijie Lv⁵, Long Xiao^{1

2}, Zhirong Wang^{1

2}

Affiliations

¹ Translational Medical Innovation Center, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China.
² Department of Orthopedics, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, China.
³ Shi's Center of Orthopedics and Traumatology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
⁴ Institute of Traumatology and Orthopedics, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China.
⁵ The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Provincial Hospital of Chinese Medicine, Hangzhou, China.

Abstract

Background: Osteoarthritis is a common chronic degenerative disease, and recently, an increasing number of studies have shown that immunity plays an important role in the progression of osteoarthritis, which is exacerbated by local inflammation. The role of N6-methyladenine (m⁶A) modification in immunity is being explored. However, the role of m⁶A modification in regulating the immune microenvironment of osteoarthritis remains unknown. In this study, we sought to discuss the association between the N6-methyladenine (m⁶A) modification and the immune microenvironment of osteoarthritis. Methods: First, the data and gene expression profiles of 139 samples, including 33 healthy samples and 106 osteoarthritis samples, were obtained from the Genetics osteoARthritis and Progression (GARP) study. Then the differences in m⁶A regulators between healthy individuals and osteoarthritis patients were analyzed. The correlation between m⁶A regulators and immune characteristics was also investigated by single-sample gene set enrichment analysis (ssGSEA). Principal component analysis (PCA), Gene Set Variation Analysis (GSVA) enrichment analysis, weighted gene coexpression network analysis (WGCNA), and Associated R packages were used to identify the m⁶A phenotype and its biological functions. Results: A total of 23 m⁶A regulators were involved in this study. We found a close correlation between most m⁶A regulators in all samples as well as in osteoarthritis samples. VIRMA and LRPPRC were the most highly correlated m⁶A regulators and showed a positive correlation, whereas VIRMA and RBM15B were the most negatively correlated. M⁶A regulators are associated with osteoarthritis immune characteristics. For example, MDSC cell abundance was strongly correlated with RBM15B and HNRNPC. Meanwhile, RBM15B and HNRNPC were important effectors of natural killer cell immune responses. IGFBP3 is an important regulator of cytolytic activity immune function. We performed an unsupervised consensus cluster analysis of the osteoarthritis samples based on the expression of 23 m⁶A regulators. Three different m⁶A subtypes of osteoarthritis were identified, including 27 samples in subtype C1, 21 samples in subtype C2, and 58 samples in subtype C3. Different m⁶A subtypes have unique biological pathways and play different roles in the immune microenvironment of osteoarthritis. Conclusion: The m⁶A modification plays a crucial role in the diversity and complexity of the immune microenvironment in osteoarthritis.

Keywords: N6-methyladenine (m6A); immune; methylation; microenvironment; osteoarthritis.

Grants and funding

This study was supported by the National Natural Science Foundation of China (82074473, and 82104892), Natural Science Foundation of Jiangsu province (BK20180001, BK20191201, and BE2020666), Project of Excellent Young Talents of Traditional Chinese Medicine of Zhejiang Province (2019ZQ016) and the “Zhejiang Medical and Health Science and Technology Young Talents Program (2019RC059)” from the Health Commission of Zhejiang Province.