Alternative splicing and intron retention: Their profiles and roles in cutaneous fibrosis of systemic sclerosis

Shasha Xie; Ding Bao; Yizhi Xiao; Hongdong Li; Muyao Guo; Bingying Dai; Sijia Liu; Jing Huang; Muyuan Li; Liqing Ding; Qiming Meng; Chun-Liu Lv; Jörg H W Distler; Hui Luo; Honglin Zhu

doi:10.1016/j.jaut.2024.103306

Alternative splicing and intron retention: Their profiles and roles in cutaneous fibrosis of systemic sclerosis

J Autoimmun. 2024 Sep 11:149:103306. doi: 10.1016/j.jaut.2024.103306. Online ahead of print.

Authors

Shasha Xie¹, Ding Bao¹, Yizhi Xiao¹, Hongdong Li², Muyao Guo¹, Bingying Dai¹, Sijia Liu¹, Jing Huang¹, Muyuan Li¹, Liqing Ding¹, Qiming Meng¹, Chun-Liu Lv³, Jörg H W Distler⁴, Hui Luo⁵, Honglin Zhu⁶

Affiliations

¹ Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
² Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, China.
³ Department of Breast Tumor Plastic Surgery, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, Hunan, 410013, China.
⁴ Department of Rheumatology, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University, 40225, Düsseldorf, Germany; Hiller Research Center, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University, 40225, Düsseldorf, Germany.
⁵ Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. Electronic address: luohui@csu.edu.cn.
⁶ Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. Electronic address: honglinzhu@csu.edu.cn.

PMID: 39265192
DOI: 10.1016/j.jaut.2024.103306

Abstract

Background: Alternative splicing (AS) and intron retention (IR) implicated in multiple pathophysiological processes, have rarely been reported in systemic sclerosis (SSc).

Methods: We integrated bulk RNA-seq and 4D label-free mass spectrometry to perform a multi-omics analysis of AS and IR in SSc skin tissue and fibroblasts. RMATS and iREAD were used to identify AS and IR, which were validated by real-time PCR. Spearman correlation and the LASSO method were employed to assess correlations among clinical features, introns, splicing factors (regulators of AS) and proteins.

Findings: AS profiles showed distinct alterations in SSc skin tissue, with the most pronounced changes occurring in IR. AS and IR were associated with total modified Rodnan skin score (mRSS) and local skin score. Upon TGF-β stimulation, fibroblasts exhibited significant alterations in IR profiles, affecting genes related to fibroblast proliferation and collagen fibril organization. A comprehensive integrated analysis of introns, exons, and proteome profiles revealed that IR exerted a negative impact on protein expression, with certain changes being under intronic control. RT-PCR confirmed the presence of intron and exon-derived sequences of CTTN, OGA, MED16 and PHYKPL. Additionally, notable changes were observed in the regulatory network of splicing factors in SSc skin tissues. These factors are also involved in fibrosis pathways and correlated with clinical features.

Conclusion: Totally, abnormal AS, IR profiles and splicing factors were identified in SSc, altered IRs and splicing factors participated in fibrosis-related pathways. IR exerted a negative impact on protein expression in TGF-β-stimulated fibroblasts. Clarification of the IR mechanisms will provide new insights into the pathophysiology of SSc.

Keywords: Alternative splicing; Intron retention; Skin fibrosis; Splicing factors; Systemic sclerosis.