Integrative lncRNA–mRNA co‐expression network analysis identifies novel lncRNA E2F3‐IT1 for rheumatoid arthritis

• Published in: Clinical and translational medicine Vol. 11; no. 2; pp. e325 - n/a
• Main Authors: Wu, Long‐Fei, Mo, Xing‐Bo, He, Jia‐Hui, He, Pei, Lu, Xin, Deng, Hong‐Wen, Deng, Fei‐Yan, Lei, Shu‐Feng
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.02.2021; John Wiley and Sons Inc; Wiley
• Subjects: Arthritis, Rheumatoid - etiology; Arthritis, Rheumatoid - genetics; Body mass index; Case-Control Studies; Cell cycle; Cell growth; Conflicts of interest; DNA methylation; E2F3 Transcription Factor - genetics; E2F3 Transcription Factor - metabolism; Epigenesis, Genetic; Epigenetics; Female; Flow cytometry; Gene expression; Gene Expression Regulation - genetics; Humans; Letter to Editor; Localization; Lymphocytes; Male; Middle Aged; Pathogenesis; Patients; Proteins; Rheumatoid arthritis; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; Roles
• ISSN: 2001-1326; 2001-1326
• DOI: 10.1002/ctm2.325

Dear Editor, Our previous study has reported that DNA methylation serves as an important epigenetic factor of gene–environment interaction, which contributes to pathogenesis of rheumatoid arthritis (RA).1 To investigate the role of another epigenetic factor (long noncoding RNA, lncRNA) in RA pathogenesis, we integrated lncRNA and mRNA transcriptomic information, constructed lncRNA→mRNA→RA regulatory network by performing co-expression networks analysis and causal inference test, and explored functional roles of the highlighted lncRNA E2F3-IT1 (E2F3 intronic transcript 1) in RA (Figure S1). Differential expression analyses identified a total of 402 lncRNAs and 832 mRNAs (fold-change > 2 and false discovery rate < 0.05) as potential targets for subsequent analyses (Table S1). Since the functions of lncRNAs are largely unknown, we performed the weighted gene co-expression network analysis (WGCNA)3 by simultaneously incorporating information of the above differential expressed genes, and two interesting co-expression modules were constructed, named yellow and magenta (Figure 1B). TABLE 1 Basic characteristics of the study subjects and the expression levels of the selected mRNA and lncRNA in PBMCs in the validation sample (A) Basic characteristics of the study subjects Discovery group Validation group Variable RA patient (n = 25) Healthy control (n = 18) RA patient (n = 35) Healthy control (n = 35) Gender Female Female Female Female Age (year) 45.6 ± 9.84 47.11 ± 14.09 46.44 ± 10.99 47.57 ± 13.99 BMI (kg/m2) 22.07 ± 3.31 22.32 ± 2.79 22.24 ± 3.67 22.32 ± 2.79 DAS28 4.46 ± 0.99 n.d. 5.08 ± 1.32 n.d. CRP (mg/L) 13.51 + 16.74 n.d. 18.37 ± 31.17 n.d. ESR (mm/h) 42.61 ± 27.5 n.d. 48.29 ± 29.46 n.d. TJC 8.64 ± 6.49 n.d. 10 ± 7.7 n.d. SJC 5.48 ± 3.83 n.d. 6.79 ± 5.43 n.d. (B) The expression levels of the selected mRNA and lncRNA in PBMCs in the validation sample lncRNA Chromosome Fold change p-Value Class CYTOR 17q11.2 1.08 0.67 Intergenic DQ593252 11q12.3 1.21 0.05 Intergenic E2F3-IT1 6p22.3 1.73 0.03 Intronic uc.265 9q31.1 1.35 0.02 Antisense INE2 Xp22.2 1.43 0.049 Antisense mRNA DDX58 9p21.1 1.06 0.67 DExD/H-box helicase 58 IFI16 1q23.1 1.09 0.35 Interferon gamma inducible protein 16 LDLR 19p13.2 2.13 <0.001 Low-density lipoprotein receptor PLSCR1 3q24 -1.67 <0.001 Phospholipid scramblase 1 PARP9 3q21.1 1.39 0.015 Poly(ADP-ribose) polymerase family member 9 Abbreviations: BMI, body mass index; DAS28,28 joint Disease Activity Score; CRP, C reactive protein; ESR, equivalent series resistance; TJC, tender joint count; SJC, swollen joint count; n.d., not determined. SEE PDF] The lncRNA E2F3-IT1 is located at chromosome 6, an intronic transcript of transcriptional factor E2F3 (Figure S2A). Since the function of lncRNA is correlated with its subcellular localization, we carried out a cellular fractionation assay.