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

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