MicroRNAs in the pathogenesis of systemic lupus erythematosus


  • Xiaochun Ma,

    1. Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, Shandong University School of Medicine, Jinan, Shandong, China
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  • Qiji Liu

    Corresponding author
    • Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, Shandong University School of Medicine, Jinan, Shandong, China
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Correspondence: Professor Qiji Liu, Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, Shandong University School of Medicine, No.44 Wenhua xi Road, Jinan, Shandong 250012, China.

Email: liuqiji@sdu.edu.cn


Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease, characterized by the production of autoantibodies against multiple organs. MicroRNAs (miRNAs) are non-coding, single-stranded small RNAs that post-transcriptionally regulate gene expression. Evidence is accumulating that miRNAs play a pivotal role in the pathogenesis of SLE. This article reviews the pertinent publications (searched from the PubMed database) involving the mechanisms of actions of miRNA associated with the pathogenesis of SLE. The search of related literature was extended as far back as 1979. In this mini-review we first introduce the miRNAs briefly and later discuss their regulatory roles in the DNA methylation pathway, type I interferon pathway, estrogen and regulatory T-cells in the pathogenesis of SLE.


Systemic lupus erythematosus (SLE) is a chronic multisystem autoimmune disorder, characteristic of the production of nuclear-targeted autoantibodies that initiate widespread immunopathological damage to various organs.[1] The pathogenesis of SLE remains to be further elucidated. Epigenetic factors have long been demonstrated to play crucial roles in disease pathogenesis, both epidemiologically and biologically.[2, 3] Three major epigenetic modifications are most often typified: DNA methylation, histone modifications and microRNAs (miRNAs), and each exerts considerable influence on multiple human diseases.[4, 5] MiRNAs play essential roles in various autoimmune diseases, including SLE.[6] The main objective of this review is to discuss the known mechanisms of miRNAs associated with the pathogenesis of SLE (Table 1).

Table 1. miRNAs in SLE
miRNATarget geneEffectReferences
  1. RasGRP1, RAS guanyl releasing protein 1; DNMT-1, DNA methyltransferase 1; IRF-5, interferon regulatory factor 5; IRAK1, interleukin-1 receptor-associated kinase 1; TRAF6, TNF receptor-associated factor 6; STAT-1, signal transducer and activator of transcription 1; IFN, interferon; IRAK-M, interleukin-1 receptor-associated kinase M; TAB 2, TGF-beta activated kinase 1; Treg cell, regulatory T-cell; FOXP3, Forkhead box P3.

DNA methylation
miR-21RasGRP1DNMT1 repression, DNA hypomethylation [19, 20, 22]
miR-148aDNMT1DNA hypomethylation [20]
miR-126DNMT1DNA hypomethylation [21]
Type I IFN
miR-146aIRF-5, IRAK1, TRAF6, STAT-1Type I IFN signaling up-regulation [29, 32]
miR-155IRAK-M, TAB 2Type I INF production [33, 34]
miR-146aUnknownIFN-γ production up-regulation [40, 41]
miR-223UnknownIFN-γ production up-regulation 
Treg cell
miR-155CD62LTreg cell alteration, deficient suppressive capacity [47]
miR-31FOXP3Deficient Treg cell development and function [48]
MiR-142-3pAC9Deficient Treg cell function [50]


MiRNAs, usually 21–24 nucleotides long, are conservative noncoding RNA (ncRNA) molecules that post-transcriptionally modulate gene expression. MiRNAs normally bind to the 3′ untranslated region (3′ UTR) of targeted messenger RNAs (mRNAs) and leads to translation inhibition and/or mRNAs degradation.[7] MiRNAs have been implicated in fine-tuning diverse physiological and pathological processes, such as cell differentiation, embryonic development and carcinogenesis.[8]

MiRNAs are first transcribed in the nucleus by RNA polymerase II to form primary miRNA (pri-miRNA) transcripts and then are processed by Drosha and its partner protein DiGeorge syndrome critical region 8 (DGCR8), an RNA polymerase III enzyme complex, into 70–100 nucleotide precursor miRNA (pre-miRNA) molecules.[9, 10] Pre-miRNAs are actively transported from the nucleus to the cytoplasm by Exportin5, a nuclear membrane transporter, and then cleaved by RNA polymerase III, Dicer, altogether with its partner protein trans-activator RNA binding protein (TRBP), into 18–25 nucleotide double-stranded miRNAs.[11, 12] One strand of these double- stranded miRNAs is selected to form the RNA-induced silencing complex (RISC) (Fig.1). Mature miRNAs in RISC target mRNAs 3′ UTR via complete or partial complementary pairing and result in either mRNA degradation or translational repression, which negatively modulates protein syntheses and their effects (Fig. 2).[13] Notably, an individual miRNA can affect multiple mRNAs, causing difficulty in predicting targeted genes of a novel miRNA.

Figure 1.

Biogenesis of microRNA (miRNA). The process of miRNA biogenesis is schemed: (1) miRNAs are transcribed in the nucleus by RNA polymerase II to form pri-miRNA; (2) pri-miRNAs are processed by Drosha and its partner protein DGCR8 (an RNA polymerase III enzyme complex) into pre-miRNAs;[9, 10] (3) pre-miRNAs are actively transported from the nucleus to the cytoplasm by Exportin5 (a nuclear membrane transporter); (4) pre-miRNAs are then cleaved by Dicer (an RNA polymerase III) together with its partner protein TRBP, into double-stranded miRNAs and one strand of the double-stranded miRNAs is selected to form the RISC;[11, 12] (5) mature miRNAs in RISC target mRNAs 3′ UTR, which results in either mRNA degradation or translational inhibition.[13] DGCR8, DiGeorge syndrome critical region 8; pri-miRNA, primary miRNA; pre-miRNA, precursor miRNA; TRBP, trans-activator RNA binding protein; RISC, RNA-induced silencing complex.

Figure 2.

Function of microRNAs (miRNAs). MiRNAs negatively modulate protein synthesis and their effects via two major mechanisms: (1) miRNAs lead to the degradation of targeted mRNAs by RISC via complete complementary pairing; (2) miRNAs interfere with protein translation via partial complementary pairing to targeted mRNAs. mRNA, messenger RNA; RISC, RNA-induced silencing complex. The 3′ poly-A tail is a chain of adenine nucleotides that is added to an mRNA molecule during RNA processing. The 5′ Cap is situated in the 5′ end of an mRNA molecule and consists of a guanine nucleotide connected to the mRNA. Symbols: The “scissor-like” symbol means the cleavage of a targeted mRNA by RISC. The “T-like” symbol means the inhibition of transcription activities by an miRNA.

miRNAs are essential regulators of the development and function of the immune system, such as the differentiation of T- and B-lymphocytes and immune responses.[14] Abnormal miRNA expression has been confirmed in patients and animal models with autoimmune diseases and functional studies have revealed the significant roles of miRNAs in the onset and/or development of autoimmune diseases. Additionally, novel miRNA-targeted therapeutic strategies have a bright prospect in the treatment and/or prevention of autoimmune disorders in the future.

DNA Methylation and MiRNA

DNA methylation is a pivotal epigenetic alteration that negatively regulates many cellular processes, including embryonic development, transcription, chromatin structure and so forth. Aberrant DNA methylation has been implicated to be involved in an increasing number of human diseases, such as cancers and autoimmune diseases. Global reduced DNA methylation in SLE patients has long been noted in early studies.[15] The degree of cluster of differentiation (CD)4+ T-cell DNA hypomethylation in SLE patients closely correlates with disease activity and severity.[16] Overexpression of several methylation-sensitive autoreactivity-related genes due to hypomethylation is as well associated with the initiation and progression of SLE.[17] Recently miRNAs have emerged to contribute to abnormal DNA methylation in the pathogenesis of SLE.

DNA methyltransferase 1 (DNMT-1), which catalyzes to maintain a specific DNA methylation pattern during DNA replication, has been noted to be down-regulated in T-cells from patients with active SLE.[18, 19] MiRNAs were demonstrated to directly or indirectly modulate DNMT-1 expression. MiR-148a and miR-126 directly down-regulate DNMT-1 expression. MiR-148a and miR-126 have proven to be up-regulated in CD4+ T-cells from both SLE patients and SLE-prone MRL/lpr (lymphoproliferation) mice and both miRNAs repress DNMT-1 expression by directly targeting their mRNAs.[20, 21] MiR-21 indirectly down-regulates DNMT-1 as there is no binding site by miR-21 in DNMT-1 3′ UTR. MiR-21 represses DNMT-1 expression via inhibiting RAS guanyl releasing protein 1 (RASGRP1). RASGRP1 can activate mitogen-activated protein kinase (MAPK) cascade, which is upstream of and up-regulates DNMT-1.[19, 22] Intriguingly, miR-21, miR-148a and miR-126-transfected primary CD4+ T-cells all over-express CD70 and CD11a, two SLE-related methylation-sensitive genes. CD11a, dimerizing with CD18 to form leukocyte function-associated antigen1 (LFA-1), is a critical integrin that mediates co-stimulation and cellular adhesion between T-cells and antigen-presenting cells. Over-expression of CD11a in CD4+ T-cells from patients with active SLE is associated with this SLE activity.[23] It is suspected that over-expression of CD11a on antigen specific CD4+ cells promotes cellular proliferation in response to subliminal immune-stimulus, including self-antigens.[24] CD70 is also a pivotal co-stimulatory molecule and its over-expression stimulates immunoglobulin G (IgG) production in normal B-cells.[25]

Type I Interferon and MiRNA

It is widely confirmed that the type I interferon (IFN) system is irregularly activated in the pathogenesis of SLE. Type I IFN-inducible gene expression, normally referred to as IFN signature, serves as an effective biological marker for screening more severe cases, involving the kidneys, hematopoetic system and central nervous system in SLE patients.[26, 27] Genetic variants of several important components of type I IFN pathway, such as IFN regulatory factor (IRF) 5, 7 and 8, have been verified to be associated with susceptibility to SLE.[28]

Aberrance in negative regulators in the type I IFN pathway results in excessive positive signaling occurring in autoimmune diseases. In 2006 a role of miR-146a in immune system was proposed in mediating a negative feedback regulatory loop by suppressing interleukin-1 receptor-associated kinase 1 (IRAK1) and TNF receptor-associated factor 6 (TRAF6).[29] IRAK1 was also identified as a critical risk gene in the pathogenesis of SLE.[30] Aberrant miR-146a expression was then confirmed in SLE patients and differential expression levels of miR-146a were inversely associated with disease activity and IFN scores. In addition, miR-146a suppresses the type I IFN pathway by directly targeting multiple key components of this pathway, including signal transducer and activator of transcription 1 (STAT-1), IRF-5, IRAK1 and TRAF6 which are crucial either for the production of type I IFN or signaling downstream of type I IFN. A functional promoter single nucleotide polymorphism (SNP) of miR-146a (rs57095329) was identified to confer SLE susceptibility in Asian and European cohorts. The SLE-associated G allele is associated with reduced miR-146a expression and reduces the protein-binding affinity of a transcription factor, v-ets erythroblastosis virus E26 oncogene homolog 1 (ETS-1). EST-1 is as well an SLE susceptibility gene that harbors SNPs with functional significance for SLE susceptibility. The additive effect of ETS-1 and miR-146a suggests a greater risk of developing SLE for individuals carrying two or more disease-associated SNPs.[31, 32] MiR-155 was recognized to be dysregulated in splenocytes from SLE-prone mice when compared to age-matched control mice and is closely related to SLE susceptibility.[33] Very recently a role of this miRNA has been clarified in type I IFN production in human plasmacytoid dendritic cells (PDC). Upon Toll-like receptor (TLR)-7 stimulation, the expression of miR-155 and its star-form partner miR-155* is greatly induced.[34] However, miR-155 and miR-155* have opposite effects on type I INF production by PDC because miR-155* positively regulates IFN-α/β production by suppressing a negative mediator of type I INF pathway, IRAK-M. While miR-155 negatively regulates IFN production by repressing a positive mediator, tumor growth factor (TGF)-β activated kinase 1 (TAB 2).[35, 36] Interestingly, miR-155* and miR-155 induction occurs at different time intervals of PDC activation, implicating their cooperative interaction in type I IFN production by PDC.[34]

Estrogen and MiRNA

Although SLE afflicts both sexes, an obvious female predominance has long been noted.[1] Abnormal estrogen metabolism was demonstrated both in diseased men and women.[37] Long-term use of estrogen is associated with an increase in risk of developing SLE.[38] Recent advances in understanding of comprehensive effects of estrogen on the immune system have promoted the elucidation of the role of this sex hormone in SLE pathogenesis. These studies with SLE-prone NZB/W mice revealed that estrogen promoted the production of autoantibodies.[39]

Abnormal miRNA expression patterns have been noted to be induced by estrogen. Estrogen can selectively up-regulate certain miRNAs, including miR-451, miR-486, miR-223, miR-148a, miR-18a and miR-708, and inhibit the expression of several SLE-related miRNAs such as miR-145, miR-125a and miR-146a.[40] The down-regulation of miR-146a and up-regulation of miR-223 by estrogen cooperatively enhance IFN-γ production in splenocytes activated by lipopolysaccharide (LPS).[41] It remains poorly understood how estrogen induces abnormal miRNA expression in autoimmune diseases. miRNAs can influence estrogen receptor (ER) expression or activity by directly targeting ERα mRNA and modulate estrogen-regulated gene expression in breast cancer.[42] Thus, miRNAs may also affect the estrogen pathway via regulating ERs and estrogen-regulated genes in the pathogenesis of SLE and this requires further investigation.

Regulatory T-Cells and miRNA

CD4+ regulatory T-cells (Tregs) play key roles in maintaining immunologic tolerance and preventing autoimmune diseases, via suppressing activation and effector function of autoreactive immune cells.[43] A reduction in proportion of circulating Tregs among other CD4+ T-cells in active SLE patients was evidenced when compared to healthy controls or inactive patients. Treg cell deficiency was also shown to be related to disease severity.[44, 45] Treg cells from active SLE patients have impaired suppressive capacity as compared to controls. Down-expression of a transcription factor that is crucial for the development and function of Treg cells, Forkhead Box P3 (FoxP3), and poor repressive function of Treg cells, both indicate a role of aberrant Treg cells in the pathogenesis of SLE. While this deficiency appears reversible because reactivation of deficient Treg cells from active SLE patients, together with elevated levels of FoxP3 mRNA and protein expression, restores their suppressive function.[46] miRNAs have been reported to play a role in the development and function of Treg cells.

Until now, there has been no widely confirmed Treg miRNA signature (a miRNA expression pattern in Treg cells), whereas several miRNAs have been indeed linked to the abnormal development and function of Treg cells. miR-155 is up-regulated in Treg cells from MRL/lpr mice as compared to non-autoimmune mice. A reversible phenotypic alteration (CD62L−CD69+) and deficient suppressive capacity, were also noted. This altered phenotype results from up-expression of miR-155 that targets CD62L. Interestingly, a profound reduction in Dicer expression noted in Treg cells from diseased mice (seemingly contradictory to the over-expression of miR-155) implies a Dicer-independent mechanism of miRNA modification.[47] In SLE-prone mice, miR-31 appears up-regulated and miR-31 negatively regulates FOXP3 expression by directly binding to the 3′ UTR of FOXP3 mRNA. Hence, miR-31 and miR-155 contribute to SLE pathogeneses by cooperatively affecting the development and function of Treg cells.[48] Type I IFN pathway is excessively activated in SLE patients and it is correlated with deficient Treg cells. In vitro type I IFN appears to be able to inhibit the expression of Dicer and affects Treg cell-related miRNAs.[49] Cyclic adenosine monophosphate (cAMP) is critical for suppressive capacity of Treg cells.[50] miR-142-3p down-regulates adenylyl cyclase 9 (AC9) mRNA and its elevated expression leads to a decrease in cAMP levels in Treg cells and abnormal function of Treg cells.[51] Specific miRNA-targeted therapy for restoration of normal Treg cell development and function may be a novel strategy worthy of efforts in the treatment and prevention of SLE. Future work is required to establish precise and comprehensive Treg miRNA signatures and elucidate the role of miRNAs in Treg cells and SLE pathogenesis.

Interactions Between miRNAs and Other Epigenetic Factors

DNA methylation and histone acetylation can both influence the expression of miRNAs. DNA demethylation and histone deacetylase 4 (HDAC4) inhibitors can up-regulate the expression of multiple miRNAs, implicating that miRNAs are regulated by DNA methylation and histone acetylation levels.[52] In return, miRNAs regulate the expression of genes involved in DNA methylation and histone modifications. Thus miRNAs can indirectly affect these epigenetic mechanisms. miR-148a, miR-126 and miR-21 can either directly or indirectly down-regulate DNMT-1 expression and contribute to the global hypomethylation noted in SLE.[19-22] The miRNA-29 family has been identified to directly target DNMT-3A and DNMT-3B and the down-regulation of this family promotes DNA hypermethylation of some methylation-silenced tumor suppressor genes, which facilitates the occurrence of lung cancer.[53] miR-140 regulates HDAC4 expression in embryonic mouse cartilage tissue.[54] In summary, the interplay between miRNAs and other epigenetic factors has added a layer of complexity to the pathogenesis of human diseases such as SLE.


miRNAs are small, conserved and non-coding RNA molecules that modulate gene expression at the post-transcriptional level. It is becoming increasingly evident that miRNAs play a vital role in the regulation of the immune system and the initiation and/or progression of autoimmune diseases. The role of miRNAs as transcriptional modulators in the pathogenesis of SLE has recently emerged and their regulatory effects on DNA methylation pathway, type I Interferon pathway, estrogen and regulatory T-cells are becoming clear. Given the diverse involvement of miRNAs in SLE, miRNA-based therapeutic approaches are expected to provide new opportunities for patients with SLE and other autoimmune diseases.


This work was supported by grants of the National Natural Science Foundation of China (81273281, 81072452).


The two authors of this article wrote this review together. Dr Qiji Liu was responsible for modifications.