Introduction
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with various clinical manifestations affecting different tissues. It is characterized by the deposition of immune complexes due to widespread loss of immune tolerance to nuclear self-antigens, as well as by excessive proinflammatory cytokine production and damage to multiple organ systems [
1]. Recent experimental and clinical studies have placed new emphasis on the role of the innate immune system in SLE. It has become apparent that Toll-like receptors (TLRs) can participate in cell activation by self molecules such as immune complexes containing DNA or RNA. Indeed, TLRs have an important role in the pathogenesis of lupus involving recruitment of adapter proteins; activation of protein kinases and transcription factors; and expression of inflammatory cytokines, chemokines, endothelial adhesion molecules and costimulatory molecules [
2]. TLR signaling also stimulates B cell proliferation, cell differentiation and immunoglobulin class switching [
2,
3].
In the past, the importance of non-protein-coding RNAs has been emphasized in many biological and pathological processes [
4]. Much research has been focused on microRNAs (miRNAs). miRNAs are small RNA molecules with a length of approximately 22 nucleotides (nt) that play a critical role in the pathogenesis of SLE by regulating gene expression at posttranscriptional levels [
5,
6]. miRNAs have also been reported to be involved in the local inflammatory response that ultimately leads to tissue injury and organ damage [
7]. Recently, several studies have shown the feasibility of using miRNAs as biomarkers in body fluids for the diagnosis of SLE [
8-
10]. Though miRNAs play important roles in SLE, they are only a small fraction of the noncoding regions of the mammalian genome. Unlike miRNAs, long noncoding RNAs (lncRNAs) are expressed abundantly, including large intergenic noncoding RNAs (lincRNAs) [
11].
lncRNAs are a class of mRNA-like transcripts ranging in length from 200 nt to over 100 kb and lacking any significant open reading frames [
12,
13]. They are highly diverse and actively present in virtually every aspect of cell biology, such as cell differentiation, cell proliferation, DNA damage response, dosage compensation and chromosomal imprinting. Recently, a number of lncRNA molecules have been reported to be involved in diverse diseases [
14-
16]. Some evidence indicates that a few samples of lncRNAs could regulate the immune system [
17-
19]. In particular, there are several emerging hypotheses on lncRNA involvement in rheumatic diseases, such as rheumatoid arthritis (RA) [
20,
21], autoimmune thyroid disease [
22] and psoriasis [
23]. Other preliminary data in a murine model system pointed to a link between the lncRNA growth arrest–specific 5 (
GAS5) and disease susceptibility to SLE [
16]. In addition, the chromosomal locus of
GAS5, 1q25, was showed to be associated with human SLE development in genetic studies [
23-
25].
Because of the heterogeneous presentation of patients with SLE and their unpredictable disease course, there is a pressing need to identify biomarkers that will facilitate better diagnosis and prognosis, and lincRNAs as biomarkers are still largely unexplored in this regard. It has been reported that four lincRNAs (
linc0949, linc0597, linc1992 and
linc3995) not only are differentially expressed following innate activation of THP-1 macrophages but also regulate induction of proinflammatory cytokines such as tumor necrosis factor (TNF)-α and interleukin (IL)-6 [
26]. Moreover, it is well-established that
IL-6 and
TNF-α are involved in SLE pathogenesis [
27-
29].
As mentioned above, we hypothesized that these lincRNAs would produce cross-linking with SLE via innate immunity and play a critical role in the pathogenesis of SLE and that they might serve as biomarkers of disease activity, organ damage and medical response. In the present study, we aimed to investigate whether the expression levels of these lincRNAs in peripheral blood mononuclear cells (PBMCs) were abnormal in patients with SLE, assess the relationship of the levels with disease activity and organ damage, and explore new biomarkers used in disease monitoring and prognostication.
Methods
Patients and healthy controls
All samples from patients with SLE and patients with RA were obtained from the Department of Rheumatology of Renji Hospital (Shanghai, China). All patients with SLE met at least four of the American College of Rheumatology (ACR) 1982 revised criteria for SLE [
30]. Patients with RA were diagnosed according to the ACR/European League Against Rheumatism 2010 classification criteria for RA [
31]. The control group comprised healthy volunteers with no history of autoimmune disease or immunosuppressive therapy. Otherwise eligible individuals with a current or recent infection were excluded from the study. Control subjects were frequency-matched with the patients for age and sex. All participants were from the Han Chinese population. The study was approved by the Research Ethics Board of Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. Informed consent was obtained from all study participants.
The patients with lupus were all receiving steroid therapy at the time of the study, and a prednisone dosage per day (dosages of other steroids were converted to prednisone equivalents) from 2.5 mg to 500 mg (mean dosage: 29.5 mg/day). In addition, 42 patients were receiving immunosuppressive therapy (azathioprine (AZA; n = 7), cyclophosphamide (CYC; n = 10), cyclosporine A (CsA; n = 6), tacrolimus (FK506; n = 1), leflunomide (LEF; n = 2), mycophenolate mofetil (MMF; n = 8), methotrexate (MTX; n = 8)), and 59 were receiving an antimalarial drug (chloroquine or hydrochloroquine). For each patient, the severity of disease was assessed with the Systemic Lupus Erythematosus Disease Activity Index 2000 (SLEDAI-2K) [
32]. Organ damage (defined as nonreversible change, not related to active inflammation, occurring since the onset of lupus and present for at least 6 months) was assessed using the Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index (SDI) score [
33]. In our cohort, nearly 51.0% of patients (52 of 102 patients with SLE) had either previous or current lupus nephritis (LN) (Table
1). Subjects were considered to have active renal disease if proteinuria was ≥0.5 g/day, hematuria was ≥5 red blood cells per high-power field (hpf), pyuria was ≥5 white blood cells/hpf or cellular casts were present. Infection, kidney stones and other causes were excluded.
Table 1
Large intergenic noncoding RNA
linc0949
by presence or absence of clinical features of systemic lupus erythematosus
a
Renal | 50 | 2.16 ± 0.152 | 52 | 1.47 ± 0.132 | 0.0014 |
Rash | 33 | 1.89 ± 0.200 | 69 | 1.87 ± 0.199 | NS |
Arthritis | 35 | 1.79 ± 0.327 | 67 | 1.97 ± 0.163 | NS |
Serositis | 21 | 1.81 ± 0.307 | 81 | 1.72 ± 0.364 | NS |
Mucosal ulcer | 19 | 2.02 ± 0.207 | 83 | 1.87 ± 0.187 | NS |
Hematologic | 30 | 1.84 ± 0.243 | 72 | 2.06 ± 0.179 | NS |
Neurologic | 9 | 1.99 ± 0.084 | 93 | 2.05 ± 0.45 | NS |
Autoantibodies | | | | | |
| Anti-dsDNA | 40 | 1.91 ± 0.274 | 62 | 1.88 ± 0.264 | NS |
| Anti-Sm | 16 | 2.07 ± 0.202 | 86 | 1.78 ± 0.193 | NS |
| Anti-nucleosome | 40 | 1.91 ± 0.204 | 62 | 1.88 ± 0.212 | NS |
| Anti-SSA/SSB | 32 | 2.03 ± 0.258 | 70 | 2.01 ± 0.176 | NS |
| Anti-RNP | 22 | 1.95 ± 0.253 | 80 | 1.96 ± 0.165 | NS |
Medical therapy | | | | | |
| Prednisone dose ≥30 mg/day | 48 | 2.08 ± 0.175 | 54 | 1.94 ± 0.181 | NS |
| Immunosuppressantsb
| 42 | 2.00 ± 0.141 | 60 | 1.54 ± 0.151 | 0.0365 |
Peripheral blood samples handling and RNA processing
Peripheral blood samples (10 ml) were obtained from each subject. The samples were collected in tubes containing ethylenediaminetetraacetic acid (EDTA). PBMCs were isolated from anticoagulated whole blood by use of Ficoll density gradient centrifugation. Then total RNA was extracted from PBMCs using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The integrity of the RNA was assessed using capillary gel electrophoresis, and the concentrations of RNA were measured using a NanoDrop™ 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) with a 260 nm/280 nm ratio above 1.8. About 200 ng of total RNA were reverse-transcribed into cDNA using a PrimeScript RT reagent kit (Takara Bio, Dalian, China). All RNA and cDNA samples were stored at −70°C before use.
Cell culture and stimulation
Peripheral blood samples were obtained from five healthy donors and five patients with SLE. The samples were collected in tubes containing EDTA. PBMCs were isolated from anticoagulated whole blood by Ficoll density gradient centrifugation. Two hours before stimulation, 1 × 106 PBMCs were cultured in 24-well flat-bottomed plates in 500 μl of RPMI 1640 medium containing 10% fetal bovine serum (FBS). Then the PBMCs were stimulated for 4 hours with the TLR2 ligand Pam3CK4 (20 ng/ml).
Cell culture and treatment with dexamethasone and immunosuppressant agents
Peripheral blood samples were obtained from two healthy donors. PBMCs were isolated from anticoagulated whole blood by use of Ficoll density gradient centrifugation. PBMCs (1 × 106) were resuspended for 2 hours in 500 μl of RPMI 1640 medium containing 10% FBS, then dexamethasone was added with the indicated concentration (Dexamethasone concentrations were 10ng/ml,100ng/ml,1000ng/ml,10ug/ml, respectively) for another 24 hours, as were CsA (200 nmol) and FK506 (20 nmol). RNA samples were then isolated, and real-time quantitative PCRs (RT-qPCRs) were performed.
Real-time quantitative polymerase chain reaction
To quantify the expression of four lincRNAs (
linc0949, linc0597, linc1992 and
linc3995), cDNA was amplified by RT-PCR with SYBR Green (SYBR Premix Ex Taq RT-PCR kit; Takara Bio). The primer sequences used for SYBR Green–based RT-PCR are given in Table
2. The ribosomal protein L13A (
RPL13A) gene was used as an internal control to normalize the amounts of cDNA. The SYBR Green assays were performed in duplicate using an ABI ViiA 7 Real-Time PCR System (Applied Biosystems, Foster City, CA, USA). The relative expression levels were calculated using the 2
−ΔCt comparative threshold cycle method.
Table 2
Primers used to amplify transcripts of large intergenic noncoding RNAs
a
RPL13A
| 5′-CTGGAGGAGAAGAGGAAAGAGA-3′ | 5′-TTGAGGACCTCTGTGTATTTGTCAA-3′ |
ENST00000500597
| 5′-TTGGATTCATCCCGTTCACCTCCA-3′ | 5′-CAGCATGACGATCAAGCGAGATTC-3′ |
ENST00000501992
| 5′-AACTCCTGACCTCAGGTGATCCAT-3′ | 5′-AAGGGAGTTTCAGAAGGTGTGGCT-3′ |
ENST00000500949
| 5′-TCCTGCAACCCAAGGTGGATACTT-3′ | 5′-CTGCAGTGAGCAGAAATCACGCAT-3′ |
ENST00000523995
| 5′-GTTTGTGGCATATGGCTCTGCTGT-3′ | 5′-CATTGCAGGAAAGAGTGCCAAGGT-3′ |
Statistical analysis
Data were analyzed with GraphPad Prism version 5.0 software (GraphPad Software, La Jolla, CA, USA). The nonparametric Mann–Whitney
U test was used to compare gene expression between two groups. The correlation between groups was evaluated using Spearman’s rank correlation coefficient test. The strength of the correlation was graded using Cohen’s criteria as follows: 0.3 to 0.5 = weak, 0.5 to 0.7 = moderate and >0.7 = strong [
34].
P-values (two-tailed) <0.05 were considered statistically significant.
Discussion
In recent years, an increasing body of evidence has shown that lncRNAs play major biological roles in embryogenesis, stem cell biology and cellular development and show developmental and tissue-specific expression patterns [
11,
38,
39]. Studies have also suggested that abnormal expression of lncRNAs might be associated with numerous diseases, indicating that these RNAs may open a new avenue for diagnostic and therapeutic targets by recognition of their roles in human disease.
In the present study, we detected four lincRNAs (
linc0949,
linc0597,
linc1992 and
linc3995) and investigated the association between their expression levels and specific clinical features of SLE. Two of these lincRNAs (
linc0949 and
linc0597) were significantly decreased in patients with SLE compared with healthy donors and disease controls.
linc0949 was associated with disease activity, as assessed using the SLEDAI-2K score and C3 level in patients with SLE. Moreover,
linc0949 expression was reduced in patients with SLE with ongoing or cumulative organ damage, as assessed based on SDI score or the presence of active LN.
linc0949 expression does not participate in clinical manifestations other than LN, which demonstrates that it has very good detection specificity for LN. Lower levels of
linc0949 may thus be helpful to identify patients with SLE who have active and severe disease. To evaluate the effect of antirheumatic drugs on the expression of
linc949, we used
in vitro studies to test whether the addition of dexamethasone, CsA or FK506 to cultured PBMCs would affect the expression of
linc0949. As shown in Figure
4C, these antirheumatic drugs did not affect the expression of
linc0949 in PBMCs, which confirmed that
linc0949 was intrinsically underexpressed in patients with SLE.
linc0949 expression of three patients with severe disease flares significantly increased after treatment (Figure
4D), indicating that
linc0949 might be responsive to treatment and might change in conjunction with disease activity and severity and suggesting that
linc0949 might be used to monitor disease progression and guide therapy.
Over the past several decades, tremendous enthusiasm and efforts have been devoted to biomarkers for SLE because the diagnosis of SLE requires a combination of clinical manifestations and biomarkers and no single test is sufficiently sensitive and specific to be diagnostic. The traditional antibodies fail to identify the pathogenic processes, organ damage and biological responses to a therapeutic intervention. Many groups, including the members of our laboratory, have found a set of potential biomarkers for SLE. For example, interferon (IFN)-induced genes and IFN-inducible chemokines may serve as new biomarkers for active and severe disease in patients with SLE [
40,
41]. Some limitations of these biomarkers are revealed gradually, however. Several studies have shown that overexpressed transcripts of the type I IFN pathway are also identified in patients with myositis, RA, Sjögren’s syndrome and scleroderma [
42-
44], so an IFN signature or chemokine is not sufficiently specific. In two longitudinal studies to date, researchers have reported conflicting results on the correlations between type I IFN gene signature score and diseases activity [
45,
46]. There is an urgent need for SLE biomarkers that can help enhance comprehension of the mechanisms of diseases or effects of therapies by relating the changes of molecular and cellular pathways to disease status or clinical responses. In our present study, we demonstrate that lower expression of
linc0949 is specific for SLE and that it is helpful in identifying disease activity, monitoring disease progression and guiding therapy. However,
linc0949 needs to be further investigated in large-scale multicenter trials.
On the basis of our present observations, we believe that
linc0949 could be a potentially readily accessible biomarker useful for diagnosing SLE. As a novel biomarker, lincRNAs have the following characteristics. First, lincRNAs display a wide range of stabilities in the samples comparable to those of mRNAs of protein-coding genes [
47]. Second, they show a greater tissue specificity compared with protein-coding mRNAs and miRNAs, which are frequently expressed in multiple tissues, and they show highly increased or decreased expression levels in disease [
15]. In addition, lincRNAs are also detectible in body fluids such as plasma and urine [
48-
50], diagnostic samples of which are easy to collect using noninvasive methods. Moreover, detection of the lincRNAs is simple, inexpensive and has high throughput, making it a suitable approach to gaining an overview of disease activity and severity in patients with SLE. These features make lincRNAs very suitable as biomarkers, and many studies have been published on this matter in recent years, both in cancer and in other human diseases such as cardiovascular diseases [
50] and neurological disorders [
51].
Most lncRNAs described to date have been found to be related to transcriptional regulation or mRNA processing, characteristics that they share with microRNAs. However, unlike microRNAs, lncRNAs show a greater complexity of their functions and have a wider spectrum of biological contexts, such as epigenetic regulation, enhancer-like function and RNA splicing, editing and export [
52]. In our ongoing experiments, we found that
linc0949 and
linc0597 could be induced by TLR2 in PBMCs of healthy donors, but they did not respond to the stimuli in patients with SLE as compared with healthy donors (Figure
5). These results validate that lincRNAs were indeed involved in the complex regulatory network of innate immunity. We hypothesized that the regulation defect of
linc0949 and
linc0597 could contribute to the pathogenesis of SLE and that lincRNAs may provide potential novel strategies for therapeutic intervention, although their function and mechanism of action need further exploration.
We have suggested the abnormal expression of linc0949 in patients with SLE, as well as the association of lincRNA level with disease activity and organ damage; however, in this study, we did not conduct a functional study of this lincRNA, and the underlying mechanism needs further investigation. We did not detect the expression of linc0949 released in the local target tissues and in specific cell subsets in PBMCs. Future studies are needed to investigate the lincRNA expression level in specific organ and cell types as well.
Competing interests
The authors declare that they have no competing interests.
Authors’ contributions
YFW, YJT and NS conceived of and designed the experiments and analyzed the data. YFW, FFZ, YJT and NS wrote the paper. YFW, FFZ, JYM, XYZ, LLW, BQ, SWX and SLC performed the experiments, collected blood samples and contributed reagents, materials and analytic tools. JYM, XYZ, LLW, BQ, SWX and SLC helped to draft the manuscript. All authors read and approved the final manuscript.