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Research Papers:

Functional polymorphisms in pre-miR146a and pre-miR499 are associated with systemic lupus erythematosus but not with rheumatoid arthritis or Graves’ disease in Mexican patients

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Oncotarget. 2017; 8:91876-91886. https://doi.org/10.18632/oncotarget.19621

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Isidro Alemán-Ávila, Mayra Jiménez-Morales, Olga Beltrán-Ramírez, Rosa Elda Barbosa-Cobos, Silvia Jiménez-Morales, Fausto Sánchez-Muñoz, Guillermo Valencia-Pacheco, Luis M. Amezcua-Guerra, Yaneli Juárez-Vicuña, Dulce Milagro Razo-Blanco Hernández, María Concepción Aguilera-Cartas, Ricardo F. López-Villanueva, Oscar Peralta-Zaragoza, Carlos Tovilla-Zárate and Julian Ramírez-Bello _

Abstract

Isidro Alemán-Ávila1,2, Mayra Jiménez-Morales1, Olga Beltrán-Ramírez1, Rosa Elda Barbosa-Cobos3, Silvia Jiménez-Morales4, Fausto Sánchez-Muñoz5, Guillermo Valencia-Pacheco6, Luis M. Amezcua-Guerra5, Yaneli Juárez-Vicuña5, Dulce Milagro Razo-Blanco Hernández7, María Concepción Aguilera-Cartas8, Ricardo F. López-Villanueva9, Oscar Peralta-Zaragoza10, Carlos Tovilla-Zárate11 and Julian Ramírez-Bello1

1Endocrine and Metabolic Disease Unit Research, Hospital Juarez of Mexico, Mexico City, Mexico

2Superior School of Medicine Postgraduate Program, National Polytechnic Institute, Mexico City, Mexico

3Rheumatology Department, Hospital Juarez of Mexico, Mexico City, Mexico

4Laboratory of Cancer Genomics, National Institute of Genomic Medicine, Mexico City, Mexico

5Immunology Department, National Institute of Cardiology, Mexico City, Mexico

6Hematology Laboratory, Regional Research Center, Autonomous University of Yucatan, Yucatan, Mexico

7Research Direction, Hospital Juarez of Mexico, Mexico City, Mexico

8Endocrinology Department, Hospital Juarez of Mexico, Mexico City, Mexico

9Rheumatology Department, Regional Hospital General (ISSSTE), Health Service Yucatan, Yucatan, Mexico

10Direction of Chronic Infections and Cancer, Research Center in Infection Diseases, National Institute of Public Health, Cuernavaca, México

11Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco, Mexico

Correspondence to:

Julian Ramírez-Bello, email: [email protected]

Keywords: systemic lupus erythematosus, rheumatoid arthritis, Graves’ disease, microRNA gene, susceptibility

Received: December 21, 2016     Accepted: June 30, 2017     Published: July 27, 2017

ABSTRACT

Recently, different microRNA (miRNA) gene polymorphisms have been evaluated in patients with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and Graves’ disease (GD). In the present study, we examined three single-nucleotide polymorphisms (SNPs) located in the pre-miR-146a (rs2910164G/C), pre-miR-196a-2 (rs11614913C/T), and pre-miR-499 (rs3746444A/G) genes. Our study population included 900 Mexican patients with RA, SLE, or GD, as well as 486 healthy control individuals with no family history of inflammatory or autoimmune diseases. Genotyping was performed using TaqMan probes and a 5′ exonuclease assay. None of the investigated SNPs were associated with RA or GD susceptibility under any genetic model (co-dominant, recessive, or dominant). Genotype and allele frequencies of the miR-196a-2 rs11614913C/T polymorphism were similar between SLE cases and controls. In contrast, the miR-146a rs2910164G/C and miR-499 rs3746444A/G polymorphisms were associated with SLE susceptibility. These SNPs were not associated with lupus nephritis (LN). Our results suggest that polymorphisms in miR-146a, miR-196a-2, and miR-499 are not associated with RA or GD susceptibility. This is the first report documenting that the miR-146a rs2910164G/C and miR-499 rs3746444 polymorphisms are associated with SLE susceptibility but not with LN.


INTRODUCTION

Autoimmune diseases (AIDs) constitute a heterogeneous group of pathologies characterized by loss of immunological tolerance, production of autoantibodies, and increased expression of cytokines with inflammatory activity [1]. In the United States, AIDs affect about 5–8% of the general population, with most showing a higher prevalence in women than in men [2]. Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease characterized by synovial inflammation, which leads to joint tissue destruction and functional disability [3]. Systemic lupus erythematosus (SLE) is the prototype of a multi-systemic AID, and is characterized by loss of immunological tolerance against self-antigens and production of pathogenic autoantibodies, ultimately resulting in damage to multiple organ systems [4]. Graves’ diseases (GD) is an organ-specific AID, in which the major antigenic target is the thyroid-stimulating hormone receptor (TSHR). TSHR-autoantibodies bind to TSHR, mimicking the action of its ligand (TSH) and causing hyperthyroidism [5].

Although the etiologies of RA, SLE, and GD remain unclear, the identified risk factors include gender; genetic background; and environmental agents, such as geography, climate, endemic microbes, and socio-cultural practices, including smoking, lifestyle, and dietary habits [67]. Investigations using a candidate gene approach and genome-wide association studies have demonstrated that RA, SLE, and GD susceptibility is conferred by different variants of protein-coding genes, including HLA-class II, PTPN22, TNFAIP3, STAT4, TNFRSF14, BLK, and TRAF1 [810]. Genetic risk factors for these AIDs may also include single-nucleotide polymorphisms (SNPs) in non-coding RNA genes, including the microRNAs (miRNAs) 146a, miR-196a-2 and miR-499 [1117].

RNA polymerase II initially transcribes miRNA genes, producing primary miRNAs (pri-miRNAs) of approximately 2 kb in length. In the nucleus, these pri-miRNAs are processed by RNase III Drosha and the DiGeorge syndrome chromosomal region 8, Microprocessor Complex Subunit (DGCR8; DiGeorge syndrome chromosomal region 8) protein, generating a precursor miRNA (pre-miRNA) of approximately 100 bp. These pre-miRNAs are transported from the nucleus to the cytoplasm via exportin-5. In the cytoplasm, pre-miRNAs are cleaved by the RNase III enzyme Dicer, in complex with the human immunodeficiency virus transactivating response RNA-binding protein (TRBP), ultimately forming small non-coding RNAs of approximately 19–22 nucleotides, termed mature miRNAs [1822]. Mature miRNAs function in the negative regulation of gene expression, acting at the post-transcriptional level by binding to the 3′ untranslated region (3′UTR) of target messenger RNAs (mRNAs), thus preventing their translation into proteins [2225].

Various miRNAs play important roles in regulating a wide array of biological functions, including proliferation, apoptosis, differentiation, immune response, and inflammation [2227]. With regards to AIDs, miR-146a is abnormally expressed in RA-affected tissues, including synovial fibroblasts, synovial tissue, serum, and peripheral blood mononuclear cells (PBMCs) [2833]. This miRNA also shows abnormal expression in PBMCs and monocytes from SLE patients [33, 34], and in PBMCs from patients with Graves’ ophthalmopathy (GO). Moreover, patients with active GO show lower serum miR-146a levels than those with inactive GO [35, 36]. Both miR-196a and miR-499 are thought to be involved in autoimmune and inflammatory diseases, because they promote the expressions of several relevant proteins, including interleukin (IL)-23a, IL-6, IL-2, C-reactive protein, IL-18R, and IL-2R. Thus, both miRNAs could potentially contribute to the pathogenesis and disease progression of several AIDs [3739].

Functional SNPs located in miRNA genes (miR-SNPs) could potentially affect pri-miRNA transcription or pri-miRNA/pre-miRNA processing, or could disrupt miRNA–mRNA interactions if located in the mature miRNA sequence or in miRNA binding sites [4042]. The functional miR-SNP rs2910164G/C, located in pre-miR-146a, has been evaluated in RA patients from different populations, yielding controversial results. Yang et al. [11], Hashemi et al. [12], and El-Shal et al. [13] reported that this polymorphism was not associated with RA susceptibility; however, Zhou et al. [43] found that the GG genotype was significantly associated with RA among women. This SNP has not been associated with SLE or GD susceptibility in patients from different populations [16, 44, 45]. Another functional miR-SNP, miR-499 rs3746444A/G, is reportedly associated with RA susceptibility, severity, and disease activity in Iranian and Egyptian populations, but not in a Chinese population [1113, 46]. This polymorphism also showed no association with SLE susceptibility in a Chinese population [44]; however, it was recently found to be associated with GD susceptibility in a Chinese population [16]. The functional miR-196a-2 rs11614913C/T SNP has only been evaluated in Egyptian patients with RA, and no evidence of association was detected [46].

In the present case-control study, we evaluated whether the polymorphisms pre-miR-146a rs2910164G/C, pre-miR-196a-2 rs11614913C/T, and pre-miR-499 rs3746444A/G conferred risk for RA, SLE, and GD in a sample of Mexican patients. We also evaluated whether these polymorphisms were associated with lupus nephritis (LN).

RESULTS

Demographic features of cases and controls

This study included 900 patients with AIDs: 412 with RA (378 female, 34 male), 407 with SLE (384 female, 23 male), and 81 with GD (72 female, 9 male). The study also included 486 healthy control individuals (431 female, 55 male). Table 1 presents demographic features of the RA, SLE, and GD patients, and the controls.

Table 1: Demographic characteristics of the patients with RA, SLE and GD from Mexico included in this study

 

Controls (n=486)

RA (n=412)

SLE (n=407)

GD (n=81)

Age (years)

50.9

51.8

39.9

36.2

SD *

(±7.3)

(±13.6)

(±12.6)

(±10.8)

Gender:

 

 

 

 

Female n (%)

431 (88.7)

378 (91.7)

384 (94.3)

72 (88.9)

Male n (%)

55 (11.3)

34 (8.3)

23 (5.7)

9 (11.1)

*SD: standard deviation; RA: rheumatoid arthritis; SLE: systemic lupus erythematosus; GD: Graves’ disease.

Hardy-Weinberg equilibrium (HWE) in the study population

In this case-control study, the genotype frequencies of the miR-146a rs2910164G/C, miR-196a-2 rs11614913C/T, and miR-499 rs3746444A/G polymorphisms were in HWE (Tables 2-4).

Table 2: Genotype and allelic frequencies of the miR-146a rs2910164G/C polymorphism and association analysis in RA, SLE and GD patients

SNP ID

Population

Allele

Genotype n (%)

 

 

 

Allele n (%)

 

 

 

12

11

12

22

OR (11vs22)

95% CI

p

1

2

OR (1vs2)

95% CI

p

miRNA146a

Controls

G C

218(44.9)

222(45.7)

46(9.4)

658(67.7)

314(32.3)

(rs2910164)

RA*

 

168(41.0)

196(47.8)

46(11.2)

1.3

(0.82-2.04)

0.261

532(64.9)

288(35.1)

1.1

(0.93-1.38)

0.208

 

SLE

 

168(41.3)

179(44.0)

60(14.7)

1.7

(1.09-2.61)

0.017

515(69.2)

229(30.8)

1.2

(1.00-1.48)

0.049

 

GD

 

29(35.8)

44(54.3)

8(9.9)

1.3

(0.56-3.04)

0.53

102(63.0)

60(37.0)

1.2

(0.87-1.74)

0.235

OR: odds ratio; CI: confidence interval; p: p value; RA: rheumatoid arthritis; SLE: systemic lupus erythematosus; GD: Graves’ disease.

Significant p-values are reported in bold type.

H-WE p values to controls (p=0.33), RA (p=0.32), SLE (p=0.28), and GD (p=0.14).

* Two RA samples were not genotyped.

Table 3: Genotype and allelic frequencies of the miR-196a-2 rs11614913C/T polymorphism and association analysis in RA, SLE, GD patients and controls

SNP ID

Population

Allele

Genotype n (%)

 

 

 

Allele n (%)

 

 

 

12

11

12

22

OR (11vs22)

95% CI

p

1

2

OR (1vs2)

95% CI

p

miRNA196a2

Controls

C T

182(37.5)

230(47.3)

74(15.2)

594(61.1)

378(38.9)

(rs11614913)

RA

 

142(34.5)

213(51.7)

57(13.8)

1.0

(0.66-1.49)

0.951

497(60.3)

327(39.7)

1.0

(0.86-1.25)

0.731

 

SLE*

 

155(38.3)

189(46.7)

61(15.0)

1.0

(0.65-1.44)

0.873

499(61.6)

311(38.4)

1.0

(0.81-1.19)

0.831

 

GD**

 

28(35.0)

39(48.8)

13(16.2)

1.1

(0.56-2.32)

0.714

95(59.4)

65(40.6)

1.1

(0.76-1.51)

0.676

OR: odds ratio; CI: confidence interval; p: p value; RA: rheumatoid arthritis; SLE: systemic lupus erythematosus; GD: Graves’ disease.

H-WE p values to controls (p=0.93), RA (p=0.10), SLE (p=0.79), and GD (p=0.93).

* Two SLE samples were not genotyped. * One GD sample was not genotyped.

Table 4: Genotype and allelic frequencies of the miR-499 rs3746444A/G polymorphism and association analysis in RA, SLE, GD patients and controls

SNP ID

Population

Allele

Genotype n (%)

 

 

 

Allele n (%)

 

 

 

12

11

12

22

OR (11vs22)

95% CI

p

1

2

OR (1vs2)

95% CI

p

miRNA499

Controls

A G

425(87.5)

60(12.3)

1(0.2)

--

--

--

910(93.6)

62(6.4)

--

--

--

(rs3746444)

RA

 

352(85.4)

57(13.8)

3(0.8)

1.2

(0.77-1.69)

0.489

761(92.4)

63(7.6)

1.2

(0.84-1.74)

0.293

 

SLE

 

336(82.6)

71(17.4)

0(0%)

1.5

(1.03-2.17)

0.033

743(91.3)

71(8.7)

1.4

(0.98-2.00)

0.060

 

GD

 

69(85.2)

12(14.8)

0(0%)

1.2

(0.63-2.40)

0.541

150(92.6)

12(7.4)

1.2

(0.62-2.23)

0.623

OR: odds ratio; CI: confidence interval; p: p value; RA: rheumatoid arthritis; SLE: systemic lupus erythematosus; GD: Graves’ disease.

Significant P-values are reported in bold type.

H-WE p values to controls (p=0.46), RA (p=0.68), SLE (p=0.054), and GD (p=0.47).

Case-control genetic association analysis

The statistical power values were 93.4% for RA, 93.3% for SLE, and 34.3% for GD. The genotype and allele frequencies of the miR-146a rs2910164G/C, miR-196a-2 rs11614913C/T, and miR-499 rs3746444A/G polymorphisms were similar between RA and GD patients and controls. Case-control analysis revealed no association between these three SNPs and RA or GD susceptibility, even when using recessive and dominant genetic models (Tables 2-7). Genotype and allele frequencies of the miR-196a-2 rs11614913C/T SNP were also similar between SLE patients and controls. However, the miR-146a rs2910164G/C and miR-499 rs3746444A/G polymorphisms were associated with SLE susceptibility (Tables 2 and 4). Comparison of the miR-146a rs2910164G/C and miR-499 rs3746444A/G polymorphisms between SLE patients and controls revealed associations with SLE susceptibility under both the recessive and dominant genetic models (Tables 5 and 7). None of the investigated SNPs showed association with LN (Table 8). Analysis with gender stratification showed no association between the three analyzed polymorphisms and RA, SLE, or GD (data not shown).

Table 5: Association analysis between the miR-146a rs2910164G/C polymorphism in RA, SLE and GD patients under different genetic models

Recessive model

SNP ID

Genotypes

Controls

RA

OR, 95 % CI, p

SLE

OR, 95 % CI, p

GD

OR, 95 % CI, p

miR-146ª (rs2910164) G/C

GG + GC

440 (90.5)

364 (88.8)

347 (85.3)

73 (90.1)

 

CC

46 (9.5)

46 (11.2)

1.2

60 (14.7)

1.7

8 (9.9)

1.0

 

 

 

(0.78-1.86)

 

(1.10-2.49)

 

(0.48-2.31)

 

 

 

0.389

 

0.015

 

0.907

Dominant model

Genotypes

Controls

RA

OR, 95 % CI, p

SLE

OR, 95 % CI, p

GD

OR, 95 % CI, p

GG

218 (44.9)

168 (41.0)

168 (41.3)

29 (35.8)

GC + CC

268 (55.1)

242 (59.0)

1.2

239 (58.7)

1.2

52 (64.2)

1.5

 

 

 

(0.90-1.53)

 

(0.89-1.51)

 

(0.84-2.38)

 

 

 

0.243

 

0.282

 

0.128

OR: odds ratio; CI: confidence interval; p: p value; RA: rheumatoid arthritis; SLE: systemic lupus erythematosus; GD: Graves’ disease.

Significant P-values are reported in bold type.

Table 6: Association analysis between the miR-196a-2 rs11614913C/T polymorphism in RA, SLE and GD patients under different genetic models

Recessive model

SNP ID

Genotypes

Controls

RA

OR, 95 % CI, p

SLE

OR, 95 % CI, p

GD

OR, 95 % CI, p

miR-196a-2 (rs11614913) C/T

CC + CT

412 (84.8)

355 (86.2)

344 (84.9)

67 (83.8)

 

TT

74 (15.2)

57 (13.8)

0.89

61 (15.1)

0.99

13 (16.2)

1.31

 

 

 

(0.62-1.30)

 

(0.68-1.43)

 

(0.68-2.53)

 

 

 

0.556

 

0.946

 

0.409

Dominant model

Genotypes

Controls

RA

OR, 95 % CI, p

SLE

OR, 95 % CI, p

GD

OR, 95 % CI, p

CC

182 (37.4)

142 (34.5)

155 (38.3)

28 (35.0)

CT + TT

304 (62.6)

270 (65.5)

1.14

250 (61.7)

0.97

52 (65.0)

1.10

 

 

 

(0.87-1.50)

 

(0.74-1.27)

 

(0.68-1.82)

 

 

 

0.354

 

0.800

 

0.674

OR: odds ratio; CI: confidence interval; p: p value; RA: rheumatoid arthritis; SLE: systemic lupus erythematosus; GD: Graves’ disease.

Table 7: Association analysis between the miR-499 rs3746444A/G polymorphism in RA, SLE and GD patients under different genetic models

Recessive model

SNP ID

Genotypes

Controls

AR

OR, 95 % CI, p

SLE

OR, 95 % CI, p

GD

OR, 95 % CI, p

miR-499 (rs3746444) A/G

AA – AG

485 (99.8)

409 (99.3)

407 (100)

81 (100)

 

GG

1 (0.2)

3 (0.7)

3.55

0 (0.0)

0 (0.0)

 

 

 

(0.36-34.3)

 

 

 

 

 

0.24

 

 

 

 

Dominant model

Genotypes

Controls

AR

OR, 95 % CI, P

SLE

OR, 95 % CI, P

GD

OR, 95 % CI, p

AA

425 (87.5)

352 (85.4)

336 (82.5)

69 (85.2)

AG - GG

61 (12.5)

60 (14.6)

1.18

71 (17.5)

1.47

12 (14.8)

1.21

 

 

 

(0.81-1.74)

 

(1.02-2.13)

 

(0.62-2.36)

 

 

 

0.379

 

0.040

 

0.573

OR: odds ratio; CI: confidence interval; p: p value; RA: rheumatoid arthritis; SLE: systemic lupus erythematosus; GD: Graves’ disease.

Significant P-values are reported in bold type.

Table 8: Association analysis of polymorphisms in pre-miR-146a, pre-miR-196a-2 and pre-miR-499 genes in patients with SLE; no nephritis vs nephritis

Gene SNP

No nephritis

Lupus nephritis

OR

95% CI

p

miR-146a

n=112 (%)

n=90 (%)

 

 

 

rs2910164

 

 

 

 

 

Genotype

 

 

 

 

 

GG

41 (36.6)

38 (42.3)

GC

47 (42.0)

40 (44.4)

0.92

0.50-1.69

0.784

CC

24 (21.4)

12 (13.3)

0.54

0.24-1.23

0.139

Allele

 

 

 

 

 

G

129 (57.6)

116 (64.4)

C

95 (42.4)

64 (35.6)

0.75

0.50-1.12

0.161

miR-196a-2

n=112 (%)

n=90 (%)

 

 

 

rs11614913

 

 

 

 

 

Genotype

 

 

 

 

 

CC

46 (41.1)

38 (42.3)

CT

44 (39.3)

40 (44.4)

1.10

0.60-2.02

0.757

TT

22 (19.6)

12 (13.3)

0.66

0.29-1.51

0.322

Allele

 

 

 

 

 

C

136 (60.7)

116 (64.4)

T

88 (39.3)

64 (35.6)

0.85

0.57-1.28

O.442

miR-499

n=112 (%)

n=90 (%)

 

 

 

rs3746444

 

 

 

 

 

Genotype

 

 

 

 

 

AA

94 (83.9)

77 (85.6)

AG

18 (16.1)

13 (14.4)

0.88

0.41-1.91

0.750

GG

0 (0.0)

0 (0.0)

1.22

0.02-62.16

1.000

Allele

 

 

 

 

 

A

206 (92.0)

167 (92.8)

G

18 (8.0)

13 (7.2)

0.89

0.42-1.87

0.760

OR: odds ratio; CI: confidence interval; p: p value; SLE: systemic lupus erythematosus.

DISCUSSION

In this study, we evaluated the miR-146a rs2910164G/C, miR-196a-2 rs11614913C/T, and miR-499 rs3746444A/G polymorphisms with regards to their potential associations with RA, SLE, and GD susceptibility in a sample of Mexican patients. Our results revealed that the miR-146a rs2910164G/C and miR-499 rs3746444 polymorphisms were associated with susceptibility to SLE.

Several recent studies have also evaluated the miR-146a rs2910164G/C, miR-196a-2 rs11614913C/T, and miR-499 rs3746444A/G polymorphisms in patients with RA, SLE, and GD [1113, 16, 4346]. Zhou et al. [43] found that the GG genotype of miR-146a rs2910164G/C was significantly associated with RA among women. In contrast, we found no association between this SNP and RA susceptibility, before or after gender stratification analysis. Our findings are in accordance with other published studies, including previous investigations in Mexican patients with juvenile rheumatoid arthritis [1113, 47, 48]. The discrepancy between studies may be at least partly explained by differences in ancestry between studied populations.

The miR-146a rs2910164G/C SNP has also been evaluated in Chinese and Sweden populations with SLE, and was not found to be associated with SLE susceptibility in either group [44, 45]. Our present study is the first to document an association between miR-146a rs2910164G/C and SLE susceptibility (OR 1.7, 95% CI 1.09–2.61, p = 0.017). This polymorphism was also previously evaluated in Mexican patients with pediatric SLE, and no association with susceptibility was identified [48]. This discrepancy could be explained by the genetic differences between adult and pediatric SLE patients. For example, investigations of the PTPN22 R620W and TNF-α −308G/A SNPs in adult Mexican patients with SLE have revealed no associations with susceptibility [49, 50], even though both of these SNPs are associated with SLE susceptibility among pediatric SLE patients [51, 52]. Our study is only the second to evaluates the association between miR-146a rs2910164G/C and GD, and we found no association, which is in agreement with the results published by Cai et al. [16].

The functional rs2910164C allele affects the processing and maturation of miR-146a, decreasing generation of the mature form compared to with the G allele [53]. Moreover, computational tools predict that the C allele causes mispairing within the mature hairpin [53, 54]. The resulting reduction of functional miR-146a could contribute to the pathogenesis of SLE and other AIDs [55, 56]. In mice, miR-146a loss causes spontaneous autoimmunity [57]. MiR-146a negatively regulates the type I interferon (IFN) pathway by targeting IRF5, STAT1, IRAK1, TRAF6, and others. A decrease of miR-146a level results in increases of type I IFN and pro-inflammatory cytokines, such as IL-1β and TNF-α, which are involved in the pathogenesis of various AIDs [58, 59].

The miR-196a-2 rs11614913C/T polymorphism alters the expression of mature miR-196a and binds to target mRNAs, and this SNP is associated with reduced survival time in patients with non-small-cell lung cancer [60]. A recent evaluation of the miR-196a-2 rs11614913C/T SNP in RA patients from Egypt found no evidence for association [46], and our present results were in accordance with this finding. Our present study is the first to evaluate this SNP in a population with SLE or GD, and we found no association of this SNP with SLE or GD susceptibility in a Mexican population. This polymorphism should be further investigated in other populations with different ancestries to assess its potential role in RA, SLE, and GD susceptibility.

Three prior studies in Iranian and Egyptian populations report that the miR-499 rs3746444A/G polymorphism is associated with RA susceptibility, severity, and disease activity; however, no such associations were found in a Han Chinese population [1113, 46]. Our present findings showed that the miR-499 rs3746444A/G polymorphism was not associated with RA susceptibility, in line with the findings in a Chinese population [11], and in contrast to the results in Iranian and Egyptian populations [12, 13, 46]. This discrepancy may be related to the differing ancestral backgrounds of the studied populations or to the small sample size. On the other hand, this polymorphism was recently found to be associated with GD susceptibility in Chinese population, while our present results showed no association of this SNP with GD. One major limitation of our present study was the small sample size of GD patients (n = 81) compared to the GD patient sample size in the study by Cai et al. (n = 701) [16].

Notably, our present study identified an association between the miR-499 rs3746444A/G polymorphism and SLE susceptibility (AA vs AG; OR 1.5, 95% CI 1.03–2.17, p = 0.033). In contrast, a prior study in a Chinese population showed no association between SLE susceptibility and miR-499 rs3746444A/G [44]. Thus, our present report is the first to document an association between miR-499 rs3746444A/G and SLE susceptibility. This polymorphism was also investigated in Mexican patients with pediatric SLE, with no detected association. As discussed above, this discrepancy may be explained by genetic background differences between pediatric and adult SLE patients. LN is a major cause of morbidity and mortality in SLE [61]; thus, we evaluated whether the miR-146a rs2910164G/C, miR-196a-2 rs11614913C/T, and miR-499 rs3746444A/G polymorphisms were associated with LN. Our data showed no association, indicating that these miR-SNPs likely do not confer LN susceptibility.

The rs3746444A/G polymorphism affects the pre-miR-499 stem region, resulting in a change from an A:U to a G:U pairing and mismatching. This alteration reduces the stability of the pre-miR-499 secondary structure. Additionally, the G allele affects miRNA maturation and binding to target mRNAs, increasing susceptibility to various diseases [62], including several AIDs. Qui F et al. recently demonstrated that relative to the miR-499 rs3746444 A allele, the G allele influences the expression of several genes related to immunity and cancer [63]. Although the role of miR-499 in the pathogenesis of SLE, RA and GD is not well understood, it has been demonstrated that miR-499 targets IL-17RB, IL6, IL-23a, IL-2RB, IL-2, and IL-18R, suggesting its potential to influence these AIDs [8, 11]. Further studies are needed to understand the role of miR-499 in these AIDs.

Our studies in SLE and RA patients reached statistical power (>80%); however, our findings in GD patients could be biased by the small sample size (low statistical power). The cases and controls in all groups were matched by gender, age, and self-reported ancestry. However, it should be noted that the Mexican-Mestizo population is a heterogeneous ethnic group with a very complex genetic structure [64], and thus our findings could be influenced by population stratification. This phenomenon represents a major limitation of this work. Additionally, insufficient clinical data limited our ability to determine whether the investigated polymorphisms could act as modifiers of disease severity in SLE, RA, or GD.

In conclusion, our present results suggest that the functional miR-146a rs2910164G/C, 196a-2 rs11614913C/T, and miR-499 rs3746444A/G polymorphisms were not associated with RA, GD, or LN in patients from Mexico. Our data further suggest that miR-196a-2 r211614913C/T was not associated with SLE in this population. Importantly, this study is the first to document associations of the miR-146a rs2910164G/C and miR-499 rs3746444A/G polymorphisms with SLE susceptibility.

MATERIALS AND METHODS

Study population

Our study population included unrelated subjects over 18 years of age, with a diagnosis of SLE, RA, or GD, recruited from the rheumatology, endocrinology, and immunology outpatient clinics at the Juarez Hospital of Mexico, the National Institute of Cardiology, and the Regional Hospital General in Yucatan. Patients were excluded if they had received a blood transfusion within the last three months; had a viral infection, such as HIV or hepatitis B or C; or had multiple AIDs (except for RA with Sjörgren syndrome). RA patients were classified following the 2010 criteria of the American College of Rheumatology (ACR) [65], GD cases were diagnosed following the criteria of the American Thyroid Association (ATA) [66], and SLE patients were classified based on the 1997 ACR criteria [67]. Data regarding LN presence were available in 202 SLE cases.

From the Juarez Hospital of Mexico, we recruited healthy unrelated control individuals, of over 18 years of age, with self-reported Mexican-Mestizo ancestry (three generations). Control subjects were excluded if they had a family history of autoimmune or chronic inflammatory disease, including obesity, asthma, food allergy, inflammatory bowel disease, chronic urticarial, and others.

All evaluated cases and controls were matched for gender and ethnicity. All study participants provided written informed consent, and this study was approved by the institutional committees of Ethics, Research, and Biosecurity.

Genomic DNA extraction

From each participant, we obtained a total of 5 ml EDTA-treated peripheral blood. Human nuclear DNA was isolated from PBMCs using an Invisorb Blood Universal Kit (Stratec Molecular GmbH; Berlin, Germany) following the manufacturer’s specifications. DNA concentrations were spectrophotometrically measured based on the default OD 260/280 absorbance algorithm. Then the DNA was diluted to a concentration of 5 ng/μl and stored at −20°C until use.

Determination of polymorphisms in pre-miRNAs

Genotypes of the miR-146a rs2910164G/C, miR-196a-2 rs11614913C/T, and miR-499 rs3746444A/G SNPs were determined using TaqMan probes (C__15946974_10 for rs2910164, C__31185852_10 for rs11614913, and C___2142612_30 for rs3746444; Applied Biosystems, Foster City, CA) with a CFX96 Touch™ Real-Time PCR Detection System (Bio-Rad, California, USA) following the manufacturer’s instructions. Allelic discrimination plots for the three miR-SNPs were constructed using Bio-Rad CFX Manager software. To evaluate the assay reproducibility, 60% of the samples were genotyped twice for all three polymorphisms, showing 100% reproducibility.

Statistical analysis

To evaluate the HWE for the three investigated miR-SNPs, we used the chi-square test as implemented in the FINETTI software (http://ihg.gsf.de/cgi-bin/hw/hwa1.pl). For all cases and controls, HWE was independently tested for each miR-SNP: miR-146a (rs2910164G/C), miR-196a-2 (rs11614913C/T), and miR-499 (rs3746444A/G). EPIDAT 3.1 software (http://www.sergas.es/Saude-publica/Epidat-3-1-descargar-Epidat-3-1-(espanol)?print=1) was used to estimate associations between RA, SLE or GD susceptibility and the alleles and genotypes of the evaluated functional miR-SNPs. These analyses included estimation of the odds ratio (OR), 95% confidence interval (95% CI), and P value. P values of less than 0.05 were considered statistically significant.

ACKNOWLEDGMENTS

We thank all participants for generously donating their blood samples. The authors would like to express their gratitude to María Guadalupe Rangel González, Blanca Elizabeth Mata Gamez, Irma Gurrión Benitez and Silvia Monserrat Flores Olivarria for the collection of biological samples from SLE patients. This study was supported by a grant of the Consejo Nacional de Ciencia y Tecnología de México (CONACyT) (FOSISS; project no. 233107).

CONFLICTS OF INTEREST

The authors declare no conflicts of interest.

REFERENCES

1. La Cava A. Putting together the autoimmunity puzzle. J Clin Invest. 2015; 125:2184-2186.

2. Ngo ST, Steyn FJ, McCombe PA. Gender differences in autoimmune disease. Front Neuroendocrinol. 2014; 35:347-369.

3. Mellado M, Martínez-Muñoz L, Cascio G, Lucas P, Pablos JL, Rodríguez-Frade MJ. T cell migration in rheumatoid arthritis. Front Immunol. 2015; 6:384.

4. Liu Z, Davidson A. Taming lupus-a new understanding of pathogenesis is leading to clinical advances. Nat Med. 2012; 18:871-882.

5. Inaba H, De Groot LJ, Akamizu T. Thyrotropin receptor epitope and human leukocyte antigen in Graves' disease. Front Endocrinol (Lausanne). 2016; 7:120.

6. Karlson EW, Deane K. Environmental and gene-environment interactions and risk of rheumatoid arthritis. Rheum Dis Clin North Am. 2012; 38:405-426.

7. Vojdani A. A potential link between environmental triggers and autoimmunity. Autoimmune Dis. 2014; 2014:437231.

8. Rodríguez Elías AK, Maldonado Murillo K, López Mendoza LF, Ramírez Bello J. Genetics and genomics in rheumatoid arthritis (RA): an update. Gac Med Mex. 2016; 152:218-227.

9. Teruel M, Alarcón-Riquelme ME. The genetic basis of systemic lupus erythematosus: what are the risk factors and what have we learned. J Autoimmun. 2016; 74:161-175.

10. Pujol-Borrell R, Giménez-Barcons M, Marín-Sánchez A, Colobran R. Genetics of Graves' disease: special focus on the role of TSHR gene. Horm Metab Res. 2015; 47:753-766.

11. Yang B, Zhang JL, Shi YY, Li DD, Chen J, Huang ZC, Cai B, Song XB, Li LX, Ying BW, Wang LL. Association study of single nucleotide polymorphisms in pre-miRNA and rheumatoid arthritis in a Han Chinese population. Mol Biol Rep. 2011; 38:4913-4919.

12. Hashemi M, Eskandari-Nasab E, Zakeri Z, Atabaki M, Bahari G, Jahantigh M, Taheri M, Ghavami S. Association of pre-miRNA-146a rs2910164 and premiRNA-499 rs3746444 polymorphisms and susceptibility to rheumatoid arthritis. Mol Med Rep. 2013; 7:287-291.

13. El-Shal AS, Aly NM, Galil SM, Moustafa MA, Kandel WA. Association of microRNAs genes polymorphisms with rheumatoid arthritis in Egyptian female patients. Joint Bone Spine. 2013; 80:626-631.

14. Fu L, Jin L, Yan L, Shi J, Wang H, Zhou B, Wu X. Comprehensive review of genetic association studies and meta-analysis on miRNA polymorphisms and rheumatoid arthritis and systemic lupus erythematosus susceptibility. Hum Immunol. 2016; 77:1-6.

15. Lee YH, Bae SC. The miR-146a polymorphism and susceptibility to systemic lupus erythematosus and rheumatoid arthritis: a meta-analysis. Z Rheumatol. 2015; 74:153-156.

16. Cai T, Li J, An X, Yan N, Li D, Jiang Y, Wang W, Shi L, Qin Q, Song R, Wang G, Jiang W, Zhang JA. Polymorphisms in MIR499A and MIR125A gene are associated with autoimmune thyroid diseases. Mol Cell Endocrinol. 2017; 440:106-115.

17. Qian L, Gao D, Wang G, Li X, Li X, Chen J, Qin M. Relationship between the single nucleotide polymorphisms in pre-miR-146a rs2910164 and expression of miR-146a in rheumatoid arthritis. Chin J Microbiol Immunol. 2012; 32:253-257.

18. Li Y, Kowdley KV. MicroRNAs in common human diseases. Genomics Proteomics Bioinformatics. 2012; 10:246-253.

19. Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, Shiekhattar R. TRBP recruits the dicer complex to Ago2 for microRNA processing and gene silencing. Nature. 2005; 436:740-744.

20. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R. The microprocessor complex mediates the genesis of microRNAs. Nature. 2004; 432:235-240.

21. Gurtan AM, Sharp PA. The role of miRNAs in regulating gene expression networks. J Mol Biol. 2013; 425:3582-3600.

22. Ha M, Kim VN. Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol. 2014; 15:509-524.

23. Saba R, Sorensen DL, Booth SA. MicroRNA-146a: a dominant, negative regulator of the innate immune response. Front Immunol. 2014; 5:578.

24. Qu Z, Li W, Fu B. MicroRNAs in autoimmune diseases. Biomed Res Int. 2014; 2014:527895.

25. Makarova JA, Maltseva DV, Galatenko VV, Abbasi A, Maximenko DG, Grigoriev AI, Tonevitsky AG, Northoff H. Exercise immunology meets MiRNAs. Exerc Immunol Rev. 2014; 20:135-164.

26. Velu VK, Ramesh R, Srinivasan AR. Circulating microRNAs as biomarkers in health and disease. J Clin Diagn Res. 2012; 6:1791-1795.

27. de Candia P, Torri A, Pagani M, Abrignani S. Serum microRNAs as biomarkers of human lymphocyte activation in health and disease. Front Immunol. 2014; 5:43.

28. Churov AV, Oleinik EK, Knip M. MicroRNAs in rheumatoid arthritis: altered expression and diagnostic potential. Autoimmun Rev. 2015; 14:1029-1037.

29. Nakasa T, Miyaki S, Okubo A, Hashimoto M, Nishida K, Ochi M, Asahara H. Expression of microRNA-146 in rheumatoid arthritis synovial tissue. Arthritis Rheum. 2008; 58:1284-1292.

30. Stanczyk J, Pedrioli DM, Brentano F, Sanchez-Pernaute O, Kolling C, Gay RE, Detmar M, Gay S, Kyburz D. Altered expression of microRNA in synovial fibroblasts and synovial tissue in rheumatoid arthritis. Arthritis Rheum. 2008; 58:1001-1009.

31. Pauley KM, Satoh M, Chan AL, Bubb MR, Reeves WH, Chan EK. Upregulated miR-146a expression in peripheral blood mononuclear cells from rheumatoid arthritis patients. Arthritis Res Ther. 2008; 10:R101.

32. Filková M, Aradi B, Senolt L, Ospelt C, Vettori S, Mann H, Filer A, Raza K, Buckley CD, Snow M, Vencovský J, Pavelka K, Michel BA, et al. Association of circulating miR-223 and miR-16 with disease activity in patients with early rheumatoid arthritis. Ann Rheum Dis. 2014; 73:1898-1904.

33. Chan EK, Satoh M, Pauley KM. Contrast in aberrant microRNA expression in systemic lupus erythematosus and rheumatoid arthritis: is microRNA-146 all we need? Arthritis Rheum. 2009; 60:912-915.

34. Pérez-Sánchez C, Aguirre MA, Ruiz-Limón P, Barbarroja N, Jiménez-Gómez Y, de la Rosa IA, Rodriguez-Ariza A, Collantes-Estévez E, Segui P, Velasco F, Cuadrado MJ, Teruel R, González-Conejero R, et al. 'Atherothrombosis-associated microRNAs in antiphospholipid syndrome and systemic lupus erythematosus patients'. Sci Rep. 2016; 6:31375.

35. Li K, Du Y, Jiang BL, He JF. Increased microRNA-155 and decreased microRNA-146a may promote ocular inflammation and proliferation in Graves' ophthalmopathy. Med Sci Monit. 2014; 20:639-643.

36. Wei H, Guan M, Qin Y, Xie C, Fu X, Gao F, Xue Y. Circulating levels of miR-146a and IL-17 are significantly correlated with the clinical activity of Graves' ophthalmopathy. Endocr J. 2014; 61:1087-1092.

37. Luo X, Ranade K, Talker R, Jallal B, Shen N, Yao Y. MicroRNA-mediated regulation of innate immune response in rheumatic diseases. Arthritis Res Ther. 2013; 15:210.

38. Makino T, Jinnin M, Etoh M, Yamane K, Kajihara I, Makino K, Ichihara A, Igata T, Sakai K, Fukushima S, Ihn H. Down-regulation of microRNA-196a in the sera and involved skin of localized scleroderma patients. Eur J Dermatol. 2014; 24:470-476.

39. Motawi TK, Mohsen DA, El-Maraghy SA, Kortam MA. MicroRNA-21, microRNA-181a and microRNA-196a as potential biomarkers in adult Egyptian patients with systemic lupus erythematosus. Chem Biol Interact. 2016; 260:110-116.

40. Slaby O, Bienertova-Vasku J, Svoboda M, Vyzula R. Genetic polymorphisms and microRNAs: new direction in molecular epidemiology of solid cancer. J Cell Mol Med. 2012; 16:8-21.

41. Saunders MA, Liang H, Li WH. Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci U S A. 2007; 104:3300-3305.

42. Sun G, Yan J, Noltner K, Feng J, Li H, Sarkis DA, Sommer SS, Rossi JJ. SNPs in human miRNA genes affect biogenesis and function. RNA. 2009; 15:1640-1651.

43. Zhou X, Zhu J, Zhang H, Zhou G, Huang Y, Liu R. Is the microRNA-146a (rs2910164) polymorphism associated with rheumatoid arthritis? Association of microRNA-146a (rs2910164) polymorphism and rheumatoid arthritis could depend on gender. Joint Bone Spine. 2015; 82:166-171.

44. Zhang J, Yang B, Ying B, Li D, Shi Y, Song X, Cai B, Huang Z, Wu Y, Wang L. Association of pre-microRNAs genetic variants with susceptibility in systemic lupus erythematosus. Mol Biol Rep. 2011; 38:1463-1468.

45. Löfgren SE, Frostegård J, Truedsson L, Pons-Estel BA, D'Alfonso S, Witte T, Lauwerys BR, Endreffy E, Kovács L, Vasconcelos C, Martins da Silva B, Kozyrev SV, Alarcón-Riquelme ME. Genetic association of miRNA-146a with systemic lupus erythematosus in Europeans through decreased expression of the gene. Genes Immun. 2012; 13:268-274.

46. Toraih EA, Ismail NM, Toraih AA, Hussein MH, Fawzy MS. Precursor miR-499a variant but not miR-196a2 is associated with rheumatoid arthritis susceptibility in an Egyptian population. Mol Diagn Ther. 2016; 20:279-295.

47. Ciccacci C, Conigliaro P, Perricone C, Rufini S, Triggianese P, Politi C, Novelli G, Perricone R, Borgiani P. Polymorphisms in STAT-4, IL-10, PSORS1C1, PTPN2 and mir146A genes are associated differently with prognostic factors in Italian patients affected by rheumatoid arthritis. Clin Exp Immunol. 2016; 186:157-163.

48. Jiménez-Morales S, Gamboa-Becerra R, Baca V, Del Río-Navarro BE, López-Ley DY, Velázquez-Cruz R, Saldaña-Alvarez Y, Salas-Martínez G, Orozco L. MiR-146a polymorphism is associated with asthma but not with systemic lupus erythematosus and juvenile rheumatoid arthritis in Mexican patients. Tissue Antigens. 2012; 80:317-321.

49. López-Cano DJ, Cadena-Sandoval D, Beltrán-Ramírez O, Barbosa-Cobos RE, Sánchez-Muñoz F, Amezcua-Guerra LM, Juárez-Vicuña Y, Aguilera-Cartas MC, Moreno J, Bautista-Olvera J, Valencia-Pacheco G, López-Villanueva RF, Ramírez-Bello J. The PTPN22 R263Q polymorphism confers protection against systemic lupus erythematosus and rheumatoid arthritis, while PTPN22 R620W confers susceptibility to Graves' disease in a Mexican population. Inflamm Res. 2017. https://doi.org/10.1007/s00011-017-1056-0.

50. Zúñiga J, Vargas-Alarcón G, Hernández-Pacheco G, Portal-Celhay C, Yamamoto-Furusho JK, Granados J. Tumor necrosis factor-alpha promoter polymorphisms in Mexican patients with systemic lupus erythematosus (SLE). Genes Immun. 2001; 2:363-366.

51. Baca V, Velázquez-Cruz R, Salas-Martínez G, Espinosa-Rosales F, Saldaña-Alvarez Y, Orozco L. Association analysis of the PTPN22 gene in childhood-onset systemic lupus erythematosus in Mexican population. Genes Immun. 2006; 7:693-695.

52. Jiménez-Morales S, Velázquez-Cruz R, Ramírez-Bello J, Bonilla-González E, Romero-Hidalgo S, Escamilla-Guerrero G, Cuevas F, Espinosa-Rosales F, Martínez-Aguilar NE, Gómez-Vera J, Baca V, Orozco L. Tumor necrosis factor-alpha is a common genetic risk factor for asthma, juvenile rheumatoid arthritis, and systemic lupus erythematosus in a Mexican pediatric population. Hum Immunol. 2009; 70:251-256.

53. Jazdzewski K, Murray EL, Franssila K, Jarzab B, Schoenberg DR, de la Chapelle A. Common SNP in pre-miR-146a decreases mature miR expression and predisposes to papillary thyroid carcinoma. Proc Natl Acad Sci U S A. 2008; 105:7269-7274.

54. Wang R, Li M, Zhou S, Zeng D, Xu X, Xu R, Sun G. Effect of a single nucleotide polymorphism in miR-146a on COX-2 protein expression and lung function in smokers with chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis. 2015; 10:463-473.

55. Chan EK, Satoh M, Pauley KM. Contrast in aberrant microRNA expression in systemic lupus erythematosus and rheumatoid arthritis: is microRNA-146 al we need? Arthritis Rheum. 2009; 60:912-915.

56. Li K, Du Y, Jiang BL, He JF. Increased microRNA-155 and decreased microRNA-146a may promote ocular inflammation and proliferation in Graves’ opthalmopathy. Med Sci Monit. 2014; 20:639-643.

57. Garo LP, Marugaiyan G. Contribution of microRNAs to autoimmune diseases. Cell Mol Life Sci. 2016; 73:2041-2051.

58. Chen JQ, Papp G, Szodoray P, Zeher M. The role of microRNAs in the pathogenesis of autoimmune diseases. Autoimmun Rev. 2016; 15:1171-1180.

59. Tang Y, Luo X, Cui H, Ni X, Yuan M, Guo Y, Huang X, Zhou H, de Vries N, Tak PP, Chen S, Shen N. MicroRNA-146a contributes to abnormal activation of the type I interferón pathway in human lupus by targeting the key signaling proteins. Arthritis Rheum. 2009; 60:1065-1075.

60. Li XD, Li ZG, Song XX, Liu CF. A variant in microRNAs-196a2 is associated with susceptibility to hepatocellular carcinoma in Chinese patients with cirrosis. Pathology. 2010; 42:669-673.

61. Nowling TK, Gilkeson GS. Mechanisms of tissue injury in lupus nephritis. Artritis Res Ther. 2011; 13:250.

62. Wang Z, Wu J, Zhang G, Cao Y, Jiang C, Ding Y. Association of miR-499 and miR-34b/c polymorphisms with susceptibility to hepatocellular carcinoma: an evidence-based evaluation. Gastroenterol Res Pract. 2013; 2013:719202.

63. Qiu F, Yang L, Ling X, Yang R, Yang X, Zhang L, Fang W, Xie C, Huang D, Zhou Y, Lu J. Sequence variation in mature microRNA-499 confers unfavorable prognosis of lung cancer patients treated with platinum-based chemotherapy. Clin Cancer Res 2015; 21:1602-1613.

64. Mendoza Rincón JF, Rodríguez Elias AK, Fragoso JM, Vargas Alarcón G, Maldonado Murillo K, Rivas Jiménez ML, Barbosa Cobos RE, Jiménez Morales S, Lugo Zamudio G, Tovilla Zárate C, Ramírez Bello J. MHC2TA and FCRL3 genes are not associated with rheumatoid arthritis in Mexican patients. Rheumatol Int. 2016; 36:249-254.

65. Aletaha D, Neogi T, Silman AJ, Funovits J, Felson DT, Bingham CO 3rd, Birnbaum NS, Burmester GR, Bykerk VP, Cohen MD, Combe B, Costenbader KH, Dougados M, et al. 2010 Rheumatoid classification criteria: an American College of Rheumatology/European League Against Rheumatism collaborative initiative. Arthritis Rheum. 2010; 62:2569-2581.

66. Ross DS, Burch HB, Cooper DS, Greenlee MC, Laurberg P, Maia AL, Rivkees SA, Samuels M, Sosa JA, Stan MN, Walter MA. 2016 American Thyroid Association guidelines for Diagnosis and management of hyperthyroidism and other causes of thyrotoxicosis. Thyroid. 2016; 26:1343-1421.

67. Hochberg MC. Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum. 1997; 40:1725.


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