Characterization of variations in IL23A and IL23R genes: possible roles in multiple sclerosis and other neuroinflammatory demyelinating diseases

Results

Clinical data

Two specialists in neurology at the Second Affiliated Hospital of Harbin Medical University, Harbin, China, conducted the diagnosis. There were no other systemic abnormalities in these IDD patients and they had no previous familial history of these diseases. The IDD patients (n = 206, male 60, female 146, the min and max ages were 15 and 73 respectively, and the average age was 41.45 years) included 84 MS, 14 myelitis, 8 NMO, 4 optic neyritis and 96 radiologically isolated syndrome (RIS) diseases that were not classified as MS, myelitis, NMO or optic neyritis. The recruited normal controls (n = 300, male 87, female 213, the min and max ages were 23 and 50 respectively, and the average age was 41.70 years) had no statistical differences in the gender composition or age with the IDD patients (Table 1).

Table 1. Clinical characteristics of study population.

Parameter	IDD	Control	F	t	P	95%CI
						Up	Low
Sample (n)	206	300	-	-	-	-	-
Male/Female (n)	60/146	87/213	-	-	0.975	-	-
Age (years)	41.45±13.30	41.70±7.06	115.938	-0.278	0.781	-2.04458	1.53778
Data are shown as mean±SD; between the two groups, there were no statistical differences of the age and gender composition.

SNP analyses

We sequenced the transcribed regions and splicing sites of the IL-23A, IL-23R and IL-12RB1 genes to test the hypothesis that common genetic variants in those genes may confer the susceptibility to IDD diseases. We found variants within or near genes of IL-23A (rs2066808, rs2371494, rs11575248 and rs11171806), IL-23R (rs1884444, rs7530511, rs10889677 and rs76418789), and IL-12RB1 (rs11575934 and rs401502). We compared genetic heterozygosity of the SNPs and found that the genetic heterozygosity of rs2066808, rs2371494, rs11575248, rs1884444, rs7530511, rs10889677, rs401502 and rs11575934 was very high (Fig. S1), whereas that of rs11171806 and rs76418789 was very low.

Polymorphism-disease association analyses

In order to test any possible associations between IL-23A, IL-23R or IL-12RB1 and IDD diseases, we conducted analyses on the SNPs and found that the variants rs2066808, rs2371494, rs11575248 in the IL-23A gene and rs1884444 in the IL-23R gene were associated with the risk of IDD diseases in the Chinese Han population (Tables 2, 3); however, the variants rs7530511, rs10889677 in the IL-23R gene and rs401502, rs11575934 in the IL-12RB1 gene were not. Of special significance, the variants rs2066808, rs2371494, rs11575248 and rs1884444 were closely associated with the risk of MS but not RIS (Tables 2, 3).

Table 2. The genotype and allele frequency of rs2066808, rs2371494, rs11575248 and rs1884444 variants in 206 Chinese Han Neuroinflammatory demyelinating diseases of the central nervous system patients and 300 non- IDD controls.

Genes	Variants	Group		Genotype frequency (%)			Allele frequency (%)
IL23A	Rs2066808	Genotype		T/T	T/C	C/C	T	C
		IDD	206	183(88.8)	23(11.2)	0(0.0)	389(94.4)	23(5.6)
		MS	84	72(85.7)	12(14.3)	0(0.0)	156(92.9)	12(7.1)
		RIS	96	87(90.6)	9(9.4)	0(0.0)	183(95.3)	9(4.7)
		Controls	300	287(95.7)	11(3.7)	2(0.7)	585(97.5)	15(2.5)
	Rs2371494	Genotype		C/C	C/A	A/A	C	A
		IDD	206	180(87.4)	26(12.6)	0(0.0)	386(93.7)	26(6.3)
		MS	84	72(85.7)	12(14.3)	0(0.0)	156(92.9)	12(7.1)
		RIS	96	85(88.5)	11(11.5)	0(0.0)	181(94.3)	11(5.7)
		Controls	300	283(94.3)	16(5.3)	1(0.3)	582(97.0)	18(3.0)
	Rs11575248	Genotype		C/C	C/A	A/A	C	A
		IDD	206	182(88.3)	24(11.7)	0(0.0)	388(94.2)	24(5.8)
		MS	84	71(84.5)	13(15.5)	0(0.0)	155(92.3)	13(7.7)
		RIS	96	86(89.6)	10(10.4)	0(0.0)	182(94.8)	10(5.2)
		Controls	300	283(94.3)	17(5.7)	0(0.0)	583(97.2)	17(2.8)
IL23R	Rs1884444	Genotype		T/T	T/G	G/G	T	G
		IDD	206	76(11.0)	108(74.0)	22(15.1)	260(63.1)	152(36.9)
		MS	84	35(41.7)	42(50.0)	7(8.3)	112(66.7)	56(33.3)
		RIS	96	33(34.4)	52(54.2)	11(11.5)	118(61.5)	74(38.5)
		Controls	300	101(33.7)	133(44.3)	66(22.0)	335(55.8)	265(44.2)
IDD: inflammatory demyelinating diseases; MS: multiple sclerosis; RIS: radiologically isolated syndrome.

Table 3. Associations of rs2066808, rs2371494, rs11575248 and rs1884444 variants within IL23A or IL23R with risk of IDD in Chinese populations.

Titles				Pearson Chi-square				Pearson’s R
Genes	Genotyped SNP	Diseases	Statistical Types	Value	Min counta	df	Asymp. Sig. (2-sided)	Value	Asymp. Std. errorb	Approx. Tc	Approx. Sig
IL23A	Rs2066808	IDD	Genotype	12.207	0.81	2	0.002	-0.109	0.047	-2.459	0.014d
			Allele	6.422	15.47	1	0.011	-0.080	0.032	-2.540	0.011d
		MS	Genotype	13.610	0.44	2	0.001	-0.139	0.062	-2.752	0.006d
			Allele	8.341	5.91	1	0.004	-0.104	0.044	-2.900	0.004d
		RIS	Genotype	5.528	0.48	2	0.063	-0.072	0.056	-1.441	0.150d
			Allele	2.369	5.82	1	0.124	-0.055	0.040	-1.539	0.124d
	Rs2371494	IDD	Genotype	9.148	0.41	2	0.010	-0.113	0.046	-2.546	0.011d
			Allele	6.438	17.91	1	0.011	-0.080	0.032	-2.543	0.011d
		MS	Genotype	8.020	0.22	2	0.018	-0.123	0.060	-2.428	0.016d
			Allele	6.001	6.56	1	0.014	-0.088	0.043	-2.456	0.014d
		RIS	Genotype	4.584	0.24	2	0.101	-0.087	0.056	-1.726	0.085d
			Allele	3.071	7.03	1	0.080	-0.062	0.040	-1.754	0.080d
	Rs11575248	IDD	Genotype	5.873	16.69	1	0.015	-0.108	0.045	-2.433	0.015d
			Allele	5.625	16.69	1	0.018	-0.075	0.032	-2.376	0.018d
		MS	Genotype	8.768	6.56	1	0.003	-0.151	0.061	-2.988	0.003d
			Allele	8.412	6.56	1	0.004	-0.105	0.044	-2.912	0.004d
		RIS	Genotype	2.583	6.55	1	0.108	-0.081	0.056	-1.608	0.109d
			Allele	2.492	6.55	1	0.114	-0.056	0.040	-1.579	0.115d
IL23R	Rs1884444	IDD	Genotype	11.043	35.83	2	0.004	-0.102	0.043	-2.298	0.022d
			Allele	5.334	169.77	1	0.021	0.073	0.031	2.313	0.021d
		MS	Genotype	8.096	15.97	2	0.017	0.125	0.046	2.453	0.015d
			Allele	6.332	70.22	1	0.012	0.091	0.035	2.523	0.012d
		RIS	Genotype	5.672	18.67	2	0.059	0.067	0.046	1.340	0.181d
			Allele	1.880	82.18	1	0.170	0.049	0.035	1.371	0.171d
a the minimum expected count; b not assuming the null hypothesis; c using the asymptotic standard error assuming the null hypothesis; d based on normal approximation; IDD: inflammatory demyelinating diseases; MS: multiple sclerosis; RIS: radiologically isolated syndrome.

The genotype frequencies in the IDD diseases and control groups were further analyzed by three genetic models: additive, dominant, and recessive. The variants rs2066808, rs2371494, rs11575248 and rs1884444 were associated with the risk of IDD diseases, however rs2066808 and rs2371494 were not in the recessive model and rs1884444 was not in the dominant model (Table 4). The experiment-wide significance threshold of the variants rs2066808, rs2371494, rs11575248 is 0.019. The Haploview software was used to conduct LD analysis in the IL23A variants, and the results from the LD analysis of the variants (rs2066808, rs2371494 and rs11575248) in the present study and the data from the HapMap CHB population were shown in Fig. 1. The data from the HapMap CHB and this work were consistent. We conducted the Hardy-Weinberg equilibrium test for the IDD diseases and controls and it was in line with equilibrium.

Table 4. Analysis of rs2066808, rs2371494, rs11575248 and rs1884444 variants in the IDD and control groups based on three genetic models.

Genes	Variants	Additive model (P value)	Dominant model (P value)	Recessive model (P value)
IL23A	Rs2066808	0.01731	0.004455	0.5163
	Rs2371494	0.01761	0.008755	1
	Rs11575248	0.01537	0.02242	0.0197
IL23R	Rs1884444	0.02291	0.5067	0.001176
IDD: inflammatory demyelinating diseases

Figure 1. LD analysis of the variants in the IL23A gene region, and the LD plots were generated using the Haploview software v4.2. (A) Data analysis between IDD patients and controls from the present study. (B) Data from the HapMap CHB. The data from the HapMap CHB and this work were very similar.

Gene expression analysis

We conducted the ELISA analysis to measure the serum level of IL23A in the IDD participants and controls between the wild type, heterozygous mutation and homozygous mutation type groups. Firstly, we drew a standard curve and calculated the regression equation (Y = 0.0385X + 0.0393, R2=0.9969; Fig. S2). We found that the serum levels of IL23A in the MS patients were higher than those in the normal group (statistically significant, two asterisks). Notably, when both the IL-23A and IL-23R genes were altered, the serum levels of IL23A were significantly higher than those in the groups in which the IL-23A and IL-23R genes were not altered or only one of them was altered (Fig.2). Remarkably, although the serum levels of IL23A in the RIS patients were higher than those in the normal group (statistically significant), there was no statistically significant difference among the three groups that had the IL-23A and IL-23R genes both altered, only one altered or neither altered (Fig. 2).

Figure 2. The serum levels of IL23A in IDD and normal groups were detected by ELISA. (A) The expression levels of IL23A in the MS patients were higher than that in the control group (two asterisk); and when both the IL-23A and IL-23R genes were altered, the serum levels of IL23A were higher than those in the groups in which neither the IL-23A nor the IL-23R gene was altered or only one of them was altered. (B) The expression levels of IL23A in the RIS patients were higher than those in the control group (two asterisks); however there was no difference between the three groups that had the IL-23A and IL-23R genes both altered, only one altered or neither altered. “WW” means neither the IL-23A nor the IL-23R gene was altered; “MM” means the IL-23A and IL-23R genes were both altered; “Homozygous variant” means the homozygous variant G/G of the rs1884444 variant in the IL-23R gene.

Materials and Methods

Study population

We included 206 IDD patients and 300 normal controls (Table 1), which were assembled at the Department of Neurology and Medical Examination Center of the Second Affiliated Hospital of Harbin Medical University, Harbin, China. In order to make the present work consistent with the 1975 Declaration of Helsinki, we obtained a written informed consent from each participant or their guardian, and this work also was approved by the Ethics Committee of Harbin Medical University. We also confirm that all experiments were performed in accordance with relevant guidelines and regulations [31]. Medical histories of the enrolled participants were recorded in detail, and the participants also received physical and neurological system examination. When necessary, some patients also received imageological examination or cerebrospinal fluid inspection. All the patients were diagnosed according to the McDonald's (2010) diagnostic criteria [32].

DNA analysis

Genomic DNA in peripheral blood leukocytes of each participant was extracted using standard protocols [33]. The transcribed regions and splicing sites of the IL-23A, IL-23R and IL-12RB1 genes were amplified by PCR with the primers shown in Table S1. The PCR products were sequenced for mutational analysis using standard protocols [34].

SNP genotyping analysis and statistical analysis

The variants within or near the genes of IL-23A (rs1884444, rs7530511, rs10889677 and rs76418789), IL-23R (rs2066808, rs2371494, rs11575248, rs11171806 and rs401502), and IL-12RB1 (rs11575934) were determined (Fig. 3) on 206 patients with IDD diseases and 300 normal controls. The DNA regions were amplified and the PCR products sequenced to determine the genotypes. And then overall IDD analysis was conducted according to the types of IDD and sample sizes.

Figure 3. Schematic diagrams of the variants. (A) the IL-23A gene variants rs2066808, rs2371494 and rs11575248; (B): the IL-23R gene variant rs1884444.

Using the SPSS software (version 19.0), we conducted the statistical analyses [35]. The continuous variables (measurement data, such as age) statistical analyses were conducted using independent-samples T test and the discrete variables (enumeration data, such as gender composition and genotype frequency) statistical analyses were conducted using Chi-Square Tests to calculate P value. P values smaller than 0.05 were considered statistically significant [36]. The Hardy-Weinberg equilibrium tests of the IDD and control populations were conducted with the online software OEGE [37]. The Fisher test was used to compare the genotype frequencies between the IDD and control groups based on three genetic models using PLINK v1.07 software (http://pngu.mgh.harvard.edu/Bpurcell/plink/). We also determined experiment-wide significance threshold, matrix of mpirwise linkage-disequilibrium (LD) correlation for the markers and haplotype diagram of LD structure using SNPSpD software(http://neurogenetics.qimrberghofer.edu.au/SNPSpD/) [38] and Haploview software(http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview) [39].

ELISA analysis and data calculation

We separated the serum and blood cells and stored the samples at -80°C prior to use. For ELISA assays, we used the Interleukins 23A (Human) ELISA testing kit (96T), No.: CK - E10077H, from Shanghai Yuanye Bio-Technology Co., Ltd. The IL23A levels were measured by ELISA using a microplate reader (BioTeK Epoch, USA).

To make a standard curve for measuring the levels of IL–23A, we put the OD values of six different concentrations of standard substance minus the OD value of blank hole on ordinate Y and the concentrations of the standard substance on the abscissa X, and then calculated the regression equation (Y = aX + b, R2 value). The concentrations of IL–23A in the samples were then determined according to their OD values. Finally, using GraphPad Prism, we conducted the T test.

Acknowledgements

The authors thank the patients and the family members for their cooperation and participation in this study.

Funding

This work was supported by grants of National Natural Science Foundation of China to SLL (NSFC81271786, 81030029, 81671980) and JF (NSFC 81070964, 81171120), and a grant from Health and Family Planning Commission of Heilongjiang province Foundation (2016-189) to FFL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Conflicts of Interest

All the authors have declared that no competing financial interests exist.

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