Genetic Polymorphisms in Genes Involved in the Type I Interferon System (IFIH1/MDA-5, TNFAIP3/A20, and STAT4): Association with SLE Risk in Egyptian Children and Adolescents

Figures & data

Figure 1 Renal biopsy classes (stage I, II, III, IV and V) in lupus nephritis cases.

Figure 2 Proliferative and non- proliferative renal biopsies in lupus nephritis cases.

Table 1 Demographic, Clinical and Laboratory Characteristics of SLE (Systemic Lupus Erythematosus) Patients and Healthy Control Subjects

Demographic/Clinical/Laboratory Manifestations	SLE, N=94	Controls, N=94	P
Sex (Males/Females) (N (%))	12 (12.8)/82 (87.2)	14 (14.9)/80 (85.1)	0.673
Age (mean±SD)	13.7±3.0	13.5±1.9	0.599
SLEDAI (medium(range))	9 (0–19)	–	–
Duration of disease (medium(range)) year	3 (1–9)	–	–
Cutaneous (%)	51 (54.3)	–	–
Malar rash (%)	37 (39.4)	–	–
Photosensitivity (%)	31 (33.0)	–	–
Oropharyngeal ulcers (%)	10 (10.6)	–	–
Non-scarring alopecia (%)	28 (29.6)	–	–
Arthritis (%)	26 (27.7)	–	–
Serositis (pleurisy or pericarditis) (%)	3 (3.2)	–	–
Renal disorder (%)	71 (75.5)	–	–
Persistent Proteinuria (%)	68 (72.3)	–	–
RBCs casts (%)	22 (23.4)	–	–
Creatinine (mean±SD) (mg/dl)	0.7±0.2	0.6±0.1	0.365
Neurologic disorder (%)	10 (10.6)	–	–
Hematological disorder (%)	70 (74.5)	–	–
Anemia (%)	62 (66.0)	–	–
Hemoglobin (mean±SD) (g/dl)	11.8±1.7	13.9±0.8	<0.001
RBCs (mean±SD) (x10^6/l)	4.5±0.6	5.6±0.4	0.003
Leucopenia or lymphopenia (%)	10 (1.6)	–	–
WBCs (mean±SD (x10^9/l)	6.5±2.2	8.7±1.5	0.007
Thrombocytopenia (%)	12 (12.8)	–	–
Platelets (mean±SD) (x10^9/l)	280.7±91.9	323.5±67.9	<0.001
Pancytopenia (%)	5 (5.3)	–	–
Immunologic disorder (%)	94 (100)	–	–
Positive anti-ds DNA (%)	65 (69.1)	–	<0.001
Positive ANA (%)	86 (91.5)	–	<0.001
Hypocomplementemia (C3 or C4) (%)	91 (96.8)	–	–
C3 (mean±SD) (mg/dl)	107.6±35.9	121.4±18.4	0.001
C4 (mean±SD) (mg/dl)	14.2±3.1	22.5±6.8	<0.001
P (mean±SD) (mg/dl)	4.9±0.7	4.7±0.5	0.230
Ca) (mean±SD) (mg/dl)	9.4±0.7	9.2±0.4	0.154

Notes: Values in parentheses are percentages or data are presented as mean ± SD; medium (range) and percentages; P < 0.05 versus control group is considered significant. Normal levels: WBCs (x109/l), 4.00–10.0; RBCs (x106/l), 4.0–6.0; Hemoglobin (g/dl), 12–18; Platelets (x109/l), 140–440; Creatinine (mg/dl), 0.3–0.7, P (mg/dl), 4.0–7.0; Ca (mg/dl), 8.6–10.3; C3 (mg/dl), 91–185; C4 (mg/dl), 9–63. C3 & C4, complement components.

Abbreviations: N, number in each group; SLE, systemic lupus erythematosus; SLEDAI, systemic lupus erythematosus Disease Activity Index; ANA, anti-nuclear Antibodies; Anti-ds-DNA, anti-double-stranded DNA; WBCs, white blood cells; RBCs, red blood cells; P, phosphorous; Ca, calcium.

Figure 3 SLE features.

Abbreviations: SLE, systemic lupus erythematosus; ANA, anti-nuclear antibodies.

Table 2 Distribution of IFIH1, TNFAIP3 and STAT4 Genotype and Allele Frequencies in the Studied SLE (Systemic Lupus Erythematosus) Patients and Healthy Control Subjects

Gene	Control (N=94) N (%)	SLE (N=94) N (%)	P	OR	95% CI
IFIH1 rs3747517 C/T
CC	44 (46.8%)	58 (61.7%)	–	1	Reference
CT	41 (43.6%)	33 (35.1%)	0.108	0.734	(0.504–1.07)
TT	9 (9.6%)	3 (3.2%)	0.040	0.429	(0.191–0.962)
CT+TT	50 (53.2%)	36 (38.3%)	0.041	0.685	(0.477–0.984)
C	129 (68.6%)	149 (79.3%)	–	1	Reference
T	59 (31.4%)	39 (20.7%)	0.019	0.705	(0.527–0.944)
HWE	0.902	0.512
TNFAIP3 rs610604 G/T
GG	16 (17.0%)	10 (10.6%)	–	1	Reference
GT	44 (46.8%)	46 (48.9%)	0.255	1.379	0.793–2.399
TT	34 (36.2%)	38 (40.4%)	0.211	1.438	0.814–2.539
GT+TT	78 (83.0%)	84 (89.4%)	0.205	1.405	0.83–2.377
G	76 (40.4%)	66 (35.1%)	–	1	Reference
T	112 (59.6%)	122 (64.9%)	0.287	1.153	0.887–1.497
HWE	0.785	0.473
STAT4 rs7574865 G/T
GG	65 (69.1%)	51 (54.3%)		1	Reference
GT	28 (29.8%)	35 (37.2%)	0.139	1.339	0.91–1.969
TT	1 (1.1%)	8 (8.5%)	0.015	3.945	1.303–11.947
GT+TT	29 (30.9%)	43 (45.7%)	0.024	1.536	1.058–2.231
G	158 (84.0%)	137 (72.9%)		1	Reference
T	30 (16.0%)	51 (27.1%)	0.009	1.522	1.113–2.082
HWE	0.284	0.572

Notes: Values in parentheses are percentages; P < 0.05 versus control group is considered statistically significant. Test, Logistic regression analysis.

Abbreviations: N, number in each group; SLE, systemic lupus erythematosus; IFIH1, interferon-induced helicase C domain 1; TNFAIP3, tumor necrosis factor alpha-induced protein 3; STAT4, signal transducer and activator of transcription 4; OR, odds ratio; CI, confidence interval; HWE, Hardy–Weinberg equilibrium (HWE).

Table 3 Association of IFIH1 rs3747517 C/T, TNFAIP3 rs610604 G/T and STAT4 rs7574865 G/T Genotypes with SLE Clinical or Laboratory Features

Clinical/Laboratory Features	IFIH1 rs3747517 C/T			P	TNFAIP3 rs610604 G/T			P	STAT4 rs7574865 G/T			P
	CC N=58	CT N=33	TT N=3		GG N=10	GT N=46	TT N=38		GG N=51	GT N=35	TT N=8
Cutaneous	27 (46.6%)	22 (66.7%)	2 (66.7%)	0.157	6 (60%)	27 (58.7%)	18 (47.4%)	0.699	27 (52.9%)	18 (51.4%)	6 (75.0%)	0.781
Ulcers	3 (5.2%)	6 (18.2%)	1 (33.3%)	0.375	2 (20%)	4 (8.7%)	4 (10.5%)	0.340	5 (9.8%)	4 (11.4%)	1 (12.5%)	0.775
Alopecia	14 (24.1%)	14 (42.4%)	0 (0.0%)	0.131	2 (20%)	16 (34.8%)	10 (26.3%)	0.467	16 (31.4%)	9 (25.7%)	3 (37.5%)	0.714
Arthritis	16 (27.6%)	9 (27.3%)	1 (33.3%)	0.984	5 (50%)	15 (32.6%)	6 (15.8%)	0.111	16 (31.4%)	8 (22.9%)	2 (25.0%)	0.380
Serositis	2 (3.4%)	1 (3.0%)	0 (0.0%)	0.857	0 (0.0%)	0 (0.0%)	3 (7.9%)	1.000	2 (3.9%)	0 (0.0%)	1 (12.5%)	0.661
Neurologic	7 (12.1%)	3 (9.1%)	0 (0.0%)	0.566	0 (0.0%)	7 (15.2%)	3 (7.9%)	0.593	7 (13.7%)	3 (8.6%)	0 (0.0%)	0.290
Hematological disorder	40 (69.0%)	27 (81.8%)	3 (100%)	0.118	6 (60%)	34 (73.9%)	30 (78.9%)	0.284	37 (72.5%)	27 (77.1%)	6 (75.0%)	0.656
Nephritis	38 (59.4%)	24 (37.5%)	2 (3.1%)	0.497	9 (14.1%)	31 (48.4%)	24 (37.5%)	0.114	35 (54.7%)	22 (34.4%)	7 (10.9%)	0.902
Renal biopsy stages I	1 (50%)	1 (50%)	0 (0.0%)	0.400	1 (50%)	1 (50%)	0 (0.0%)	0.191	0 (0.0%)	2 (100%)	0 (0.0%)	0.140
II	7 (77%)	1 (11.1%)	1 (11.1%)		0 (0.0%)	7 (77.8%)	2 (22.2%)		6 (66.7%)	1 (11.1%)	2 (22.2%)
III	17 (58.6%)	12 (41.4%)	0 (0.0%)		2 (6.90%)	14 (48.3%)	13 (44.8%)		16 (55.2%)	9 (31%)	4 (13.8%)
IV	10 (50%)	9 (45%)	1 (5%)		5 (25%)	7 (35%)	8 (40%)		9 (45%)	10 (50%)	1 (5%)
V	3 (75%)	1 (25%)	0 (0.0%)		1 (25%)	2 (50%)	1 (25%)		4 (100%)	0 (0.0%)	0 (0.0%)
Non proliferative	4 (66.7%)	2 (33.3%)	0 (0.0%)	0.701	2 (33.3%)	3 (50%)	1 (16.7%)	0.192	4 (66.7%)	2 (33.3%)	0 (0.0%)	0.535
Proliferative	34 (58.6%)	22 (37.9%)	2 (3.4%)		7 (12.1%)	28 (48.3%)	23 (39.7%)		31 (53.4%)	20 (34.5%)	7 (12.1%)
SLEDAI (medium (range))	8 (0–19)	11 (5–9)	4 (4–6)	0.177	6.5 (0–12)	10 (4–19)	8 (0–19)	0.177	8 (0–19)	10 (0–19)	9.5 (6–17)	0.382
Active SLE	28 (48.3%)	19 (57.6%)	0 (0.0%)	0.671	4 (40%)	27 (58.7%)	16 (42.1%)	0.504	25 (49%)	18 (51.4%)	4 (50%)	0.836
Anti-ds-DNA	37 (63.8%)	26 (78.8%)	2 (66.7%)	0.152	9 (90%)	29 (63.0%)	27 (71.1%)	0.128	37 (72.5%)	23 (65.7%)	5 (62.5%)	0.438
ANA	52 (89.7%)	31 (93.9%)	3 (100%)	0.416	9 (90%)	43 (93.5%)	34 (89.5%)	0.860	47 (92.2%)	32 (91.4%)	7 (87.5%)	0.801
Hypocomplementemia	56 (96.6%)	32 (97.0%)	3 (100%)	0.857	9 (90%)	45 (97.8%)	37 (97.4%)	0.257	49 (96.1%)	35 (100%)	7 (87.5%)	0.661

Notes: Values in parentheses are percentages or data are presented as percentages and medium(range); P>0.05 is statistically non-significant. Test, Chi-square for categorical data, Kruskal Wallis test for numerical data.

Abbreviations: N, number in each group; SLE, systemic lupus erythematosus; SLEDAI, systemic lupus erythematosus Disease Activity Index; ANA, anti-nuclear Antibodies; Anti-ds-DNA, anti-double-stranded DNA; IFIH1, interferon-induced helicase C domain 1; TNFAIP3, tumor necrosis factor alpha-induced protein 3; STAT4, signal transducer and activator of transcription 4.

Table 4 Regression Analysis for Prediction of SLE Susceptibility

	Univariable			Multivariable
	P	OR	95% CI	P	OR	95% CI
Age	0.597	1.019	0.949–1.095
Gender	0.673	1.119	0.665–1.881
IFIH1 (CT+TT)	0.041	0.685	0.477–0.984	0.018	0.638	0.440–0.924
TNFAIP3 (GT+TT)	0.205	1.405	0.83–2.377
STAT4 (GT+TT)	0.024	1.536	1.058–2.231	0.011	1.644	1.122–2.408

Notes: Logistic regression analysis was used. P<0.05 is statistically significant.

Abbreviations: SLE, systemic lupus erythematosus; IFIH1, interferon-induced helicase C domain 1; TNFAIP3, tumor necrosis factor alpha-induced protein 3; STAT4, signal transducer and activator of transcription 4; OR, odds ratio; CI, confidence interval.