Replication of interleukin 23 receptor and autophagy-related 16-like 1 association in adult- and pediatric-onset inflammatory bowel disease in Italy

Table 1 Demographic and clinical features of CD and UC according to the Montreal classification[39]

	CD (n = 763)	UC (n = 843)
Sex (M/F)	435/328	492/351
Duration of follow-up, mean ± SD (range)	8 ± 7 (1-37)	9 ± 7 (1-41)
Age at diagnosis (yr), mean ± SD (range)	29 ± 15 (1-79)	32 ± 16 (1-76)
≤ 16 (A1)	173 (22%)	155 (18%)
17-40 (A2)	431 (57%)	458 (55%)
> 40 (A3)	159 (21%)	230 (27%)
Disease localization CD, n (%)
Ileum (L1 ± L4)	241 (31%)
Colon (L2 ± L4)	200 (26%)
Ileo-colon (L3 ± L4)	315 (41%)
Upper GI (L4)	7 (2%)
Disease extent UC, n (%)
Rectum (E1)		102 (13%)
Left colon (E2)		416 (49%)
Pancolitis (E3)		325 (38%)
Disease behavior CD, n (%)
Inflammatory (B1 ± p)	346 (46%)
Stricturing (B2 ± p)	177 (23%)
Penetrating (B3 ± p)	240 (31%)
Perianal disease y/n (%)	137/626 (18%)	17/826 (2%)
Smoking history
Yes	242 (33%)	119 (15%)
No	423 (55%)	510 (60%)
Ex	98 (12%)	214 (25%)
Family history of IBD y/n (%)	74/689 (10%)	53/790 (6%)
Surgery y/n, n (%)	237/526 (31%)	95/748 (13%)
Extra-intestinal manifestations y/n (%)	304/459 (40%)	182/661 (21%)

Table 2 Genotypes and alleles distribution for ATG16L1 and IL23R SNPS in CD, UC and controls

	Genotypes							Alleles
	AA	Aa	aa	Total	P	OR (95% CI)		Freq	P	OR (95% CI)
ATG16L1
rs2241880					(AA Aa vs aa)		G
CD Total	227 (34%)	335 (50%)	105 (16%)	667	0.008	1.44 (1.10-1.89)		0.59	0.003	1.25 (1.08-1.45)
CD adult	165 (34%)	254 (52%)	72 (15%)	491	0.004	1.57 (1.16-2.13)		0.59	0.004	1.27 (1.08-1.49)
CD pediatric	62 (35%)	81 (46%)	33 (19%)	176	0.466	1.17 (0.77-1.77)		0.58	0.122	1.20 (0.95-1.52)
UC Total	212 (32%)	315 (47%)	141 (21%)	668	0.956	1.01 (0.78-1.30)		0.55	0.381	1.07 (0.92-1.24)
UC adult	157 (31%)	244 (48%)	105 (21%)	506	0.839	1.03 (0.78-1.36)		0.55	0.469	1.06 (0.90-1.25)
UC pediatric	55 (34%)	71 (44%)	36 (22%)	162	0.779	0.94 (0.63-1.42)		0.56	0.473	1.09 (0.86-1.39)
Controls	214 (29%)	376 (50%)	159 (21%)	749	-			0.54
IL23R
rs7517847					(Aa aa vs AA)		G
CD Total	366 (51%)	305 (42%)	52 (7%)	723	< 0.01	0.63 (0.51-0.77)		0.28	< 0.01	0.64 (0.55-0.75)
CD adult	273 (51%)	225 (42%)	42 (8%)	540	< 0.01	0.63 (0.50-0.79)		0.29	< 0.01	0.65 (0.55-0.78)
CD pediatric	93 (51%)	80 (44%)	10 (5%)	183	< 0.01	0.62 (0.45-0.86)		0.27	< 0.01	0.61 (0.48-0.79)
UC Total	326 (41%)	390 (49%)	88 (11%)	804	0.567	0.94 (0.77-1.16)		0.35	0.111	0.89 (0.76-1.03)
UC adult	259 (41%)	301 (48%)	71 (11%)	631	0.468	0.92 (0.74-1.15)		0.35	0.121	0.88 (0.75-1.03)
UC pediatric	67 (39%)	89 (51%)	17 (10%)	173	0.927	1.02 (0.72-1.43)		0.36	0.400	0.90 (0.70-1.15)
Controls	280 (39%)	328 (46%)	108 (15%)	716	-			0.38
rs11209026							A
CD Total	675 (92%)	60 (8%)	0 (0%)	735	0.005	0.61 (0.43-0.86)		0.04	0.005	0.62 (0.45-0.87)
CD adult	502 (91%)	50 (9%)	0 (0%)	552	0.042	0.69 (0.48-0.99)		0.05	0.041	0.69 (0.49-0.99)
CD pediatric	173 (95%)	10 (5%)	0 (0%)	183	0.006	0.40 (0.20-0.78)		0.03	0.007	0.41 (0.21-0.80)
UC Total	750 (91%)	72 (9%)	1 (0%)	823	0.015	0.67 (0.48 - 0.93)		0.04	0.019	0.69 (0.50-0.94)
UC adult	589 (91%)	58 (9%)	1(0%)	648	0.035	0.69 (0.49-0.98)		0.05	0.043	0.71 (0.51-0.99)
UC pediatric	161 (92%)	14 (8%)	0 (0%)	175	0.085	0.60 (0.33-1.08)		0.04	0.087	0.61 (0.34-1.08)
Controls	634 (87%)	91 (13%)	1 (0%)	726	-			0.06

“A” refers to wild type and “a” to mutated allele. Adult and pediatric subgroups are divided on the basis of the age at diagnosis (≥ 19 years and < 19 years, respectively).

Table 3 Haplotypes frequency of he two IL23R variants in IBD patients and controls

Haplotype		IBD		CD		UC
rs7517847	rs11209026	Cases/Controls (% Haplotype)	P	Cases/Controls (% Haplotype)	P	Cases/Controls (% Haplotype)	P
T	G	68/62	0.0032	71/62	< 0.01	65/62	0.2166
G	G	28/32	0.0548	25/32	< 0.01	31/32	0.7398
G	A	4/6	0.0121	4/6	0.0088	4/6	0.0578

Table 4 Transmission disequilibrium test (TDT) for rs7517847 and rs11209026 IL23R SNPs for IBD, CD, and UC

Marker	Over-trans	Haplotype	IBD (n = 273)			CD (n = 138)			UC (n = 135)
			T	U	P	T	U	P	T	U	P
rs7517847	T		137	101	0.0196	74	40	0.0015	63	61	0.8575
rs11209026	G		34	19	0.0394	18	9	0.0833	16	10	0.2393
		TG	141	100	0.0084	52	60	0.0012	45	34	0.5947
		GG	97	123	0.0790	50	39	0.0098	28	28	0.9940
		GA	14	24	0.1088	12	20	0.0585	9	13	0.6555
		TA	5	10	0.1831	13	8	0.7037	-	-	-
rs2241880	G		-	-	-	90	62	0.0231	-	-	-

TDT haplotypes are also included. Data of over-transmitted allele are given, with counts of transmitted (T) and un-transmitted (U) alleles.

Table 5 Genotype and allele frequency distribution of ATG16L1 and IL23R SNPs in CD cases stratified by phenotypic subgroups, (n)

SNP/gene genotype	rs2241880 ATG16L1					rs7517847 IL23R					rs11209026 IL23R
	AA (105)	AG (335)	GG (227)	Total (667)	Freq (G) 0.501	GG (52)	GT (305)	TT (366)	Total (723)	Freq (G) 0.283	AA (0)	AG (60)	GG (675)	Total (735)	Freq (A) 0.041
Sex
Male	54	193	126	373	0.597	28	169	212	409	0.275	0	27	390	417	0.032
Female	51	142	101	294	0.585	24	136	154	314	0.293	0	33	285	318	0.052
Age at diagnosis (yr)
≤ 16 (A1)	28	72	53	153	0.582	9	76	74	159	0.296	0	9	150	159	0.028
17-40 (A2)	56	180	123	359	0.593	24	160	209	393	0.265	0	29	378	407	0.036
> 40 (A3)	20	71	40	131	0.576	14	57	73	144	0.295	0	19	123	142	0.067
Disease localization
Ileum (L1 ± L4)	28	97	67	192	0.602	12	86	118	216	0.255	0	21	200	221	0.048
Colon (L2 ± L4)	31	92	48	171	0.550	10	76	104	190	0.253	0	18	170	188	0.048
Ileo-colon (L3 ± L4)	43	131	101	275	0.605	25	131	129	285	0.318	0	19	276	295	0.032
Upper GI (L4)	2	4	1	7	0.429	0	2	4	6	0.167	0	0	6	6	0.000
Disease behavior
Inflammatory (B1)	44	154	98	296	0.591	21	133	162	316	0.277	0	25	294	319	0.039
Stricturing (B2)	22	79	46	147	0.582	10	64	82	156	0.269	0	16	145	161	0.050
Penetrating (B3)	38	85	70	193	0.583	17	93	103	213	0.298	0	17	201	218	0.039
Perianal disease
Yes	14	52	37	103	0.612	8	54	59	121	0.289	0	11	113	124	0.044
No	89	269	175	533	0.581	40	233	293	566	0.277	0	46	529	575	0.040
Smoking history
No	57	168	116	341	0.587	24	149	191	364	0.271	0	29	339	368	0.039
Yes	32	105	71	208	0.594	20	100	107	227	0.308	0	20	213	233	0.043
Ex	14	39	30	83	0.596	3	41	49	93	0.253	0	8	88	96	0.042
Surgery
Yes	34	91	68	193	0.588	15	83	113	211	0.268	0	16	202	218	0.037
No	70	231	149	450	0.588	32	211	241	484	0.284	0	42	447	489	0.043

Only patients with at least 2 years of follow-up from diagnosis were included.

Table 6 Genotype and allele frequencies of ATG16L1 and IL23R SNPs in UC cases stratified by phenotypic subgroups, (n)

SNP/gene genotype	rs2241880 ATG16L1					rs7517847 IL23R					rs11209026 IL23R
	AA (141)	AG (315)	GG (212)	Total (668)	Freq (G) 0.553	GG (88)	GT (390)	TT (326)	Total (804)	Freq (G) 0.352	AA (1)	AG (72)	GG (750)	Total (823)	Freq (A) 0.045
Sex
Male	77	183	112	372	0.547	41	236	185	462	0.344	0	45	432	477	0.047
Female	64	132	100	296	0.561	47	154	141	342	0.363	1	27	318	346	0.042
Age at diagnosis (yr)
≤ 16 (A1)	30	58	48	136	0.566	15	76	49	140	0.379	0	11	129	140	0.039
17-40 (A2)	79	159	102	340	0.534	40	213	170	423	0.346	0	33	401	434	0.038
> 40 (A3)	24	84	55	163	0.595	28	86	89	203	0.350	1	25	184	210	0.064
Disease localization
Rectum	18	41	15	74	0.480	13	38	39	90	0.356	1	8	80	89	0.056
Rectum-sigmoid	20	55	39	114	0.583	20	82	46	148	0.412	0	21	134	155	0.068
Left colon	41	101	64	206	0.556	27	104	100	231	0.342	0	19	215	234	0.041
Colon	54	104	86	244	0.566	24	148	124	296	0.331	0	22	283	305	0.036
Perianal disease
Yes	3	3	6	12	0.625	0	6	8	14	0.214	0	2	13	15	0.067
No	129	298	198	625	0.555	82	367	301	750	0.354	1	67	699	767	0.045
Smoking history
No	81	173	125	379	0.558	51	203	185	439	0.347	1	38	408	447	0.045
Yes	25	54	25	104	0.500	10	65	41	116	0.366	0	12	104	116	0.052
Ex	25	72	51	148	0.588	20	105	77	202	0.359	0	18	191	209	0.043
Surgery
Yes	11	33	26	70	0.607	9	37	35	81	0.340	0	9	74	83	0.054
No	122	268	178	568	0.549	74	337	274	685	0.354	1	61	638	700	0.045

Only patients with at least 2 years of follow-up from diagnosis were included.

Table 7 Logistic regression analysis

Genes	P	OR	95% CI
CARD15	2.34E-14	2.908	2.211-3.825
ATG	0.008	1.442	1.099-1.894
ATG (adj CARD15)	0.014	1.439	1.077-1.924
ATG* CARD15	0.692	0.851	0.382-1.894
IL23	0.005	0.613	0.435-0.863
IL23 (adj CARD15)	0.029	0.629	0.414-0.954
IL23* CARD15	0.981	1.010	0.432-2.360
OCTN	0.028	1.434	1.039-1.980
OCTN (adj CARD15)	0.021	1.479	1.061-2.061
TTCC* CARD15	0.632	0.821	0.367-1.839
ATG*IL23*OCTN*CARD15	0.428	0.651	0.226-1.880

Individual contribution of CARD15 (at least 1 variant), ATG16L1 (GG/AG vs AA), IL23R rs11209026 (AG/AA vs GG), and OCTN dyploype (TTCC) to risk CD. adj CARD15: Contribution from the term after adjustment for CARD15 genotype.