Clinical factors
1. Patients’ characteristics and baseline data
The study design is summarized in Figure 1.
In the anti-TNF naïve group, the cumulative clinical relapse rates were analyzed in 373 patients; 75.9% (283 patients) in IFX-treated and 24.1% (90 patients) in ADA-treated. The baseline characteristics of patients are summarized in Table 1. The median age at initial CD diagnosis and disease duration at the start of the anti-TNF therapy were 21.0 and 6.2 years, respectively. The identified disease locations were as follows: 51 ileal, 54 colonic, and 268 ileocolonic. As for disease behavior, 152, 144, and 77 patients had inflammation, stenosis, and fistula types, respectively. Two hundred and fifty-four patients (68.1%) had perianal lesions, and 203 patients (54.4%) had a history of intestinal resection. Fifty-six patients (15.0%) were treated with concomitant thiopurine.
In the anti-TNF switch group, the cumulative clinical relapse rates were analyzed in 91 cases (IFX to ADA, N = 80; 87.9% and ADA to IFX, N = 11; 12.1%). The baseline characteristics of patients are summarized in Table 2. The median age at CD diagnosis and disease duration at the start of the anti-TNF were 21.0 and 12.4 years, respectively. The identified disease locations were as follows: 5 ileal, 16 colonic, and 70 ileocolonic. As for disease behavior, 32, 32, and 27 patients had inflammation, stenosis, and fistula types. Seventy-four patients (81.3%) had anal lesions, and 63 patients (69.2%) had a history of intestinal resection. Twenty-two patients (24.2%) were treated with concomitant thiopurine. The reason for ADA to IFX switch was LOR, whereas the reasons for IFX to ADA switch were LOR in 45 patients (56.2 %), adverse events in 31 patients (38.8 %), and other reasons in four patients (5.0 %).
2. Overall relapse-free survival
The cumulative relapse-free survival rates of the anti-TNF naïve group were 73.5%, 52.6%, and 35.5% at 1, 3, and 5 years, respectively (Supplementary Figure 1). Among patients in the anti-TNF switch group, 75 had a clinical relapse during their disease course. The cumulative relapse-free survival rates of the anti-TNF switch group were 59.0%, 32.8%, and 19.3% at 1, 3, and 5 years, respectively. The cumulative relapse-free survival rate was significantly higher in the anti-TNF naïve group than in the anti-TNF switch group (P = 3.32E-5).
3. Factors Associated with relapse-free survival
3-1. Univariate Analysis
The association between clinical factors and relapse-free survival rate of the anti-TNF naïve group is summarized in Table 1. The cumulative relapse-free survival rates were significantly higher when the age at diagnosis was ≥ 21 years (P = 0.012), in the group without anal disease (P = 0.026), and in the group with baseline serum albumin levels ≥ 3.7 g/dL (P = 0.00022). Kaplan–Meier curves for each clinical factor are shown in Figures 2a, 2b, and 2c.
The association between clinical factors and relapse-free survival rate of the anti-TNF switch group is summarized in Table 2. The cumulative relapse-free survival rates were significantly lower in the group treated with IFX after ADA (P = 2.95E-7), the group with inflammatory disease behavior (P = 0.045), the group without previous intestinal resection (P = 8.42E-5), and those with baseline serum albumin levels < 3.6 g/dL (P = 0.014) (Supplementary Figures 2 a, 2b, 2c and 2d).
3-2. Multivariate Analysis
The results of the multivariate analysis of the anti-TNF naïve group are summarized in Table 1. Age at diagnosis < 21 years, anal disease, and baseline serum albumin levels < 3.7 g/dL were identified as independent risk factors for the early clinical relapse (hazard ratio: HR = 1.76, 1.43 and 1.36; P = 0.00029, 0.044 and 0.045, respectively).
The results of the multivariate analysis of the anti-TNF switch group are summarized in Table 2. Previous intestinal resection was significantly associated with the cumulative relapse-free survival rates (HR = 0.42; P = 0.0075).
Genetic factors
1. GWAS of clinical relapse-free rates
A total of 275 patients with CD were analyzed in the study. The independent risk factors that were identified by the univariate and multivariate analysis were used as covariates in GWAS (age at diagnosis, anal disease, and baseline serum albumin levels).
The Manhattan plot of the GWAS is shown in Figure 3. The genomic inflation factor (lambda GC) was 1.03. Although no SNPs reached genome-wide significance, 80 SNPs were identified as candidate SNPs for relapse-free survival. These candidate SNPs were summarized into 15 loci (Table 3). The SNP with the lowest P-value was rs12613485 (HR = 2.44; P = 3.42E-7). The regional plot around rs12613485 is shown in Figure 4a. This SNP was located near Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Regulatory Factor X 8 (RFX8). Additionally, rs1029898 (HR = 1.76; P = 2.71E-7) and rs338887 (HR = 2.78; P = 6.15E-7) showed relatively strong associations to relapse (P < 1E-6). Rs1029898 is located near DnaJ Heat Shock Protein Family (Hsp40) Member B6 (DNAJB6) and rs338887 is an intronic variant of PRELI Domain-Containing Protein 2 (PRELID2). Rs338887 is associated with the expression of PRELID2 in multiple tissues with the strongest association in the colon (P = 3.0E-52). The regional plots around rs1029898 and rs338887 are shown in Figures 4b and 4c. Kaplan–Meier curves for the each SNP are shown in Supplementary Figures 3a, 3b and 3c.
Furthermore, we conducted a replication analysis of the SNPs which were reportedly associated with the therapeutic outcomes of anti-TNFα for inflammatory bowel disease (IBD) 21 22 23 24 25 (Supplementary Table 1). Only one out of the 13 candidate SNPs (rs1801274) was associated with clinical relapse in our study (P =1.96E-2).
2. Pathway analysis
Pathway analysis found nominally significant associations with several pathways (Supplementary Table 2). The top two pathways were REACTOME Signaling by transforming growth factor (TGF) β family members (P = 3.06E-4) and REACTOME Signaling by TGF β receptor complex (P = 7.80E-4).