Ts with established/late lesions and normal controls. doi:10.1371/journal.pone.0054562.gimmunological events that drive the initial lesions of CD. To this end, we collected biopsies from CD patients 
with or without endoscopic recurrence and looked at the T cell and macrophage mucosal infiltration by immunofluorescence. The number of CD3+ cells was significantly higher in biopsies taken from the neoterminal ileum of CD patients without endoscopic recurrence than in normal control biopsies and was further increased in biopsies taken from patients with endoscopic recurrence and in surgical specimens with established lesions, with no significant difference between these later two groups (Fig. 1A and C). Similarly, biopsies taken from the neo-terminal ileum of CD patients with no endoscopic recurrence contained more CD68+ cells than control biopsies (Fig. 1B and D). Moreover, CD68+ cells were moreabundant in biopsies with endoscopic recurrence and in SR3029 web samples with established lesions than in biopsies without endoscopic lesions (Fig. 1B and D). These data indicate that, even in the absence of endoscopic lesions, the mucosa of the neo-terminal ileum of CD patients is markedly infiltrated with inflammatory cells.The Early Stage of CD Inflammation is Dominated by Th1 Cytokines while a Mixed Th1/Th17 Response is Seen in Areas with Early or Established LesionsNext we examined various Th cell-related cytokines in CD and control samples by real-time PCR and flow-cytometry. Expression of IFN-c 
transcripts was more pronounced in the biopsies takenDistinct Cytokine Patterns in CDTable 1. Cytokine expression in pre-operative (established) and post-operative ileal samples of Crohn’s disease patients.Table 2. Cytokine expression in pre-operative (established) and post-operative ileal samples of Crohn’s disease patients.Established CD (n = 4) Z-360 web Median (range) IFN-c IL-21 IL-17A IL-4 IL-5 IL-13 TNF-a IL-6 18 (15?9) 2,9 (2,2?,2) 16,5 (10,9?6) 7,7 (7,4?) 49,9 (30?6,2) 23,6 (9?0) 5,2 (4,9?,3) 78,4 (14,3?94)CD recurrence i0-i1 (n = 4) Median (range) 76 (92?34) 4,3 (3,6?0,8) 9 (5?0) 4,5 (1?0,4) 2,1 (1,8?3,8) 12,4 (4,7?2) 20,1 (19,9?2,8) 10,4 (7?3,8) IFN-c IL-21 IL-17A IL-4 IL-5 IL-13 TNF-a IL-Established CD (n = 5) Median (range) 140,8 (18?26) 3 (2,5?,9) 57,6 (10?68) 225,5 (36,2?96) 47,1 (24,2?91,7) 30 (12?09) 7,8 (1,4?0,7) 92,4 (32,6?88,9)CD recurrence i2-i4 (n = 5) Median (range) 68,3 (32,5?60) 4,6 (2?0,2) 50 (45,7?43,4) 38,3 (17,3?4,6) 41,5 (29?27,5) 32,7 (13,3?20) 21,6 (7,8?0,7) 60,7 (13,8?42)Post-operative samples were taken from areas with no endoscopic lesions. doi:10.1371/journal.pone.0054562.tPost-operative samples were taken from areas with endoscopic recurrence. doi:10.1371/journal.pone.0054562.tfrom the 1326631 neo-terminal ileum, either with or without endoscopic recurrence, and specimens with established lesions in comparison to control samples (Fig. 2A). Although there was variability in the content of transcripts among samples, no significant difference in terms of IFN-c RNA was seen in mucosal samples taken from the 3 subgroups of CD patients (Fig. 2A). These data were confirmed by analysis of the percentages of IFN-c-secreting cells in CD3+ LPMC samples isolated from biopsies and specimens of patients and controls (Fig. 2B). Since, in CD, IFN-c-secreting cells produce IL-21, [24] we analysed IL-21in the same samples used for measuring IFN-c. Up-regulation of IL-21 RNA and protein was seen in CD samples taken from the neo-terminal ileum, either with or wit.Ts with established/late lesions and normal controls. doi:10.1371/journal.pone.0054562.gimmunological events that drive the initial lesions of CD. To this end, we collected biopsies from CD patients with or without endoscopic recurrence and looked at the T cell and macrophage mucosal infiltration by immunofluorescence. The number of CD3+ cells was significantly higher in biopsies taken from the neoterminal ileum of CD patients without endoscopic recurrence than in normal control biopsies and was further increased in biopsies taken from patients with endoscopic recurrence and in surgical specimens with established lesions, with no significant difference between these later two groups (Fig. 1A and C). Similarly, biopsies taken from the neo-terminal ileum of CD patients with no endoscopic recurrence contained more CD68+ cells than control biopsies (Fig. 1B and D). Moreover, CD68+ cells were moreabundant in biopsies with endoscopic recurrence and in samples with established lesions than in biopsies without endoscopic lesions (Fig. 1B and D). These data indicate that, even in the absence of endoscopic lesions, the mucosa of the neo-terminal ileum of CD patients is markedly infiltrated with inflammatory cells.The Early Stage of CD Inflammation is Dominated by Th1 Cytokines while a Mixed Th1/Th17 Response is Seen in Areas with Early or Established LesionsNext we examined various Th cell-related cytokines in CD and control samples by real-time PCR and flow-cytometry. Expression of IFN-c transcripts was more pronounced in the biopsies takenDistinct Cytokine Patterns in CDTable 1. Cytokine expression in pre-operative (established) and post-operative ileal samples of Crohn’s disease patients.Table 2. Cytokine expression in pre-operative (established) and post-operative ileal samples of Crohn’s disease patients.Established CD (n = 4) Median (range) IFN-c IL-21 IL-17A IL-4 IL-5 IL-13 TNF-a IL-6 18 (15?9) 2,9 (2,2?,2) 16,5 (10,9?6) 7,7 (7,4?) 49,9 (30?6,2) 23,6 (9?0) 5,2 (4,9?,3) 78,4 (14,3?94)CD recurrence i0-i1 (n = 4) Median (range) 76 (92?34) 4,3 (3,6?0,8) 9 (5?0) 4,5 (1?0,4) 2,1 (1,8?3,8) 12,4 (4,7?2) 20,1 (19,9?2,8) 10,4 (7?3,8) IFN-c IL-21 IL-17A IL-4 IL-5 IL-13 TNF-a IL-Established CD (n = 5) Median (range) 140,8 (18?26) 3 (2,5?,9) 57,6 (10?68) 225,5 (36,2?96) 47,1 (24,2?91,7) 30 (12?09) 7,8 (1,4?0,7) 92,4 (32,6?88,9)CD recurrence i2-i4 (n = 5) Median (range) 68,3 (32,5?60) 4,6 (2?0,2) 50 (45,7?43,4) 38,3 (17,3?4,6) 41,5 (29?27,5) 32,7 (13,3?20) 21,6 (7,8?0,7) 60,7 (13,8?42)Post-operative samples were taken from areas with no endoscopic lesions. doi:10.1371/journal.pone.0054562.tPost-operative samples were taken from areas with endoscopic recurrence. doi:10.1371/journal.pone.0054562.tfrom the 1326631 neo-terminal ileum, either with or without endoscopic recurrence, and specimens with established lesions in comparison to control samples (Fig. 2A). Although there was variability in the content of transcripts among samples, no significant difference in terms of IFN-c RNA was seen in mucosal samples taken from the 3 subgroups of CD patients (Fig. 2A). These data were confirmed by analysis of the percentages of IFN-c-secreting cells in CD3+ LPMC samples isolated from biopsies and specimens of patients and controls (Fig. 2B). Since, in CD, IFN-c-secreting cells produce IL-21, [24] we analysed IL-21in the same samples used for measuring IFN-c. Up-regulation of IL-21 RNA and protein was seen in CD samples taken from the neo-terminal ileum, either with or wit.
