Reagents were from Sigma-Aldrich (Milan, Italy) unless specified. Lamina propria mononuclear cells (LPMC) were SR-3029 isolated from ileal biopsies and get Nafarelin intestinal resection specimens of CD patients and normal controls as described elsewhere. [5] LPMC were suspended in RPMI 1640 medium, supplemented with 10 inactivated fetal bovine serum (FBS), penicillin (P) (100 U/ml), and streptomycin (S) (100 mg/ml) (Life TechnologiesGibcoCRL, Milan, Italy). LPMC were used to assess cytokine expression by flow cytometry.Statistical AnalysisStatistical differences were assessed with the 11967625 GraphPad Prism statistical PC program (GraphPad Software, San Diego, CA). Comparisons were made between each CD subgroup and normal controls, and in CD group between early and established lesions using the Mann-Whitney U test (for cytokine expression) and the Student t-test (for CD3- and CD68-infiltrates). A p value of less than 0.05 was considered statistically significant.RNA Extraction, cDNA Preparation, and Real-time PCRRNA was extracted from fresh mucosal samples of CD patients and normal controls using Trizol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). A constant amount of RNA (1 mg per sample) was reverse-transcribed into cDNA, and this was amplified using a buy 548-04-9 sybergreen-based PCR (BioRad, Hercules, CA). PCR conditions were as follows: denaturation 1 min at 95uC, annealing 30 s at 61uC for IL-17A and IL-6; 58uC for IFN-c, IL-21, IL-13 and IL-23p19; 62uC for TNF-a and IL-5, and 60uC for b-actin followed by 30 s extension at 72uC. PrimerResults Clinical and Endoscopic DataNo endoscopic recurrence was documented in 8 out of 19 (42 ) patients. Of the remaining 11 patients with endoscopic recurrence,Distinct Cytokine Patterns in CDFigure 2. IFN-c and IL-21 are up-regulated in the initial phase of CD inflammation. Transcripts for IFN-c (A) and IL-21 (C) were analysed in ileal samples taken from CD patients with no endoscopic recurrence (i0 1), CD patients with endoscopic recurrence (i2 4), CD patients with established/late lesions and normal controls by real-time PCR and normalized to b-actin. Data indicate individual values of cytokines in single biopsies and horizontal bars represent the median value. B . Flow cytometry analysis of IFN-c- and CASIN web IL-21-producing cells in CD3+LPMC isolated from CD patients with no endoscopic recurrence (i0 1), CD patients with endoscopic recurrence (i2 4), CD patients with established/late lesions and normal controls. LPMC were gated on CD3+ cells and subsequently analysed for the expression of IFN-c (B) and IL-21 (D). Data indicate individual values and horizontal bars represent the median value. Right insets: representative histograms of IFN-c- and IL-21-producing CD3+cells in LPMC isolated from 1 CD patient with no endoscopic recurrence (i0), 1 CD patient with endoscopic recurrence (i4), 1 CD patient with established/late lesions and 1 normal control. Staining with a control IgG is also shown. Numbers above lines indicate the percentages of positive cells. doi:10.1371/journal.pone.0054562.g6 had diffuse inflammation and large ulcers (i4 grade), 2 had diffuse aphthous ileitis (i3 grade) and 3 had more than 5 aphthous lesion with normal mucosa between the lesions (i2 grade). The 5 patients with CDAI .150 had endoscopic recurrence (i2-i4).CD3+ and CD68+ Cells Infiltrate the Neo-terminal Ileum of CD Patients Independently of the Presence of Endoscopic RecurrenceFollowing ileocolonic resection, the new CD lesion.Reagents were from Sigma-Aldrich (Milan, Italy) unless specified. Lamina propria mononuclear cells (LPMC) were isolated from ileal biopsies and intestinal resection specimens of CD patients and normal controls as described elsewhere. [5] LPMC were suspended in RPMI 1640 medium, supplemented with 10 inactivated fetal bovine serum (FBS), penicillin (P) (100 U/ml), and streptomycin (S) (100 mg/ml) (Life TechnologiesGibcoCRL, Milan, Italy). LPMC were used to assess cytokine expression by flow cytometry.Statistical AnalysisStatistical differences were assessed with the 11967625 GraphPad Prism statistical PC program (GraphPad Software, San Diego, CA). Comparisons were made between each CD subgroup and normal controls, and in CD group between early and established lesions using the Mann-Whitney U test (for cytokine expression) and the Student t-test (for CD3- and CD68-infiltrates). A p value of less than 0.05 was considered statistically significant.RNA Extraction, cDNA Preparation, and Real-time PCRRNA was extracted from fresh mucosal samples of CD patients and normal controls using Trizol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). A constant amount of RNA (1 mg per sample) was reverse-transcribed into cDNA, and this was amplified using a sybergreen-based PCR (BioRad, Hercules, CA). PCR conditions were as follows: denaturation 1 min at 95uC, annealing 30 s at 61uC for IL-17A and IL-6; 58uC for IFN-c, IL-21, IL-13 and IL-23p19; 62uC for TNF-a and IL-5, and 60uC for b-actin followed by 30 s extension at 72uC. PrimerResults Clinical and Endoscopic DataNo endoscopic recurrence was documented in 8 out of 19 (42 ) patients. Of the remaining 11 patients with endoscopic recurrence,Distinct Cytokine Patterns in CDFigure 2. IFN-c and IL-21 are up-regulated in the initial phase of CD inflammation. Transcripts for IFN-c (A) and IL-21 (C) were analysed in ileal samples taken from CD patients with no endoscopic recurrence (i0 1), CD patients with endoscopic recurrence (i2 4), CD patients with established/late lesions and normal controls by real-time PCR and normalized to b-actin. Data indicate individual values of cytokines in single biopsies and horizontal bars represent the median value. B . Flow cytometry analysis of IFN-c- and IL-21-producing cells in CD3+LPMC isolated from CD patients with no endoscopic recurrence (i0 1), CD patients with endoscopic recurrence (i2 4), CD patients with established/late lesions and normal controls. LPMC were gated on CD3+ cells and subsequently analysed for the expression of IFN-c (B) and IL-21 (D). Data indicate individual values and horizontal bars represent the median value. Right insets: representative histograms of IFN-c- and IL-21-producing CD3+cells in LPMC isolated from 1 CD patient with no endoscopic recurrence (i0), 1 CD patient with endoscopic recurrence (i4), 1 CD patient with established/late lesions and 1 normal control. Staining with a control IgG is also shown. Numbers above lines indicate the percentages of positive cells. doi:10.1371/journal.pone.0054562.g6 had diffuse inflammation and large ulcers (i4 grade), 2 had diffuse aphthous ileitis (i3 grade) and 3 had more than 5 aphthous lesion with normal mucosa between the lesions (i2 grade). The 5 patients with CDAI .150 had endoscopic recurrence (i2-i4).CD3+ and CD68+ Cells Infiltrate the Neo-terminal Ileum of CD Patients Independently of the Presence of Endoscopic RecurrenceFollowing ileocolonic resection, the new CD lesion.Reagents were from Sigma-Aldrich (Milan, Italy) unless specified. Lamina propria mononuclear cells (LPMC) were isolated from ileal biopsies and intestinal resection specimens of CD patients and normal controls as described elsewhere. [5] LPMC were suspended in RPMI 1640 medium, supplemented with 10 inactivated fetal bovine serum (FBS), penicillin (P) (100 U/ml), and streptomycin (S) (100 mg/ml) (Life TechnologiesGibcoCRL, Milan, Italy). LPMC were used to assess cytokine expression by flow cytometry.Statistical AnalysisStatistical differences were assessed with the 11967625 GraphPad Prism statistical PC program (GraphPad Software, San Diego, CA). Comparisons were made between each CD subgroup and normal controls, and in CD group between early and established lesions using the Mann-Whitney U test (for cytokine expression) and the Student t-test (for CD3- and CD68-infiltrates). A p value of less than 0.05 was considered statistically significant.RNA Extraction, cDNA Preparation, and Real-time PCRRNA was extracted from fresh mucosal samples of CD patients and normal controls using Trizol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). A constant amount of RNA (1 mg per sample) was reverse-transcribed into cDNA, and this was amplified using a sybergreen-based PCR (BioRad, Hercules, CA). PCR conditions were as follows: denaturation 1 min at 95uC, annealing 30 s at 61uC for IL-17A and IL-6; 58uC for IFN-c, IL-21, IL-13 and IL-23p19; 62uC for TNF-a and IL-5, and 60uC for b-actin followed by 30 s extension at 72uC. PrimerResults Clinical and Endoscopic DataNo endoscopic recurrence was documented in 8 out of 19 (42 ) patients. Of the remaining 11 patients with endoscopic recurrence,Distinct Cytokine Patterns in CDFigure 2. IFN-c and IL-21 are up-regulated in the initial phase of CD inflammation. Transcripts for IFN-c (A) and IL-21 (C) were analysed in ileal samples taken from CD patients with no endoscopic recurrence (i0 1), CD patients with endoscopic recurrence (i2 4), CD patients with established/late lesions and normal controls by real-time PCR and normalized to b-actin. Data indicate individual values of cytokines in single biopsies and horizontal bars represent the median value. B . Flow cytometry analysis of IFN-c- and IL-21-producing cells in CD3+LPMC isolated from CD patients with no endoscopic recurrence (i0 1), CD patients with endoscopic recurrence (i2 4), CD patients with established/late lesions and normal controls. LPMC were gated on CD3+ cells and subsequently analysed for the expression of IFN-c (B) and IL-21 (D). Data indicate individual values and horizontal bars represent the median value. Right insets: representative histograms of IFN-c- and IL-21-producing CD3+cells in LPMC isolated from 1 CD patient with no endoscopic recurrence (i0), 1 CD patient with endoscopic recurrence (i4), 1 CD patient with established/late lesions and 1 normal control. Staining with a control IgG is also shown. Numbers above lines indicate the percentages of positive cells. doi:10.1371/journal.pone.0054562.g6 had diffuse inflammation and large ulcers (i4 grade), 2 had diffuse aphthous ileitis (i3 grade) and 3 had more than 5 aphthous lesion with normal mucosa between the lesions (i2 grade). The 5 patients with CDAI .150 had endoscopic recurrence (i2-i4).CD3+ and CD68+ Cells Infiltrate the Neo-terminal Ileum of CD Patients Independently of the Presence of Endoscopic RecurrenceFollowing ileocolonic resection, the new CD lesion.Reagents were from Sigma-Aldrich (Milan, Italy) unless specified. Lamina propria mononuclear cells (LPMC) were isolated from ileal biopsies and intestinal resection specimens of CD patients and normal controls as described elsewhere. [5] LPMC were suspended in RPMI 1640 medium, supplemented with 10 inactivated fetal bovine serum (FBS), penicillin (P) (100 U/ml), and streptomycin (S) (100 mg/ml) (Life TechnologiesGibcoCRL, Milan, Italy). LPMC were used to assess cytokine expression by flow cytometry.Statistical AnalysisStatistical differences were assessed with the 11967625 GraphPad Prism statistical PC program (GraphPad Software, San Diego, CA). Comparisons were made between each CD subgroup and normal controls, and in CD group between early and established lesions using the Mann-Whitney U test (for cytokine expression) and the Student t-test (for CD3- and CD68-infiltrates). A p value of less than 0.05 was considered statistically significant.RNA Extraction, cDNA Preparation, and Real-time PCRRNA was extracted from fresh mucosal samples of CD patients and normal controls using Trizol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). A constant amount of RNA (1 mg per sample) was reverse-transcribed into cDNA, and this was amplified using a sybergreen-based PCR (BioRad, Hercules, CA). PCR conditions were as follows: denaturation 1 min at 95uC, annealing 30 s at 61uC for IL-17A and IL-6; 58uC for IFN-c, IL-21, IL-13 and IL-23p19; 62uC for TNF-a and IL-5, and 60uC for b-actin followed by 30 s extension at 72uC. PrimerResults Clinical and Endoscopic DataNo endoscopic recurrence was documented in 8 out of 19 (42 ) patients. Of the remaining 11 patients with endoscopic recurrence,Distinct Cytokine Patterns in CDFigure 2. IFN-c and IL-21 are up-regulated in the initial phase of CD inflammation. Transcripts for IFN-c (A) and IL-21 (C) were analysed in ileal samples taken from CD patients with no endoscopic recurrence (i0 1), CD patients with endoscopic recurrence (i2 4), CD patients with established/late lesions and normal controls by real-time PCR and normalized to b-actin. Data indicate individual values of cytokines in single biopsies and horizontal bars represent the median value. B . Flow cytometry analysis of IFN-c- and IL-21-producing cells in CD3+LPMC isolated from CD patients with no endoscopic recurrence (i0 1), CD patients with endoscopic recurrence (i2 4), CD patients with established/late lesions and normal controls. LPMC were gated on CD3+ cells and subsequently analysed for the expression of IFN-c (B) and IL-21 (D). Data indicate individual values and horizontal bars represent the median value. Right insets: representative histograms of IFN-c- and IL-21-producing CD3+cells in LPMC isolated from 1 CD patient with no endoscopic recurrence (i0), 1 CD patient with endoscopic recurrence (i4), 1 CD patient with established/late lesions and 1 normal control. Staining with a control IgG is also shown. Numbers above lines indicate the percentages of positive cells. doi:10.1371/journal.pone.0054562.g6 had diffuse inflammation and large ulcers (i4 grade), 2 had diffuse aphthous ileitis (i3 grade) and 3 had more than 5 aphthous lesion with normal mucosa between the lesions (i2 grade). The 5 patients with CDAI .150 had endoscopic recurrence (i2-i4).CD3+ and CD68+ Cells Infiltrate the Neo-terminal Ileum of CD Patients Independently of the Presence of Endoscopic RecurrenceFollowing ileocolonic resection, the new CD lesion.