TABLE 1.
Abnormal STP activity in patients with various forms of IBD (diagnosis), and in responder versus non-responder patients, pre-treatment and during treatment. Diagnosis: Comparison between IBD and healthy control STP activity; indicated STPs have higher PAS in IBD group. Pre-treatment prediction of response to anti-TNFα treatment: comparison between pre-treatment STP activity of responder versus non-responder groups; indicated STPs have higher PAS in responder patient group. Individual patient response assessment during treatment: comparison between delta (for individual patients) in STP activity before - during treatment of responder versus delta in non-responder groups; indicated STPs have higher delta PAS in responder patients. Patient group response assessment during treatment: Comparison patient responder with non-responder groups during treatment; indicated STPs have higher PAS in responder group during treatment. Indicated STPs in the table: STPs with significantly higher PAS (p < 0.01); between brackets: STPs with marginal significance (p < 0.05). See Supplementary Table S1 for absolute p-values. For specifics of patient inclusion, dosing and sample type, see Methods for description of datasets. NA: Not applicable.
| CD GSE52746 | CDc GSE16879 | CDi GSE16879 | UC GSE16879 | UC GSE23597 | UC GSE23597 | |
|---|---|---|---|---|---|---|
| Disease localization | Colon and ileum | Colon | Ileum | Colon | Colon | Colon |
| Biopsy | Colon, inflamed lesion, before and after 12 weeks | Colon, inflamed lesion; before and after 4–6 weeks | Colon, inflamed lesion; Before and after 4–6 weeks | Colon, inflamed lesion; Before and after 4–6 weeks | Colon, 15–20 cm from anal verge (irrespective of lesions), before and after 8 weeks | Colon, 15–20 cm from anal verge (irrespective of lesions), before and after 30 weeks |
| Treatment | Remission induction; Adalimumab (s.c.) or infliximab, details in Methods | Remission induction; Infliximab, 5 mg/kg, details in Methods | Remission induction; Infliximab, 5 mg/kg, details in Methods | Remission induction; Infliximab, 5 mg/kg, details in Methods | Remission induction; Infliximab (groups with 5 and 10 mg/kg combined), details in Methods | Maintenance; Infliximab (groups with 5 and 10 mg/kg combined), details in Methods |
| Diagnosis (Figure 1; Supplementary Table S1) | AR | AR | AR | |||
| MAPK | MAPK | MAPK | MAPK | |||
| NFκB | NFκB | (NFκB) | NFκB | |||
| TGFβ | TGFβ | |||||
| JAK-STAT1/2 | JAK-STAT1/2 | |||||
| JAK-STAT3 | JAK-STAT3 | JAK-STAT3 | ||||
| Wnt | Wnt | (Wnt) | Wnt | |||
| Pre-treatment prediction of response to anti-TNFα treatment (Figure 2 and Supplementary Table S1) | (MAPK) | (Wnt) | NFκB | NFκB | (TGFβ) | |
| NFκB | TGFβ | TGFβ | ||||
| TGFβ | JAK-STAT3 | |||||
| JAK-STAT3 | ||||||
| Wnt | ||||||
| Individual patient, response assessment during treatment (decrease in STP PAS during treatment) Supplementary Table S1 | NA | (MAPK) | AR | MAPK | (AR) | |
| (NFκB) | MAPK | MAPK (NFκB) | ||||
| (JAK-STAT1/2) | (TGFβ) | |||||
| JAK-STAT3 (Wnt) | ||||||
| Patient group response assessment during treatment (Supplementary Table S1) | (AR) | MAPK | MAPK | AR | MAPK | (AR) |
| (Wnt) | NFκB (TGFβ) | NFκB | MAPK | NFκB | MAPK | |
| JAK-STAT3 | Wnt | NFκB | (TGFβ) | NFκB (TGFβ) | ||
| Wnt | TGFβ | JAK-STAT1/2 | ||||
| (JAK-STAT1/2) | JAK-STAT3 | |||||
| JAK-STAT3 | (JAK-STAT3) | Wnt |