Table 1.
Upregulated genes in all three types of intestinal granulomas (D7 B, D21 B and D21 T, Log2fold>1 in all groups).
| Gene | Function | Nematode Host Response | D21B (BOLUS infection) | D21T (Trickle infection) | D7B (BOLUS infection) | ||||
|---|---|---|---|---|---|---|---|---|---|
| Fold Change | Adjusted p-value | Fold Change | Adjustedp-value | Fold Change | Adjusted p-value | ||||
| Upregulated in all groups compared to Naive | |||||||||
| 1 | Chil4 | AAM marker Ym2 involved in ECM remodeling | (93) | 27756.05 | 2.14E-18 | 27070.52 | 1.06E-18 | 4384.16 | 2.17E-12 |
| 2 | Rnase2a | Encodes for eosinophil derived cationic proteins and neurotoxins and involved in neutrophil recruitment | (94) | 3400.94 | 3.42E-13 | 1864.72 | 1.46E-11 | 743.17 | 9.28E-09 |
| 3 | Chil3 | AAM marker Ym1 involved in ECM remodeling | (20, 87, 95) | 1886.21 | 2.82E-48 | 1868.95 | 2.17E-50 | 303.00 | 1.64E-27 |
| 4 | Mmp12 | ECM remodeling | (96) | 341.87 | 1.59E-21 | 345.71 | 3.59E-22 | 29.93 | 1.66E-07 |
| 5 | Serpine1 | Involved in ECM remodeling | (97) | 286.56 | 7.26E-07 | 151.28 | 1.29E-05 | 317.39 | 5.62E-07 |
| 6 | Ccl7 | Chemokine involved in cell migration | (98) | 180.60 | 1.87E-05 | 259.64 | 3.42E-06 | 917.22 | 1.30E-08 |
| 7 | Retnla | AAM marker, involved in ECM remodeling | (20, 99–101) | 123.55 | 4.20E-65 | 70.37 | 6.07E-55 | 23.52 | 1.03E-27 |
| 8 | Arg1 | Alternatively Activated Macrophage marker involved in ECM remodeling | (7, 16, 35, 87, 102) | 86.61 | 5.17E-45 | 84.28 | 8.53E-48 | 80.52 | 8.98E-43 |
| 9 | Ccl8 | Eosinophil chemotactic factor | (103) | 57.52 | 1.66E-53 | 68.74 | 1.58E-62 | 29.93 | 3.31E-37 |
| 10 | Cxcl3 | Chemokine controlling the adhesion and/or migration of monocytes | (102) | 33.53 | 4.74E-02 | 41.25 | 2.86E-02 | 67.64 | 1.54E-02 |
| 11 | Adam8 | Metalloproteinase, ECM remodeling | (104) | 24.23 | 2.60E-35 | 21.32 | 3.94E-33 | 8.98 | 3.20E-16 |
| 12 | Cxcr4 | Myeloid cell recruitment | (105) | 22.27 | 2.82E-07 | 4.49 | 2.00E-02 | 5.04 | 1.65E-02 |
| 13 | Cd163 | M2 macrophage marker | (106) | 14.96 | 9.12E-07 | 13.91 | 4.98E-07 | 3.92 | 2.66E-02 |
| 14 | Retnlb | Blocks nematode feeding | (107) | 14.78 | 3.98E-18 | 31.67 | 1.40E-32 | 28.93 | 8.28E-28 |
| 15 | Ccl24 | Eotaxin 2, Eosinophil chemotaxis | (108) | 14.62 | 8.44E-10 | 32.63 | 1.28E-17 | 34.57 | 2.33E-16 |
| 16 | Fn1 | Fibronectin 1, ECM remodeling | (109) | 13.63 | 8.92E-24 | 9.80 | 3.26E-20 | 2.87 | 1.93E-04 |
| 17 | Ccl12 | Chemokine; attracts myeloid cells | (110) | 10.48 | 1.71E-06 | 15.19 | 4.54E-09 | 8.38 | 2.30E-05 |
| 18 | Mrc1 | Mannose Receptor, CD206 | (93) | 8.92 | 3.45E-11 | 7.88 | 4.84E-11 | 5.12 | 1.97E-06 |
| 19 | Col1a2 | Collagen I | (111) | 8.61 | 3.02E-84 | 5.68 | 1.30E-58 | 3.03 | 1.37E-21 |
| 20 | Cyp1b1 | Gene involved in the M2 macrophage phenotype | No study found | 7.24 | 4.52E-05 | 6.14 | 1.80E-04 | 9.40 | 4.04E-06 |
| 21 | Mmp19 | Matrix metallopeptidase, breakdown of extracellular matrix | (112) | 7.13 | 1.64E-02 | 5.55 | 3.36E-02 | 8.56 | 8.32E-03 |
| 22 | Pf4 | Chemokine released by platelets that promotes coagulation | (113) | 6.24 | 5.67E-04 | 7.60 | 5.88E-05 | 4.93 | 3.67E-03 |
| 23 | Ccl2 | Monocyte chemoattractant | (114) | 6.24 | 1.01E-04 | 11.00 | 4.69E-08 | 31.38 | 1.51E-14 |
| 24 | Itga5 | Fibronectin receptor alpha | (115) | 5.74 | 7.91E-05 | 4.87 | 2.81E-04 | 3.91 | 3.61E-03 |
| 25 | C3 | Complement component | (116) | 5.53 | 6.31E-16 | 5.74 | 2.28E-18 | 2.76 | 5.37E-06 |
| 26 | Plau | Urokinase-type plasminogen activator, involved in fibrosis | (117) | 5.39 | 1.82E-10 | 6.48 | 1.41E-13 | 3.37 | 1.31E-05 |
| 27 | Cd68 | Scavenger receptor | (118) | 4.67 | 1.02E-14 | 4.27 | 3.00E-14 | 2.54 | 1.17E-05 |
| 28 | C3ar1 | Complement receptor, inflammatory response | (110) | 4.07 | 3.91E-22 | 2.74 | 2.86E-12 | 2.51 | 2.31E-09 |
| 29 | Col3a1 | Collagen, type III, alpha 1 | (119) | 3.92 | 3.84E-09 | 3.36 | 4.39E-08 | 2.00 | 6.11E-03 |
| 30 | Ccl17 | Chemokine, chemoattractant for T-helper cells and Tregs | (120) | 3.87 | 3.65E-03 | 3.69 | 3.94E-03 | 4.83 | 6.07E-04 |
| 31 | Fcgr2b | IgG receptor | (119) | 3.24 | 2.13E-06 | 3.90 | 4.54E-09 | 2.83 | 4.22E-05 |
| 32 | Plaur | Plau receptor, involved in the degradation of the ECM | No study found | 2.58 | 3.41E-06 | 2.57 | 1.81E-06 | 2.12 | 4.53E-04 |
| 33 | C5ar1 | Complement 5a receptor, inflammatory response | (121) | 2.38 | 3.59E-05 | 2.14 | 2.38E-04 | 2.28 | 1.31E-04 |
| Downregulated in all groups compared to Naive | |||||||||
| 1 | Nos2 | Inducible Nitric Oxide Synthase involved in Nitric Oxide production | (122) | 21.68 | 6.70E-18 | 7.42 | 1.57E-10 | 10.74 | 3.52E-12 |
| 2 | Enpep | Glutamyl aminopeptidase | (123) | 3.53 | 2.59E-07 | 5.72 | 8.72E-15 | 2.96 | 1.48E-05 |
| 3 | Crip1 | Involved in fibrosis | (124) | 2.79 | 4.63E-07 | 3.36 | 1.33E-10 | 2.08 | 5.74E-04 |
| 4 | Lamb3 | Regulates cell growth, motility & adhesion. Role in ECM remodeling. | No study found | 2.42 | 4.35E-02 | 9.34 | 8.92E-09 | 5.54 | 3.87E-05 |
| 5 | Hpgd | Degrades eicosinoids | No study found | 2.37 | 2.46E-03 | 3.57 | 7.50E-07 | 2.18 | 7.51E-03 |