The macrophages from Crohn’s Disease (CD) patients are defective to control the replication of CD-associated adherent-invasive E. coli (AIEC). We aimed to identify the host factors associated with AIEC replication focusing on polymorphisms related to autophagy. Peripheral blood monocyte-derived macrophages (MDM), obtained from 95 CD patient, 30 ulcerative colitis (UC) patients and 15 healthy subjects, were genotyped for several CD-associated polymorphisms. AIEC bacteria survival increased within MDM from CD patients compared to UC (p = 0.0019). AIEC bacteria survival increased in patients with CD-associated polymorphism IRGM (p = 0.05) and reduced in those with CD-associated polymorphisms XBP-1 (p = 0.026) and ULK-1 (p = 0.033). AIEC infection led to an increase of pro-inflammatory cytokines IL-1β (p < 0.0001) and TNF-α (p < 0.0001) in CD macrophages. ULK-1 expression increased in AIEC-infected MDM from CD patients compared to MDM from UC patients or healthy subjects (p = 0.0056) and correlated with AIEC survival (p = 0.0013). Moreover, the expression of ULK-1 phosphorylation on Serine 757 decreased following to AIEC infection (p < 0.0001). Short-term silencing of ULK-1 and IRGM genes restricted and promote, respectively, AIEC survival within MDM (p = 0.0018 and p = 0.0291). In conclusion, the macrophage defect to mediate AIEC clearance in CD patients is linked to polymorphisms related to autophagy such as IRGM and ULK-1.

Background & Aims The mechanism of action of anti-TNF agents could implicate macrophages modulation in Crohn’s disease (CD). As CD macrophages are defective to control CD-associated adherent-invasive E. coli (AIEC), anti-TNF agents could limit AIEC replication within macrophages. We assessed the effect of anti-TNF agents on AIEC survival within monocytes-derived macrophages (MDM) from CD patients and attempted to identify the implicated proteins. Methods Peripheral blood monocyte-derived macrophages (MDM) were obtained from 44 CD patients including 22 with and 22 without anti-TNF agents. MDM were infected with AIEC-LF82 reference strain. Proteomic analysis was performed before and 6h after AIEC-LF82 infection. Results AIEC-LF82 survival was lower in MDM from CD patients receiving anti-TNF agents compared to those who did not (-73%, p=0.006). After AIEC-LF82 infection, the levels of CD82 (p=0.007), ILF3 (Interleukin enhancer-binding factor 3; p=0.001), FLOT-1 (Flotillin-1; p=0.007) and CHI3L1 (Chitinase 3-like 1; p=0.035) proteins were different within CD-MDM depending on anti-TNF exposure. FLOT-1 (ϱ=- 0.44; p=0.038) and CHI3L1 (ϱ=0.57, p=0.006) levels were inversely and positively correlated with AIEC survival within MDM from CD patients with or without anti-TNF, respectively. We observed a dose-dependent decrease of AIEC-LF82 survival after adjunction of anti-TNF within MDM inducing increase of FLOT-1 and decrease of CHI3L1 mRNA levels. Neutralization of intra-macrophagic CHI3L1 protein using anti-CHI3L1 antibodies reduced AIEC survival within macrophages 6h after infection (p&lt;0.05). Conclusion Anti-TNF agents are able to restrict replication of pathobiont, such as AIEC, within macrophages by modulating FLOT-1 and CHI3L1 expressions in CD patients.