AXL-dependent autophagy impairment differentiates monocyte-derived macrophages from Crohn's disease and intestinal...

Macrophages are critical to maintaining intestinal homeostasis and contribute to localized inflammation once dysregulated. Here, we aimed at understanding innate macrophage dysfunction in subjects with chronic idiopathic gut inflammation Crohn's disease (CD) and chronic infection-related gut inflammation, intestinal tuberculosis (ITB).

The study population involved subjects aged 18 years or above, including males and females, who met the inclusion/exclusion criteria (CD: n = 42; ITB: n = 41). RNA-seq analysis of ex vivo Mtb-infected or uninfected monocyte-derived macrophages (MDMs) from CD, ITB and healthy controls was done. The MDMs from a cohort of patients, including CD (n = 42) and ITB (n = 41), were characterized for innate immune responses such as autophagy (CD, n = 15: ITB, n = 09), mitochondrial depolarization (CD, n = 08: ITB, n = 08) and bactericidal capacity (CD, n = 25: ITB, n = 28). Finally, the role of AXL downregulation in impaired autophagy was tested.

The MDMs from CD and ITB subjects showed differential regulation of autophagy-associated genes. Functionally, CD MDMs showed significant autophagy impairment compared to ITB MDMs (average MFI-201 in CD vs. 414 in ITB). Both CD and ITB MDMs were permissive to Mtb uptake; however, CD MDMs were more permissive (44% CD samples vs. 28% ITB samples). We noted that AXL was consistently downregulated in CD MDMs and biopsies compared to ITB. AXL knockdown in macrophages impaired autophagy, suggesting a causal relationship between AXL expression and impaired autophagy in CD MDMs.

We experimentally demonstrate distinct autophagy regulation between CD and ITB MDMs. Impaired autophagy in CD MDMs could explain the heightened chronic inflammation observed in CD subjects. The association of AXL downregulation with autophagy impairment could facilitate novel diagnostic and intervention approaches against CD.