Axl-Dependent Autophagy Impairment Differentiates Monocyte-Derived Macrophages from Crohn's Disease and Intestinal Tuberculosis

Abstract

Macrophages are critical to maintain intestinal homeostasis and contribute to localized inflammation once dysregulated. Here, we aimed to understand innate macrophage dysfunction in the subjects with chronic idiopathic gut inflammation [Crohn’s Disease (CD)] and chronic infection-related gut inflammation [Intestinal Tuberculosis (ITB)]. RNA-seq analysis of ex vivo Mtb-infected or uninfected monocyte-derived macrophages (MDMs) from CD, ITB and healthy controls was done. Subsequently, MDMs from a cohort of patients, including CD (n=42) and ITB (n=41) were characterised for innate immune responses like 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. Both CD and ITB MDMs were permissive to Mtb uptake; however, CD MDMs were more permissive. We noted that AXL was consistently downregulated in CD MDMs compared to ITB, which was also reflected in the tissue biopsies. AXL knockdown in Thp-1 macrophages impaired autophagy flux, suggesting a causal relationship between reduced AXL expression and impaired autophagy in CD MDMs. This is the first report experimentally demonstrating distinct autophagy regulation between CD and ITB MDMs and their response to ex vivo bacterial infections. 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.