Mtb and LC3 Trafficking

A major focus of the Philips laboratory is to understand why autophagy and the autophagy-related pathway LC3-associated phagocytosis (LAP) do not effectively clear Mtb.

One way that we found that Mtb undermine autophagy is by inducing expression of the host miR-33 locus. MiR-33 was known to impair mitochondrial fatty acid oxidation and promote lipid body accumulation. We found that miR-33 and its passenger strand miR-33* also repress key autophagy effectors (ATG5, ATG12, LC3B, LAMP1) and impair AMPK-dependent activation of the transcription factors FOXO3 and TFEB. Consequently, silencing of miR-33 and miR-33* promotes autophagy, lipid body clearance, and elimination of Mtb. Together, these experiments defined a molecular mechanism by which Mtb coordinately inhibits autophagy and reprograms host lipid metabolism to promote its intracellular survival and persistence in the host. Ongoing work involves elucidating the role of host lipid metabolism in Mtb pathogenesis.

Recent work has defined a LC3-trafficking pathway that is distinct from autophagy, called LC3-associated phagocytosis (LAP). LAP is characterized by the recruitment of NADPH oxidase to phagosomes, followed by phagosomal association with LC3 and delivery of the bacteria to a degradative lysosome. We found that LAP does not effectively clear Mtb. The ability of Mtb to inhibit LAP and therefore cause disease depends upon the protein CpsA, a member of the LytR-CpsA-Psr (LCP) protein family. We found that Mtb CpsA plays an unexpected role in antagonizing host innate immunity by inhibiting NADPH oxidase and LAP. Ongoing work involves elucidating how CpsA blocks the NADPH oxidase and LAP.

Macrophages that are activated by the cytokine interferon-gamma are better able to control Mtb through autophagy. We found that that the host protein ubiquilin 1 (UBQLN1) promotes IFN-gamma-mediated autophagic clearance of Mtb. Ubiquilin family members have previously been shown to recognize proteins that aggregate in neurodegenerative disorders. In IFN-gamma activated macrophages, UBQLN1 co-localizes with Mtb and promotes the anti-mycobacterial activity of IFN-gamma. Our data suggest a model in which activating autophagy with IFN-gamma promotes UBQLN1 recruitment to Mtb, which in turn leads to recruitment of the autophagy machinery, autophagy-mediated degradation of the bacteria, and antigen presentation. Since IFN-gamma is critical in human control of Mtb, our study suggests that polymorphisms in ubiquilins, known to influence susceptibility to neurodegenerative illnesses, might also play a role in host defense against Mtb. Ongoing work involves elucidating the molecular mechanism behind Ubqln1 function and its role in host susceptibility to Mtb. 

Read more about our work on TB and LC3 trafficking:

Köster S, Upadhyay S, Philips JA. Why macrophages cannot LAP up TB. Autophagy. 2018 Jan 9:1-5. doi: 10.1080/15548627.2018.1425054. [Epub ahead of print] PMID:29313424

Köster S, Upadhyay S, Chandra P, Papavinasasundaram K, Yang G, Hassan A, Grigsby S, Mittal E, Park HS, Jones V, Hsu F, Jackson M, Sassetti C, Philips, JA. Mycobacterium tuberculosis is protected from NADPH oxidase and LC3-associated phagocytosis by the LCP protein CpsA, Proc. Natl. Acad. Sci., 2017: pii:20107792. doi: 10.1073/pnas.1707792114 (Epub ahead of print).

Köster S, Klevorn T, Papavinasasundaram K, Sassetti C, Portal-Celhay C, Philips, JA. Consequences of enhanced LC3-trafficking for a live, attenuated M. tuberculosis vaccine. Vaccine, https://doi.org/10.1016/j.vaccine.2018.01.012

Ouimet M, Koster S, Sakowski, E, Ramkhelawon B, Van Solingen C, Oldebeken S, Karunakaran D, Portal-Celhay C, Sheedy FJ, Ray TD, Cecchini K, Zamore PD, Rayner KJ, Marcel YL, Philips JA,* Moore KJ.* Mycobacterium tuberculosis induces the miR-33 locus to reprogram autophagy and host lipid metabolism, Nat Immunol 2016; 17 , 677-686. PMCID: PMC4873392. (*equal contribution)

Sakowski E, Koster S, Portal Celhay C, Park HS, Shrestha E, Hetzenecker SE, Maurer K, Cadwell K, Philips JA. Ubiquilin 1 Promotes IFN-gamma-induced xenophagy of Mycobacterium tuberculosis. PLOS Pathogens. 2015 Jul 30;11(7):e1005076.