Unconventional Autophagy in Health and Disease

Autophagy is a catabolic process that degrades cytoplasmic components in response to stressful situations. Considering the pathological phenotypes exhibited by mice deficient in critical effectors of the autophagic machinery (the so-called ATG proteins), autophagy prevents different diseases, including cancer, neurodegeneration or deranged inflammation, suggesting that its modulation may have therapeutic value. However, a number of atypical activities are being discovered where ATGs function in unconventional ways to mediate processes apparently unrelated to the canonical autophagic route. To what extent these non-canonical activities contribute to protect from the diseases caused by ATG deletion is unclear, but this is an important issue because it could determine which ATG functions (canonical or atypical) that should be modulated for possible therapeutic applications.

ATG16L1 is a central autophagic effector that induces lipidation of ATG8/LC3 to promote autophagosome formation. Interestingly, ATG16L1 has a WD40 repeat-containing domain (WDD) that is not required for canonical autophagy but critical for a variety of unconventional functions where LC3 becomes lipidated in single-membrane compartments unrelated to canonical doublemembrane autophagosomes. The physiological roles of these atypical processes have remained unclear. However, previous publications from our group show that a coding allele of ATG16L1 (T300A; rs2241880) that increases the risk of a number of pathologies (including, for example, Crohn’s disease) specifically impairs the non-autophagic functions of the WDD without altering canonical autophagy, indicating that the atypical roles of ATG16L1 truly contribute to disease prevention. Therefore, identification of these non-autophagic functions is important to understand exactly how ATG16L1 prevents disease and how modulation of its activity could be used as a valid therapeutic strategy. In the last few years we have made relevant contributions to this topic by describing new roles of the WDD in the xenophagic response against bacterial infection induced by the transmembrane protein TMEM59, the regulation of the anti-inflammatory activity of A20, a ubiquitin editor, or the control of the signaling output of cytokine receptors that include a novel aminoacid motif able to bind the WDD.

In our laboratory we focus on the identification and characterization of new unconventional functions carried out by ATG16L1 from three different perspectives. First, building on our previous identification of transmembrane molecules harboring the WDD-binding motif, we intend to identify those unable to bind the ATG16L1-A300 pathological allele. We are currently characterizing how ATG16L1 regulates the biology of these molecules, and establish how their normal function is derailed by the A300 protein. Second, we are studying the role of TMEM59 in xenophagy against gram-positive bacteria and to what extent this molecule, as a validated WDD interactor that cannot bind the ATG16L1-A300 protein, mediates the pathological effects of the A300 allele. Third, we are characterizing in detail a novel unconventional autophagic pathway that is induced by Bcl2-family members during apoptotic cell death. We intend to explore its possible role in the control of the immunogenic features of apoptosis and how it may be influenced by ATG16L1-A300. We expect these studies to reveal novel unconventional activities of ATG16L1 and how they impact human pathology.