Yes / Autophagy is the central cellular mechanism for delivering organelles and cytoplasm to lysosomes for degradation and recycling of their molecular components. To determine the contribution of autophagy to melanocyte (MC) biology, we inactivated the essential autophagy gene Atg7 specifically in MCs using the Cre-loxP system. This gene deletion efficiently suppressed a key step in autophagy, lipidation of microtubule-associated protein 1 light chain 3 beta (LC3), in MCs and induced slight hypopigmentation of the epidermis in mice. The melanin content of hair was decreased by 10–15% in mice with autophagy-deficient MC as compared with control animals. When cultured in vitro, MCs from mutant and control mice produced equal amounts of melanin per cell. However, Atg7-deficient MCs entered into premature growth arrest and accumulated reactive oxygen species (ROS) damage, ubiquitinated proteins, and the multi-functional adapter protein SQSTM1/p62. Moreover, nuclear factor erythroid 2–related factor 2 (Nrf2)–dependent expression of NAD(P)H dehydrogenase, quinone 1, and glutathione S-transferase Mu 1 was increased, indicating a contribution of autophagy to redox homeostasis in MCs. In summary, the results of our study suggest that Atg7-dependent autophagy is dispensable for melanogenesis but necessary for achieving the full proliferative capacity of MCs.

Macroautophagy (hereafter referred to as autophagy) is the bulk degradation and recycling of cytoplasmic materials by forming a double membrane vesicle called the autophagosome. Autophagosome formation is regulated by the coordinated action of a set of proteins. ATG9A is the only multispanning transmembrane protein that plays an essential role in autophagosome formation, yet its function is largely elusive. Previous studies have shown that the C-terminus of ATG9A plays an important role in regulating its trafficking and proper function in autophagy. In line with that idea, we previously identified an AMPK- and ULK1- mediated phosphorylation on the C terminus of ATG9A at S761, which is required for proper ATG9A trafficking and autophagic flux. In our current study, we employed a BioID-based proteomics approach and identified a network of ATG9A C terminal interactors that include members of the ULK1 complex, ATG13, and ATG101, as well as protein complexes within the ER, Golgi, and endosomal trafficking pathways, many of which provide new insight into ATG9A trafficking mechanisms. We discovered that ATG9A exists with ATG13 and ATG101 in a separate subcomplex outside the canonical ULK1 complex. We show that the ATG13-ATG101 subcomplex regulates ATG9A trafficking and basal P62 degradation.

Huntington's disease, an autosomal dominant neurodegenerative disease, affects the cell in several toxical ways. One of them is accumulation of protein aggregates in cytoplasma, which could become a serious problem especially for long-lived cells such as neurons. Autophagy (macroautophagy) is an important catabolic pathway, crucial for cell survival. If fully functional, it should eliminate protein aggregates and reduce the toxic effect on the cell. However, recent works show that this pathway might be defective, most probably in the cytoplasmic cargo recognition. In my work I used a transgenic miniature pig model of Huntington's disease to verify the hypothesis of autophagical dysfunction in individuals suffering from Huntington's disease. I studied levels of autophagosomal markers - LC3 and p62 in mesenchymal stem cells after different autophagy stimulation treatments, and ammonium chloride was found the most effective. In addition I evaluated the effect of age of the animals on autophagic function, but no significant changes were identified, even if animal genotype was considered. Moreover I had an opportunity to study proteins levels in three porcine brain tissues - cortex, cerebellum and striatum. Even though there is no significant diference, we can observe a trend of LC3 II and p62 increase in...

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

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La macroautophagie est un processus catabolique, situé au carrefour entre l’homéostasie et le métabolisme cellulaire. Dans le système immunitaire, elle joue des rôles spécialisés, en contribuant notamment à la régulation de l’inflammation et la présentation antigènique. En utilisant deux modèles murins, nous avons pu démontrer que la macroautophagy est nécessaire à la lignée lymphocytaire B et contribue à l’élaboration d’une réponse humorale optimale. En effet, la macroautophagie contribue à la survie des cellules sécrétrices d’antigènes, notamment la population plasmocytaire, ainsi que des cellules à longue durée de vie, telles que les lymphocytes B mémoire. Nous avons également démontré qu’une forme d’autophagie non-canonique était nécessaire pour la présentation efficace d’antigènes particulaires reconnus par le récepteur des lymphocytes B. Dans ce contexte, la machinerie macroautophagique contribue à la polarisation du cytosquelette des lymphocytes B, afin de former une synapse immunologique, nécessaire au chargement efficace du complexe majeur d’histocompatibilité de classe II, et ainsi, à la présentation antigènique. A l’aide d’un troisième modèle de souris transgénique, nous avons caractérisé un rôle jusqu’alors inconnu de la macroautophagie dans le maintient de l’homéostasie des cellules de Langerhans. L’inhibition de la macroautophagie altère la survie de ces cellules, en les exposant à potentiel stress du réticulum endoplasmique, potentiellement non compensé. En somme, nous avons démontré que la macroautophagie était un acteur majeur au sein des cellules présentatrices d’antigènes. / Macroautophagy is a catabolic process at the crossroad between homeostasis and metabolism. In the immune system it also possesses specialized roles such as inflammation regulation and antigen presentation. Here we demonstrated in two mice models that macroautophagy is integral to B cell lineage for proper humoral responses. Indeed it insures the survival of secreting cells such as plasma cells and long living cells such as memory B cells. We also report that non-canonical autophagy is also needed for an efficient presentation of particulate antigen recognized by the B cell receptor. In this context it drives B cell cytoskeleton polarization to form an immune synapse necessary for the efficient loading of class two major histocompatibility complexes and the subsequent antigen presentation. Using a third mice model we unveiled a yet uncharacterized function of macroautophagy in Langerhans cells, a subset of epidermal dendritic cells, homeostasis. Macroautophagy inhibition impairs their survival by exposing them to a potentially uncompensated endoplasmic reticulum stress response. Altogether we demonstrated that macroautophagy is a major actor in several types of antigen presenting cells.

<p>The Immunity-Related GTPases (IRGs) are a family of dynamin-like proteins found in vertebrates that play critical roles in cell-autonomous resistance to bacteria and protozoa. The IRGs are divided into two subfamilies, with the GMS IRGs exerting a regulatory function over the GKS IRGs, affecting GKS IRG expression, localization, and ultimately function. The profound loss of host resistance seen in mice lacking the GMS protein Irgm1 suggests that GMS IRGs may additionally have broader functions beyond the regulation of GKS IRGs, though the nature of these functions remains poorly understood. In this dissertation, we address the regulatory functions of GMS IRGs in mouse cells.</p><p>We first addressed regulation of GKS IRGs (Irga6 and Irgb6) by GMS IRGs (Irgm1 and Irgm3). We found that in both fibroblasts and macrophages lacking these GMS IRGs, that the GKS IRGs relocalized to form punctate structures that were ubiquitin-, p62-, and LC3-positive. A biochemical analysis indicated that the GKS IRGs were directly ubiquitinated through K63 linkages. Collectively, these results suggested that GMS IRGs regulate aggregation of GKS IRGs and their transfer to autophagosomes through one of at least two possible mechanisms -- by the direct association of GMS IRGs with GKS IRGs to block their aggregation that subsequently leads to autophagic removal, and/or by directly promoting autophagic removal of spontaneously forming GKS aggregates. The latter hypothesis was addressed using a series of complementary assays, which ultimately showed that absence of Irgm1 has no effect on the maturation of autophagosomes in fibroblasts, and only a very small and statistically insignificant effect in macrophages. Thus, we conclude that the major mechanism through which GMS IRGs regulate GKS IRGs is by directly inhibiting their aggregation, rather than through general effects on autophagic initiation or maturation of GKS IRG-containing autophagosomes.</p><p>We also addressed the possibility of broad regulatory functions of GMS IRGs beyond the regulation of GKS IRGs by examining whether GMS IRGs can affect another family of dynamin-like GTPases, the guanylate-binding proteins (GBPs). Despite no previous evidence of interactions between these two protein families, we found that the absence of GMS IRGs had striking effects on the localization of the murine Gbp2, leading it to colocalize with GKS IRG aggregates formed as a consequence of GMS IRG deficiency. We further demonstrated that unlike the GKS IRGs, Gbp2 was not tagged with K63-linked ubiquitin chains, which might have targeted it for specific macroautophagy, implying that Gbp2 is not aggregating in the absence of Irgm1. We then showed both that Gbp2 forms puncta in the presence of generic protein aggregates, and that guanylate-binding proteins including Gbp2 promote the degradation of GKS IRG protein aggregates. These findings suggest that GMS IRGs do not exert direct control over GBPs, but rather that GBPs are involved in the macroautophagic degradation of protein aggregates as a primary function, and are thus influenced indirectly by GMS IRGs.</p><p>In total, our experiments contribute to the understanding of regulatory interactions among GMS IRGs, GKS IRGs, and GBPs. These results will be important in establishing the mechanisms through which these important families of proteins influence eradication of bacterial and protozoan pathogens through key innate immune mechanisms.</p> / Dissertation

Autophagy, as the name suggests, is a cellular process of self-eating in which cytoplasmic debris is engulfed by a double membrane vesicle dubbed the autophagosome and is ultimately degraded and recycled by proteases in the lysosome. The process is initiated by a group of core ATG proteins, including a multi-pass transmembrane protein called ATG9A. Although ATG9A has been shown to be essential for both stress induced and basal autophagy, its mechanism and interaction network remain largely illusive. Our current study employs BioID proteomics to identify a network of interactors, including regulators of membrane fusion and vesicle trafficking, such as TRAPP, EARP, GARP, exocyst, AP-1 and AP-4 complexes, as well as members of the ULK1 autophagy kinase complex. Further investigations confirm that two components of the ULK1 complex, ATG13 and ATG101, directly interact with ATG9A. Using CRISPR, we show that deletion of ATG13 or ATG101 disrupts ATG9A trafficking and causes an accumulation of ATG9A at p62/SQSTM1-positive ubiquitin clusters. Lentivirus reconstitution and split-mVenus approaches using an ULK1 binding deficient mutant of ATG13 reveal that ATG9A interacts with ATG13 and ATG101 in an ULK1-independent manner. Together, these data reveal ATG9A interactions in vesicle trafficking and autophagy pathways, including a role for an ULK1- independent ATG13 complex in regulating ATG9A.

No / Tenovin-6 (Tnv-6) is a bioactive small molecule with anti-neoplastic activity. Inhibition of the Sirtuin class of protein deacetylases with activation of p53 function is associated with the pro-apoptotic effects of Tnv-6 in many tumors. Here, we demonstrate that in chronic lymphocytic leukemia (CLL) cells, Tnv-6 causes non-genotoxic cytotoxicity, without adversely affecting human clonogenic hematopoietic progenitors in vitro, or murine hematopoiesis. Mechanistically, exposure of CLL cells to Tnv-6 did not induce cellular apoptosis or p53-pathway activity. Transcriptomic profiling identified a gene program influenced by Tnv-6 that included autophagy-lysosomal pathway genes. The dysregulation of autophagy was confirmed by changes in cellular ultrastructure and increases in the autophagy-regulatory proteins LC3 (LC3-II) and p62/Sequestosome. Adding bafilomycin-A1, an autophagy inhibitor to Tnv-6 containing cultures did not cause synergistic accumulation of LC3-II, suggesting inhibition of late-stage autophagy by Tnv-6. Thus, in CLL, the cytotoxic effects of Tnv-6 result from dysregulation of protective autophagy pathways.