Understanding the importance of autophagy in human diseases using Drosophila

Nanotherapeutics targeting autophagy regulation for improved cancer therapy

The clinical efficacy of current cancer therapies falls short, and there is a pressing demand to integrate new targets with conventional therapies. Autophagy, a highly conserved self-degradation process, has received considerable attention as an emerging therapeutic target for cancer. With the rapid development of nanomedicine, nanomaterials have been widely utilized in cancer therapy due to their unrivaled delivery performance. Hence, considering the potential benefits of integrating autophagy and nanotechnology in cancer therapy, we outline the latest advances in autophagy-based nanotherapeutics. Based on a brief background related to autophagy and nanotherapeutics and their impact on tumor progression, the feasibility of autophagy-based nanotherapeutics for cancer treatment is demonstrated. Further, emerging nanotherapeutics developed to modulate autophagy are reviewed from the perspective of cell signaling pathways, including modulation of the mammalian target of rapamycin (mTOR) pathway, autophagy-related (ATG) and its complex expression, reactive oxygen species (ROS) and mitophagy, interference with autophagosome-lysosome fusion, and inhibition of hypoxia-mediated autophagy. In addition, combination therapies in which nano-autophagy modulation is combined with chemotherapy, phototherapy, and immunotherapy are also described. Finally, the prospects and challenges of autophagy-based nanotherapeutics for efficient cancer treatment are envisioned.

Toxicity by descent: A comparative approach for chemical hazard assessment

Toxicology is traditionally divided between human and eco-toxicology. In the shared pursuit of environmental health, this separation does not account for discoveries made in the comparative studies of animal genomes. Here, we provide evidence on the feasibility of understanding the health impact of chemicals on all animals, including ecological keystone species and humans, based on a significant number of conserved genes and their functional associations to health-related outcomes across much of animal diversity. We test four conditions to understand the value of comparative genomics data to inform mechanism-based human and environmental hazard assessment: (1) genes that are most fundamental for health evolved early during animal evolution; (2) the molecular functions of pathways are better conserved among distantly related species than the individual genes that are members of these pathways; (3) the most conserved pathways among animals are those that cause adverse health outcomes when disrupted; (4) gene sets that serve as molecular signatures of biological processes or disease-states are largely enriched by evolutionarily conserved genes across the animal phylogeny. The concept of homology is applied in a comparative analysis of gene families and pathways among invertebrate and vertebrate species compared with humans. Results show that over 70% of gene families associated with disease are shared among the greatest variety of animal species through evolution. Pathway conservation between invertebrates and humans is based on the degree of conservation within vertebrates and the number of interacting genes within the human network. Human gene sets that already serve as biomarkers are enriched by evolutionarily conserved genes across the animal phylogeny. By implementing a comparative method for chemical hazard assessment, human and eco-toxicology converge towards a more holistic and mechanistic understanding of toxicity disrupting biological processes that are important for health and shared among animals (including humans).

The role of K63-linked polyubiquitin in several types of autophagy

Lysosomal-dependent self-degradative (autophagic) mechanisms are essential for the maintenance of normal homeostasis in all eukaryotic cells. Several types of such self-degradative and recycling pathways have been identified, based on how the cellular self material can incorporate into the lysosomal lumen. Ubiquitination, a well-known and frequently occurred posttranslational modification has essential role in all cell biological processes, thus in autophagy too. The second most common type of polyubiquitin chain is the K63-linked polyubiquitin, which strongly connects to some self-degradative mechanisms in the cells. In this review, we discuss the role of this type of polyubiquitin pattern in numerous autophagic processes.

The roles, controversies, and combination therapies of autophagy in lung cancer

Lung cancer is one of the leading causes of death among men and women worldwide. The disease initially has a silent phenotype, which leads to the progression of the disease and ultimately the lack of proper response to routine treatments. Autophagy, known as an intracellular "recycle bin" for the degradation of defective proteins and molecules, is one of the mechanisms that has been considered in the context of cancer in recent years. This study aims to provide a comprehensive review of published articles on autophagy in the context of lung cancer to have a complete view of the role of autophagy in lung cancer and its possible treatments. PubMed, Scopus, and Google Scholar were searched until June 15 to find related articles. No specific search filters or restrictions were applied. The results were entered into reference management software for aggregation and management. The full text of all articles was screened and studied. In conclusion, studies on the exact function of autophagy in lung cancer are contradictory, but what can be concluded from a review of literature on lung cancer is that targeting autophagy combined with traditional routine therapies such as chemotherapy, especially in advanced stages of lung cancer, can be an effective anticancer approach.

Lipid profiles of autophagic structures isolated from wild type and Atg2 mutant Drosophila

Autophagy is mediated by membrane-bound organelles and it is an intrinsic catabolic and recycling process of the cell, which is very important for the health of organisms. The biogenesis of autophagic membranes is still incompletely understood. In vitro studies suggest that Atg2 protein transports lipids presumably from the ER to the expanding autophagic structures. Autophagy research has focused heavily on proteins and very little is known about the lipid composition of autophagic membranes. Here we describe a method for immunopurification of autophagic structures from Drosophila melanogaster (an excellent model to study autophagy in a complete organism) for subsequent lipidomic analysis. Western blots of several organelle markers indicate the high purity of the isolated autophagic vesicles, visualized by various microscopy techniques. Mass spectrometry results show that phosphatidylethanolamine (PE) is the dominant lipid class in wild type (control) membranes. We demonstrate that in Atg2 mutants (Atg2^-), phosphatidylinositol (PI), negatively charged phosphatidylserine (PS), and phosphatidic acid (PA) with longer fatty acyl chains accumulate on stalled, negatively charged phagophores. Tandem mass spectrometry analysis of lipid species composing the lipid classes reveal the enrichment of unsaturated PE and phosphatidylcholine (PC) in controls versus PI, PS and PA species in Atg2^-. Significant differences in the lipid profiles of control and Atg2^- flies suggest that the lipid composition of autophagic membranes dynamically changes during their maturation. These lipidomic results also point to the in vivo lipid transport function of the Atg2 protein, pointing to its specific role in the transport of short fatty acyl chain PE species.

Xenophagy in innate immunity: A battle between host and pathogen

Autophagy is a fundamental bulk intracellular degradation and recycling process that directly eliminates intracellular microorganisms through "xenophagy" in various types of cells, especially in macrophages. Meanwhile, bacteria have evolved strategies and cellular self-defense mechanisms to prevent autophagosomal degradation and even attack the immune system of host. The lack of knowledge about the roles of autophagy in innate immunity severely limits our understanding of host defensive system and the development of farmed industry consisting of aquaculture. Increasing evidence in recent decades has shown the importance of autophagy. This review focuses on the triggering of xenophagy, targeting of invading pathogens to autophagosomes and elimination in the autophagolysosomes during pathogen infection. How the pathogen can escape from the xenophagy pathway was also discussed. Overall, we aim to reduce diseases and improve industrial production in aquaculture by providing theoretical and technical guidance on xenophagy.

The Role of Deubiquitinating Enzymes in the Various Forms of Autophagy

Deubiquitinating enzymes (DUBs) have an essential role in several cell biological processes via removing the various ubiquitin patterns as posttranslational modification forms from the target proteins. These enzymes also contribute to the normal cytoplasmic ubiquitin pool during the recycling of this molecule. Autophagy, a summary name of the lysosome dependent self-degradative processes, is necessary for maintaining normal cellular homeostatic equilibrium. Numerous forms of autophagy are known depending on how the cellular self-material is delivered into the lysosomal lumen. In this review we focus on the colorful role of DUBs in autophagic processes and discuss the mechanistic contribution of these molecules to normal cellular homeostasis via the possible regulation forms of autophagic mechanisms.

Necrotic cell death induces melanotic mass formation in Drosophila

The immune system protects its host from not only invading parasites and parasitoids, but also altered self tissue, including dying cells. Necrotic cells are strongly immunogenic, but in Drosophila this has not been directly addressed, due partially to the fact that knowledge about necrosis in Drosophila currently lags behind that for other models. Upon the loss of cell matrix attachment, endocycling polyploid tissues of the Drosophila larva undergo autophagy instead of apoptosis; we employed this system as a model to examine cell death modalities and immunity. Here, we report that larval fat body cells depleted of integrin undergo not only autophagy, but also necrotic cell death, and that a blockade of reaper, grim, hid, or the downstream caspases enhances necrosis. These cells elicit melanotic mass formation, an autoimmune-like response. We also show that necrosis is the main cause of melanotic mass formation in these anchorage-depleted polyploid cells.

Silencing of PARP2 Blocks Autophagic Degradation

Poly(ADP-Ribose) polymerases (PARPs) are enzymes that metabolize NAD⁺. PARP1 and PARP10 were previously implicated in the regulation of autophagy. Here we showed that cytosolic electron-dense particles appear in the cytoplasm of C2C12 myoblasts in which PARP2 is silenced by shRNA. The cytosolic electron-dense bodies resemble autophagic vesicles and, in line with that, we observed an increased number of LC3-positive and Lysotracker-stained vesicles. Silencing of PARP2 did not influence the maximal number of LC3-positive vesicles seen upon chloroquine treatment or serum starvation, suggesting that the absence of PARP2 inhibits autophagic breakdown. Silencing of PARP2 inhibited the activity of AMP-activated kinase (AMPK) and the mammalian target of rapamycin complex 2 (mTORC2). Treatment of PARP2-silenced C2C12 cells with AICAR, an AMPK activator, nicotinamide-riboside (an NAD⁺ precursor), or EX-527 (a SIRT1 inhibitor) decreased the number of LC3-positive vesicles cells to similar levels as in control (scPARP2) cells, suggesting that these pathways inhibit autophagic flux upon PARP2 silencing. We observed a similar increase in the number of LC3 vesicles in primary PARP2 knockout murine embryonic fibroblasts. We provided evidence that the enzymatic activity of PARP2 is important in regulating autophagy. Finally, we showed that the silencing of PARP2 induces myoblast differentiation. Taken together, PARP2 is a positive regulator of autophagic breakdown in mammalian transformed cells and its absence blocks the progression of autophagy.

The Controversial Role of Autophagy in Tumor Development: A Systematic Review

Autophagy is a natural regulatory mechanism of the cell that eliminates unnecessary and dysfunctional cellular components to maintain homeostasis. Several authors have demonstrated that this mechanism can be induced by pathological conditions as cancer. However, their role in tumor development is still a controversial issue in cancer research. Here, we discussed the most relevant findings concerning autophagy in tumor development. In this critical review performed with studies published between 2002 and 2018, we found that the main pathway involved in the autophagy process is the PI3K/AKT/mTOR intracellular signaling pathway. Regarding their role in cancer development, breast cancer is the main study target, followed by lung, prostate and colon cancer. In these issues, 46% of the works consulted suggesting that autophagy inhibits tumor progression by favor a better antitumor response, 4% suggest that favors growth and tumor progression and, 50% of the authors failed to establish whether autophagy inhibits or favors tumor development. Herein, we concluded that depending on the study model, autophagy may favor or inhibits growth and cancer progression.

Mechanisms and Pathophysiological Roles of the ATG8 Conjugation Machinery

Since their initial discovery around two decades ago, the yeast autophagy-related (Atg)8 protein and its mammalian homologues of the light chain 3 (LC3) and γ-aminobutyric acid receptor associated proteins (GABARAP) families have been key for the tremendous expansion of our knowledge about autophagy, a process in which cytoplasmic material become targeted for lysosomal degradation. These proteins are ubiquitin-like proteins that become directly conjugated to a lipid in the autophagy membrane upon induction of autophagy, thus providing a marker of the pathway, allowing studies of autophagosome biogenesis and maturation. Moreover, the ATG8 proteins function to recruit components of the core autophagy machinery as well as cargo for selective degradation. Importantly, comprehensive structural and biochemical in vitro studies of the machinery required for ATG8 protein lipidation, as well as their genetic manipulation in various model organisms, have provided novel insight into the molecular mechanisms and pathophysiological roles of the mATG8 proteins. Recently, it has become evident that the ATG8 proteins and their conjugation machinery are also involved in intracellular pathways and processes not related to autophagy. This review focuses on the molecular functions of ATG8 proteins and their conjugation machinery in autophagy and other pathways, as well as their links to disease.

Impact of Autophagy and Aging on Iron Load and Ferritin in Drosophila Brain

Biometals such as iron, copper, potassium, and zinc are essential regulatory elements of several biological processes. The homeostasis of biometals is often affected in age-related pathologies. Notably, impaired iron metabolism has been linked to several neurodegenerative disorders. Autophagy, an intracellular degradative process dependent on the lysosomes, is involved in the regulation of ferritin and iron levels. Impaired autophagy has been associated with normal pathological aging, and neurodegeneration. Non-mammalian model organisms such as Drosophila have proven to be appropriate for the investigation of age-related pathologies. Here, we show that ferritin is expressed in adult Drosophila brain and that iron and holoferritin accumulate with aging. At whole-brain level we found no direct relationship between the accumulation of holoferritin and a deficit in autophagy in aged Drosophila brain. However, synchrotron X-ray spectromicroscopy revealed an additional spectral feature in the iron-richest region of autophagy-deficient fly brains, consistent with iron-sulfur. This potentially arises from iron-sulfur clusters associated with altered mitochondrial iron homeostasis.