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1.  Using LC3 to Monitor Autophagy Flux in the Retinal Pigment Epithelium 
Autophagy  2009;5(8):1190-1193.
Autophagy is a highly conserved housekeeping pathway that plays a critical role in the removal of aged or damaged intracellular organelles and their delivery to lysosomes for degradation.1,2 Autophagy begins with the formation of membranes arising in part from the endoplasmic reticulum, that elongate and fuse engulfing cytoplasmic constituents into a classic double-membrane bound nascent autophagosome. These early autophagosomes undergo a stepwise maturation process to form the late autophagosome or amphisome that ultimately fuses with a lysosome. Efficient autophagy is dependent on an equilibrium between the formation and elimination of autophagosomes; thus, a deficit in any part of this pathway will cause autophagic dysfunction. Autophagy plays a role in aging and age-related diseases. 1,2,7 However, few studies of autophagy in retinal disease have been reported.
Recent studies show that autophagy and changes in lysosomal activity are associated with both retinal aging and age-related macular degeneration (AMD).3,4 This article describes methods which employ the target protein LC3 to monitor autophagic flux in retinal pigment epithelial cells. During autophagy, the cytosolic form of LC3 (LC3-I) is processed and recruited to the phagophore where it undergoes site specific proteolysis and lipidation near the C terminus to form LC3-II.5 Monitoring the formation of cellular autophagosome puncta containing LC3 and measuring the ratio of LC3-II to LC3-I provides the ability to monitor autophagy flux in the retina.
PMCID: PMC3704326  PMID: 19855195
autophagy flux; LC3; retinal pigment epithelium; lysosomes; age-related macular degeneration; aging
2.  Autophagic control of RLR signaling 
Autophagy  2009;5(5):749-750.
Innate immunity to viral infection is initiated within the infected cells through the recognition of unique viral signatures by pattern recognition receptors (PRRs) that mediate the induction of potent antiviral factor, type I interferons (IFNs). Infection with RNA viruses is recognized by the members of the retinoic acid inducible gene I (RIG-I)-like receptor (RLR) family in the cytosol. Our recent study demonstrates that IFN production in response to RNA viral ligands is increased in the absence of autophagy. The process of autophagy functions as an internal clean-up crew within the cell, shuttling damaged cellular organelles and long-lived proteins to the lysosomes for degradation. Our data show that the absence of autophagy leads to the amplification of RLR signaling in two ways. First, in the absence of autophagy, mitochondria accumulate within the cell leading to the build up of mitochondrial associated protein, IPS-1, a key signaling protein for RLRs. Second, damaged mitochondria that are not degraded in the absence of autophagy provide a source of reactive oxygen species (ROS), which amplify RLR signaling in Atg5 knockout cells. Our study provides the first link between ROS and cytosolic signaling mediated by the RLRs, and suggests the importance of autophagy in the regulation of signaling emanating from mitochondria.
PMCID: PMC3693554  PMID: 19571662
3.  Autophagy is required for extension of yeast chronological life span by rapamycin 
Autophagy  2009;5(6):847-849.
Rapamycin is an antibiotic that stimulates autophagy in a wide variety of eukaryotes, including the budding yeast Saccharomyces cerevisiae. Low concentrations of rapamycin extend yeast chronological life span (CLS). We have recently shown that autophagy is required for chronological longevity in yeast, which is attributable in part to a role for autophagy in amino acid homeostasis. We report herein that low concentrations of rapamycin stimulate macroautophagy during chronological aging and extend CLS.
PMCID: PMC3586265  PMID: 19458476
autophagy; aging; chronological life span; rapamycin; Saccharomyces cerevisiae
4.  Ceramide-induced autophagy 
Autophagy  2009;5(4):558-560.
Ceramide is a sphingolipid bioactive molecule that induces apoptosis and other forms of cell death, and triggers macroautophagy (referred to below as autophagy). Like amino acid starvation, ceramide triggers autophagy by interfering with the mTOR-signaling pathway, and by dissociating the Beclin 1:Bcl-2 complex in a c-Jun N-terminal kinase 1 (JNK1)-mediated Bcl-2 phosphorylation-dependent manner. Dissociation of the Beclin 1:Bcl-2 complex, and the subsequent stimulation of autophagy have been observed in various contexts in which the cellular level of long-chain ceramides was increased. It is notable that the conversion of short-chain ceramides (C2-ceramide and C6-ceramide) into long-chain ceramide via the activity of ceramide synthase is required to trigger autophagy. The dissociation of the Beclin 1:Bcl-2 complex has also been observed in response to tamoxifen and PDMP (an inhibitor of the enzyme that converts ceramide to glucosylceramide), drugs that increase the intracellular level of long-chain ceramides. However, and in contrast to starvation, over-expression of Bcl-2 does not blunt ceramide-induced autophagy. Whether this autophagy that is unchecked by forced dissociation of the Beclin 1:Bcl-2 complex is related to the ability of ceramide to trigger cell death remains an open question. More generally, the question of whether ceramide-induced autophagy is a dedicated cell death mechanism deserves closer scrutiny.
PMCID: PMC3501009  PMID: 19337026
macroautophagy; Bcl-2; Beclin 1; c-Jun N-terminal kinase; cell death; sphingolipids
5.  Autophagy discriminates between Alix and ESCRTs 
Autophagy  2009;5(1):106-107.
Alix and ESCRT proteins are required for membrane fission during viral budding and egress and during the abscission stage of cytokinesis. These common roles have suggested that Alix functions as an ESCRT protein, a conclusion challenged by the finding that unlike ESCRTs, which control the formation of multivesicular endosomes, Alix does not influence the degradation of the EGF receptor. We previously showed that Alix controls neuronal death by an unknown mechanism, but dependent on its interaction with ESCRT proteins. Since then, numerous reports have shown that ESCRTs participate in macroautophagy. Given the direct interaction between ESCRTs and Alix, together with the known contribution of autophagy to cell death, it was hypothesized that Alix controls autophagy and thereby cell death. Our recent published results show that this is not the case. ESCRT protein activity therefore needs Alix for viral budding and cytokinesis but not for autophagy. The function of ESCRT can thus be clearly be disconnected from that of Alix.
PMCID: PMC3325908  PMID: 19029801
Animals; Autophagy; Biological Transport; Calcium-Binding Proteins; metabolism; Caspases; metabolism; Endosomes; metabolism; Humans; Multiprotein Complexes; metabolism; Alix; Autophagy; ESCRT; endocytosis; MVB
6.  When more is less 
Autophagy  2009;5(1):111-113.
The role of autophagy, a catabolic lysosome-dependent pathway, has recently been recognized in a variety of disorders, including Pompe disease, which results from a deficiency of the glycogen-degrading lysosomal hydrolase acid-alpha glucosidase (GAA). Skeletal and cardiac muscle are most severely affected by the progressive expansion of glycogen-filled lysosomes. In both humans and an animal model of the disease (GAA KO), skeletal muscle pathology also involves massive accumulation of autophagic vesicles and autophagic buildup in the core of myofibers, suggesting an induction of autophagy. Only when we suppressed autophagy in the skeletal muscle of the GAA KO mice did we realize that the excess of autophagy manifests as a functional deficiency. This failure of productive autophagy is responsible for the accumulation of potentially toxic aggregate-prone ubiquitinated proteins, which likely cause profound muscle damage in Pompe mice. Also, by generating muscle-specific autophagy-deficient wild-type mice, we were able to analyze the role of autophagy in healthy skeletal muscle.
PMCID: PMC3257549  PMID: 19001870
Pompe disease; lysosome; muscle-specific autophagy deficiency; protein inclusions
7.  On the level 
Autophagy  2009;5(1):96-99.
Crohn disease is a complex, multigenic, chronic inflammatory bowel disease of uncertain etiology. Recent advances in genetics, including high-throughput single-nucleotide polymorphism typing platforms and deep sequencing technologies have begun to shed light upon disease predisposition and pathogenesis. Autophagy is emerging as a key player in both innate and adaptive immunity, as well as tissue homeostasis and development in the gut. Here we describe our recent studies into the Crohn disease-associated Immunity-Related GTPase family, M (IRGM) gene and our discovery of a large risk-conferring upstream deletion. We discuss the effects of this deletion upon expression levels of IRGM alleles and how tissue-specific expression might be affected by the promoter polymorphism. In addition, we comment upon the potential roles of IRGM in autophagy of intracellular pathogens, and the challenges ahead for further elucidating IRGM function.
PMCID: PMC3204672  PMID: 19029815
Crohn disease; inflammation; infection; bacteria; host-pathogen interaction; innate immunity
8.  Macroautophagy 
Autophagy  2009;5(2):140-151.
Dietary compounds can influence the risk of cancer and other diseases through diverse mechanisms which include the activation or inhibition of macroautophagy. Macroautophagy is a catabolic process for the lysosomal degradation and recycling of cytoplasmic constituents which has been implicated in several pathologies, including cancer and neurodegeneration. In some instances, macroautophagy acts to suppress tumor formation and neural degeneration. Thus, it may be feasible to design diets, supplements or therapeutics that can alter the level of macroautophagy within cells to prevent or treat disease. While critical questions still need to be answered before we can safely and effectively implement such a strategy, we provide here a review of the literature regarding dietary constituents that have a demonstrated macroautophagy-modulating function.
PMCID: PMC3135626  PMID: 19098459 CAMSID: cams1839
macroautophagy; autophagy; diet; nutrition; natural compounds; LC3; cancer; prevention
9.  An executioner caspase regulates autophagy 
Autophagy  2009;5(4):530-533.
The relationships between autophagy and cell death are complex and still not well understood. To advance our understanding of the molecular connections between autophagy and apoptosis, we performed an RNAi-based screen of Drosophila melanogaster apoptosis-related genes for their ability to enhance or suppress starvation-induced autophagy. We discovered that six apoptosis-related genes, Dcp-1, hid, Bruce, buffy, debcl and p53 as well as Ras/ Raf/MAPK signaling pathway components play a role in autophagy regulation in Drosophila cultured cells. Our study also provides the first in vivo evidence that the effector caspase Dcp-1 and IAP protein Bruce regulate both autophagy and starvation-induced cell death at two nutrient status checkpoints, germarium and mid-oogenesis, in the Drosophila ovary. Analysis of degenerating mid-stage egg chambers in DmAtg1 and DmAtg7 mutants reveal a reduction in TUNEL staining though DNA condensation appears unaffected. Based on these and previous findings, we propose here a putative molecular pathway that might regulate the sensitivity threshold of apoptotic and autophagic responses. We also discuss multiple interpretations of the Atg mutant egg chamber TUNEL phenotype that are consistent with a possible role for autophagy in either suppressing or enhancing the efficiency of cell degradation and/or promoting cell clearance associated with the death process.
PMCID: PMC3135627  PMID: 19242106 CAMSID: cams1682
autophagy; apoptosis; caspase; Dcp-1; Bruce
11.  Self-eating in skeletal development 
Autophagy  2009;5(2):228-229.
Macroautophagy (a.k.a. autophagy) is a cellular process aimed at the recycling of proteins and organelles that is achieved when autophagosomes fuse with lysosomes. Accordingly, lysosomal dysfunctions are often associated with impaired autophagy. We demonstrated that inactivation of the sulfatase modifying factor 1 gene (Sumf1), a gene mutated in multiple sulfatase deficiency (MSD), causes glycosaminoglycans (GAGs) to accumulate in lysosomes, which in turn disrupts autophagy. We utilized a murine model of MSD to study how impairment of this process affects chondrocyte viability and thus skeletal development.
PMCID: PMC3052986  PMID: 19029806
chondrocytes; macroautophagy; lysosomes; LSD; skeletal abnormalities
12.  Protein turnover differences between neurons and other cells 
Autophagy  2009;5(7):1037-1038.
In a recent study, we investigated the relationship between formation of an inclusion body (IB) and activity of the ubiquitin-proteasome system (UPS) in a primary neuron model of Huntington disease. We applied single-cell longitudinal acquisition and analysis to simultaneously monitor mutant huntingtin, which causes Huntington disease, IB formation, UPS function, and neuronal toxicity. We found that proteasome inhibition is toxic to striatal neurons in a dose-dependent fashion. The UPS is more impaired in neurons that go on to form IBs than in those that do not; however, after IBs form, UPS function improves. Our findings suggest that IBs are a protective cellular response to mutant protein mediated, in part, by improving intracellular protein degradation. The study also revealed some surprising differences in the ways that neurons regulate protein turnover compared with non-neuronal cells, which we discuss further in this article.
PMCID: PMC2892253  PMID: 19838079
Huntington disease; autophagy; neurodegeneration; rapamycin; everolimus; LC3
13.  Quantitation of selective autophagic protein aggregate degradation in vitro and in vivo using luciferase reporters 
Autophagy  2009;5(4):511-519.
The analysis of autophagy in cells and tissue has principally been performed via qualitative measures. These assays identify autophagosomes or measure the conversion of LC3I to LC3II. However, qualitative assays fail to quantitate the degradation of an autophagic substrate and therefore only indirectly measure an intact autophagic system. “Autophagic flux” can be measured using long-lived proteins that are degraded via autophagy. We developed a quantifiable luciferase reporter assay that measures the degradation of a long-lived polyglutamine protein aggregate, polyQ80-luciferase. Using this reporter, the induction of autophagy via starvation or rapamycin in cells preferentially decreases polyQ80-luciferase when compared with a non-aggregating polyQ19-luciferase after four hours of treatment. This response was both time- and concentration-dependent, prevented by autophagy inhibitors and absent in ATG5 knockout cells. We adapted this assay to living animals by electroporating polyQ19-luciferase and polyQ80-luciferase expression constructs into the right and left tibialis anterior (TA) muscles of mice, respectively. The change in the ratio of polyQ80-luciferase to polyQ19-luciferase signal before and after autophagic stimulation or inhibition was quantified via in vivo bioluminescent imaging. Following two days of starvation or treatment with intraperitoneal rapamycin, there was a ~35% reduction in the ratio of polyQ80:polyQ19-luciferase activity, consistent with the selective autophagic degradation of polyQ80 protein. This autophagic response in skeletal muscle in vivo was abrogated by co-treatment with chloroquine and in ATG16L1 hypomorphic mice. Our study demonstrates a method to quantify the autophagic flux of an expanded polyglutamine via luciferase reporters in vitro and in vivo.
PMCID: PMC2992796  PMID: 19305149
14.  Monitoring mitophagy in yeast: The Om45-GFP processing assay 
Autophagy  2009;5(8):1186-1189.
Macroautophagy (hereafter autophagy) is a ubiquitous degradative process in eukaryotic cells.1 Mitochondria autophagy (mitophagy) is a type of specific autophagy that degrades mitochondria selectively.2 Mitophagy is thought to play an important role for maintaining the quality of these organelles by eliminating damaged mitochondria, and it is involved in cellular differentiation, whereas dysfunctional mitophagy is related with neurodegenerative diseases;3-5 however, the mechanism of mitophagy is poorly understood. To facilitate the analysis of mitophagy, we recently established a simple method to monitor mitophagy in yeast, the Om45-GFP processing assay.6 Om45-GFP is a mitochondrial outer membrane protein. Following the uptake of mitochondria into the vacuole, Om45-GFP is degraded, releasing the intact form of GFP, which is detected by immunoblotting. Therefore, the amount of free GFP reflects the level of mitophagy.
PMCID: PMC2850110  PMID: 19806021
mitochondria; autophagy; vacuole; Om45; GFP
15.  Autophagy-dependent and -independent mechanisms of mitochondrial clearance during reticulocyte maturation 
Autophagy  2009;5(7):1064-1065.
Erythrocyte formation involves the elimination of mitochondria at the reticulocyte stage of development. Nix−/− reticulocytes fail to eliminate their mitochondria at this step due to a defect in the targeting of mitochondria to autophagosomes. To determine the role of autophagy in this process, we generated Atg7−/− transplant mice. Atg7−/− reticulocytes exhibit a partial defect in mitochondrial clearance, demonstrating that there are both autophagy-dependent and -independent mechanisms of mitochondrial clearance. We used Atg7−/− autophagy-defective reticulocytes to study temporal events in mitochondrial clearance. Mitochondrial depolarization precedes elimination, but in Atg7−/− reticulocytes the depolarization event is markedly delayed. Since Atg7 regulates autophagosome formation, we infer that mitochondrial depolarization occurs downstream of autophagosome formation in reticulocytes. We propose that there are two mechanisms of mitochondrial clearance: one that is triggered by mitochondrial depolarization, and a second NIX-dependent mechanism, which is not. The NIX-dependent mechanism remains to be elucidated.
PMCID: PMC2763954  PMID: 19713771
reticulocyte; autophagy; mitophagy; mitochondria; NIX; Atg7; mitochondrial depolarization; mitochondrial clearance
16.  Indirect estimation of the area density of Atg8 on the phagophore 
Autophagy  2009;5(2):217-220.
Atg8 is a ubiquitin-like protein that controls the expansion of the phagophore during autophagosome formation. It is recruited to the phagophore during the expansion stage and released upon the completion of the autophagosome. One possible model explaining the function of Atg8 is that it acts as an adaptor of a coat complex. Here, we tested the coat-adaptor model by estimating the area density of Atg8 molecules on the phagophore. We developed a computational process to simulate the random sectioning of vesicles heterogeneous in size. This method can be applied to estimate the original sizes of intracellular vesicles from sizes of their random sections obtained through transmission electron microscopy. Using this method, we found that the estimated area density of Atg8 is comparable with that of proteins that form the COPII coat.
PMCID: PMC2941343  PMID: 19088501
Autophagy; lysosome; stress; vacuole; yeast
17.  A common role for Atg16L1, Atg5, and Atg7 in small intestinal Paneth cells and Crohn’s disease 
Autophagy  2009;5(2):250-252.
Recently identified genetic determinants for enhanced susceptibility to Crohn’s disease (CD) included polymorphisms in the ATG16L1 and IRGM1 loci suggesting that the autophagy pathway plays a role in the pathogenesis of this disease. We have generated and analyzed three mouse models with diminished expression of autophagy proteins and show how the loss of function of various autophagy components contributes to CD pathogenesis. In the mouse small intestine, the common cellular target of Atg16L1, Atg5, and Atg7 is the Paneth cell, a specialized epithelial cell whose main function is the delivery of antimicrobial factors into the intestinal lumen by production and secretion of its characteristic cytoplasmic granules. Autophagy-deficient Paneth cells exhibited a striking loss of function in this granule exocytosis pathway. Transcriptional analysis revealed a gain of function whereby the gene expression associated with inflammatory responses was increased in autophagy-deficient Paneth cells. Importantly, we validated these findings by analyzing intestinal tissues from CD patients. Similar Paneth cell abnormalities were observed in CD patients homozygous for the ATG16L1 risk allele. Thus, one role for the autophagy pathway in CD pathogenesis is through selective effects on the biology and specialized properties of Paneth cells.
PMCID: PMC2940227  PMID: 19139628
ATG16L1; ATG5; ATG7; Paneth cell; Crohn’s disease; inflammatory bowel disease; intestine; exocytosis; adipocytokine; PPAR
18.  Toxoplasma - induced autophagy: a window into nutritional futile cycles in mammalian cells? 
Autophagy  2009;5(3):404-406.
The regulation and function of autophagy in response to metabolic signals is not yet well understood. A recent study from our laboratory indicates than an intracellular parasite, Toxoplasma gondii, derives nutritive benefit from the upregulation of host cell autophagy. We discuss these and related findings suggesting that autophagy in infected cells functions as part of a metabolic futile cycle. The hypothesis is presented that endogenous autophagy-based futile cycles may operate in normal mammalian cells, providing a substrate for manipulation by pathogens.
PMCID: PMC2891286  PMID: 19305153
Toxoplasma; parasites; autophagy; futile cycles; protein metabolism; mTOR; amino acids
19.  Regulation of autophagy by a beclin 1-targeted microRNA, miR-30a, in cancer cells 
Autophagy  2009;5(6):816-823.
beclin 1, the mammalian homologue of the yeast Atg6, is a key autophagy-promoting gene that plays a critical role in the regulation of cell death and survival of various types of cells. However, recent studies have observed that the expression of beclin 1 is altered in certain diseases including cancers. The causes underlying the aberrant expression of beclin 1 remain largely unknown. We report here that microRNAs (miRNAs), a class of endogenous, 22–24 nucleotide noncoding RNA molecules able to affect stability and translation of mRNA, may represent a previously unrecognized mechanism for regulating beclin 1 expression and autophagy. We demonstrated that beclin 1 is a potential target for miRNA miR-30a, and this miRNA could negatively regulate beclin 1 expression resulting in decreased autophagic activity. Treatment of tumor cells with the miR-30a mimic decreased, and with the antagomir increased, the expression of beclin 1 mRNA and protein. Dual luciferase reporter assay confirmed that the miR-30a binding sequences in the 3′-UTR of beclin 1 contribute to the modulation of beclin 1 expression by miR-30a. Furthermore, inhibition of beclin 1 expression by the miR-30a mimic blunted activation of autophagy induced by rapamycin. Our study of the role of miR-30a in regulating beclin 1 expression and autophagy reveals a novel function for miRNA in a critical cellular event with significant impacts in cancer development, progression and treatment, and in other diseases.
PMCID: PMC3669137  PMID: 19535919
beclin 1; autophagy; microRNA; miR-30a; gene expression
20.  PCD and autophagy in the unicellular green alga Micrasterias denticulata 
Autophagy  2009;5(6):854-855.
Programmed cell death (PCD) plays a central role in normal plant development and is also induced by various biotic and abiotic stress factors. In the unicellular freshwater green alga Micrasterias denticulata morphological and biochemical hallmarks such as the appearance of autophagosomes, increased production of ROS and degradation of genomic DNA into small fragments (“DNA laddering”) indicate PCD. Our data not only demonstrate that Micrasterias is capable of performing PCD under salt stress, but also that it is triggered by the ionic and not osmotic component of salinity. Additionally, results from the present and previous studies suggest that different inducers may lead to different cell death pathways in one and the same organism.
PMCID: PMC2912524  PMID: 19430197
autophagy; green alga; Micrasterias denticulata; programmed cell death; ROS; salt stress; ultrastructure
21.  Tap42-associated protein phosphatase type 2A negatively regulates induction of autophagy 
Autophagy  2009;5(5):616-624.
Autophagy is a highly conserved degradative process in eukaryotic cells. This process plays an integral role in cellular physiology, and the levels of autophagy must be precisely controlled to prevent cellular dysfunction. The rapamycin-sensitive Tor kinase complex 1 (TORC1) has a major role in regulating the induction of autophagy; however, the regulatory mechanisms are not fully understood. Here, we find that Tap42 and protein phosphatase type 2A (PP2A) are involved in the regulation of autophagy in yeast. Temperature-sensitive mutant alleles of TAP42 revealed that autophagy was induced without inactivation of TORC1. Absence of the Tap42-interacting protein Tip41 abolished autophagy induction in the tap42 mutants, whereas overexpression of Tip41 activated autophagy. Furthermore, inactivation of PP2A stimulated autophagy and overexpression of a catalytic subunit of PP2A blocked rapamycin-induced autophagy. Our data support a model in which autophagy is negatively regulated by the Tap42-PP2A pathway.
PMCID: PMC2738980  PMID: 19223769
autophagy; lysosome; stress; vacuole; yeast
22.  A multiple ATG gene knockout strain for yeast two-hybrid analysis 
Autophagy  2009;5(5):699-705.
Autophagy is a major intracellular degradative pathway that is involved in many human diseases. The molecular mechanism of autophagy has been elucidated largely through studies on autophagy-related (Atg) proteins. One difficulty in understanding the mechanism of autophagy has been the lack of functional motifs in most of the Atg proteins. In the absence of this information, studies that have focused on the interactions between Atg proteins have shed light on their functions. However, in most studies, it is difficult to determine whether an interaction is direct or occurs through other Atg proteins, particularly in vivo. Here, we took advantage of a new reagent, a multiple knockout (MKO) strain lacking 24 ATG genes, and converted the strain into a yeast two-hybrid (Y2H) host strain. We introduced three reporter genes into the existing MKO strain, and analyzed known interactions in the new MKO Y2H strain background to verify its utility. We also probed a new interaction using the MKO Y2H strain, and our results suggest that Atg29 and Atg31 interact independently of other known Atg proteins, and this interaction may mediate the interaction between Atg17 and Atg29.
PMCID: PMC2754276  PMID: 19337029
autophagy; protein-protein interaction; Atg1 complex; Atg29; Atg31
23.  Identification of Atg5-dependent transcriptional changes and increases in mitochondrial mass in Atg5-deficient T lymphocytes 
Autophagy  2009;5(5):625-635.
Autophagy is implicated in many functions of mammalian cells such as organelle recycling, survival and differentiation, and is essential for the maintenance of T and B lymphocytes. Here, we demonstrate that autophagy is a constitutive process during T cell development. Deletion of the essential autophagy genes Atg5 or Atg7 in T cells resulted in decreased thymocyte and peripheral T cell numbers, and Atg5-deficient T cells had a decrease in cell survival. We employed functional-genetic and integrative computational analyses to elucidate specific functions of the autophagic process in developing T-lineage lymphocytes. Our whole-genome transcriptional profiling identified a set of 699 genes differentially expressed in Atg5-deficient and Atg5-sufficient thymocytes (Atg5-dependent gene set). Strikingly, the Atg5-dependent gene set was dramatically enriched in genes encoding proteins associated with the mitochondrion. In support of a role for autophagy in mitochondrial maintenance in T lineage cells, the deletion of Atg5 led to increased mitochondrial mass in peripheral T cells. We also observed a correlation between mitochondrial mass and Annexin-V staining in peripheral T cells. We propose that autophagy is critical for mitochondrial maintenance and T cell survival. We speculate that, similar to its role in yeast or mammalian liver cells, autophagy is required in T cells for the removal of damaged or aging mitochondria and that this contributes to the cell death of autophagy-deficient T cells.
PMCID: PMC3737142  PMID: 19276668
T cells; cell differentiation and development; transgenic/knockout mice; ATG5; mitochondria
24.  Targeted deletion of autophagy-related 5 (atg5) impairs adipogenesis in a cellular model and in mice 
Autophagy  2009;5(8):1118-1130.
Mammalian white adipocytes have a unique structure in which nearly the entire cell volume is occupied by a single large lipid droplet, while the surrounding cytoplasm occupies minimal space. The massive cytoplasmic remodeling processes involved in the formation of this unique cellular structure are poorly defined. Autophagy is a membrane trafficking process leading to lysosomal degradation of cytoplasmic components. Here, we investigated the functional role of atg5, a gene encoding an essential protein required for autophagy, in adipocyte differentiation in a cellular model and in mice. Massive autophagy was activated when wild-type primary mouse embryonic fibroblasts (MEFs) were induced for adipocyte differentiation. Importantly, the autophagy deficient primary atg5-/- MEFs exhibited dramatically reduced efficiency in adipogenesis. Time-lapse microscopy revealed that atg5-/- MEFs initially appeared to differentiate normally; however, a majority of the differentiating atg5-/- cells ultimately failed to undergo further morphological transformation and eventually died, likely through apoptosis. Consistent with these in vitro results, histological analysis revealed that the atg5-/- late-stage embryos and neonatal pups had much less subcutaneous perilipin A-positive adipocytes. Consistently, when treated with chloroquine, a functional inhibitor of autophagy, wild-type MEFs exhibited drastically reduced efficiency of adipocyte differentiation. Taken together, these findings demonstrated that Atg5 is involved in normal adipocyte differentiation, suggesting an important role of autophagy in adipogenesis.
PMCID: PMC2873687  PMID: 19844159
Atg5; autophagy; adipogenesis; WAT; adipocyte differentiation
25.  Mitochondrial autophagy as a compensatory response to PINK1 deficiency 
Autophagy  2009;5(8):1213-1214.
Macroautophagy (hereafter, autophagy) plays a critical role in maintaining cellular homeostasis by degrading protein aggregates and dysfunctional/damaged organelles. We recently reported that silencing the recessive familial Parkinson disease gene encoding PTEN-induced kinase 1 (PINK1) leads to neuronal cell death accompanied by mitochondrial dysfunction and Drp1-dependent fragmentation. In this model, mitochondrial fission and Beclin 1-dependent autophagy play protective roles, cooperating to sequester and eliminate damaged mitochondria. We discuss the role of superoxide and other reactive oxygen species upstream of mitochondrial depolarization, fission and autophagy in PINK1 knockdown lines. PINK1 deficiency appears to trigger several compensatory responses that together facilitate clearance of depolarized mitochondria, through a mechanism that is further enhanced by increased expression of parkin. These data offer additional insights that broaden the spectrum of potential interactions between PINK1 and parkin with respect to the regulation of mitochondrial homeostasis and mitophagy.
PMCID: PMC2841445  PMID: 19786829
mitochondria; PINK1; autophagy; cell death; parkinson disease; parkin; beclin 1

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