In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

[Abstract unavailable

TRPML1 (mucolipin-1/MCOLN1) is predicted to be an intracellular late endosomal and lysosomal ion channel protein belonging to the mucolipin subfamily of Transient Receptor Potential (TRP) proteins 1–3. Mutations in the human TRPML1 gene cause mucolipidosis type IV disease (ML4) 4, 5. ML4 patients exhibit motor impairment, mental retardation, retinal degeneration, and iron-deficiency anemia. Since aberrant iron metabolism may cause neural and retinal degeneration 6, 7, it may be a primary cause of ML4 phenotypes. In most mammalian cells, release of iron from endosomes and lysosomes following iron uptake via endocytosis of Fe3+-bound transferrin receptors 6, or following lysosomal degradation of ferritin-Fe complexes and autophagic ingestion of iron-containing macromolecules 6, 8, is the major source of cellular iron. The Divalent Metal Transporter protein (DMT1) is the only endosomal Fe2+ transporter currently known and is highly expressed in erythroid precursors 6, 9, but genetic studies suggest the existence of a DMT1-independent endosomal/lysosomal Fe2+ transport protein 9. Here, by measuring radiolabeled iron uptake, monitoring the levels of cytosolic and intra-lysosomal iron and directly patch-clamping the late endosomal/lysosomal membrane, we show that TRPML1 functions as a Fe2+ permeable channel in late endosomes and lysosomes. ML4 mutations are shown to impair TRPML1’s ability to permeate Fe2+ at varying degrees, which correlate well with the disease severity. A comparison of TRPML1−/− ML4 and control skin fibroblasts showed a reduction of cytosolic Fe2+ levels, an increase of intra-lysosomal Fe2+ levels, and an accumulation of lipofuscin-like molecules in TRPML1−/− cells. We propose that TRPML1 mediates a mechanism by which Fe2+ is released from late endosomes/lysosomes. Our results suggest that impaired iron transport may contribute to both hematological and degenerative symptoms of ML4 patients.

It is now generally accepted that aging and eventual death of multicellular organisms is to a large extent related to macromolecular damage by mitochondrially produced reactive oxygen species, mostly affecting long-lived postmitotic cells, such as neurons and cardiac myocytes. These cells are rarely or not at all replaced during life and can be as old as the whole organism. The inherent inability of autophagy and other cellular-degradation mechanisms to remove damaged structures completely results in the progressive accumulation of garbage, including cytosolic protein aggregates, defective mitochondria, and lipofuscin, an intralysosomal indigestible material. In this review, we stress the importance of crosstalk between mitochondria and lysosomes in aging. The slow accumulation of lipofuscin within lysosomes seems to depress autophagy, resulting in reduced turnover of effective mitochondria. The latter not only are functionally deficient but also produce increased amounts of reactive oxygen species, prompting lipofuscinogenesis. Moreover, defective and enlarged mitochondria are poorly autophagocytosed and constitute a growing population of badly functioning organelles that do not fuse and exchange their contents with normal mitochondria. The progress of these changes seems to result in enhanced oxidative stress, decreased ATP production, and collapse of the cellular catabolic machinery, which eventually is incompatible with survival. Antioxid. Redox Signal. 12, 503-535.

The lysosomal compartment is essential for a variety of cellular functions, including the normal turnover of most long-lived proteins and all organelles. The compartment consists of numerous acidic vesicles (pH *4 to 5) that constantly fuse and divide. It receives a large number of hydrolases (*50) from the trans-Golgi network, and substrates from both the cells' outside (heterophagy) and inside (autophagy). Many macromolecules contain iron that gives rise to an iron-rich environment in lysosomes that recently have degraded such macromolecules. Iron-rich lysosomes are sensitive to oxidative stress, while 'resting' lysosomes, which have not recently participated in autophagic events, are not. The magnitude of oxidative stress determines the degree of lysosomal destabilization and, consequently, whether arrested growth, reparative autophagy, apoptosis, or necrosis will follow. Heterophagy is the first step in the process by which immunocompetent cells modify antigens and produce antibodies, while exocytosis of lysosomal enzymes may promote tumor invasion, angiogenesis, and metastasis. Apart from being an essential turnover process, autophagy is also a mechanism by which cells will be able to sustain temporary starvation and rid themselves of intracellular organisms that have invaded, although some pathogens have evolved mechanisms to prevent their destruction. Mutated lysosomal enzymes are the underlying cause of a number of lysosomal storage diseases involving the accumulation of materials that would be the substrate for the corresponding hydrolases, were they not defective. The normal, low-level diffusion of hydrogen peroxide into iron-rich lysosomes causes the slow formation of lipofuscin in long-lived postmitotic cells, where it occupies a substantial part of the lysosomal compartment at the end of the life span. This seems to result in the diversion of newly produced lysosomal enzymes away from autophagosomes, leading to the accumulation of malfunctioning mitochondria and proteins with consequent cellular dysfunction. If autophagy were a perfect turnover process, postmitotic ageing and several age-related neurodegenerative diseases would, perhaps, not take place.

H(2)DCF-DA (dihydrodichlorofluorescein diacetate) is widely used to evaluate 'cellular oxidative stress'. After passing through the plasma membrane, this lipophilic and non-fluorescent compound is de-esterified to a hydrophilic alcohol [H(2)DCF (dihydrodichlorofluorescein)] that may be oxidized to fluorescent DCF (2',7'-dichlorofluorescein) by a process usually considered to involve ROS (reactive oxygen species). It is, however, not always recognized that, being a hydrophilic molecule, H(2)DCF does not cross membranes, except for the outer fenestrated mitochondrial ones. It is also not generally realized that oxidation of H(2)DCF is dependent either on Fenton-type reactions or on unspecific enzymatic oxidation by cytochrome c, for neither superoxide, nor H(2)O(2), directly oxidizes H(2)DCF. Consequently, oxidation of H(2)DCF requires the presence of either cytochrome c or of both redox-active transition metals and H(2)O(2). Redox-active metals exist mainly within lysosomes, whereas cytochrome c resides bound to the outer side of the inner mitochondrial membrane. Following exposure to H(2)DCF-DA, weak mitochondrial fluorescence was found in both the oxidation-resistant ARPE-19 cells and the much more sensitive J774 cells. This fluorescence was only marginally enhanced following short exposure to H(2)O(2), showing that by itself it is unable to oxidize H(2)DCF. Cells that were either exposed to the lysosomotropic detergent MSDH (O-methylserine dodecylamide hydrochloride), exposed to prolonged oxidative stress, or spontaneously apoptotic showed lysosomal permeabilization and strong DCF-induced fluorescence. The results suggest that DCF-dependent fluorescence largely reflects relocation to the cytosol of lysosomal iron and/or mitochondrial cytochrome c.

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TRPML1 (mucolipin-1/MCOLN1) is predicted to be an intracellular late endosomal and lysosomal ion channel protein belonging to the mucolipin subfamily of Transient Receptor Potential (TRP) proteins 1-3. Mutations in the human TRPML1 gene cause mucolipidosis type IV disease (ML4) 4, 5. ML4 patients exhibit motor impairment, mental retardation, retinal degeneration, and iron-deficiency anemia. Since aberrant iron metabolism may cause neural and retinal degeneration 6, 7 , it may be a primary cause of ML4 phenotypes. In most mammalian cells, release of iron from endosomes and lysosomes following iron uptake via endocytosis of Fe 3+bound transferrin receptors 6 , or following lysosomal degradation of ferritin-Fe complexes and autophagic ingestion of iron-containing macromolecules 6, 8 , is the major source of cellular iron. The Divalent Metal Transporter protein (DMT1) is the only endosomal Fe 2+ transporter currently known and is highly expressed in erythroid precursors 6, 9 , but genetic studies suggest the existence of a DMT1-independent endosomal/lysosomal Fe 2+ transport protein 9. Here, by measuring radiolabeled iron uptake, monitoring the levels of cytosolic and intra-lysosomal iron and directly patch-clamping the late endosomal/lysosomal membrane, we show that TRPML1 functions as a Fe 2+ permeable channel in late endosomes and lysosomes. ML4 mutations are shown to impair TRPML1's ability to permeate Fe 2+ at varying degrees, which correlate well with the disease severity. A comparison of TRPML1 −/− ML4 and control skin fibroblasts showed a reduction of cytosolic Fe 2+ levels, an increase of intra-lysosomal Fe 2+ levels, and an accumulation of lipofuscin-like molecules in TRPML1 −/− cells. We propose that TRPML1 mediates a mechanism by which Fe 2+ is released from late endosomes/lysosomes. Our results suggest that impaired iron transport may contribute to both hematological and degenerative symptoms of ML4 patients.