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

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Recent studies indicate that regulation of cellular oxidative capacity through enhancing mitochondrial biogenesis may be beneficial for neuronal recovery and survival in human neurodegenerative disorders. The peroxisome proliferator-activated receptor ␥ coactivator-1␣ (PGC-1␣) has been shown to be a master regulator of mitochondrial biogenesis and cellular energy metabolism in muscle and liver. The aim of our study was to establish whether PGC-1␣ and PGC-1␤ control mitochondrial density also in neurons and if these coactivators could be up-regulated by deacetylation. The results demonstrate that PGC-1␣ and PGC-1␤ control mitochondrial capacity in an additive and independent manner. This effect was observed in all studied subtypes of neurons, in cortical, midbrain, and cerebellar granule neurons. We also observed that endogenous neuronal PGC-1␣ but not PGC-1␤ could be activated through its repressor domain by suppressing it. Results demonstrate also that overexpression of SIRT1 deacetylase or suppression of GCN5 acetyltransferase activates transcriptional activity of PGC-1␣ in neurons and increases mitochondrial density. These effects were mediated exclusively via PGC-1␣, since overexpression of SIRT1 or suppression of GCN5 was ineffective where PGC-1␣ was suppressed by short hairpin RNA. Moreover, the results demonstrate that overexpression of PGC-1␤ or PGC-1␣ or activation of the latter by SIRT1 protected neurons from mutant ␣-synuclein-or mutant huntingtin-induced mitochondrial loss. These evidences demonstrate that activation or overexpression of the PGC-1 family of coactivators could be used to compensate for neuronal mitochondrial loss and suggest that therapeutic agents activating PGC-1 would be valuable for treating neurodegenerative diseases in which mitochondrial dysfunction and oxidative damage play an important pathogenic role.Previous studies have shown that the PGC-1 family of coactivators, particularly PGC-1␣, are potent stimulators of mitochondrial respiration and gene transcription in liver, heart, and skeletal muscle. It has been shown that PGC-1␣ acts by activating the nuclear respiratory factors NRF1 and NRF2 that in turn regulate expression of Tfam (mitochondrial transcription factor A), essential for replication, maintenance, and transcription of mitochondrial DNA. PGC-1␣ is also important for the expression of nuclear genes encoding respiratory chain subunits and other proteins that are required for proper mitochondrial functions (1-4).Apart from gene expression, the activity of PGC-1␣ is influenced by posttranscriptional regulation by means of protein phosphorylation, acetylation, and methylation. PGC-1␣ is known to be regulated by p38 mitogen-activated protein kinase through the inhibition of the p160 Myb-binding protein (p160 MBP ) 2 in brown fat cells and myotubes (5, 6). AMPK (AMP-activated protein kinase) phosphorylation of PGC-1␣ initiates many of the important gene-regulatory functions of AMPK in skeletal muscle (7). Acetylation status of PGC-1␣ is, on the other hand, regulated by t...

Parkinson disease is characterized by the accumulation of aggregated ␣-synuclein as the major component of the Lewy bodies. ␣-Synuclein accumulation in turn leads to compensatory effects that may include the up-regulation of autophagy. Another common feature of Parkinson disease (PD) is mitochondrial dysfunction. Here, we provide evidence that the overactivation of autophagy may be a link that connects the intracellular accumulation of ␣-synuclein with mitochondrial dysfunction. We found that the activation of macroautophagy in primary cortical neurons that overexpress mutant A53T ␣-synuclein leads to massive mitochondrial destruction and loss, which is associated with a bioenergetic deficit and neuronal degeneration. No mitochondrial removal or net loss was observed when we suppressed the targeting of mitochondria to autophagosomes by silencing Parkin, overexpressing wild-type Mitofusin 2 and dominant negative Dynamin-related protein 1 or blocking autophagy by silencing autophagy-related genes. The inhibition of targeting mitochondria to autophagosomes or autophagy was also partially protective against mutant A53T ␣-synuclein-induced neuronal cell death. These data suggest that overactivated mitochondrial removal could be one of the contributing factors that leads to the mitochondrial loss observed in PD models. Mitochondrial dysfunction is one of the hallmarks of Parkinson disease (PD).2 The link between mitochondrial dysfunction and PD was made after the discovery of mitochondrial complex I deficiency in the substantia nigra (1). This connection has been supported by the finding that the products of several PDrelated genes show mitochondrial localization under certain conditions, including SNCA, Parkin, PINK1, DJ-1, LRRK2, and HTR2A (2), and that the mitochondrial toxins MPTP, rotenone, and acetogenins can cause PD (3). A variety of mechanisms have been proposed to explain mitochondrial dysfunction. Oxidative stress, mitochondrial DNA deletions, pathological mutations in genes encoding mitochondrial proteins, altered mitochondrial morphology, and the interaction of pathogenic proteins with mitochondria can all lead to mitochondrial dysfunction and neuronal demise (4).In this study, we propose an intriguing possibility whereby mitochondrial dysfunction may arise from the loss of mitochondria because of the overactivation of autophagy. Signs of autophagy have been detected in the brains of PD patients, whereas autophagosomes are rarely detected in normal brain (5-6). Moreover, several studies have also demonstrated that the overexpression of mutant A53T ␣-synuclein in PC12 cells, cultured neurons, and nigrostriatal systems activates autophagy (7-10). Here, we provide evidence that shows that the up-regulation of macroautophagy by mutant A53T ␣-synuclein can augment mitochondrial removal, which results in a net mitochondrial loss, energetic failure, and neuronal cell death. EXPERIMENTAL PROCEDURESNeuronal Cultures-Primary cultures of rat cortical cells were prepared from neonatal Wistar rats. Briefly, cortices w...

Deficiency of the protein Wolfram syndrome 1 (WFS1) is associated with multiple neurological and psychiatric abnormalities similar to those observed in pathologies showing alterations in mitochondrial dynamics. The aim of this study was to examine the hypothesis that WFS1 deficiency affects neuronal function via mitochondrial abnormalities. We show that down-regulation of WFS1 in neurons leads to dramatic changes in mitochondrial dynamics (inhibited mitochondrial fusion, altered mitochondrial trafficking, and augmented mitophagy), delaying neuronal development. WFS1 deficiency induces endoplasmic reticulum (ER) stress, leading to inositol 1,4,5-trisphosphate receptor (IP3R) dysfunction and disturbed cytosolic Ca2+ homeostasis, which, in turn, alters mitochondrial dynamics. Importantly, ER stress, impaired Ca2+ homeostasis, altered mitochondrial dynamics, and delayed neuronal development are causatively related events because interventions at all these levels improved the downstream processes. Our data shed light on the mechanisms of neuronal abnormalities in Wolfram syndrome and point out potential therapeutic targets. This work may have broader implications for understanding the role of mitochondrial dynamics in neuropsychiatric diseases.