Name: Protocol for Measuring Mitophagy in Caenorhabditis elegans
Uploaded: 2023-05-19T13:40:00
Description: Watch this Scientific Journal Video about Protocol for Measuring Mitophagy in Caenorhabditis elegans at JoVE.com

protocol for measuring mitophagy in caenorhabditis elegans

Quantifizierung der Mitophagie in C. elegans und einer Leberkrebszelllinie

Mitochondria are essential for all aerobic animals, including humans. They convert the chemical energy of biomolecules to adenosine triphosphate (ATP) via oxidative phosphorylation1, synthesize heme2, degrade fatty acids through &#946; oxidation3, regulate calcium4 and iron5 homeostasis, control cell death by apoptosis6, and generate reactive oxygen species (ROS), which play a vital role in redox homeostasis7. Two complementary and opposite processes maintain the integrity and proper function of the mitochondria: the synthesis of new mitochondrial components (biogenesis) and the selective removal of damaged ones through mitochondrial autophagy (i.e., mitophagy)8.
Several mitophagy pathways are mediated by enzymes, such as PINK1/Parkin, and receptors, including FUNDC1, FKBP8, and BNIP/NIX9,10. Notably, the selective degradation of mitochondrial components can occur independently of the autophagosome machinery (i.e., through mitochondrial-derived vesicles)11. However, the endpoints of the different selective mitophagy pathways are similar&#160;(i.e.,mitochondrial degradation by lysosomal enzymes)12,13. For this reason, various methods for identifying and measuring mitophagy rely on the colocalization of mitochondrial and lysosomal markers14,15,16,17 and decreased levels of mitochondrial proteins/mitochondrial DNA18.
Below is a concise description of the existing experimental methodologies for measuring mitophagy in animal cells using fluorescence microscopy, emphasizing the mitophagy endpoint phase.
Mitophagy biosensors 
Mitochondrial degradation occurs within the acidic environment of the lysosome19. Therefore, mitochondrial components, including proteins, experience a shift from a neutral to an acidic pH at the endpoint of the mitophagy process. This pattern underpins the mechanism of action of several mitophagy biosensors, including mito-Rosella18 and tandem mCherry-GFP-FIS114. These sensors contain a pH-sensitive green fluorescence protein (GFP) and a pH-insensitive red fluorescence protein (RFP). Therefore, at the endpoint of mitophagy, the green-to-red fluorescence ratio drops significantly due to the quenching of the GFP fluorophore. The major limitations of these sensors are (1) possible F&#246;rster resonance energy transfer (FRET) between the fluorophores; (2) the differential maturation rate of GFP and RFP; (3) dissociation between the GFP and RFP due to proteolytic cleavage of the polypeptide that connects them; (4) fluorescence-emission overlap; and (5) differential fluorophore brightness and quenching15,16.
A sensor that overcomes some of these limitations is the Keima mitochondrial sensor17. The mt-Keima sensor (derived from the coral protein Keima) displays a single emission peak (620 nm). However, its excitation peaks are pH-sensitive. As a result, there is a transition from a green excitation (440 nm) to a red one (586 nm) when shifting from a high pH to an acidic pH16,17. A more recent mitophagy sensor, Mito-SRAI, has advanced the field by allowing for measurements in fixed biological samples20. However, despite the many advantages of genetic sensors, such as the ability to express them in specific tissues/cells and target them to distinct mitochondrial compartments, they also have limitations. One limitation is that the genetic sensors need to be expressed in cells or animals, which can be time-consuming and resource-intensive.
Additionally, the expression of the sensors within mitochondria themselves may influence the mitochondrial function. For example, expressing mitochondrial GFP (mtGFP) in the C. elegans worm body wall muscles expands the mitochondrial network21. This phenotype depends on the function of the stress-activated transcription factor ATFS-1, which plays an essential role in the activation of unfolded protein response in mitochondria (UPRmt)21. Therefore, although genetically encoded mitochondria/mitophagy biosensors are extremely useful for monitoring mitochondria homeostasis in vivo, they may affect the very process they are designed to measure.
Mitochondria/lysosome-specific antibodies and dyes 
Another strategy for testing mitochondrial/lysosome colocalization is to use antibodies against mitochondrial/lysosomal proteins, such as the mitochondrial outer membrane protein TOM20 and lysosomal-associated membrane protein 1 (LAMP1)22. In most cases, secondary antibodies that are conjugated to a fluorophore are used to detect the fluorescence signal via microscopy. Another strategy is to combine genetic constructs with mitochondrial/lysosomal dyes, such as expressing a LAMP1::GFP fusion construct in cells while staining them with a red mitochondrial dye (e.g., Mitotracker Red)16. These methodologies, while effective, require specific antibodies and often involve working with fixed specimens or generating cells/transgenic animals expressing fluorescently labeled mitochondria/lysosomes.
Here, we outline the utilization of a commercial lysosome/mitochondria/nuclear staining kit for assessing the mitophagy-activating properties of synthetic diamine O,O (octane-1,8-diyl)bis(hydroxylamine), hereafter referred to as VL-85023, in C. elegans worms and the human cancer cell line Hep-3B (Figure 1). The staining kit contains a mixture of lysosomal/mitochondrial/nuclear-targeted dyes that specifically stain these organelles23. We previously used this kit to demonstrate the mitophagy activity of 1,8 diaminooctane (hereafter referred to as VL-004) in C. elegans23. Importantly, we validated the staining kit results with the mito-Rosella biosensor and qPCR measurements of the mitochondrial:nuclear DNA content23. This staining kit offers the following advantages. First, there is no need to generate transgenic animals or cells expressing a mitochondrial biosensor. Therefore, we can study unmodified wild-type animals or cells and, thus, save much time, money, and labor. Moreover, as mentioned, expressing mitochondrial biosensors can change the mitochondrial function. Second, the kit is cost-effective, easy to use, and fast. Third, although we demonstrate the method in C. elegans and human cells, it could be modified for other cell types and organisms.
With that said, like any method, the staining kit protocol has drawbacks. For example, the incubation of the worms with the reagent is carried out in the absence of food (we have seen that even dead bacteria significantly decrease the staining efficiency). Although the incubation time is relatively short, it is possible that even in this time frame, homeostatic responses may be altered, including mitophagy. In addition, the binding of the dyes to the ER/mitochondrial/nuclear proteins and other biomolecules may affect the activities of these organelles. Moreover, unlike mitophagy measurement with genetic sensors, we work with worms and cells that have undergone chemical fixation. Therefore, it is impossible to continue monitoring the same worms/cells at different times. Hence, we recommend combining different methodologies to validate the function of mitophagy in a particular physiological process. Below, we present new data demonstrating that VL-850 induces robust mitophagy in C. elegans worms and Hep-3B cells. Therefore, these data further support the hypothesis that VL-850 extends the lifespan of C. elegans and protects C. elegans from oxidative damage through the induction of healthy mitophagy. We have used the proton ionophore carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP), which is a potent mitophagy inducer24, as a positive control.

Autor im Rampenlicht: Nachweis der Mitophagie in Caenorhabditis elegans und Säugetierzellen mit organellenspezifischen Farbstoffen  

Nachweis von Mitophagie in Caenorhabditis elegans und Säugetierzellen mit organellenspezifischen Farbstoffen

Degradation of damaged mitochondria by mitophagy is essential for the function of the mitochondrial network. Unfortunately, this process declines with age. We develop and use drugs that activate mitophagy, thereby promoting healthy aging to understand the function of mitophagy in aging and age-related diseases, including Alzheimer's.One of the biggest challenges is to measure the mitophagy process without affecting it. Recent studies have shown that GFP expression in the mitochondria of muscle cells induces stress that is MT UPR. Therefore, using dyes in non-transgenic animals or cells is essential and complements genetic technologies.Our protocol has three main advantages. First, there is no need to generate transgenic animals or cells expressing mitophagy biosensors. Second, no need for expensive infrastructure and expertise such as in case of electron microscopy.And third, the organelle dye cocktail is commercially available and the protocol is simple and fast. The new mitophagy-activating compound VL-850 induces robust mitophagy, and in this way protects from oxidative stress and promote lifespan. Now the big question is to determine the underlying mechanism of action.We explored the mechanism at multiple levels, from the cellular to the organismal using C.elegans and mammalian cells.

Watch this Scientific Journal Video about Protocol for Measuring Mitophagy in Caenorhabditis elegans at JoVE.com

Protocol for Measuring Mitophagy in Caenorhabditis elegans  

Protokoll zur Messung der Mitophagie bei Caenorhabditis elegans

Nehmen Sie zunächst die synchronisierten jungen erwachsenen C.Elegans-Hermaphroditen in einem Mikrozentrifugenröhrchen ein. Fügen Sie dem Wurmpellet 200 Mikroliter M9-Puffer hinzu, der Poloxamer 188, Pluronic F127 und zwei Mikroliter des Färbekit-Reagenzes enthält. Decken Sie die Röhrchen mit Alufolie ab, um die Farbstoffe vor Licht zu schützen.Lassen Sie die Mischung eine Stunde lang bei Raumtemperatur bei 20 U/min rotieren. Dann schleudern Sie die Würmer eine Minute lang bei 500 G. Entfernen Sie danach die Färbelösung, ohne das Wurmpellet zu stören.Waschen Sie die Würmer dreimal mit M9-Puffer und geben Sie sie in eine gesäte NGM-Agarplatte, die die entsprechende Behandlung enthält. Waschen Sie die Würmer von den Platten in frische Mikrozentrifugenröhrchen mit einem Milliliter M9-Puffer. Danach fixieren Sie die Würmer 30 Minuten lang mit 1%Formaldehyd auf Eis.Und waschen Sie die Würmer dreimal mit einem Milliliter M9-Puffer, um Formaldehydreste zu entfernen. Saugen Sie nach dem Pelletieren der Würmer die maximale Menge Überstand an und halten Sie das Pellet in 10 Mikrolitern M9 intakt. Um 2,5 % Agarose herzustellen, wiegen Sie als nächstes 0,125 Gramm Agarose in ein 10-Milliliter-Reagenzglas aus Borosilikatglas. Fügen Sie fünf Milliliter M9-Puffer hinzu und lösen Sie die Agarose auf, indem Sie das Rohr vorsichtig mit einem Bunsenbrenner erhitzen.Übertragen Sie die geschmolzene Agarose in ein Trockenbad bei 75 Grad Celsius. Geben Sie 100 Mikroliter der geschmolzenen Agarose mit einer Ein-Milliliter-Spitze auf ein Deck-Glosser-Mikroskop-Deckglas. Legen Sie sofort eine weitere Folie senkrecht auf den Agarosetropfen und bilden Sie eine Kreuzform.Trennen Sie die Objektträger nach zwei Minuten vorsichtig, indem Sie das obere Deckglas drücken und das Agarosepad auf dem unteren Deckobjektträger belassen. Übertragen Sie die Würmer mit einer Pasteur-Glaspipette auf das Agarosepad. Verwenden Sie einen Docht aus einem Labortuch, um überschüssige Flüssigkeit zu entfernen.Decken Sie dann die Würmer mit einem kleineren Deckglas ab und tragen Sie transparenten Nagellack auf den Rand auf, um ein Verdunsten zu verhindern. Legen Sie den Objektträger in eine dunkle Box, um ihn vor Licht zu schützen. Verwenden Sie ein konfokales Mikroskop, um die Würmer innerhalb von 24 Stunden bei den entsprechenden Wellenlängen mit einem Objektiv mit 60-facher Vergrößerung abzubilden.Öffnen Sie als Nächstes die Bildbearbeitungssoftware und klicken Sie mit der rechten Maustaste auf den grauen Bereich. Wählen Sie im angezeigten Popup-Fenster die Option Akquisition aus. Ti2 Vollpolster.ND-Erfassungs- und Lookup-Tabellen. Wählen Sie unter Ti2 Full Pad 60 Mal aus und stellen Sie den Mikroskop-Feinfokusknopf ein, um die Würmer in den Fokus zu bringen. Wählen Sie dann Spinning Disc und wählen Sie die Option 16 Bit ohne Binning.Stellen Sie für jeden Fluoreszenzfilter die Belichtungszeit auf 500 Millisekunden und für das Hellfeld auf 20 Millisekunden ein. Sobald diese Parameter festgelegt sind, wählen Sie Jetzt ausführen und warten Sie, bis das Ausgabebild als ND2-Datei generiert wurde.

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Biology

Protocol for Measuring Mitophagy in Caenorhabditis elegans

Detection of Mitophagy in Caenorhabditis elegans and Mammalian Cells Using Organelle-Specific Dyes

Mitochondria are essential for various biological functions, including energy production, lipid metabolism, calcium homeostasis, heme biosynthesis, ...