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Method Article
* Wspomniani autorzy wnieśli do projektu równy wkład.
Here a simple and well-validated protocol for measuring bulk autophagic sequestration activity in mammalian cells is described. The method is based on quantifying the proportion of lactate dehydrogenase (LDH) in sedimentable cell fractions compared to total cellular LDH levels.
Bulk autophagy is characterized by the sequestration of large portions of cytoplasm into double/multi-membrane structures termed autophagosomes. Here a simple protocol to monitor this process is described. Moreover, typical results and experimental validation of the method under autophagy-inducing conditions in various types of cultured mammalian cells are provided. During bulk autophagy, autophagosomes sequester cytosol, and thereby also soluble cytosolic proteins, alongside other autophagic cargo. LDH is a stable and highly abundant, soluble cytosolic enzyme that is non-selectively sequestered into autophagosomes. The amount of LDH sequestration therefore reflects the amount of bulk autophagic sequestration. To efficiently and accurately determine LDH sequestration in cells, we employ an electrodisruption-based fractionation protocol that effectively separates sedimentable from cytosolic LDH, followed by measurement of enzymatic activity in sedimentable fractions versus whole-cell samples. Autophagic sequestration is determined by subtracting the proportion of sedimentable LDH in untreated cells from that in treated cells. The advantage of the LDH sequestration assay is that it gives a quantitative measure of the autophagic sequestration of endogenous cargo, as opposed to other methods that either involve ectopic expression of sequestration probes or semi-quantitative protease protection analyses of autophagy markers or receptors.
Autophagy (Greek for "self-eating") is an evolutionary conserved process for vacuolar/lysosomal degradation of intracellular material. Upon discovery of the autophagy-related ("ATG") genes, which are important for autophagy in yeast and humans, and the realization that autophagy plays a significant role in human health and disease (acknowledged by the 2016 Nobel Prize in Medicine or Physiology to Yoshinori Ohsumi), autophagy has quickly become one of the most intensely studied processes in cell biology1,2.
Macroautophagy (hereafter referred to as "autophagy") is characterized by the expansion and folding of intracellular membrane cisternae ("phagophores") into sealed, double- or multi-membrane structures ("autophagosomes") that effectively sequester the enwrapped material from the rest of the cytoplasm. Upon fusion of autophagosomes with lysosomes, the inner autophagosomal membrane and the sequestered cargo is degraded and recycled. Autophagosomes can sequester cytoplasmic material in both random (non-selective autophagy) and selective (selective autophagy) manners. Bulk autophagy most likely represents a mix of non-selective and selective autophagy.
In the 1960's and 70's ("the morphological era" of autophagy research), autophagic sequestration was mainly assessed through ultrastructural analyses. In the 1980's and beginning of the 1990's ("the biochemical era") Per Seglen and co-workers — who studied autophagy in primary rat hepatocytes — developed the first methods to quantitatively measure autophagic sequestration activity3. Using these assays, Seglen defined and characterized different steps of the autophagic-lysosomal pathway4,5, discovered and coined the amphisome6 (the product of endosome-autophagosome fusion), and was the first to describe the role of protein phosphorylation in autophagy regulation7. However, after the discovery of the ATGs in the 1990's ("the molecular era") and the first characterization of a mammalian ATG8 protein, microtubule-associated protein 1A/1B-light chain 3 (LC3) in 20008, the use of ATG proteins as markers for the autophagic process quickly gained popularity, and the older and more laborious biochemical methods were left behind. In fact, over the last 18 years, western blot and fluorescence microscopy analyses of LC3 have become the by far most popular (and in many cases the only) means of studying autophagy in mammalian cells. The advantage is the relative ease by which these methods can be carried out. The disadvantage is that one is studying a cart component (LC3) rather than actual autophagic cargo. This is a rather serious disadvantage, because the relationship between the states and/or flux of LC3 through the pathway versus the sequestration and flux of cargo is highly unclear. In fact, we have shown that bulk cargo flux can be maintained at high levels under conditions where there is no LC3 flux, despite the presence of conjugated LC3 in the cells9. Moreover, we demonstrated that bulk autophagy is unaffected by efficient LC3 depletion, and thus likely is LC3-independent9. This finding has later been confirmed by LC3 knock-out studies10,11, which also indicate that Parkin-dependent mitophagy (the selective autophagy of mitochondria) is independent of LC310,11.
In summary, there is a clear need for cargo-based assays to monitor autophagic activity. Optimally such assays should be broadly applicable, well-defined, and easy to perform. Over the last few years we have taken a particular interest in the LDH sequestration assay, which was developed by Per Seglen in the 1980's12, and is based on measuring the transfer of cytosolic LDH to sedimentable, autophagic vacuole-containing cell fractions. LDH is a stable, soluble cytosolic protein that is readily co-sequestered when phagophores enwrap cytoplasmic cargo. Sequestration of LDH is therefore a general measure of autophagic sequestration. LDH is exclusively degraded by the autophagic-lysosomal pathway12. Thus, in the presence of lysosomal degradation inhibitors, e.g., bafilomycin A1 (Baf)13, experimental treatment effects directly reflect alterations in autophagic sequestration activity. In the absence of degradation inhibitors, the net effect of alterations in LDH sequestration and degradation can be measured.
The LDH sequestration assay is broadly applicable, since LDH is highly and ubiquitously expressed in all cell types, and LDH levels can be accurately quantified by an enzymatic assay14,15. However, the original protocol12 — established in primary rat hepatocytes — was rather time-consuming and required a high amount of starting material as well as a custom-made electric discharge capacitor. In a step-wise manner, we have gradually transformed the assay into an easy and versatile method. First, the original protocol was adapted for use in mammalian cell lines16. Second, the method was substantially downscaled3,9. Third, several steps in the protocol were eliminated, including a laborious density cushion step17. This simultaneously enabled an even further downscaling of the method, from the original starting point of using a 10 cm plate per sample16 to using a single well from a 12-well plate per sample (i.e., approximately 15-fold less starting material)17. Fourth, we identified a commercial electroporation apparatus that could replace the custom-made electric discharge capacitor17.
Here our most up-to-date protocol of the LDH sequestration assay, which includes some further simplifications of the method as compared to the previously published17 is presented. Furthermore, a set of typical results obtained in a number of different cell types is shown, and importantly, multiple lines of experimental validations of the method using pharmacological as well as genetic knockdown and knockout approaches are provided. For an overall flow scheme of the whole protocol, see Figure 1.
1. Cell Seeding and Treatment
2. Cell Harvest and Preparation for Electrodisruption
3. Plasma Membrane Electrodisruption and Separation of Sedimentable- and Total-cell Fractions
4. LDH Extraction and Measurement of LDH Enzymatic Activity
5. Calculation of LDH Sequestration
Using the protocol described here, bulk autophagic sequestration activity in a number of different mammalian cell lines, including LAPC4, DU145, Huh7, PNT2A, HeLa, VCaP, H3122, Hec1A, MCF-7, T47D, U2OS, PC3, G361, mouse embryonic fibroblasts (MEFs), RPE-1, HEK293, BJ, and LNCaP cells was measured. Sequestration was assessed under basal conditions (in complete, nutrient-rich medium), or in cells acutely starved for serum and amino acids (a bona fide autophagy-inducing condition
In summary, the protocol described here represents a reliable and widely applicable method to monitor bulk autophagic sequestration activity in mammalian cells. Compared to the original method12,16, we have removed a number of unnecessary steps, simplified several of the remaining steps, and introduced a substantial downscaling. As a result, the protocol is greatly improved in relation to cost- and time-efficiency, and the same amount of samples can now be handle...
The authors have no conflict of interest.
This work was financially supported by the Research Council of Norway, the University of Oslo, the Anders Jahre Foundation, the Nansen Foundation, and the Legacy in the memory of Henrik Homan. We thank Dr. Noboru Mizushima for the ATG5+/+ MEFs and ATG5-/- MEFs, Dr. Masaaki Komatsu for the ATG7+/+ MEFs and ATG7-/- MEFs, and Dr. Shizuo Akira for the ATG9A+/+ MEFs and ATG9A-/- MEFs. We thank Frank Sætre for technical assistance, and Dr. Per O. Seglen for constructive methodological discussions.
Name | Company | Catalog Number | Comments |
1.5 ml and 2 ml microcentrifuge tubes | Eppendorf | 211-2130 and 211-2120 | |
12-well plates | Falcon | 353043 | |
Accumax cell detachment solution | Innovative Cell Technologies | A7089 | Keep aliquots at -20 °C for years, and in fridge for a few months |
Bafilomycin A1 | Enzo | BML-CM110-0100 | Dissolve in DMSO |
BJ cells | ATCC | CRL-2522 | use at passage <30 |
Bovine serum albumin (BSA) | VWR | 422361V | |
Burker counting chamber | Fisher Scientific | 139-658585 | |
Countess Cell Counting Chamber Slides | ThermoFisher Scientfic | C10228 | |
Countess II Automated Cell Counter | ThermoFisher Scientfic | AMQAX1000 | |
Cover glass for the Burker counting chamber | Fisher Scientific | 139-658586 | |
Criterion Tris-HCl Gel, 4–20%, 26-well, 15 µl, 13.3 x 8.7 cm (W x L) | Bio-Rad | 3450034 | |
DTT | Sigma-Aldrich | D0632 | |
Earle's balanced salt solution (EBSS) | Gibco | 24010-043 | conatains 0.1% glucose |
EDTA | Sigma-Aldrich | E7889 | |
Electroporation cuvette (4 mm) | Bio-Rad | 1652088 | |
Exponential decay wave electroporator | BTX Harvard Apparatus | EMC 630 | |
Fetal bovine serum (FBS) | Sigma | F7524 | 10% final concentration in RPMI 1640 medium |
HEK293 cells | ATCC | CRL-1573 | |
Imidazole | Sigma-Aldrich | 56750 | Autoclave a 65 mM solution and keep in fridge for months |
Incubator; Autoflow IR Direct Heat CO2 incubator | NuAire | NU-5510E | |
Lipofectamine RNAiMAX Transfection Reagent | ThermoFisher | 13778150 | |
LNCaP cells | ATCC | CRL-1740 | use at passage <30 |
3-Methyl Adenine (3MA) | Sigma-Aldrich | M9281 | Stock 100 mM in RPMI in -20 °C. Heat stock to 65 °C for 10 minutes, and use at 10 mM final concentration |
Refridgerated Microcentrifuge | Beckman Coulter Life Sciences | 368831 | |
Refridgerated Microcentrifuge with soft-mode function | Eppendorf | Eppendorf 5417R | |
MRT67307 hydrochloride (ULKi) | Sigma-Aldrich | SML0702 | Inhibits ULK kinase activity. Dissolve in DMSO. |
MaxMat Multianalyzer instrument | Erba Diagnostics | PL-II | |
MCF7 cells | ATCC | HTB-22 | |
NADH | Merck-Millipore | 1.24644.001 | |
Nycodenz | Axis-Shield | 1002424 | |
Opti-MEM Reduced Serum Medium | ThermoFisher | 31985062 | |
Phosphate-buffered saline (PBS) | Gibco | 20012-019 | |
Pipette tips 3 (0.5-20 µl) | VWR | 732-2223 | Thermo Fischer ART Barrier tips |
Pipette tips (1-200 µl) | VWR | 732-2207 | Thermo Fischer ART Barrier tips |
Pipette tips (100-1000µl) | VWR | 732-2355 | Thermo Fischer ART Barrier tips |
Pipettes | ThermoFisher | 4701070 | Finnpipette F2 GLP Kit |
Poly-D-lysine | Sigma-Aldrich | P6407-10X5MG | Make a 1 mg/ml stock solution in sterile H2O. This solution is stable at -20 °C for at least 1 year. |
Pyruvate | Merck-Millipore | 1066190050 | |
RPE-1 cells (hTERT RPE-1) | ATCC | CRL-4000 | |
RPMI 1640 | Gibco | 21875-037 | |
SAR-405 | ApexBio | A8883 | Inhibits phosphoinositide 3-kinase class III (PIK3C3). Dissolve in DMSO. |
Silencer Select Negative Control #1 (siCtrl) | ThermoFisher/Ambion | 4390843 | |
Silencer Select ATG9-targeting siRNA (siATG9A) | ThermoFisher/Ambion | s35504 | |
Silencer Select FIP200-targeting siRNA (siFIP200) | ThermoFisher/Ambion | s18995 | |
Silencer Select ULK1-targeting siRNA (siULK1) | ThermoFisher/Ambion | s15964 | |
Silencer Select ULK2-targeting siRNA (siULK2) | ThermoFisher/Ambion | s18705 | |
Silencer Select GABARAP-targeting siRNA (siGABARAP) | ThermoFisher/Ambion | s22362 | |
Silencer Select GABARAPL1-targeting siRNA (siGABARAPL1) | ThermoFisher/Ambion | s24333 | |
Silencer Select GABARAPL2-targeting siRNA (siGABARAPL2) | ThermoFisher/Ambion | s22387 | |
Sodium phosphate monobasic dihydrate (NaH2PO4 • 2H2O) | Merck-Millipore | 1.06580.1000 | |
Sodium phosphate dibasic dihydrate (Na2HPO4 • 2H2O ) | Prolabo | 28014.291 | |
Sucrose | VWR | 443816T | 10% final concentration in water; filter through 0.45 µm filter and keep in fridge for months |
Thapsigargin | Sigma-Aldrich | T9033 | Inhibits the SERCA ER Ca2+ pump. Dissolve in DMSO. |
Triton X-405 | Sigma-Aldrich | X405 | 1% final |
Trypan Blue stain 0.4% | Molecular Probes | T10282 | |
Trypsin-EDTA (0.25% w/v Trypsin) | Gibco | 25200-056 | |
Tween-20 | Sigma-Aldrich | P2287 | 0.01% final |
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