Autophagy profiling in single cells with open source CellProfiler-based image analysis

References

• Ohsumi Y. Historical landmarks of autophagy research. Cell Res. 2014;24(1):9–23.
   PubMed Web of Science ®Google Scholar
• Gomez-Sanchez R, Tooze SA, Reggiori F. Membrane supply and remodeling during autophagosome biogenesis. Curr Opin Cell Biol. 2021;71:112–119.
   PubMed Web of Science ®Google Scholar
• Melia TJ, Lystad AH, Simonsen A. Autophagosome biogenesis: from membrane growth to closure. J Cell Biol. 2020;219(6):e202002085.
   PubMed Web of Science ®Google Scholar
• Dikic I, Elazar Z. Mechanism and medical implications of mammalian autophagy. Nat Rev Mol Cell Biol. 2018;19(6):349–364.
   PubMed Web of Science ®Google Scholar
• Mizushima N, Levine B. Autophagy In Human Diseases. N Engl J Med. 2020;383(16):1564–1576.
   PubMed Web of Science ®Google Scholar
• Mizushima N, Murphy LO. Autophagy assays for biological discovery and therapeutic development. Trends Biochem Sci. 2020;45(12):1080–1093.
   PubMed Web of Science ®Google Scholar
• Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, et al. Guidelines for the use and interpretation of assays for monitoring autophagy. 4th edition)(1). Autophagy. 2021;17(1): 1–382
   Google Scholar
• Kabeya Y, Mizushima N, Ueno T et al. LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J. 2007;19(21):5720–5728.
   Google Scholar
• Kimura S, Noda T, Yoshimori T Dissection of the autophagosome maturation process by a novel reporter protein, tandem fluorescent-tagged LC3. Autophagy. 2007;3(5):452–460. DOI:10.4161/auto.4451
   PubMed Web of Science ®Google Scholar
• Lamark T, Svenning S, Johansen T. Regulation of selective autophagy: the p62/SQSTM1 paradigm. Essays Biochem. 2017;61(6):609–624.
   PubMed Web of Science ®Google Scholar
• Pankiv S, Clausen TH, Lamark T, et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem. 2007;282(33):24131–24145.
   PubMed Web of Science ®Google Scholar
• Roberts MA, Olzmann JA. Protein quality control and lipid droplet metabolism. Annu Rev Cell Dev Biol. 2020;36:115–139.
   PubMed Web of Science ®Google Scholar
• Schepers J, Behl C. Lipid droplets and autophagy-links and regulations from yeast to humans. J Cell Biochem. 2021;122(6):602–611.
   PubMed Web of Science ®Google Scholar
• Kirkin V. History of the selective autophagy research: how did it begin and where does it stand today? J Mol Biol. 2020;432(1):3–27.
   PubMed Web of Science ®Google Scholar
• Lamark T, Johansen T. Mechanisms of selective autophagy. Annu Rev Cell Dev Biol. 2021;37:143–169.
   PubMed Web of Science ®Google Scholar
• Stolz A, Ernst A, Dikic I. Cargo recognition and trafficking in selective autophagy. Nat Cell Biol. 2014;16(6):495–501.
   PubMed Web of Science ®Google Scholar
• Mueller AJ, Proikas-Cezanne T. Automated detection of autophagy response using single cell-based microscopy assays. Methods Mol Biol. 2019;1880:429–445.
   PubMedGoogle Scholar
• Proikas-Cezanne T, Ruckerbauer S, Stierhof YD, et al. Human WIPI-1 puncta-formation: a novel assay to assess mammalian autophagy. FEBS Lett. 2007;581(18):3396–3404.
   PubMed Web of Science ®Google Scholar
• Thost AK, Donnes P, Kohlbacher O, et al. Fluorescence-based imaging of autophagy progression by human WIPI protein detection. Methods. 2015;75:69–78.
   PubMed Web of Science ®Google Scholar
• Proikas-Cezanne T, Takacs Z, Donnes P, et al. WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome. J Cell Sci. 2015;128(2):207–217.
   PubMed Web of Science ®Google Scholar
• Proikas-Cezanne T, Waddell S, Gaugel A, et al. WIPI-1alpha (WIPI49), a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is linked to starvation-induced autophagy. Oncogene. 2004;23(58):9314–9325.
   PubMed Web of Science ®Google Scholar
• Bakula D, Muller AJ, Zuleger T, et al. WIPI3 and WIPI4 beta-propellers are scaffolds for LKB1-AMPK-TSC signalling circuits in the control of autophagy. Nat Commun. 2017;8:15637.
   PubMed Web of Science ®Google Scholar
• Dooley HC, Wilson MI, Tooze SA. WIPI2B links PtdIns3P to LC3 lipidation through binding ATG16L1. Autophagy. 2015;11(1):190–191.
   PubMed Web of Science ®Google Scholar
• Dooley HC, Razi M, Polson HE, et al. WIPI2 links LC3 conjugation with PI3P, autophagosome formation, and pathogen clearance by recruiting Atg12-5-16L1. Mol Cell. 2014;55(2):238–252.
   PubMed Web of Science ®Google Scholar
• Dobson ETA, Cimini B, Klemm AH, et al. ImageJ and CellProfiler: complements in open-source bioimage analysis. Curr Protoc. 2021;1(5): e89
   Google Scholar
• McQuin C, Goodman A, Chernyshev V, et al. CellProfiler 3.0: next-generation image processing for biology. PLoS Biol. 2018;16(7):e2005970.
   PubMed Web of Science ®Google Scholar
• Dao D, Fraser AN, Hung J, et al. CellProfiler analyst: interactive data exploration, analysis and classification of large biological image sets. Bioinformatics. 2016;32(20):3210–3212.
   PubMed Web of Science ®Google Scholar
• Bray MA, Carpenter AE. CellProfiler tracer: exploring and validating high-throughput, time-lapse microscopy image data. BMC Bioinformatics. 2015;16:368.
   PubMed Web of Science ®Google Scholar
• Stoter M, Niederlein A, Barsacchi R, et al. CellProfiler and KNIME: open source tools for high content screening. Methods Mol Biol. 2013;986:105–122.
   PubMedGoogle Scholar
• Kamentsky L, Jones TR, Fraser A, et al. Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinformatics. 2011;27(8):1179–1180.
   PubMed Web of Science ®Google Scholar
• Vokes MS, Carpenter AE. Using CellProfiler for automatic identification and measurement of biological objects in images. Curr Protoc Mol Biol. 2008;Chapter 14:Unit 14.17.
   PubMedGoogle Scholar
• Jones TR, Kang IH, Wheeler DB, et al. CellProfiler analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics. 2008;9:482.
   PubMed Web of Science ®Google Scholar
• Lamprecht MR, Sabatini DM, Carpenter AE. CellProfiler: free, versatile software for automated biological image analysis. Biotechniques. 2007;42(1):71–75.
   PubMed Web of Science ®Google Scholar
• Carpenter AE, Jones TR, Lamprecht MR, et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006;7(10):R100.
   PubMed Web of Science ®Google Scholar
• Stoter M, Janosch A, Barsacchi R, et al. CellProfiler and KNIME: open-source tools for high-content screening. Methods Mol Biol. 2019;1953:43–60.
   PubMedGoogle Scholar
• Scipioni L, Lanzano L, Diaspro A, et al. Comprehensive correlation analysis for super-resolution dynamic fingerprinting of cellular compartments using the zeiss airyscan detector. Nat Commun. 2018;9(1):5120.
   PubMedGoogle Scholar
• Grotemeier A, Alers S, Pfisterer SG, et al. AMPK-independent induction of autophagy by cytosolic Ca2+ increase. Cell Signal. 2010;22(6):914–925.
   PubMed Web of Science ®Google Scholar
• Caicedo JC, Cooper S, Heigwer F, et al. Data-analysis strategies for image-based cell profiling. Nat Methods. 2017;14(9):849–863.
   PubMed Web of Science ®Google Scholar
• Jin M, Klionsky DJ. Regulation of autophagy: modulation of the size and number of autophagosomes. FEBS Lett. 2014;588(15):2457–2463.
   PubMed Web of Science ®Google Scholar
• Munafo DB, Colombo MI. A novel assay to study autophagy: regulation of autophagosome vacuole size by amino acid deprivation. J Cell Sci. 2001;114(Pt 20):3619–3629.
   PubMed Web of Science ®Google Scholar
• Pol A, Luetterforst R, Lindsay M, et al. A caveolin dominant negative mutant associates with lipid bodies and induces intracellular cholesterol imbalance. J Cell Biol. 2001;152(5):1057–1070.
   PubMed Web of Science ®Google Scholar
• Ronan B, Flamand O, Vescovi L, et al. A highly potent and selective Vps34 inhibitor alters vesicle trafficking and autophagy. Nat Chem Biol. 2014;10(12):1013–1019.
   PubMed Web of Science ®Google Scholar
• Klionsky DJ, Elazar Z, Seglen PO, et al. Does bafilomycin A1 block the fusion of autophagosomes with lysosomes? Autophagy. 2008;4(7):849–850.
   PubMed Web of Science ®Google Scholar
• Yamamoto A, Tagawa Y, Yoshimori T, et al. Bafilomycin A1 prevents maturation of autophagic vacuoles by inhibiting fusion between autophagosomes and lysosomes in rat hepatoma cell line, H-4-II-E cells. Cell Struct Funct. 1998;23(1):33–42.
   PubMed Web of Science ®Google Scholar
• Liu Q, Chang JW, Wang J, et al. Discovery of 1-(4-(4-propionylpiperazin-1-yl)-3-(trifluoromethyl)phenyl)-9-(quinolin-3-yl)benz o[h][1,6]naphthyridin-2(1H)-one as a highly potent, selective mammalian target of rapamycin (mTOR) inhibitor for the treatment of cancer. J Med Chem. 2010;53(19):7146–7155.
   PubMed Web of Science ®Google Scholar
• Muralidharan C, Conteh AM, Marasco MR, et al. Pancreatic beta cell autophagy is impaired in type 1 diabetes. Diabetologia. 2021;64(4):865–877.
   PubMed Web of Science ®Google Scholar
• Adomshick V, Pu Y, Veiga-Lopez A. Automated lipid droplet quantification system for phenotypic analysis of adipocytes using CellProfiler. Toxicol Mech Methods. 2020;30(5):378–387.
   PubMed Web of Science ®Google Scholar
• Arias-Fuenzalida J, Jarazo J, Walter J, et al. Automated high-throughput high-content autophagy and mitophagy analysis platform. Sci Rep. 2019;9(1):9455
   PubMedGoogle Scholar
• Kolla L, Heo DS, Rosenberg DP, et al. High content screen for identifying small-molecule LC3B-localization modulators in a renal cancer cell line. Sci Data. 2018;5:180116
   PubMed Web of Science ®Google Scholar