C. F. Bento, M. Renna, G. Ghislat, C. Puri, A. Ashkenazi et al., Autophagy: How Does It Work?, Annu. Rev. Biochem, vol.85, pp.685-713, 2016.

D. Gatica, V. Lahiri, and D. J. Klionsky, Cargo recognition and degradation by selective autophagy, Nature, vol.20, pp.233-242, 2018.

V. Kirkin and V. V. Rogov, A Diversity of Selective Autophagy Receptors Determines the Specificity of the Autophagy Pathway, Mol. Cell, vol.76, pp.268-285, 2019.

B. Levine and G. Kroemer, Biological Functions of Autophagy Genes: A Disease Perspective, Cell, vol.176, pp.11-42, 2019.

E. Arias and A. M. Cuervo, Pros and Cons of Chaperone-Mediated Autophagy in Cancer Biology, Trends Endocrinol. Metab, vol.31, pp.53-66, 2019.

J. Li, F. Cao, H. Yin, Z. Huang, Z. Lin et al., Ferroptosis: Past, present and future, Cell Death Dis, vol.11, pp.1-13, 2020.

S. R. Bonam, F. Wang, and S. Muller, Autophagy: A new concept in autoimmunity regulation and a novel therapeutic option, J. Autoimmun, vol.94, pp.16-32, 2018.

J. M. Levy and A. Thorburn, Autophagy in cancer: Moving from understanding mechanism to improving therapy responses in patients, Cell Death Differ, vol.27, pp.843-857, 2019.

S. R. Bonam, F. Wang, and S. Muller, Lysosomes as a therapeutic target, Nat. Rev. Drug Discov, vol.18, pp.923-948, 2019.

S. V. Retnakumar and S. Muller, Pharmacological Autophagy Regulators as Therapeutic Agents for Inflammatory Bowel Diseases, Trends Mol. Med, vol.25, pp.516-537, 2019.

Y. Hazari, J. M. Pedro, B. Hetz, C. Galluzzi, L. Kroemer et al., Autophagy in hepatic adaptation to stress, J. Hepatol, vol.2020, pp.183-196

M. Das, A. Karnam, E. Stephen-victor, L. Gilardin, B. Bhatt et al., Intravenous immunoglobulin mediates anti-inflammatory effects in peripheral blood mononuclear cells by inducing autophagy
URL : https://hal.archives-ouvertes.fr/inserm-02455428

D. J. Klionsky, E. L. Eskelinen, and V. Deretic, Autophagosomes, phagosomes, autolysosomes, phagolysosomes, autophagolysosomes. wait, I'm confused, Autophagy, vol.10, pp.549-551, 2014.

A. Kuma, M. Komatsu, and N. Mizushima, Autophagy-monitoring and autophagy-deficient mice, Autophagy, vol.13, pp.1619-1628, 2017.

K. Tekirdag and A. M. Cuervo, Chaperone-mediated autophagy and endosomal microautophagy: Joint by a chaperone, J. Biol. Chem, vol.293, pp.5414-5424, 2017.

S. A. Walker and N. T. Ktistakis, Autophagosome Biogenesis Machinery, J. Mol. Biol, vol.2020, pp.2449-2461

L. Galluzzi, J. M. Pedro, B. Levine, B. Green, D. R. Kroemer et al., Pharmacological modulation of autophagy: Therapeutic potential and persisting obstacles, Nat. Rev. Drug Discov, vol.16, pp.487-511, 2017.

D. C. Rubinsztein, P. Codogno, and B. Levine, Autophagy modulation as a potential therapeutic target for diverse diseases, Nat. Rev. Drug Discov, vol.11, 2012.

Y. Cheng, X. Ren, W. N. Hait, and J. Yang, Therapeutic targeting of autophagy in disease: Biology and pharmacology, Pharmacol. Rev, vol.65, pp.1162-1197, 2013.

F. Gros and S. Muller, Pharmacological regulators of autophagy and their link with modulators of lupus disease, Br. J. Pharmacol, vol.171, pp.4337-4359, 2014.

H. Vakifahmetoglu-norberg, H. Xia, and J. Yuan, Pharmacologic agents targeting autophagy, J. Clin. Investig, vol.125, pp.5-13, 2015.

D. J. Klionsky, K. Abdelmohsen, A. Abe, J. Abedin, H. Abeliovich et al., Guidelines for the use and interpretation of assays for monitoring autophagy, Autophagy, vol.12, pp.1-222, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02641288

S. R. Bonam, M. Ruff, and S. Muller, Hspa8/Hsc70 in Immune Disorders: A Molecular Rheostat that Adjusts Chaperone-Mediated Autophagy Substrates, vol.8, p.849, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02361769

M. Mauthe, I. Orhon, C. Rocchi, X. Zhou, M. Luhr et al., Chloroquine inhibits autophagic flux by decreasing autophagosome-lysosome fusion, Autophagy, vol.14, pp.1435-1455, 2018.

J. A. Sobota, N. Back, B. A. Eipper, and R. E. Mains, Inhibitors of the V0 subunit of the vacuolar H + ATPase prevent segregation of lysosomal and secretory-pathway proteins, J. Cell Sci, vol.122, pp.3542-3553, 2009.

N. Schall, N. Page, C. Macri, O. Chaloin, J. Briand et al., Peptide-based approaches to treat lupus and other autoimmune diseases, J. Autoimmun, vol.39, pp.143-153, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00742448

S. Muller, S. Brun, F. Rene, J. De-seze, J. Loeffler et al., Autophagy in neuroinflammatory diseases, Autoimmun. Rev, vol.16, pp.856-874, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02347273

S. Brun, N. Schall, S. R. Bonam, K. Bigaut, A. Mensah-nyagan et al., An autophagy-targeting peptide to treat chronic inflammatory demyelinating polyneuropathies, J. Autoimmun, vol.92, pp.114-125, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02544054

B. Li, F. Wang, N. Schall, and S. Muller, Rescue of autophagy and lysosome defects in salivary glands of Mrl/lpr mice by a therapeutic phosphopeptide, J. Autoimmun, vol.90, pp.132-145, 2018.

E. Voynova, F. Lefebvre, A. Qadri, and S. Muller, Correction of autophagy impairment inhibits pathology in the Nod.H-2h4 mouse model of primary Sjögren's syndrome, J. Autoimmun, vol.108, 2020.

R. Zimmer, H. R. Scherbarth, O. L. Rillo, J. J. Gomez-reino, S. Muller et al., P140 peptide in patients with systemic lupus erythematosus: A randomised, double-blind, placebo-controlled phase IIb clinical trial, Ann. Rheum. Dis, vol.72, pp.1830-1835, 2012.

M. Wilhelm, F. Wang, N. Schall, J. Kleinmann, M. Faludi et al., Lupus Regulator Peptide P140 Represses B Cell Differentiation by Reducing HLA Class II Molecule Overexpression, Arthritis Rheumatol, vol.70, pp.1077-1088, 2018.

N. Page, F. Gros, N. Schall, M. Décossas, D. Bagnard et al., Hsc70 blockade by the therapeutic peptide P140 affects autophagic processes and endogenous MHII presentation in murine lupus, Ann. Rheum. Dis, vol.70, pp.837-843, 2010.

C. Macri, F. Wang, I. Tasset, N. Schall, N. Page et al., Modulation of deregulated chaperone-mediated autophagy by a phosphopeptide, Autophagy, vol.11, pp.472-486, 2015.

F. Wang and S. Muller, Manipulating Autophagic Processes in Autoimmune Diseases: A Special Focus on Modulating Chaperone-Mediated Autophagy, an Emerging Therapeutic Target, Front. Immunol, vol.6, 2015.

S. Shoji-kawata, R. Sumpter, M. Leveno, G. R. Campbell, Z. Zou et al., Identification of a candidate therapeutic autophagy-inducing peptide, Nature, vol.494, pp.201-206, 2013.

Z. Gong, I. Tasset, A. Diaz, J. Anguiano, E. Tas et al., Humanin is an endogenous activator of chaperone-mediated autophagy, J. Cell Biol, vol.217, pp.635-647, 2017.

M. Tsukada and Y. Ohsumi, Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae, FEBS Lett, vol.333, pp.169-174, 1993.

H. Nakatogawa, K. Suzuki, Y. Kamada, and Y. Ohsumi, Dynamics and diversity in autophagy mechanisms: Lessons from yeast, Nat. Rev. Mol. Cell Biol, vol.10, pp.458-467, 2009.

D. H. Kwon, L. Kim, B. Kim, J. H. Kim, K. Roh et al., A novel conformation of the LC3-interacting region motif revealed by the structure of a complex between Lc3B and RavZ, Biochem. Biophys. Res. Commun, vol.490, pp.1093-1099, 2017.

Y. Kabeya, N. Mizushima, T. Ueno, A. Yamamoto, T. Kirisako et al., Lc3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing, EMBO J, vol.19, pp.5720-5728, 2000.

E. Shvets, E. Fass, R. Scherz-shouval, and Z. Elazar, The N-terminus and Phe52 residue of Lc3 recruit p62/Sqatm1 into autophagosomes, J. Cell Sci, vol.121, pp.2685-2695, 2008.

J. N. Le-grand, F. Z. Chakrama, S. Seguin-py, A. Fraichard, R. Delage-mourroux et al., Gabarapl1 (GEC1): Original or copycat?, Autophagy, vol.7, pp.1098-1107, 2011.

A. Jacomin, S. Samavedam, and V. J. Promponas, Nezis, I. iLIR database: A web resource for Lir motif-containing proteins in eukaryotes, Autophagy, vol.12, pp.1945-1953, 2016.

H. Nakatogawa, Two ubiquitin-like conjugation systems that mediate membrane formation during autophagy, Essays Biochem, vol.55, pp.39-50, 2013.

S. Martens and D. Fracchiolla, Activation and targeting of ATG8 protein lipidation

T. Maruyama and N. N. Noda, Autophagy-regulating protease Atg4: Structure, function, regulation and inhibition, J. Antibiot, vol.71, pp.72-78, 2017.

H. Popelka and D. J. Klionsky, Analysis of the native conformation of the Lir/Aim motif in the Atg8/Lc3/Gabarap-binding proteins, Autophagy, vol.11, pp.2153-2159, 2015.

A. B. Birgisdottir, T. Lamark, and T. Johansen, The Lir motif-crucial for selective autophagy, J. Cell Sci, vol.126, pp.3237-3247, 2013.

P. Wild and D. G. Mcewan, Dikic, I. The LC3 interactome at a glance, J. Cell Sci, vol.127, pp.3-9, 2013.

Y. Lee and J. Lee, Role of the mammalian Atg8/Lc3 family in autophagy: Differential and compensatory roles in the spatiotemporal regulation of autophagy, BMB Rep, vol.49, 2016.

D. S. Wilkinson, J. S. Jariwala, E. Anderson, K. Mitra, J. Meisenhelder et al., Phosphorylation of Lc3 by the Hippo kinases Stk3/Stk4 is essential for autophagy, Mol. Cell, vol.57, pp.55-68, 2015.

S. J. Cherra, S. M. Kulich, G. Uechi, M. Balasubramani, J. Mountzouris et al., Regulation of the autophagy protein LC3 by phosphorylation, J. Cell Biol, vol.190, pp.533-539, 2010.

R. Huang, Y. Xu, W. Wan, X. Shou, J. Qian et al., Deacetylation of Nuclear Lc3 Drives Autophagy Initiation under Starvation, Mol. Cell, vol.57, pp.456-466, 2015.

S. Barth, D. Glick, and K. Macleod, Autophagy: Assays and artifacts, J. Pathol, vol.221, pp.117-124, 2010.

N. Mizushima, T. Yoshimori, B. Levine, and T. Yoshimorim, Methods in Mammalian Autophagy Research. Cell, vol.140, pp.313-326, 2010.

F. Wang, B. Li, N. Schall, M. Wilhelm, and S. Muller, Assessing Autophagy in Mouse Models and Patients with Systemic Autoimmune Diseases, vol.6, 2017.

G. Runwal, E. Stamatakou, F. H. Siddiqi, C. Puri, Y. Zhu et al., Lc3-positive structures are prominent in autophagy-deficient cells, Sci. Rep, vol.9, 2019.

D. C. Rubinsztein, A. M. Cuervo, B. Ravikumar, S. Sarkar, V. I. Korolchuk et al., In search of an "autophagomometer, Autophagy, vol.5, pp.585-589, 2009.

M. Jung, H. Choi, and J. Y. Mun, The autophagy research in electron microscopy, Appl. Microsc, vol.49, pp.1-7, 2019.

R. Zoncu, L. Bar-peled, A. Efeyan, S. Wang, Y. Sancak et al., Mtrc1 Senses Lysosomal Amino Acids Through an Inside-Out Mechanism That Requires the Vacuolar H+ ATPase, Science, vol.334, pp.678-683, 2011.

G. Juhász, Interpretation of bafilomycin, pH neutralizing or protease inhibitor treatments in autophagic flux experiments: Novel considerations, Autophagy, vol.8, pp.1875-1876, 2012.

O. Florey, N. Gammoh, S. E. Kim, X. Jiang, and M. Overholtzer, V-ATPase and osmotic imbalances activate endolysosomal LC3 lipidation, Autophagy, vol.11, pp.88-99, 2014.

C. E. Zois, A. Giatromanolaki, E. Sivridis, M. Papaiakovou, H. Kainulainen et al., Autophagic flux" in normal mouse tissues: Focus on endogenous Lc3A processing, Autophagy, vol.7, pp.1371-1378, 2011.

M. Koukourakis, A. Giatromanolaki, and C. Zois, Sivridis, E. Lc3 immunostaining pitfalls, Histopathology, vol.62, pp.962-963, 2013.

M. Moulis and C. Vindis, Methods for Measuring Autophagy in Mice, vol.6, 2017.

N. Mizushima, Chapter 2 Methods for Monitoring Autophagy Using Gfp-Lc3 Transgenic Mice, Methods Enzymol, vol.452, pp.13-23, 2009.

E. Shvets, E. Fass, and Z. Elazar, Utilizing flow cytometry to monitor autophagy in living mammalian cells, Autophagy, vol.4, pp.621-628, 2008.

H. Morishita, T. Kaizuka, Y. Hama, and N. Mizushima, A new probe to measure autophagic flux in vitro and in vivo, Autophagy, vol.13, pp.757-758, 2017.

T. Kaizuka, H. Morishita, Y. Hama, S. Tsukamoto, T. Matsui et al., An Autophagic Flux Probe that Releases an Internal Control, Mol. Cell, vol.64, pp.835-849, 2016.

S. Yoshii and N. Mizushima, Monitoring and Measuring Autophagy, Int. J. Mol. Sci, vol.18, 1865.

K. E. Eng, M. D. Panas, G. B. Hedestam, and G. M. Mcinerney, A novel quantitative flow cytometry-based assay for autophagy, Autophagy, vol.6, pp.634-641, 2010.

A. Demishtein, Z. Porat, Z. Elazar, and E. Shvets, Applications of flow cytometry for measurement of autophagy, Methods, vol.75, pp.87-95, 2015.

K. Phadwal, J. Alegre-abarrategui, A. S. Watson, L. Pike, S. Anbalagan et al., A novel method for autophagy detection in primary cells, Autophagy, vol.8, pp.677-689, 2012.

H. R. Pugsley, Quantifying autophagy: Measuring Lc3 puncta and autolysosome formation in cells using multispectral imaging flow cytometry, vol.112, pp.147-156, 2017.

M. K. Schwinn, T. Machleidt, K. Zimmerman, C. T. Eggers, A. S. Dixon et al., Crispr-Mediated Tagging of Endogenous Proteins with a Luminescent Peptide, ACS Chem. Biol, vol.13, pp.467-474, 2017.

A. Bresciani, M. C. Spiezia, R. Boggio, C. Cariulo, A. Nordheim et al., Quantifying autophagy using novel Lc3B and p62 Tr-Fret assays, PLoS ONE, vol.13, 2018.

E. Eskelinen, F. Reggiori, M. Baba, A. L. Kovács, and P. O. Seglen, Seeing is believing: The impact of electron microscopy on autophagy research, Autophagy, vol.7, pp.935-956, 2011.

N. Dupont, C. Leroy, A. Hamaï, and P. Codogno, Long-Lived Protein Degradation During Autophagy, Methods Enzymol, vol.588, pp.31-40, 2017.

P. O. Seglen, A. Overbye, and F. Saetre, Chapter 5 Sequestration Assays for Mammalian Autophagy, In Methods in Enzymology, pp.63-83, 2009.

E. Donohue, A. Tovey, A. W. Vogl, S. Arns, E. Sternberg et al., Inhibition of Autophagosome Formation by the Benzoporphyrin Derivative Verteporfin, J. Biol. Chem, vol.286, pp.7290-7300, 2010.

D. B. Munafó and M. Colombo, A novel assay to study autophagy: Regulation of autophagosome vacuole size by amino acid deprivation, J. Cell Sci, vol.114, pp.3619-3629, 2001.

L. Galluzzi, I. Vitale, S. A. Aaronson, J. M. Abrams, D. Adam et al., Molecular mechanisms of cell death: Recommendations of the Nomenclature Committee on Cell Death, Cell Death Differ, vol.25, pp.486-541, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01727577

A. M. Schläfli, O. Adams, J. A. Galván, M. Gugger, S. Savic et al., Prognostic value of the autophagy markers Lc3 and p62/Sqstm1 in early-stage non-small cell lung cancer, Oncotarget, vol.7, pp.39544-39555, 2016.

A. Dhingra, D. Alexander, J. Reyes-reveles, R. Sharp, and K. Boesze-battaglia, Microtubule-Associated Protein 1 Light Chain 3 (LC3) Isoforms in RPE and Retina; Retinal Degenerative Diseases, pp.609-616, 2018.

R. Langer, C. Neppl, M. D. Keller, R. Schmid, M. P. Tschan et al., Expression Analysis of Autophagy Related Markers Lc3B, p62 and Hmgb1 Indicate an Autophagy-Independent Negative Prognostic Impact of High p62 Expression in Pulmonary Squamous Cell Carcinomas, Cancers, vol.10, p.281, 2018.

A. Schläfli, S. Berezowska, O. Adams, R. Langer, and M. P. Tschan, Reliable Lc3 and p62 Autophagy Marker Detection in Formalin Fixed Paraffin Embedded Human Tissue by Immunohistochemistry, Eur. J. Histochem. EJH, vol.59, 2015.

L. Li, Z. V. Wang, J. Hill, and F. Lin, New Autophagy Reporter Mice Reveal Dynamics of Proximal Tubular Autophagy, J. Am. Soc. Nephrol, vol.25, pp.305-315, 2013.

A. Rocchi, S. Yamamoto, T. C. Ting, Y. Fan, K. Sadleir et al., A Becn1 mutation mediates hyperactive autophagic sequestration of amyloid oligomers and improved cognition in Alzheimer's disease, PLoS Genet, vol.13, 2017.

Y. R. Juste and A. M. Cuervo, Analysis of Chaperone-Mediated Autophagy, In Methods in Molecular Biology

P. Jiang and N. Mizushima, Autophagy and human diseases, Cell Res, vol.24, pp.69-79, 2013.

J. K. Ching, S. V. Elizabeth, J. Ju, C. Lusk, S. K. Pittman et al., Mtor dysfunction contributes to vacuolar pathology and weakness in valosin-containing protein associated inclusion body myopathy, Hum. Mol. Genet, vol.22, pp.1167-1179, 2012.

N. Ramachandran, I. Munteanu, P. Wang, A. Ruggieri, J. J. Rilstone et al., Vma21 deficiency prevents vacuolar ATPase assembly and causes autophagic vacuolar myopathy, Acta Neuropathol, vol.125, pp.439-457, 2013.

L. Galluzzi and D. R. Green, Autophagy-Independent Functions of the Autophagy Machinery, Cell, vol.177, pp.1682-1699, 2019.

V. Oikonomou, G. Renga, A. De-luca, M. Borghi, M. Pariano et al., Autophagy and Lap in the Fight against Fungal Infections: Regulation and Therapeutics. Mediat. Inflamm, pp.1-7, 2018.

L. D. Cunha, M. Yang, R. Carter, C. Guy, L. Harris et al., LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance, Cell, vol.175, pp.429-441, 2018.

B. L. Heckmann, E. B. Romero, L. D. Cunha, J. Magne, and D. R. Green, Lc3-Associated Phagocytosis and Inflammation, J. Mol. Biol, vol.429, pp.3561-3576, 2017.

J. Wan, E. Weiss, S. Ben-mkaddem, M. Mabire, P. Choinier et al., Lc3-associated phagocytosis protects against inflammation and liver fibrosis via immunoreceptor inhibitory signaling, Sci. Transl

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