{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T21:32:25Z","timestamp":1791322345707,"version":"4.3.1"},"reference-count":93,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2017,6,28]],"date-time":"2017-06-28T00:00:00Z","timestamp":1498608000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cells"],"abstract":"<jats:p>Autophagy is a tightly regulated mechanism that allows cells to renew themselves through the lysosomal degradation of proteins, which are misfolded or produced in excess, and of damaged organelles. In the context of immunity, recent research has specially attempted to clarify its roles in infection, inflammation and autoimmunity. Autophagy has emerged as a spotlight in several molecular pathways and trafficking events that participate to innate and adaptive immunity. Deregulation of autophagy has been associated to several autoimmune diseases, in particular to systemic lupus erythematosus. Nowadays, however, experimental data on the implication of autophagy in animal models of autoimmunity or patients remain limited. In our investigations, we use Murphy Roths Large (MRL)\/lymphoproliferation (lpr) lupus-prone mice as a mouse model for lupus and secondary Sj\u00f6gren\u2019s syndrome, and, herein, we describe methods applied routinely to analyze different autophagic pathways in different lymphoid organs and tissues (spleen, lymph nodes, salivary glands). We also depict some techniques used to analyze autophagy in lupus patient\u2019s blood samples. These methods can be adapted to the analysis of autophagy in other mouse models of autoinflammatory diseases. The understanding of autophagy implication in autoimmune diseases could prove to be very useful for developing novel immunomodulatory strategies. Our attention should be focused on the fact that autophagy processes are interconnected and that distinct pathways can be independently hyper-activated or downregulated in distinct organs and tissues of the same individual.<\/jats:p>","DOI":"10.3390\/cells6030016","type":"journal-article","created":{"date-parts":[[2017,6,28]],"date-time":"2017-06-28T10:25:56Z","timestamp":1498645556000},"page":"16","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["Assessing Autophagy in Mouse Models and Patients with Systemic Autoimmune Diseases"],"prefix":"10.3390","volume":"6","author":[{"given":"Fengjuan","family":"Wang","sequence":"first","affiliation":[{"name":"Centre National de la Recherche Scientifique (CNRS), Immunopathology and Therapeutic Chemistry\/Laboratory of Excellence Medalis, Institut de Biologie Mol\u00e9culaire et Cellulaire, Strasbourg 67000, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baihui","family":"Li","sequence":"additional","affiliation":[{"name":"Centre National de la Recherche Scientifique (CNRS), Immunopathology and Therapeutic Chemistry\/Laboratory of Excellence Medalis, Institut de Biologie Mol\u00e9culaire et Cellulaire, Strasbourg 67000, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Schall","sequence":"additional","affiliation":[{"name":"Centre National de la Recherche Scientifique (CNRS), Immunopathology and Therapeutic Chemistry\/Laboratory of Excellence Medalis, Institut de Biologie Mol\u00e9culaire et Cellulaire, Strasbourg 67000, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maud","family":"Wilhelm","sequence":"additional","affiliation":[{"name":"Centre National de la Recherche Scientifique (CNRS), Immunopathology and Therapeutic Chemistry\/Laboratory of Excellence Medalis, Institut de Biologie Mol\u00e9culaire et Cellulaire, Strasbourg 67000, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0481-0620","authenticated-orcid":false,"given":"Sylviane","family":"Muller","sequence":"additional","affiliation":[{"name":"Centre National de la Recherche Scientifique (CNRS), Immunopathology and Therapeutic Chemistry\/Laboratory of Excellence Medalis, Institut de Biologie Mol\u00e9culaire et Cellulaire, Strasbourg 67000, France"},{"name":"University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg 67000, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2017,6,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2861","DOI":"10.1101\/gad.1599207","article-title":"Autophagy: Process and function","volume":"21","author":"Mizushima","year":"2007","journal-title":"Genes Dev."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"549","DOI":"10.4161\/auto.28448","article-title":"Autophagosomes, phagosomes, autolysosomes, phagolysosomes, autophagolysosomes\u2026 Wait, I\u2019m confused","volume":"10","author":"Klionsky","year":"2014","journal-title":"Autophagy"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/cr.2013.153","article-title":"Chaperone-mediated autophagy: Roles in disease and aging","volume":"24","author":"Cuervo","year":"2014","journal-title":"Cell Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1007\/s00018-011-0865-5","article-title":"Microautophagy: Lesser-known self-eating","volume":"69","author":"Li","year":"2012","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"15","DOI":"10.4049\/jimmunol.1102108","article-title":"Autophagy: An emerging immunological paradigm","volume":"189","author":"Deretic","year":"2012","journal-title":"J. Immunol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/nri3532","article-title":"Autophagy in infection, inflammation and immunity","volume":"13","author":"Deretic","year":"2013","journal-title":"Nat. Rev. Immunol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/nature09782","article-title":"Autophagy in immunity and inflammation","volume":"469","author":"Levine","year":"2011","journal-title":"Nature"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.immuni.2013.07.017","article-title":"Autophagy and cellular immune responses","volume":"39","author":"Ma","year":"2013","journal-title":"Immunity"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/icb.2014.98","article-title":"Autophagy and immunity","volume":"93","author":"Mintern","year":"2015","journal-title":"Immunol. Cell Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"4337","DOI":"10.1111\/bph.12792","article-title":"Pharmacological regulators of autophagy and their link with modulators of lupus disease","volume":"171","author":"Gros","year":"2014","journal-title":"Br. J. Pharmacol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1016\/j.it.2016.08.017","article-title":"Autophagy beyond intracellular MHC Class II antigen presentation","volume":"37","year":"2016","journal-title":"Trends Immunol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3335","DOI":"10.4049\/jimmunol.0803458","article-title":"Autophagy and its role in MHC-mediated antigen presentation","volume":"182","author":"Crotzer","year":"2009","journal-title":"J. Immunol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1002\/eji.200323730","article-title":"Major histocompatibility complex class II-restricted presentation of a cytosolic antigen by autophagy","volume":"33","author":"Nimmerjahn","year":"2003","journal-title":"Eur. J. Immunol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.immuni.2009.12.006","article-title":"In vivo requirement for Atg5 in antigen presentation by dendritic cells","volume":"32","author":"Lee","year":"2010","journal-title":"Immunity"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.immuni.2006.10.018","article-title":"Antigen-loading compartments for major histocompatibility complex class II molecules continuously receive input from autophagosomes","volume":"26","author":"Schmid","year":"2007","journal-title":"Immunity"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"16133","DOI":"10.1038\/nmicrobiol.2016.133","article-title":"Suppression of autophagy and antigen presentation by Mycobacterium tuberculosis PE_PGRS47","volume":"1","author":"Saini","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1016\/j.immuni.2010.04.011","article-title":"Human immunodeficiency virus-1 inhibition of immunoamphisomes in dendritic cells impairs early innate and adaptive immune responses","volume":"32","author":"Blanchet","year":"2010","journal-title":"Immunity"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/j.immuni.2005.03.009","article-title":"Lamp-2a facilitates MHC class II presentation of cytoplasmic antigens","volume":"22","author":"Zhou","year":"2005","journal-title":"Immunity"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1080\/15548627.2015.1071759","article-title":"Modulation of inflammation by autophagy: Consequences for human disease","volume":"12","author":"Plantinga","year":"2016","journal-title":"Autophagy"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1111\/j.1600-065X.2012.01143.x","article-title":"The contribution of autophagy to lymphocyte survival and homeostasis","volume":"249","author":"McLeod","year":"2012","journal-title":"Immunol. Rev."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1007\/s13238-012-2097-3","article-title":"Intersection of autophagy with pathways of antigen presentation","volume":"3","author":"Patterson","year":"2012","journal-title":"Protein Cell"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1056\/NEJMra071297","article-title":"Systemic lupus erythematosus","volume":"358","author":"Rahman","year":"2008","journal-title":"N. Engl. J. Med."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Maiuri, M.C., and Stefano, D.D. (2016). Target autophagy as a novel therapeutic strategy in autoimmune diseases. Autophagy Networks in Inflammation, Springer.","DOI":"10.1007\/978-3-319-30079-5"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1038\/nrneurol.2014.148","article-title":"Neuropsychiatric systemic lupus erythematosus: Pathogenesis and biomarkers","volume":"10","author":"Muller","year":"2014","journal-title":"Nat. Rev. Neurol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"International Consortium for Systemic Lupus Erythematosus Genetics (SLEGEN), Harley, J.B., Alarc\u00f3n-Riquelme, M.E., Criswell, L.A., Jacob, C.O., Kimberly, R.P., Moser, K.L., Tsao, B.P., Vyse, T.J., and Langefeld, C.D. (2008). Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat. Genet., 40, 204\u2013210.","DOI":"10.1038\/ng.81"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.ajhg.2012.11.018","article-title":"Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in asians","volume":"92","author":"Yang","year":"2013","journal-title":"Am. J. Hum. Genet."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1330","DOI":"10.1136\/ard.2010.140111","article-title":"Genetic association of PRDM1-ATG5 intergenic region and autophagy with systemic lupus erythematosus in a Chinese population","volume":"70","author":"Zhou","year":"2011","journal-title":"Ann. Rheum. Dis."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1111\/1756-185X.12768","article-title":"Gene-gene interaction of ATG5, ATG7, BLK and BANK1 in systemic lupus erythematosus","volume":"19","author":"Dang","year":"2016","journal-title":"Int. J. Rheum. Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.4161\/auto.20275","article-title":"Macroautophagy is deregulated in murine and human lupus T lymphocytes","volume":"8","author":"Gros","year":"2012","journal-title":"Autophagy"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1080\/15548627.2015.1017179","article-title":"Modulation of deregulated chaperone-mediated autophagy by a phosphopeptide","volume":"11","author":"Macri","year":"2015","journal-title":"Autophagy"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1136\/annrheumdis-2013-204343","article-title":"Autophagy is activated in systemic lupus erythematosus and required for plasmablast development","volume":"74","author":"Clarke","year":"2015","journal-title":"Ann. Rheum. Dis."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"4722","DOI":"10.1096\/fj.12-206060","article-title":"T lymphocytes from patients with systemic lupus erythematosus are resistant to induction of autophagy","volume":"26","author":"Alessandri","year":"2012","journal-title":"FASEB J."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1080\/08830180490452602","article-title":"Dissecting the molecular mechanisms of TCR \u03b6 chain downregulation and T cell signaling abnormalities in human systemic lupus erythematosus","volume":"23","author":"Nambiar","year":"2004","journal-title":"Int. Rev. Immunol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1038\/nrrheum.2015.119","article-title":"Autoimmunity: Antigen presentation by B cells contributes to murine lupus","volume":"11","author":"Duarte","year":"2015","journal-title":"Nat. Rev. Rheumatol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1016\/j.biocel.2009.10.011","article-title":"The role of B cells in lupus pathogenesis","volume":"42","author":"Nashi","year":"2010","journal-title":"Int. J. Biochem. Cell Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"252","DOI":"10.3389\/fimmu.2015.00252","article-title":"Manipulating autophagic processes in autoimmune diseases: A special focus on modulating chaperone-mediated autophagy, an emerging therapeutic target","volume":"6","author":"Wang","year":"2015","journal-title":"Front. Immunol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1080\/15548627.2015.1052206","article-title":"B cell autophagy mediates TLR7-dependent autoimmunity and inflammation","volume":"11","author":"Weindel","year":"2015","journal-title":"Autophagy"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Muller, S., Brun, S., Ren\u00e9, F., de S\u00e8ze, J., Loeffler, J.-P., and Jeltsch-David, H. Autophagy in neuroinflammatory diseases. Autoimmun. Rev., in press, available online 29 May 2017.","DOI":"10.1016\/j.autrev.2017.05.015"},{"key":"ref_39","first-page":"1","article-title":"Expression of autophagy related genes mTOR, Becline-1, LC3 and p62 in the peripheral blood mononuclear cells of systemic lupus erythematosus","volume":"6","author":"Wu","year":"2017","journal-title":"Am. J. Clin. Exp. Immunol."},{"key":"ref_40","first-page":"705","article-title":"Blockade of macrophage autophagy ameliorates activated lymphocytes-derived DNA induced murine lupus possibly via inhibition of proinflammatory cytokine production","volume":"32","author":"Li","year":"2014","journal-title":"Clin. Exp. Rheumatol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1136\/ard.2010.139832","article-title":"HSC70 blockade by the therapeutic peptide P140 affects autophagic processes and endogenous MHCII presentation in murine lupus","volume":"70","author":"Page","year":"2011","journal-title":"Ann. Rheum. Dis."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e2341","DOI":"10.1038\/cddis.2016.244","article-title":"Notch-Hes-1 axis controls TLR7-mediated autophagic death of macrophage via induction of P62 in mice with lupus","volume":"7","author":"Li","year":"2016","journal-title":"Cell Death Dis."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/ng1954","article-title":"A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1","volume":"39","author":"Hampe","year":"2007","journal-title":"Nat. Genet."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1038\/ng2032","article-title":"Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis","volume":"39","author":"Rioux","year":"2007","journal-title":"Nat. Genet."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Glas, J., Seiderer, J., Bues, S., Stallhofer, J., Fries, C., Olszak, T., Tsekeri, E., Wetzke, M., Beigel, F., and Steib, C. (2013). IRGM variants and susceptibility to inflammatory bowel disease in the german population. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0054338"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Lu, X.C., Tao, Y., Wu, C., Zhao, P.L., Li, K., Zheng, J.Y., and Li, L.X. (2013). Association between variants of the autophagy related gene\u2014IRGM and susceptibility to Crohn\u2019s disease and ulcerative colitis: A meta-analysis. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0080602"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1136\/annrheumdis-2012-201671","article-title":"Autophagy regulates TNF\u03b1-mediated joint destruction in experimental arthritis","volume":"72","author":"Lin","year":"2013","journal-title":"Ann. Rheum. Dis."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1136\/ard.2010.137174","article-title":"Study of the common genetic background for rheumatoid arthritis and systemic lupus erythematosus","volume":"70","author":"Orozco","year":"2011","journal-title":"Ann. Rheum. Dis."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"e7623145","DOI":"10.1155\/2017\/7623145","article-title":"The autophagy level is increased in the synovial tissues of patients with active rheumatoid arthritis and is correlated with disease severity","volume":"2017","author":"Zhu","year":"2017","journal-title":"Mediators Inflamm."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1002\/art.38190","article-title":"Dual role of autophagy in stress-induced cell death in rheumatoid arthritis synovial fibroblasts","volume":"66","author":"Kato","year":"2014","journal-title":"Arthritis Rheumatol. Hoboken NJ"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.2353\/ajpath.2010.100050","article-title":"Impaired autophagy in sporadic inclusion-body myositis and in endoplasmic reticulum stress-provoked cultured human muscle fibers","volume":"177","author":"Nogalska","year":"2010","journal-title":"Am. J. Pathol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"152","DOI":"10.4161\/auto.5.2.7348","article-title":"Elevated ATG5 expression in autoimmune demyelination and multiple sclerosis","volume":"5","author":"Alirezaei","year":"2009","journal-title":"Autophagy"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.gene.2016.04.042","article-title":"Gene expression profiles of autophagy-related genes in multiple sclerosis","volume":"588","author":"Igci","year":"2016","journal-title":"Gene"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"18077","DOI":"10.1074\/jbc.M113.474650","article-title":"Diminished autophagy limits cardiac injury in mouse models of type 1 diabetes","volume":"288","author":"Xu","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1084\/jem.148.5.1198","article-title":"Spontaneous murine lupus-like syndromes. Clinical and immunopathological manifestations in several strains","volume":"148","author":"Andrews","year":"1978","journal-title":"J. Exp. Med."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1007\/978-1-4939-0326-9_9","article-title":"Induced murine models of systemic lupus erythematosus","volume":"1134","author":"Xu","year":"2014","journal-title":"Methods Mol. Biol. Clifton NJ"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s00281-006-0030-7","article-title":"Genetics of SLE in mice","volume":"28","author":"Kono","year":"2006","journal-title":"Springer Semin. Immunopathol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1038\/nrrheum.2010.63","article-title":"Genetics of SLE: Evidence from mouse models","volume":"6","author":"Morel","year":"2010","journal-title":"Nat. Rev. Rheumatol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"e271694","DOI":"10.1155\/2011\/271694","article-title":"Murine models of systemic lupus erythematosus","volume":"2011","author":"Perry","year":"2011","journal-title":"BioMed Res. Int."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/S0065-2776(08)60342-9","article-title":"Murine models of systemic lupus erythematosus","volume":"37","author":"Theofilopoulos","year":"1985","journal-title":"Adv. Immunol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1007\/978-1-4939-6780-3_21","article-title":"CD95 and the MRL-lpr Mouse Model","volume":"1557","author":"Flynn","year":"2017","journal-title":"Methods Mol. Biol. Clifton NJ"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1038\/icb.2014.99","article-title":"Double negative (DN) \u03b1\u03b2 T cells: Misperception and overdue recognition","volume":"93","author":"Martina","year":"2015","journal-title":"Immunol. Cell Biol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"2225","DOI":"10.1084\/jem.178.6.2225","article-title":"Double-negative T cells from MRL-lpr\/lpr mice mediate cytolytic activity when triggered through adhesion molecules and constitutively express perforin gene","volume":"178","author":"Hammond","year":"1993","journal-title":"J. Exp. Med."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1016\/j.autrev.2014.08.015","article-title":"Neuropsychiatric systemic lupus erythematosus and cognitive dysfunction: The MRL-lpr mouse strain as a model","volume":"13","author":"Muller","year":"2014","journal-title":"Autoimmun. Rev."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1111\/j.1440-1827.1994.tb01716.x","article-title":"Pathogenesis of Sj\u00f6gren\u2019s syndrome-like autoimmune lesions in MRL\/lpr mice","volume":"44","author":"Hayashi","year":"1994","journal-title":"Pathol. Int."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Gulinello, M., and Putterman, C. (2011). The MRL\/lpr mouse strain as a model for neuropsychiatric systemic lupus erythematosus. J. Biomed. Biotechnol., 2011.","DOI":"10.1155\/2011\/207504"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.cell.2010.01.028","article-title":"Methods in mammalian autophagy research","volume":"140","author":"Mizushima","year":"2010","journal-title":"Cell"},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Deretic, V. (2008). Methods for asssessing autophagy and autophagic cell death. Autophagosome and Phagosome, Humana Press. Methods in Molecular Biology.","DOI":"10.1007\/978-1-59745-157-4"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"585","DOI":"10.4161\/auto.5.5.8823","article-title":"In search of an \u201cautophagomometer\u201d","volume":"5","author":"Rubinsztein","year":"2009","journal-title":"Autophagy"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/15548627.2015.1100356","article-title":"Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)","volume":"12","author":"Klionsky","year":"2016","journal-title":"Autophagy"},{"key":"ref_71","unstructured":"Reeves, J.P., and Reeves, P.A. (2001). Removal of lymphoid organs. Curr. Protoc. Immunol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/S0022-1759(00)00256-8","article-title":"Laboratory protocols for the identification of Th cell epitopes on self-antigens in mice with systemic autoimmune diseases","volume":"244","author":"Monneaux","year":"2000","journal-title":"J. Immunol. Methods"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1002\/1521-4141(2000)30:8<2191::AID-IMMU2191>3.0.CO;2-R","article-title":"B and T cell immune response to small nuclear ribonucleoprotein particles in lupus mice: Autoreactive CD4(+) T cells recognize a T cell epitope located within the RNP80 motif of the 70K protein","volume":"30","author":"Monneaux","year":"2000","journal-title":"Eur. J. Immunol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"741","DOI":"10.4049\/jimmunol.167.2.741","article-title":"The Dendritic Cell Populations of Mouse Lymph Nodes","volume":"167","author":"Henri","year":"2001","journal-title":"J. Immunol."},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Broggi, M.A.S., Schmaler, M., Lagarde, N., and Rossi, S.W. (2014). Isolation of Murine Lymph Node Stromal Cells. J. Vis. Exp. JoVE.","DOI":"10.3791\/51803-v"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1267\/ahc.12013","article-title":"Anatomy and histology of rodent and human major salivary glands","volume":"45","author":"Amano","year":"2012","journal-title":"Acta Histochem. Cytochem."},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Fuss, I.J., Kanof, M.E., Smith, P.D., and Zola, H. (2009). Isolation of whole mononuclear cells from peripheral blood and cord blood. Curr. Protoc. Immunol.","DOI":"10.1002\/0471142735.im0701s85"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"2439","DOI":"10.1038\/nprot.2007.304","article-title":"Processing tissue and cells for transmission electron microscopy in diagnostic pathology and research","volume":"2","author":"Graham","year":"2007","journal-title":"Nat. Protoc."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"257","DOI":"10.4161\/auto.5179","article-title":"To be or not to be? Examples of incorrect identification of autophagic compartments in conventional transmission electron microscopy of mammalian cells","volume":"4","author":"Eskelinen","year":"2008","journal-title":"Autophagy"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1007\/978-1-59745-157-4_4","article-title":"LC3 and autophagy","volume":"445","author":"Tanida","year":"2008","journal-title":"Methods Mol. Biol. Clifton NJ"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"542","DOI":"10.4161\/auto.4600","article-title":"How to interpret LC3 immunoblotting","volume":"3","author":"Mizushima","year":"2007","journal-title":"Autophagy"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/j.dib.2016.02.085","article-title":"mRNA and protein dataset of autophagy markers (LC3 and p62) in several cell lines","volume":"7","author":"Fuentes","year":"2016","journal-title":"Data Brief"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.ab.2015.02.020","article-title":"Routine Western blot to check autophagic flux: Cautions and recommendations","volume":"477","author":"Fuentes","year":"2015","journal-title":"Anal. Biochem."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1002\/cyto.a.22652","article-title":"Quantifying autophagosomes and autolysosomes in cells using imaging flow cytometry","volume":"87","author":"Rajan","year":"2015","journal-title":"Cytom. Part J. Int. Soc. Anal. Cytol."},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Lin, C.-W., Lo, S., Hsu, C., Hsieh, C.-H., Chang, Y.-F., Hou, B.-S., Kao, Y.-H., Lin, C.-C., Yu, M.-L., and Yuan, S.-S. (2014). T-cell autophagy deficiency increases mortality and suppresses immune responses after sepsis. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0102066"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1080\/15548627.2015.1017181","article-title":"A rapid and high content assay that measures cyto-ID-stained autophagic compartments and estimates autophagy flux with potential clinical applications","volume":"11","author":"Guo","year":"2015","journal-title":"Autophagy"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/S0076-6879(08)03609-4","article-title":"Chapter 9 Flow cytometric analysis of autophagy in living mammalian cells","volume":"Volume 452","author":"Klionsky","year":"2009","journal-title":"Autophagy in Mammalian Systems, Part B"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.4161\/auto.29394","article-title":"Sorting cells for basal and induced autophagic flux by quantitative ratiometric flow cytometry","volume":"10","author":"Gump","year":"2014","journal-title":"Autophagy"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/S0076-6879(08)03619-7","article-title":"Methods to monitor chaperone-mediated autophagy","volume":"452","author":"Kaushik","year":"2009","journal-title":"Methods Enzymol."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.ymeth.2015.01.003","article-title":"Methods to study chaperone-mediated autophagy","volume":"75","author":"Patel","year":"2015","journal-title":"Methods San Diego Calif."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1007\/978-1-59745-157-4_15","article-title":"Chaperone-mediated autophagy","volume":"445","author":"Kaushik","year":"2008","journal-title":"Methods Mol. Biol. Clifton NJ"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1038\/ncomms1393","article-title":"A photoconvertible fluorescent reporter to track chaperone-mediated autophagy","volume":"2","author":"Koga","year":"2011","journal-title":"Nat. Commun."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"5606","DOI":"10.1074\/jbc.272.9.5606","article-title":"A population of rat liver lysosomes responsible for the selective uptake and degradation of cytosolic proteins","volume":"272","author":"Cuervo","year":"1997","journal-title":"J. Biol. Chem."}],"container-title":["Cells"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4409\/6\/3\/16\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T18:40:39Z","timestamp":1760208039000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4409\/6\/3\/16"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,6,28]]},"references-count":93,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2017,9]]}},"alternative-id":["cells6030016"],"URL":"https:\/\/doi.org\/10.3390\/cells6030016","relation":{},"ISSN":["2073-4409"],"issn-type":[{"value":"2073-4409","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,6,28]]}}}