{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T18:50:35Z","timestamp":1790794235365,"version":"4.1.0"},"reference-count":172,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T00:00:00Z","timestamp":1548028800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Research Foundation of Korea(NRF) grant funded by the Korea government(MSIP)","award":["NRF-2015M3C9A2054326"],"award-info":[{"award-number":["NRF-2015M3C9A2054326"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cells"],"abstract":"<jats:p>Autophagy is an intracellular catabolic process that is essential for a variety of cellular responses. Due to its role in the maintenance of biological homeostasis in conditions of stress, dysregulation or disruption of autophagy may be linked to human diseases such as inflammatory bowel disease (IBD). IBD is a complicated inflammatory colitis disorder; Crohn\u2019s disease and ulcerative colitis are the principal types. Genetic studies have shown the clinical relevance of several autophagy-related genes (ATGs) in the pathogenesis of IBD. Additionally, recent studies using conditional knockout mice have led to a comprehensive understanding of ATGs that affect intestinal inflammation, Paneth cell abnormality and enteric pathogenic infection during colitis. In this review, we discuss the various ATGs involved in macroautophagy and selective autophagy, including ATG16L1, IRGM, LRRK2, ATG7, p62, optineurin and TFEB in the maintenance of intestinal homeostasis. Although advances have been made regarding the involvement of ATGs in maintaining intestinal homeostasis, determining the precise contribution of autophagy has remained elusive. Recent efforts based on direct targeting of ATGs and autophagy will further facilitate the development of new therapeutic opportunities for IBD.<\/jats:p>","DOI":"10.3390\/cells8010077","type":"journal-article","created":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T03:08:22Z","timestamp":1548126502000},"page":"77","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":102,"title":["Roles of Autophagy-Related Genes in the Pathogenesis of Inflammatory Bowel Disease"],"prefix":"10.3390","volume":"8","author":[{"given":"Sup","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Microbiology, Chungnam National University School of Medicine, Daejeon 35015, Korea"},{"name":"Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Korea"},{"name":"Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon 35015, Korea"},{"name":"Department of Radiation Oncology, Chungnam National University Hospital, 282, Munwha-ro, Jung-gu, Daejeon 34952, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0485-0072","authenticated-orcid":false,"given":"Hyuk Soo","family":"Eun","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Chungnam National University Hospital, 282, Munwha-ro, Jung-gu, Daejeon 34952, Korea"},{"name":"Department of Internal Medicine, School of Medicine, Chungnam National University, 266, Munwha-ro, Jung-gu, Daejeon 35015, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eun-Kyeong","family":"Jo","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Chungnam National University School of Medicine, Daejeon 35015, Korea"},{"name":"Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Korea"},{"name":"Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon 35015, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,1,21]]},"reference":[{"key":"ref_1","first-page":"695","article-title":"Intestinal Autophagy and Its Pharmacological Control in Inflammatory Bowel Disease","volume":"7","author":"Ke","year":"2016","journal-title":"Front. Immunol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1056\/NEJMra020831","article-title":"Inflammatory bowel disease","volume":"347","author":"Podolsky","year":"2002","journal-title":"N. Engl. J. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/nature06005","article-title":"Unravelling the pathogenesis of inflammatory bowel disease","volume":"448","author":"Xavier","year":"2007","journal-title":"Nature"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"4447","DOI":"10.3748\/wjg.v19.i28.4447","article-title":"Interplay of autophagy and innate immunity in Crohn\u2019s disease: A key immunobiologic feature","volume":"19","author":"Muzes","year":"2013","journal-title":"World J. Gastroenterol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1580","DOI":"10.1136\/gut.2009.206466","article-title":"Crohn\u2019s disease: NOD2, autophagy and ER stress converge","volume":"60","author":"Fritz","year":"2011","journal-title":"Gut"},{"key":"ref_6","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_7","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1007\/s10059-013-0140-8","article-title":"Autophagy: A critical regulator of cellular metabolism and homeostasis","volume":"36","author":"Ryter","year":"2013","journal-title":"Mol. Cells"},{"key":"ref_8","first-page":"54","article-title":"Autophagic clearance of bacterial pathogens: Molecular recognition of intracellular microorganisms","volume":"3","author":"Pareja","year":"2013","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.3389\/fimmu.2017.01483","article-title":"Macrophage Autophagy and Bacterial Infections","volume":"8","author":"Bah","year":"2017","journal-title":"Front. Immunol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2233","DOI":"10.1089\/ars.2010.3485","article-title":"Autophagy shapes inflammation","volume":"14","author":"Fesus","year":"2011","journal-title":"Antioxid. Redox Signal."},{"key":"ref_11","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_12","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1038\/gene.2009.25","article-title":"Association of ATG16L1 and IRGM genes polymorphisms with inflammatory bowel disease: A meta-analysis approach","volume":"10","author":"Oliver","year":"2009","journal-title":"Genes Immun."},{"key":"ref_13","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_14","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1016\/j.dld.2008.03.022","article-title":"ATG16L1 and IL23 receptor (IL23R) genes are associated with disease susceptibility in Hungarian CD patients","volume":"40","author":"Lakatos","year":"2008","journal-title":"Dig. Liver Dis."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1080\/15548627.2015.1017187","article-title":"ATG16L1: A multifunctional susceptibility factor in Crohn disease","volume":"11","author":"Salem","year":"2015","journal-title":"Autophagy"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1038\/ng2061","article-title":"Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn\u2019s disease susceptibility","volume":"39","author":"Parkes","year":"2007","journal-title":"Nat. Genet."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1002\/ibd.22972","article-title":"Associations between genetic variants in the IRGM gene and inflammatory bowel diseases in the Korean population","volume":"19","author":"Moon","year":"2013","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1038\/ng.215","article-title":"Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn\u2019s disease","volume":"40","author":"McCarroll","year":"2008","journal-title":"Nat. Genet."},{"key":"ref_19","first-page":"817","article-title":"Optineurin deficiency in mice contributes to impaired cytokine secretion and neutrophil recruitment in bacteria-driven colitis","volume":"8","author":"Chew","year":"2015","journal-title":"Dis. Models Mech."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1111\/imm.12338","article-title":"Disruption of macrophage pro-inflammatory cytokine release in Crohn\u2019s disease is associated with reduced optineurin expression in a subset of patients","volume":"144","author":"Smith","year":"2015","journal-title":"Immunology"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"13938","DOI":"10.1038\/s41598-017-14370-4","article-title":"Transcription factor TFEB cell-autonomously modulates susceptibility to intestinal epithelial cell injury in vivo","volume":"7","author":"Murano","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e91917","DOI":"10.1172\/jci.insight.91917","article-title":"LRRK2 but not ATG16L1 is associated with Paneth cell defect in Japanese Crohn\u2019s disease patients","volume":"2","author":"Liu","year":"2017","journal-title":"JCI Insight"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1038\/ni.2113","article-title":"The kinase LRRK2 is a regulator of the transcription factor NFAT that modulates the severity of inflammatory bowel disease","volume":"12","author":"Liu","year":"2011","journal-title":"Nat. Immunol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1092","DOI":"10.1038\/cr.2012.42","article-title":"The role of LRRK2 in inflammatory bowel disease","volume":"22","author":"Liu","year":"2012","journal-title":"Cell Res."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Takagawa, T., and Kitani, A. (2018). An increase in LRRK2 suppresses autophagy and enhances Dectin-1-induced immunity in a mouse model of colitis. Sci. Transl. Med., 10.","DOI":"10.1126\/scitranslmed.aan8162"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1038\/ncb1007-1102","article-title":"Autophagosome formation: Core machinery and adaptations","volume":"9","author":"Xie","year":"2007","journal-title":"Nat. Cell Biol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1146\/annurev-immunol-020711-074948","article-title":"Autophagy and the immune system","volume":"30","author":"Kuballa","year":"2012","journal-title":"Annu. Rev. Immunol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1002\/path.2697","article-title":"Autophagy: Cellular and molecular mechanisms","volume":"221","author":"Glick","year":"2010","journal-title":"J. Pathol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.cell.2007.12.018","article-title":"Autophagy in the pathogenesis of disease","volume":"132","author":"Levine","year":"2008","journal-title":"Cell"},{"key":"ref_30","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_31","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1242\/jcs.196352","article-title":"New insights into autophagosome-lysosome fusion","volume":"130","author":"Nakamura","year":"2017","journal-title":"J. Cell Sci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"588","DOI":"10.15698\/mic2016.12.546","article-title":"Autophagy: Machinery and regulation","volume":"3","author":"Yin","year":"2016","journal-title":"Microb. Cell"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2457","DOI":"10.1016\/j.febslet.2014.06.015","article-title":"Regulation of autophagy: Modulation of the size and number of autophagosomes","volume":"588","author":"Jin","year":"2014","journal-title":"FEBS Lett."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Puertollano, R., and Ferguson, S.M. (2018). The complex relationship between TFEB transcription factor phosphorylation and subcellular localization. EMBO J., 37.","DOI":"10.15252\/embj.201798804"},{"key":"ref_35","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_36","doi-asserted-by":"crossref","first-page":"244","DOI":"10.3389\/fphar.2014.00244","article-title":"Emerging role of selective autophagy in human diseases","volume":"5","author":"Mizumura","year":"2014","journal-title":"Front. Pharmacol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/nrm3028","article-title":"Mechanisms of mitophagy","volume":"12","author":"Youle","year":"2011","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.nbd.2010.08.015","article-title":"The elimination of accumulated and aggregated proteins: A role for aggrephagy in neurodegeneration","volume":"43","author":"Yamamoto","year":"2011","journal-title":"Neurobiol. Dis."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1038\/cdd.2012.72","article-title":"Ubiquitination and selective autophagy","volume":"20","author":"Shaid","year":"2013","journal-title":"Cell Death Differ."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1659","DOI":"10.1016\/j.jmb.2016.02.027","article-title":"Mechanisms of Selective Autophagy in Normal Physiology and Cancer","volume":"428","author":"Mancias","year":"2016","journal-title":"J. Mol. Biol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1083\/jcb.200507002","article-title":"p62\/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death","volume":"171","author":"Bjorkoy","year":"2005","journal-title":"J. Cell Biol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/j.molcel.2009.01.020","article-title":"A role for NBR1 in autophagosomal degradation of ubiquitinated substrates","volume":"33","author":"Kirkin","year":"2009","journal-title":"Mol. Cell"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1126\/science.1205405","article-title":"Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth","volume":"333","author":"Wild","year":"2011","journal-title":"Science"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1038\/ni.1800","article-title":"The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria","volume":"10","author":"Thurston","year":"2009","journal-title":"Nat. Immunol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1714","DOI":"10.1016\/j.jmb.2016.02.004","article-title":"Mechanisms of Selective Autophagy","volume":"428","author":"Zaffagnini","year":"2016","journal-title":"J. Mol. Biol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.molcel.2013.12.014","article-title":"Interactions between autophagy receptors and ubiquitin-like proteins form the molecular basis for selective autophagy","volume":"53","author":"Rogov","year":"2014","journal-title":"Mol. Cell"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1016\/j.tcb.2015.02.002","article-title":"How to control self-digestion: Transcriptional, post-transcriptional, and post-translational regulation of autophagy","volume":"25","author":"Feng","year":"2015","journal-title":"Trends Cell Biol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"973","DOI":"10.4161\/auto.5.7.9296","article-title":"Atg101, a novel mammalian autophagy protein interacting with Atg13","volume":"5","author":"Hosokawa","year":"2009","journal-title":"Autophagy"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"649","DOI":"10.4161\/auto.5.5.8249","article-title":"A novel, human Atg13 binding protein, Atg101, interacts with ULK1 and is essential for macroautophagy","volume":"5","author":"Mercer","year":"2009","journal-title":"Autophagy"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"4721","DOI":"10.1007\/s00018-015-2034-8","article-title":"Autophagy signal transduction by ATG proteins: From hierarchies to networks","volume":"72","author":"Wesselborg","year":"2015","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1080\/15548627.2017.1343770","article-title":"Autophagy-monitoring and autophagy-deficient mice","volume":"13","author":"Kuma","year":"2017","journal-title":"Autophagy"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"3237","DOI":"10.1242\/jcs.126128","article-title":"The LIR motif\u2014Crucial for selective autophagy","volume":"126","author":"Birgisdottir","year":"2013","journal-title":"J. Cell Sci."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1056\/NEJM199109263251306","article-title":"Inflammatory bowel disease (1)","volume":"325","author":"Podolsky","year":"1991","journal-title":"N. Engl. J. Med."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"107","DOI":"10.3389\/fimmu.2012.00107","article-title":"Chronic intestinal inflammation: Inflammatory bowel disease and colitis-associated colon cancer","volume":"3","author":"Rubin","year":"2012","journal-title":"Front. Immunol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"2066","DOI":"10.1056\/NEJMra0804647","article-title":"Inflammatory bowel disease","volume":"361","author":"Abraham","year":"2009","journal-title":"N. Engl. J. Med."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"276","DOI":"10.4110\/in.2017.17.5.276","article-title":"IL-17A-Producing Foxp3(+) Regulatory T Cells and Human Diseases","volume":"17","author":"Jung","year":"2017","journal-title":"Immune Netw."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1136\/gut.2010.224154","article-title":"Guidelines for the management of inflammatory bowel disease in adults","volume":"60","author":"Mowat","year":"2011","journal-title":"Gut"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"25","DOI":"10.4110\/in.2017.17.1.25","article-title":"Pathogenesis of Inflammatory Bowel Disease and Recent Advances in Biologic Therapies","volume":"17","author":"Kim","year":"2017","journal-title":"Immune Netw."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1802","DOI":"10.1136\/gut.2005.068601","article-title":"Paneth cells: Their role in innate immunity and inflammatory disease","volume":"54","author":"Elphick","year":"2005","journal-title":"Gut"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"2702","DOI":"10.1016\/j.yexcr.2011.09.006","article-title":"Intestinal development and differentiation","volume":"317","author":"Noah","year":"2011","journal-title":"Exp. Cell Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"10335","DOI":"10.1073\/pnas.91.22.10335","article-title":"Paneth cell differentiation in the developing intestine of normal and transgenic mice","volume":"91","author":"Bry","year":"1994","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1002\/aja.1001410407","article-title":"Origin, differentiation and renewal of the four main epithelial cell types in the mouse small intestine. V. Unitarian Theory of the origin of the four epithelial cell types","volume":"141","author":"Cheng","year":"1974","journal-title":"Am. J. Anat."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1097\/MOG.0b013e32833dccde","article-title":"Paneth cells and innate mucosal immunity","volume":"26","author":"Ouellette","year":"2010","journal-title":"Curr. Opin. Gastroenterol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"3942","DOI":"10.1111\/j.1742-4658.2011.08302.x","article-title":"Antimicrobial peptides important in innate immunity","volume":"278","author":"Cederlund","year":"2011","journal-title":"FEBS J."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1002\/(SICI)1096-9896(200001)190:1<107::AID-PATH504>3.0.CO;2-V","article-title":"Proliferative populations in intestinal metaplasia: Evidence of deregulation in Paneth and goblet cells, but not endocrine cells","volume":"190","author":"Wong","year":"2000","journal-title":"J. Pathol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nature10400","article-title":"Caspase-8 regulates TNF-alpha-induced epithelial necroptosis and terminal ileitis","volume":"477","author":"Gunther","year":"2011","journal-title":"Nature"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1053\/j.gastro.2010.10.040","article-title":"Level of activation of the unfolded protein response correlates with Paneth cell apoptosis in human small intestine exposed to ischemia\/reperfusion","volume":"140","author":"Grootjans","year":"2011","journal-title":"Gastroenterology"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1007\/s00428-011-1129-3","article-title":"Lysozyme-rich mucus metaplasia in duodenal crypts supersedes Paneth cells in celiac disease","volume":"459","author":"Rubio","year":"2011","journal-title":"Virchows Arch."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1097\/MOG.0000000000000134","article-title":"Autophagy and checkpoints for intracellular pathogen defense","volume":"31","author":"Paulus","year":"2015","journal-title":"Curr. Opin. Gastroenterol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1016\/j.coi.2012.08.001","article-title":"Common alleles that influence autophagy and the risk for inflammatory bowel disease","volume":"24","author":"Gardet","year":"2012","journal-title":"Curr. Opin. Immunol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1016\/j.smim.2013.09.006","article-title":"Dysbiosis--a consequence of Paneth cell dysfunction","volume":"25","author":"Salzman","year":"2013","journal-title":"Semin. Immunol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1053\/j.gastro.2004.04.061","article-title":"High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn\u2019s disease","volume":"127","author":"Boudeau","year":"2004","journal-title":"Gastroenterology"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1016\/S0016-5085(98)70019-8","article-title":"Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn\u2019s disease","volume":"115","author":"Neut","year":"1998","journal-title":"Gastroenterology"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1053\/j.gastro.2014.02.009","article-title":"The microbiome in inflammatory bowel disease: Current status and the future ahead","volume":"146","author":"Kostic","year":"2014","journal-title":"Gastroenterology"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1016\/j.cell.2010.01.023","article-title":"Homeostasis and inflammation in the intestine","volume":"140","author":"Garrett","year":"2010","journal-title":"Cell"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/nature07416","article-title":"A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells","volume":"456","author":"Cadwell","year":"2008","journal-title":"Nature"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1126\/science.1104911","article-title":"Nod2-dependent regulation of innate and adaptive immunity in the intestinal tract","volume":"307","author":"Kobayashi","year":"2005","journal-title":"Science"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1038\/ng.175","article-title":"Genome-wide association defines more than 30 distinct susceptibility loci for Crohn\u2019s disease","volume":"40","author":"Barrett","year":"2008","journal-title":"Nat. Genet."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/ng.764","article-title":"Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47","volume":"43","author":"Anderson","year":"2011","journal-title":"Nat. Genet."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1038\/ng.717","article-title":"Genome-wide meta-analysis increases to 71 the number of confirmed Crohn\u2019s disease susceptibility loci","volume":"42","author":"Franke","year":"2010","journal-title":"Nat. Genet."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.jaut.2015.07.013","article-title":"Understanding inflammatory bowel disease via immunogenetics","volume":"64","author":"Barrett","year":"2015","journal-title":"J. Autoimmun."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1038\/ng.3359","article-title":"Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations","volume":"47","author":"Liu","year":"2015","journal-title":"Nat. Genet."},{"key":"ref_83","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_84","doi-asserted-by":"crossref","first-page":"486","DOI":"10.2174\/156652410791608252","article-title":"Autophagy and Crohn\u2019s disease: At the crossroads of infection, inflammation, immunity, and cancer","volume":"10","author":"Brest","year":"2010","journal-title":"Curr. Mol. Med."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1084\/jem.20160791","article-title":"Defective ATG16L1-mediated removal of IRE1alpha drives Crohn\u2019s disease-like ileitis","volume":"214","author":"Tschurtschenthaler","year":"2017","journal-title":"J. Exp. Med."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.chom.2017.12.017","article-title":"Intestinal Epithelial Cell Autophagy Is Required to Protect against TNF-Induced Apoptosis during Chronic Colitis in Mice","volume":"23","author":"Pott","year":"2018","journal-title":"Cell Host Microbe"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1038\/nature07383","article-title":"Loss of the autophagy protein Atg16L1 enhances endotoxin-induced IL-1beta production","volume":"456","author":"Saitoh","year":"2008","journal-title":"Nature"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"2133","DOI":"10.4049\/jimmunol.1601293","article-title":"Myeloid ATG16L1 Facilitates Host-Bacteria Interactions in Maintaining Intestinal Homeostasis","volume":"198","author":"Zhang","year":"2017","journal-title":"J. Immunol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.abb.2012.03.019","article-title":"Autophagy in the intestinal epithelium regulates Citrobacter rodentium infection","volume":"521","author":"Inoue","year":"2012","journal-title":"Arch. Biochem. Biophys."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/nature17186","article-title":"The amino acid sensor GCN2 controls gut inflammation by inhibiting inflammasome activation","volume":"531","author":"Ravindran","year":"2016","journal-title":"Nature"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"1390","DOI":"10.1080\/15548627.2016.1184799","article-title":"Autophagy deficiency in myeloid cells increases susceptibility to obesity-induced diabetes and experimental colitis","volume":"12","author":"Lee","year":"2016","journal-title":"Autophagy"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1002\/ibd.20162","article-title":"Confirmation of the role of ATG16L1 as a Crohn\u2019s disease susceptibility gene","volume":"13","author":"Cummings","year":"2007","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1053\/j.gastro.2007.03.034","article-title":"A nonsynonymous SNP in ATG16L1 predisposes to ileal Crohn\u2019s disease and is independent of CARD15 and IBD5","volume":"132","author":"Prescott","year":"2007","journal-title":"Gastroenterology"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1007\/s10038-007-0156-z","article-title":"Association analysis of genetic variants in IL23R, ATG16L1 and 5p13.1 loci with Crohn\u2019s disease in Japanese patients","volume":"52","author":"Yamazaki","year":"2007","journal-title":"J. Hum. Genet."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"2754","DOI":"10.1111\/j.1572-0241.2007.01525.x","article-title":"IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn\u2019s disease in a study of New Zealand Caucasians with inflammatory bowel disease","volume":"102","author":"Roberts","year":"2007","journal-title":"Am. J. Gastroenterol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.gene.2017.12.029","article-title":"Genetic profile of patients with early onset inflammatory bowel disease","volume":"645","author":"Girardelli","year":"2018","journal-title":"Gene"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"3888","DOI":"10.1093\/emboj\/18.14.3888","article-title":"Apg16p is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway","volume":"18","author":"Mizushima","year":"1999","journal-title":"EMBO J."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1242\/jcs.00381","article-title":"Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic isolation membrane with the Apg12-Apg5 conjugate","volume":"116","author":"Mizushima","year":"2003","journal-title":"J. Cell Sci."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1084\/jem.20161867","article-title":"IKKalpha controls ATG16L1 degradation to prevent ER stress during inflammation","volume":"214","author":"Diamanti","year":"2017","journal-title":"J. Exp. Med."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nature12599","article-title":"Paneth cells as a site of origin for intestinal inflammation","volume":"503","author":"Adolph","year":"2013","journal-title":"Nature"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1136\/gut.2010.228908","article-title":"Crohn\u2019s disease-associated ATG16L1 polymorphism modulates pro-inflammatory cytokine responses selectively upon activation of NOD2","volume":"60","author":"Plantinga","year":"2011","journal-title":"Gut"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/s41590-017-0042-6","article-title":"Selective autophagy of the adaptor TRIF regulates innate inflammatory signaling","volume":"19","author":"Samie","year":"2018","journal-title":"Nat. Immunol."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1186\/s12967-017-1355-9","article-title":"Genetic polymorphism in ATG16L1 gene is associated with adalimumab use in inflammatory bowel disease","volume":"15","author":"Nuij","year":"2017","journal-title":"J. Transl. Med."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1038\/nature13044","article-title":"A Crohn\u2019s disease variant in Atg16l1 enhances its degradation by caspase 3","volume":"506","author":"Murthy","year":"2014","journal-title":"Nature"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.ceb.2009.12.009","article-title":"Autophagy in infection","volume":"22","author":"Deretic","year":"2010","journal-title":"Curr. Opin. Cell Biol."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1080\/15548627.2015.1084457","article-title":"Mechanism of action of the tuberculosis and Crohn disease risk factor IRGM in autophagy","volume":"12","author":"Chauhan","year":"2016","journal-title":"Autophagy"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1038\/ng.145","article-title":"Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn\u2019s disease","volume":"40","author":"Fisher","year":"2008","journal-title":"Nat. Genet."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1007\/s00335-010-9293-3","article-title":"The immunity-related GTPases in mammals: A fast-evolving cell-autonomous resistance system against intracellular pathogens","volume":"22","author":"Hunn","year":"2011","journal-title":"Mamm. Genome"},{"key":"ref_109","doi-asserted-by":"crossref","unstructured":"Bekpen, C., Marques-Bonet, T., Alkan, C., Antonacci, F., Leogrande, M.B., Ventura, M., Kidd, J.M., Siswara, P., Howard, J.C., and Eichler, E.E. (2009). Death and resurrection of the human IRGM gene. PLoS Genet., 5.","DOI":"10.1371\/journal.pgen.1000403"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1016\/j.cell.2004.11.038","article-title":"Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages","volume":"119","author":"Gutierrez","year":"2004","journal-title":"Cell"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.1126\/science.1129577","article-title":"Human IRGM induces autophagy to eliminate intracellular mycobacteria","volume":"313","author":"Singh","year":"2006","journal-title":"Science"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/ni.1759","article-title":"Targeting of the GTPase Irgm1 to the phagosomal membrane via PtdIns(3,4)P(2) and PtdIns(3,4,5)P(3) promotes immunity to mycobacteria","volume":"10","author":"Tiwari","year":"2009","journal-title":"Nat. Immunol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1038\/ncb2119","article-title":"Human IRGM regulates autophagy and cell-autonomous immunity functions through mitochondria","volume":"12","author":"Singh","year":"2010","journal-title":"Nat. Cell Biol."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1038\/nri1270","article-title":"p47 GTPases: Regulators of immunity to intracellular pathogens","volume":"4","author":"Taylor","year":"2004","journal-title":"Nat. Rev. Immunol."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"6963","DOI":"10.4049\/jimmunol.179.10.6963","article-title":"Impaired macrophage function underscores susceptibility to Salmonella in mice lacking Irgm1 (LRG-47)","volume":"179","author":"Henry","year":"2007","journal-title":"J. Immunol."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1084\/jem.194.2.181","article-title":"Inactivation of LRG-47 and IRG-47 reveals a family of interferon gamma-inducible genes with essential, pathogen-specific roles in resistance to infection","volume":"194","author":"Collazo","year":"2001","journal-title":"J. Exp. Med."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1016\/j.chom.2012.09.007","article-title":"IFN-inducible GTPases in host cell defense","volume":"12","author":"Kim","year":"2012","journal-title":"Cell Host Microbe"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1126\/science.1201711","article-title":"A family of IFN-gamma-inducible 65-kD GTPases protects against bacterial infection","volume":"332","author":"Kim","year":"2011","journal-title":"Science"},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"30471","DOI":"10.1074\/jbc.M111.251967","article-title":"Immunity-related GTPase M (IRGM) proteins influence the localization of guanylate-binding protein 2 (GBP2) by modulating macroautophagy","volume":"286","author":"Traver","year":"2011","journal-title":"J. Biol. Chem."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/ng.762","article-title":"A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn\u2019s disease","volume":"43","author":"Brest","year":"2011","journal-title":"Nat. Genet."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1111\/j.1462-5822.2009.01381.x","article-title":"Crohn\u2019s disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly","volume":"12","author":"Lapaquette","year":"2010","journal-title":"Cell Microbiol."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1083\/jcb.201708039","article-title":"Mechanism of Stx17 recruitment to autophagosomes via IRGM and mammalian Atg8 proteins","volume":"217","author":"Kumar","year":"2018","journal-title":"J. Cell Biol."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"E3462","DOI":"10.1073\/pnas.1616683114","article-title":"Hepatitis C virus triggers Golgi fragmentation and autophagy through the immunity-related GTPase M","volume":"114","author":"Hansen","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"G573","DOI":"10.1152\/ajpgi.00071.2013","article-title":"Irgm1-deficient mice exhibit Paneth cell abnormalities and increased susceptibility to acute intestinal inflammation","volume":"305","author":"Liu","year":"2013","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1002\/ibd.20176","article-title":"Adherent-invasive Escherichia coli in inflammatory bowel disease","volume":"13","author":"Rolhion","year":"2007","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"2247","DOI":"10.1093\/ibd\/izy128","article-title":"IRGM Gene Variants Modify the Relationship Between Visceral Adipose Tissue and NAFLD in Patients With Crohn\u2019s Disease","volume":"24","author":"Simon","year":"2018","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1053\/j.gastro.2012.01.031","article-title":"Abnormal activation of autophagy-induced crinophagy in Paneth cells from patients with Crohn\u2019s disease","volume":"142","author":"Thachil","year":"2012","journal-title":"Gastroenterology"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1097\/MIB.0000000000000034","article-title":"Autophagy suppression by appendicitis and appendectomy protects against colitis","volume":"20","author":"Cheluvappa","year":"2014","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"806","DOI":"10.3389\/fimmu.2018.00806","article-title":"Type I Interferons, Autophagy and Host Metabolism in Leprosy","volume":"9","author":"Medeiros","year":"2018","journal-title":"Front. Immunol."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1016\/j.neuron.2004.11.005","article-title":"Mutations in LRRK2 cause autosomal-dominant parkinsonism with pleomorphic pathology","volume":"44","author":"Zimprich","year":"2004","journal-title":"Neuron"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/j.neuron.2004.10.023","article-title":"Cloning of the gene containing mutations that cause PARK8-linked Parkinson\u2019s disease","volume":"44","author":"Jain","year":"2004","journal-title":"Neuron"},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"2609","DOI":"10.1056\/NEJMoa0903753","article-title":"Genomewide association study of leprosy","volume":"361","author":"Zhang","year":"2009","journal-title":"N. Engl. J. Med."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"5577","DOI":"10.4049\/jimmunol.1000548","article-title":"LRRK2 is involved in the IFN-gamma response and host response to pathogens","volume":"185","author":"Gardet","year":"2010","journal-title":"J. Immunol."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/ni.3233","article-title":"Commensal bacteria direct selective cargo sorting to promote symbiosis","volume":"16","author":"Zhang","year":"2015","journal-title":"Nat. Immunol."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1002\/ana.10113","article-title":"A new locus for Parkinson\u2019s disease (PARK8) maps to chromosome 12p11.2-q13.1","volume":"51","author":"Funayama","year":"2002","journal-title":"Ann. Neurol."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1001\/jamaneurol.2017.0469","article-title":"Genome-wide Pleiotropy Between Parkinson Disease and Autoimmune Diseases","volume":"74","author":"Witoelar","year":"2017","journal-title":"JAMA Neurol."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nature09191","article-title":"Pathogenic LRRK2 negatively regulates microRNA-mediated translational repression","volume":"466","author":"Gehrke","year":"2010","journal-title":"Nature"},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"5649","DOI":"10.1093\/hmg\/ddu281","article-title":"Genetic dissection reveals that Akt is the critical kinase downstream of LRRK2 to phosphorylate and inhibit FOXO1, and promotes neuron survival","volume":"23","author":"Chuang","year":"2014","journal-title":"Hum. Mol. Genet."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"9879","DOI":"10.1073\/pnas.1004676107","article-title":"Loss of leucine-rich repeat kinase 2 causes impairment of protein degradation pathways, accumulation of alpha-synuclein, and apoptotic cell death in aged mice","volume":"107","author":"Tong","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.1080\/15548627.2017.1327511","article-title":"Destructive cellular paths underlying familial and sporadic Parkinson disease converge on mitophagy","volume":"13","author":"Wang","year":"2017","journal-title":"Autophagy"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1111\/jnc.12668","article-title":"Interferon-gamma induces leucine-rich repeat kinase LRRK2 via extracellular signal-regulated kinase ERK5 in macrophages","volume":"129","author":"Kuss","year":"2014","journal-title":"J. Neurochem."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"250","DOI":"10.4161\/auto.5.2.7560","article-title":"A common role for Atg16L1, Atg5 and Atg7 in small intestinal Paneth cells and Crohn disease","volume":"5","author":"Cadwell","year":"2009","journal-title":"Autophagy"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"278059","DOI":"10.1155\/2012\/278059","article-title":"Lack of intestinal epithelial atg7 affects paneth cell granule formation but does not compromise immune homeostasis in the gut","volume":"2012","author":"Wittkopf","year":"2012","journal-title":"Clin. Dev. Immunol."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/j.abb.2010.12.009","article-title":"Autophagy in the intestinal epithelium reduces endotoxin-induced inflammatory responses by inhibiting NF-kappaB activation","volume":"506","author":"Fujishima","year":"2011","journal-title":"Arch. Biochem. Biophys."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"20511","DOI":"10.1074\/jbc.M114.632257","article-title":"Autophagy Protects against Colitis by the Maintenance of Normal Gut Microflora and Secretion of Mucus","volume":"290","author":"Tsuboi","year":"2015","journal-title":"J. Biol. Chem."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1038\/mi.2013.108","article-title":"Hypoxic macrophages impair autophagy in epithelial cells through Wnt1: Relevance in IBD","volume":"7","author":"Calatayud","year":"2014","journal-title":"Mucosal Immunol."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"1256","DOI":"10.4161\/auto.25483","article-title":"Autophagy receptor CALCOCO2\/NDP52 takes center stage in Crohn disease","volume":"9","author":"Till","year":"2013","journal-title":"Autophagy"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1053\/j.gastro.2013.04.040","article-title":"Association between variants of PRDM1 and NDP52 and Crohn\u2019s disease, based on exome sequencing and functional studies","volume":"145","author":"Ellinghaus","year":"2013","journal-title":"Gastroenterology"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"5991","DOI":"10.1073\/pnas.93.12.5991","article-title":"Molecular cloning of a phosphotyrosine-independent ligand of the p56lck SH2 domain","volume":"93","author":"Joung","year":"1996","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1086\/340731","article-title":"Recurrent mutation of the gene encoding sequestosome 1 (SQSTM1\/p62) in Paget disease of bone","volume":"70","author":"Laurin","year":"2002","journal-title":"Am. J. Hum. Genet."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"24131","DOI":"10.1074\/jbc.M702824200","article-title":"p62\/SQSTM1 binds directly to Atg8\/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy","volume":"282","author":"Pankiv","year":"2007","journal-title":"J. Biol. Chem."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1016\/j.cell.2007.10.035","article-title":"Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice","volume":"131","author":"Komatsu","year":"2007","journal-title":"Cell"},{"key":"ref_153","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_154","doi-asserted-by":"crossref","first-page":"832704","DOI":"10.1155\/2014\/832704","article-title":"The role of the selective adaptor p62 and ubiquitin-like proteins in autophagy","volume":"2014","author":"Lippai","year":"2014","journal-title":"BioMed Res. Int."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1038\/s41467-017-00213-3","article-title":"Hypoxia ameliorates intestinal inflammation through NLRP3\/mTOR downregulation and autophagy activation","volume":"8","author":"Simmen","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"2619","DOI":"10.1038\/s41598-018-20938-5","article-title":"Ileal pouch of ulcerative colitis and familial adenomatous polyposis patients exhibit modulation of autophagy markers","volume":"8","author":"Paiva","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"2333","DOI":"10.4161\/15548627.2014.984275","article-title":"HIF1A regulates xenophagic degradation of adherent and invasive Escherichia coli (AIEC)","volume":"10","author":"Mimouna","year":"2014","journal-title":"Autophagy"},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"3452","DOI":"10.1093\/hmg\/ddx268","article-title":"Defects in optineurin- and myosin VI-mediated cellular trafficking in amyotrophic lateral sclerosis","volume":"26","author":"Sundaramoorthy","year":"2017","journal-title":"Hum. Mol. Genet."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.exer.2015.06.029","article-title":"Optineurin: The autophagy connection","volume":"144","author":"Ying","year":"2016","journal-title":"Exp. Eye Res."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.3389\/fimmu.2018.01024","article-title":"Optineurin: A Coordinator of Membrane-Associated Cargo Trafficking and Autophagy","volume":"9","author":"Ryan","year":"2018","journal-title":"Front. Immunol."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1038\/ng.562","article-title":"Genome-wide association study identifies variants at CSF1, OPTN and TNFRSF11A as genetic risk factors for Paget\u2019s disease of bone","volume":"42","author":"Albagha","year":"2010","journal-title":"Nat. Genet."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1007\/s00439-010-0888-2","article-title":"The majority of the genetic risk for Paget\u2019s disease of bone is explained by genetic variants close to the CSF1, OPTN, TM7SF4, and TNFRSF11A genes","volume":"128","author":"Chung","year":"2010","journal-title":"Hum. Genet."},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/nature08971","article-title":"Mutations of optineurin in amyotrophic lateral sclerosis","volume":"465","author":"Maruyama","year":"2010","journal-title":"Nature"},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.gde.2017.01.016","article-title":"PINK1\/Parkin mitophagy and neurodegeneration-what do we really know in vivo?","volume":"44","author":"Whitworth","year":"2017","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_165","doi-asserted-by":"crossref","unstructured":"Puri, M., La Pietra, L., Mraheil, M.A., Lucas, R., Chakraborty, T., and Pillich, H. (2017). Listeriolysin O Regulates the Expression of Optineurin, an Autophagy Adaptor That Inhibits the Growth of Listeria monocytogenes. Toxins (Basel), 9.","DOI":"10.3390\/toxins9090273"},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1126\/science.1204592","article-title":"TFEB links autophagy to lysosomal biogenesis","volume":"332","author":"Settembre","year":"2011","journal-title":"Science"},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1126\/science.1174447","article-title":"A gene network regulating lysosomal biogenesis and function","volume":"325","author":"Sardiello","year":"2009","journal-title":"Science"},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"2475","DOI":"10.1242\/jcs.146365","article-title":"TFEB at a glance","volume":"129","author":"Napolitano","year":"2016","journal-title":"J. Cell Sci."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"3852","DOI":"10.1093\/hmg\/ddr306","article-title":"Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways","volume":"20","author":"Palmieri","year":"2011","journal-title":"Hum. Mol. Genet."},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"E1817","DOI":"10.1073\/pnas.1305623110","article-title":"TFEB-mediated autophagy rescues midbrain dopamine neurons from alpha-synuclein toxicity","volume":"110","author":"Decressac","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.tins.2016.02.002","article-title":"The Autophagy-Lysosomal Pathway in Neurodegeneration: A TFEB Perspective","volume":"39","author":"Xu","year":"2016","journal-title":"Trends Neurosci."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.15252\/emmm.201303671","article-title":"Selective clearance of aberrant tau proteins and rescue of neurotoxicity by transcription factor EB","volume":"6","author":"Polito","year":"2014","journal-title":"EMBO Mol. Med."}],"container-title":["Cells"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4409\/8\/1\/77\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T12:27:39Z","timestamp":1760185659000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4409\/8\/1\/77"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,21]]},"references-count":172,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,1]]}},"alternative-id":["cells8010077"],"URL":"https:\/\/doi.org\/10.3390\/cells8010077","relation":{},"ISSN":["2073-4409"],"issn-type":[{"value":"2073-4409","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,1,21]]}}}