title: Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.
abstract: A coding polymorphism (Thr300Ala) in the essential autophagy gene, autophagy related 16-like 1 (ATG16L1), confers increased risk for the development of Crohn disease, although the mechanisms by which single disease-associated polymorphisms contribute to pathogenesis have been difficult to dissect given that environmental factors likely influence disease initiation in these patients. Here we introduce a knock-in mouse model expressing the Atg16L1 T300A variant. Consistent with the human polymorphism, T300A knock-in mice do not develop spontaneous intestinal inflammation, but exhibit morphological defects in Paneth and goblet cells. Selective autophagy is reduced in multiple cell types from T300A knock-in mice compared with WT mice. The T300A polymorphism significantly increases caspase 3- and caspase 7-mediated cleavage of Atg16L1, resulting in lower levels of full-length Atg16Ll T300A protein. Moreover, Atg16L1 T300A is associated with decreased antibacterial autophagy and increased IL-1β production in primary cells and in vivo. Quantitative proteomics for protein interactors of ATG16L1 identified previously unknown nonoverlapping sets of proteins involved in ATG16L1-dependent antibacterial autophagy or IL-1β production. These findings demonstrate how the T300A polymorphism leads to cell type- and pathway-specific disruptions of selective autophagy and suggest a mechanism by which this polymorphism contributes to disease.
authors.affiliation: Broad Institute, Cambridge, MA 02142;Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114;
authors.forename: Kara G
authors.initials: KG
authors.lastname: Lassen
authors.affiliation: Broad Institute, Cambridge, MA 02142;Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114;
authors.forename: Petric
authors.initials: P
authors.lastname: Kuballa
authors.affiliation: Broad Institute, Cambridge, MA 02142;Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114;Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114;
authors.forename: Kara L
authors.initials: KL
authors.lastname: Conway
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;
authors.forename: Khushbu K
authors.initials: KK
authors.lastname: Patel
authors.affiliation: Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114;
authors.forename: Christine E
authors.initials: CE
authors.lastname: Becker
authors.affiliation: Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114;Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114;
authors.forename: Joanna M
authors.initials: JM
authors.lastname: Peloquin
authors.affiliation: Broad Institute, Cambridge, MA 02142;Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114;Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114;
authors.forename: Eduardo J
authors.initials: EJ
authors.lastname: Villablanca
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;
authors.forename: Jason M
authors.initials: JM
authors.lastname: Norman
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;
authors.forename: Ta-Chiang
authors.initials: TC
authors.lastname: Liu
authors.affiliation: Broad Institute, Cambridge, MA 02142;Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114;
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Heath
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;
authors.forename: Morgan L
authors.initials: ML
authors.lastname: Becker
authors.affiliation: Broad Institute, Cambridge, MA 02142;
authors.forename: Lola
authors.initials: L
authors.lastname: Fagbami
authors.affiliation: Broad Institute, Cambridge, MA 02142;Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114;
authors.forename: Heiko
authors.initials: H
authors.lastname: Horn
authors.affiliation: Broad Institute, Cambridge, MA 02142;
authors.forename: Johnathan
authors.initials: J
authors.lastname: Mercer
authors.affiliation: Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139;Pathology Department, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114;
authors.forename: Omer H
authors.initials: OH
authors.lastname: Yilmaz
authors.affiliation: Broad Institute, Cambridge, MA 02142;
authors.forename: Jacob D
authors.initials: JD
authors.lastname: Jaffe
authors.affiliation: Center for the Science of Therapeutics, Broad Institute, Cambridge, MA 02142;
authors.forename: Alykhan F
authors.initials: AF
authors.lastname: Shamji
authors.affiliation: Pathology Department, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114;Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114;
authors.forename: Atul K
authors.initials: AK
authors.lastname: Bhan
authors.affiliation: Broad Institute, Cambridge, MA 02142;
authors.forename: Steven A
authors.initials: SA
authors.lastname: Carr
authors.affiliation: Broad Institute, Cambridge, MA 02142;Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114;Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114;
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Daly
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110; and.
authors.forename: Herbert W
authors.initials: HW
authors.lastname: Virgin
authors.affiliation: Center for the Science of Therapeutics, Broad Institute, Cambridge, MA 02142;Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 stuart_schreiber@harvard.edu xavier@molbio.mgh.harvard.edu.
authors.forename: Stuart L
authors.initials: SL
authors.lastname: Schreiber
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;
authors.forename: Thaddeus S
authors.initials: TS
authors.lastname: Stappenbeck
authors.affiliation: Broad Institute, Cambridge, MA 02142;Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114;Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114;Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114; stuart_schreiber@harvard.edu xavier@molbio.mgh.harvard.edu.
authors.forename: Ramnik J
authors.initials: RJ
authors.lastname: Xavier
mesh_terms: D000818:Animals; D001343:Autophagy / Q000235:genetics; D000071183:Autophagy-Related Proteins; D015153:Blotting, Western; D002352:Carrier Proteins / Q000235:genetics*; D002853:Chromatography, Liquid; D003424:Crohn Disease / Q000235:genetics / Q000276:immunology*; D004797:Enzyme-Linked Immunosorbent Assay; D005434:Flow Cytometry; D055879:Gene Knock-In Techniques; D020397:Goblet Cells / Q000473:pathology; D051379:Mice; D019879:Paneth Cells / Q000473:pathology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040901:Proteomics; D060888:Real-Time Polymerase Chain Reaction; D012480:Salmonella Infections / Q000276:immunology*; D053719:Tandem Mass Spectrometry
chemical_list: C532820:Atg16l1 protein, mouse; D000071183:Autophagy-Related Proteins; D002352:Carrier Proteins