The role of ATG16L2 in autophagy and disease

References

• Dikic I, Elazar Z. Mechanism and medical implications of mammalian autophagy. Nature reviews Molecular cell biology 2018; 19:349–364.
   PubMed Web of Science ®Google Scholar
• Feng Y, He D, Yao Z, Klionsky DJ. The machinery of macroautophagy. Cell research 2014; 24:24–41.
   PubMed Web of Science ®Google Scholar
• Yu L, Chen Y, Tooze SA. Autophagy pathway: Cellular and molecular mechanisms. Autophagy 2018; 14:207–215.
   PubMed Web of Science ®Google Scholar
• Kimmey JM, Stallings CL. Bacterial Pathogens versus Autophagy: Implications for Therapeutic Interventions. Trends in molecular medicine 2016; 22:1060–1076.
   PubMed Web of Science ®Google Scholar
• Mitchell G, Isberg RR. Innate Immunity to Intracellular Pathogens: Balancing Microbial Elimination and Inflammation. Cell host & microbe 2017; 22:166–175.
   PubMed Web of Science ®Google Scholar
• Gatica D, Lahiri V, Klionsky DJ. Cargo recognition and degradation by selective autophagy. Nature cell biology 2018; 20:233–242.
   PubMed Web of Science ®Google Scholar
• Lamark T, Johansen T. Mechanisms of Selective Autophagy. Annual review of cell and developmental biology 2021; 37:143–169.
   PubMed Web of Science ®Google Scholar
• Mizushima N. Autophagy: process and function. Genes & development 2007; 21:2861–2873.
   PubMed Web of Science ®Google Scholar
• Nishimura T, Tooze SA. Emerging roles of ATG proteins and membrane lipids in autophagosome formation. Cell discovery 2020; 6:32.
   PubMed Web of Science ®Google Scholar
• Ktistakis NT, Tooze SA. Digesting the Expanding Mechanisms of Autophagy. Trends in cell biology 2016; 26:624–635.
   PubMed Web of Science ®Google Scholar
• Chavez-Dominguez R, Perez-Medina M, Lopez-Gonzalez JS, Galicia-Velasco M, Aguilar-Cazares D. The Double-Edge Sword of Autophagy in Cancer: From Tumor Suppression to Pro-tumor Activity. Frontiers in oncology 2020; 10:578418.
   PubMed Web of Science ®Google Scholar
• Yang Z, Goronzy JJ, Weyand CM. Autophagy in autoimmune disease. Journal of molecular medicine 2015; 93:707–717.
   PubMed Web of Science ®Google Scholar
• Saha S, Panigrahi DP, Patil S, Bhutia SK. Autophagy in health and disease: A comprehensive review. Biomedicine & pharmacotherapy 2018; 104:485–495.
   PubMed Web of Science ®Google Scholar
• Pinto G, Shtaif B, Phillip M, Gat-Yablonski G. Growth attenuation is associated with histone deacetylase 10-induced autophagy in the liver. The Journal of nutritional biochemistry 2016; 27:171–180.
   PubMed Web of Science ®Google Scholar
• Gerovska D, Araúzo-Bravo MJ. Does mouse embryo primordial germ cell activation start before implantation as suggested by single-cell transcriptomics dynamics? Molecular human reproduction 2016; 22:208–225.
   PubMed Web of Science ®Google Scholar
• Tang J, Wang D, Shen Y, Xue F. ATG16L2 overexpression is associated with a good prognosis in colorectal cancer. Journal of gastrointestinal oncology 2021; 12:2192–2202.
   PubMed Web of Science ®Google Scholar
• Dunwell T, Hesson L, Rauch TA, Wang L, Clark RE, Dallol A, et al. A genome-wide screen identifies frequently methylated genes in haematological and epithelial cancers. Molecular cancer 2010; 9:44.
   PubMed Web of Science ®Google Scholar
• Ma T, Wu S, Yan W, Xie R, Zhou C. A functional variant of ATG16L2 is associated with Crohn’s disease in the Chinese population. Colorectal disease 2016; 18:O420–O426.
   Google Scholar
• Ishibashi K, Fujita N, Kanno E, Omori H, Yoshimori T, Itoh T, et al. Atg16L2, a novel isoform of mammalian Atg16L that is not essential for canonical autophagy despite forming an Atg12–5-16L2 complex. Autophagy 2011; 7:1500–1513.
   PubMed Web of Science ®Google Scholar
• Zhang H, Wu F, Wang X, Du H, Wang X, Zhang H. The two C. elegans ATG-16 homologs have partially redundant functions in the basal autophagy pathway. Autophagy 2013; 9:1965–1974.
   PubMed Web of Science ®Google Scholar
• Fletcher K, Ulferts R, Jacquin E, Veith T, Gammoh N, Arasteh JM, et al. The WD40 domain of ATG16L1 is required for its non-canonical role in lipidation of LC3 at single membranes. The EMBO journal 2018; 37.
   Web of Science ®Google Scholar
• Dooley HC, Razi M, Polson HE, Girardin SE, Wilson MI, Tooze SA. WIPI2 links LC3 conjugation with PI3P, autophagosome formation, and pathogen clearance by recruiting Atg12-5-16L1. Molecular cell 2014; 55:238–252.
   PubMed Web of Science ®Google Scholar
• Gammoh N, Florey O, Overholtzer M, Jiang X. Interaction between FIP200 and ATG16L1 distinguishes ULK1 complex-dependent and -independent autophagy. Nature structural & molecular biology 2013; 20:144–149.
   PubMed Web of Science ®Google Scholar
• Nishimura T, Kaizuka T, Cadwell K, Sahani MH, Saitoh T, Akira S, et al. FIP200 regulates targeting of Atg16L1 to the isolation membrane. EMBO reports 2013; 14:284–291.
   PubMed Web of Science ®Google Scholar
• Pantoom S, Konstantinidis G, Voss S, Han H, Hofnagel O, Li Z, et al. RAB33B recruits the ATG16L1 complex to the phagophore via a noncanonical RAB binding protein. Autophagy 2020:1–15.
   PubMed Web of Science ®Google Scholar
• Gammoh N. The multifaceted functions of ATG16L1 in autophagy and related processes. Journal of cell science 2020; 133.
   Web of Science ®Google Scholar
• Saitoh T, Fujita N, Jang MH, Uematsu S, Yang BG, Satoh T, et al. Loss of the autophagy protein Atg16L1 enhances endotoxin-induced IL-1beta production. Nature 2008; 456:264–268.
   PubMed Web of Science ®Google Scholar
• Li N, Wu X, Holzer RG, Lee JH, Todoric J, Park EJ, et al. Loss of acinar cell IKKα triggers spontaneous pancreatitis in mice. The Journal of clinical investigation 2013; 123:2231–2243.
   PubMed Web of Science ®Google Scholar
• Khor B, Conway KL, Omar AS, Biton M, Haber AL, Rogel N, et al. Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1. Journal of immunology 2019; 203:1820–1829.
   PubMed Web of Science ®Google Scholar
• Wible DJ, Chao HP, Tang DG, Bratton SB. ATG5 cancer mutations and alternative mRNA splicing reveal a conjugation switch that regulates ATG12-ATG5-ATG16L1 complex assembly and autophagy. Cell discovery 2019; 5:42.
   PubMed Web of Science ®Google Scholar
• Stanfill AG, Cao XJBRFN. Enhancing Research Through the Use of the Genotype-Tissue Expression (GTEx) Database. Biological research for nursing 2021:1099800421994186.
   Web of Science ®Google Scholar
• Huang Y, Chuang AY, Ratovitski EA. Phospho-ΔNp63α/miR-885-3p axis in tumor cell life and cell death upon cisplatin exposure. Cell cycle 2011; 10:3938–3947.
   PubMed Web of Science ®Google Scholar
• Xiong Q, Li W, Li P, Yang M, Wu C, Eichinger L. The Role of ATG16 in Autophagy and The Ubiquitin Proteasome System. Cells 2018; 8.
   Web of Science ®Google Scholar
• Feizi N, Mehrbod P, Romani B, Soleimanjahi H, Bamdad T, Feizi A, et al. Autophagy induction regulates influenza virus replication in a time-dependent manner. Journal of medical microbiology 2017; 66:536–541.
   PubMed Web of Science ®Google Scholar
• Birmingham CL, Smith AC, Bakowski MA, Yoshimori T, Brumell JH. Autophagy controls Salmonella infection in response to damage to the Salmonella-containing vacuole. The Journal of biological chemistry 2006; 281:11374–11383.
   PubMed Web of Science ®Google Scholar
• Wang YH, Wu JJ, Lei HY. The autophagic induction in Helicobacter pylori-infected macrophage. Experimental biology and medicine 2009; 234:171–180.
   PubMed Web of Science ®Google Scholar
• Burgos-Portugal JA, Mitchell HM, Castaño-Rodríguez N, Kaakoush NO. The role of autophagy in the intracellular survival of Campylobacter concisus. FEBS Open Bio 2014; 4:301–309.
   PubMed Web of Science ®Google Scholar
• Kanayama M, Inoue M, Danzaki K, Hammer G, He YW, Shinohara ML. Autophagy enhances NFκB activity in specific tissue macrophages by sequestering A20 to boost antifungal immunity. Nature communications 2015; 6:5779.
   PubMed Web of Science ®Google Scholar
• Campbell-Valois FX, Sachse M, Sansonetti PJ, Parsot C. Escape of Actively Secreting Shigella flexneri from ATG8/LC3-Positive Vacuoles Formed during Cell-To-Cell Spread Is Facilitated by IcsB and VirA. mBio 2015; 6:e02567–14.
   PubMed Web of Science ®Google Scholar
• Al-Younes HM, Al-Zeer MA, Khalil H, Gussmann J, Karlas A, Machuy N, et al. Autophagy-independent function of MAP-LC3 during intracellular propagation of Chlamydia trachomatis. Autophagy 2011; 7:814–828.
   PubMed Web of Science ®Google Scholar
• Newton HJ, Kohler LJ, McDonough JA, Temoche-Diaz M, Crabill E, Hartland EL, et al. A screen of Coxiella burnetii mutants reveals important roles for Dot/Icm effectors and host autophagy in vacuole biogenesis. PLoS pathogens 2014; 10:e1004286.
   PubMed Web of Science ®Google Scholar
• Conway KL, Kuballa P, Song JH, Patel KK, Castoreno AB, Yilmaz OH, et al. Atg16l1 is required for autophagy in intestinal epithelial cells and protection of mice from Salmonella infection. Gastroenterology 2013; 145:1347–1357.
   PubMed Web of Science ®Google Scholar
• Castaño‐Rodríguez N, Kaakoush NO, Goh KL, Fock KM, Mitchell HM. Autophagy in Helicobacter pylori infection and related gastric cancer. Helicobacter 2015; 20:353–369.
   PubMed Web of Science ®Google Scholar
• Songane M, Kleinnijenhuis J, Alisjahbana B, Sahiratmadja E, Parwati I, Oosting M, et al. Polymorphisms in autophagy genes and susceptibility to tuberculosis. PloS one 2012; 7:e41618.
   PubMed Web of Science ®Google Scholar
• Marchiando AM, Ramanan D, Ding Y, Gomez LE, Hubbard-Lucey VM, Maurer K, et al. A deficiency in the autophagy gene Atg16L1 enhances resistance to enteric bacterial infection. Cell host & microbe 2013; 14:216–224.
   PubMed Web of Science ®Google Scholar
• Germic N, Hosseini A, Stojkov D, Oberson K, Claus M, Benarafa C, et al. ATG5 promotes eosinopoiesis but inhibits eosinophil effector functions. Blood 2021; 137:2958–2969.
   PubMed Web of Science ®Google Scholar
• Inoue J, Nishiumi S, Fujishima Y, Masuda A, Shiomi H, Yamamoto K, et al. Autophagy in the intestinal epithelium regulates Citrobacter rodentium infection. Archives of biochemistry and biophysics 2012; 521:95–101.
   PubMed Web of Science ®Google Scholar
• Chauhan S, Mandell MA, Deretic V. IRGM governs the core autophagy machinery to conduct antimicrobial defense. Molecular cell 2015; 58:507–521.
   PubMed Web of Science ®Google Scholar
• Taylor GA, Huang HI, Fee BE, Youssef N, Jewell ML, Cantillana V, et al. Irgm1-deficiency leads to myeloid dysfunction in colon lamina propria and susceptibility to the intestinal pathogen Citrobacter rodentium. PLoS pathogens 2020; 16:e1008553.
   PubMed Web of Science ®Google Scholar
• Santoni M, Piva F, De Giorgi U, Mosca A, Basso U, Santini D, et al. Autophagic Gene Polymorphisms in Liquid Biopsies and Outcome of Patients with Metastatic Clear Cell Renal Cell Carcinoma. Anticancer research 2018; 38:5773–5782.
   PubMed Web of Science ®Google Scholar
• Wang M, Jing J, Li H, Liu J, Yuan Y, Sun L. The expression characteristics and prognostic roles of autophagy-related genes in gastric cancer. PeerJ 2021; 9:e10814.
   PubMed Web of Science ®Google Scholar
• Wan B, Liu B, Yu G, Huang Y, Lv C. Differentially expressed autophagy-related genes are potential prognostic and diagnostic biomarkers in clear-cell renal cell carcinoma. Aging 2019; 11:9025–9042.
   PubMedGoogle Scholar
• Mo S, Dai W, Xiang W, Li Y, Feng Y, Zhang L, et al. Prognostic and predictive value of an autophagy-related signature for early relapse in stages I-III colon cancer. Carcinogenesis 2019; 40:861–870.
   PubMed Web of Science ®Google Scholar
• Ren M, Wei CY, Wang L, Deng XY, Lu NH, Gu JY. Integration of individual prediction index based on autophagy-related genes and clinical phenomes in melanoma patients. Clinical and translational medicine 2020; 10:e132.
   PubMed Web of Science ®Google Scholar
• Wen J, Liu H, Wang L, Wang X, Gu N, Liu Z, et al. Potentially Functional Variants of ATG16L2 Predict Radiation Pneumonitis and Outcomes in Patients with Non-Small Cell Lung Cancer after Definitive Radiotherapy. Journal of thoracic oncology 2018; 13:660–675.
   PubMed Web of Science ®Google Scholar
• Bai H, He Y, Lin Y, Leng Q, Carrillo JA, Liu J, et al. Identification of a novel differentially methylated region adjacent to ATG16L2 in lung cancer cells using methyl-CpG binding domain protein-enriched genome sequencing. Genome 2021; 64:533–546.
   PubMed Web of Science ®Google Scholar
• Gewirtz DA. The four faces of autophagy: implications for cancer therapy. Cancer research 2014; 74:647–651.
   PubMed Web of Science ®Google Scholar
• Yuan J, Zhang N, Yin L, Zhu H, Zhang L, Zhou L, et al. Clinical Implications of the Autophagy Core Gene Variations in Advanced Lung Adenocarcinoma Treated with Gefitinib. Scientific reports 2017; 7:17814.
   PubMed Web of Science ®Google Scholar
• Yang Z, Liu Z. Potentially functional variants of autophagy-related genes are associated with the efficacy and toxicity of radiotherapy in patients with nasopharyngeal carcinoma. Molecular genetics & genomic medicine 2019; 7:e1030.
   PubMed Web of Science ®Google Scholar
• Shen M, Duan WM, Wu MY, Wang WJ, Liu L, Xu MD, et al. Participation of autophagy in the cytotoxicity against breast cancer cells by cisplatin. Oncology reports 2015; 34:359–367.
   PubMed Web of Science ®Google Scholar
• Palomino-Morales RJ, Oliver J, Gómez-García M, López-Nevot MA, Rodrigo L, Nieto A, et al. Association of ATG16L1 and IRGM genes polymorphisms with inflammatory bowel disease: a meta-analysis approach. Genes and immunity 2009; 10:356–364.
   PubMed Web of Science ®Google Scholar
• Murthy A, Li Y, Peng I, Reichelt M, Katakam AK, Noubade R, et al. A Crohn’s disease variant in Atg16l1 enhances its degradation by caspase 3. Nature 2014; 506:456–462.
   PubMed Web of Science ®Google Scholar
• Lassen KG, Kuballa P, Conway KL, Patel KK, Becker CE, Peloquin JM, et al. Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense. Proceedings of the National Academy of Sciences 2014; 111:7741–7746.
   Google Scholar
• Yang SK, Hong M, Zhao W, Jung Y, Baek J, Tayebi N, et al. Genome-wide association study of Crohn’s disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations. Gut 2014; 63:80–87.
   PubMed Web of Science ®Google Scholar
• Fuyuno Y, Yamazaki K, Takahashi A, Esaki M, Kawaguchi T, Takazoe M, et al. Genetic characteristics of inflammatory bowel disease in a Japanese population. Journal of gastroenterology 2016; 51:672–681.
   PubMed Web of Science ®Google Scholar
• Luu LDW, Popple G, Tsang SPW, Vinasco K, Hilmi I, Ng RT, et al. Genetic variants involved in innate immunity modulate the risk of inflammatory bowel diseases in an understudied Malaysian population. Journal of gastroenterology and hepatology 2021; n/a.
   PubMed Web of Science ®Google Scholar
• Lessard CJ, Sajuthi S, Zhao J, Kim K, Ice JA, Li H, et al. Identification of a Systemic Lupus Erythematosus Risk Locus Spanning ATG16L2, FCHSD2, and P2RY2 in Koreans. Arthritis & rheumatology 2016; 68:1197–1209.
   PubMedGoogle Scholar
• Molineros JE, Yang W, Zhou XJ, Sun C, Okada Y, Zhang H, et al. Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci. Human molecular genetics 2017; 26:1205–1216.
   PubMed Web of Science ®Google Scholar
• Grigoras CA, Ziakas PD, Jayamani E, Mylonakis E. ATG16L1 and IL23R variants and genetic susceptibility to crohn’s disease: mode of inheritance based on meta-analysis of genetic association studies. Inflammatory bowel diseases 2015; 21:768–776.
   PubMed Web of Science ®Google Scholar
• Ramos PS, Criswell LA, Moser KL, Comeau ME, Williams AH, Pajewski NM, et al. A comprehensive analysis of shared loci between systemic lupus erythematosus (SLE) and sixteen autoimmune diseases reveals limited genetic overlap. PLoS genetics 2011; 7:e1002406.
   PubMed Web of Science ®Google Scholar
• Richard-Miceli C, Criswell LA. Emerging patterns of genetic overlap across autoimmune disorders. Genome medicine 2012; 4:6.
   PubMed Web of Science ®Google Scholar
• Clarke AJ, Ellinghaus U, Cortini A, Stranks A, Simon AK, Botto M, et al. Autophagy is activated in systemic lupus erythematosus and required for plasmablast development. Annals of the rheumatic diseases 2015; 74:912–920.
   PubMed Web of Science ®Google Scholar
• Ishigaki K, Akiyama M, Kanai M, Takahashi A, Kawakami E, Sugishita H, et al. Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases. Nature genetics 2020; 52:669–679.
   PubMed Web of Science ®Google Scholar
• Mo JJ, Zhang W, Wen QW, Wang TH, Qin W, Zhang Z, et al. Genetic association analysis of ATG16L1 rs2241880, rs6758317 and ATG16L2 rs11235604 polymorphisms with rheumatoid arthritis in a Chinese population. International immunopharmacology 2021; 93:107378.
   PubMed Web of Science ®Google Scholar
• Saez-Atienzar S, Bandres-Ciga S, Langston RG, Kim JJ, Choi SW, Reynolds RH, et al. Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types. Science advances 2021; 7.
   PubMed Web of Science ®Google Scholar
• Caberlotto L, Nguyen TP, Lauria M, Priami C, Rimondini R, Maioli S, et al. Cross-disease analysis of Alzheimer’s disease and type-2 Diabetes highlights the role of autophagy in the pathophysiology of two highly comorbid diseases. Scientific reports 2019; 9:3965.
   PubMed Web of Science ®Google Scholar
• Sittler A, Muriel MP, Marinello M, Brice A, den Dunnen W, Alves S. Deregulation of autophagy in postmortem brains of Machado-Joseph disease patients. Neuropathology 2018; 38:113–124.
   PubMed Web of Science ®Google Scholar
• Yin L, Liu J, Dong H, Xu E, Qiao Y, Wang L, et al. Autophagy-related gene16L2, a potential serum biomarker of multiple sclerosis evaluated by bead-based proteomic technology. Neuroscience letters 2014; 562:34–38.
   PubMed Web of Science ®Google Scholar
• Igci M, Baysan M, Yigiter R, Ulasli M, Geyik S, Bayraktar R, et al. Gene expression profiles of autophagy-related genes in multiple sclerosis. Gene 2016; 588:38–46.
   PubMed Web of Science ®Google Scholar
• Liu TC, Kern JT, VanDussen KL, Xiong S, Kaiko GE, Wilen CB, et al. Interaction between smoking and ATG16L1T300A triggers Paneth cell defects in Crohn’s disease. The Journal of clinical investigation 2018; 128:5110–5122.
   PubMed Web of Science ®Google Scholar
• Matsuzawa-Ishimoto Y, Shono Y, Gomez LE, Hubbard-Lucey VM, Cammer M, Neil J, et al. Autophagy protein ATG16L1 prevents necroptosis in the intestinal epithelium. The Journal of experimental medicine 2017; 214:3687–3705.
   PubMed Web of Science ®Google Scholar
• Deuring JJ, Fuhler GM, Konstantinov SR, Peppelenbosch MP, Kuipers EJ, de Haar C, et al. Genomic ATG16L1 risk allele-restricted Paneth cell ER stress in quiescent Crohn’s disease. Gut 2014; 63:1081–1091.
   PubMed Web of Science ®Google Scholar
• Molineros JE, Yang W, Zhou X-j, Sun C, Okada Y, Zhang H, et al. Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci. Human molecular genetics 2017; 26:1205–1216.
   PubMed Web of Science ®Google Scholar
• Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic acids research 2017; 45:W98–W102.
   PubMed Web of Science ®Google Scholar