The role of ATG16L2 in autophagy and disease

Figures & data

Figure 1. The phylogenetic relationship, domain structure comparison and tissue gene expression of ATG16L1 and ATG16L2. (A) The phylogenetic relationship of ATG16L1 and ATG16L2 sequences in selected species from UniProt. The maximum likelihood tree was constructed using Mega X and illustrates two distinct ATG16L branches corresponding to ATG16L1 (blue) and ATG16L2 (green). Bootstrap values are shown. UniProt identifiers are shown in brackets. (B) Comparison of the domain structures in human ATG16L1 and ATG16L2. The UniProt canonical isoform for each protein (ATG16L1β and ATG16L2β) is depicted with the major domains and SNPs highlighted. The three ATG16L regions (N, M and C) are shown. Known domains and interaction sites are highlighted in colored blocks (coiled coil, yellow; ATG5 binding site, green; RB1CC1, blue; and WIPI2, magenta). ATG16L1 and RAB33B interact with ATG16L1 and L2 in the M-region as shown. ATG16L2 rs11235604 (R220W) and ATG16L1 rs2241880 (T300A) are displayed in red. (C) Heatmap illustrating the expression of ATG16L1 and ATG16L2 in different tissues. The color indicates the relative expression, in transcripts per million (TPM), of ATG16L1 and ATG16L2. The gene expression data shown in this manuscript were obtained from the Genotype-Tissue Expression (GTEx) Multi gene query[31] on 31/08/2021.

Figure 2. Schematic overview summarizing the role of ATG16L1 and ATG16L2 in autophagy. (A) ATG16L1 (purple circle) complexes with ATG12–ATG5 (red and blue circles, respectively), leads to LC3 lipidation and autophagosome formation. (B) Effect of ATG16L2 overexpression. ATG16L2 (orange circle) is a putative dominant negative inhibitor of ATG16L1, therefore, ATG16L2 competes with ATG16L1 to bind with ATG12–ATG5 complexes. ATG16L2 lacks WIPI2 and RB1CC1 interaction sites, hence ATG12–ATG5-ATG16L2 complexes are not recruited to the phagophore membrane resulting in reduced LC3 lipidation and autophagy.

Table 1. ATG16L2 SNPs implicated in human disease

SNP	Nucleotide change	Gene consequence	Disease	Population	Cases	Controls	OR	95% CI	P-value	Risk/ Protective	Reference
rs11235667	A>G	-	Crohn disease	Malaysian	36	75	3.83	1.03-14.2	0.04	Risk	[66]
rs11235667	A>G	-	Crohn disease	Korean	2311	2442	1.46	1.28-1.66	7.15x10^−09	Risk	[64]
rs11235667	A>G	-	Systemic lupus erythematosus	Korean	1174	4246	0.59	0.5-0.71	1.03x10^−08	Protective	[67]
rs11235604	C>T	Missense	Systemic lupus erythematosus	Han Chinese/ Asian	11,656	23,968	0.78	0.71-0.85	8.87x10^−12	Protective	[83]
rs11235604	C>T	Missense	Crohn disease	Han Chinese	363	486	1.31	1.04-1.67	0.02	Risk	[18]
rs11235604	C>T	Missense	Inflammatory Bowel Diseases	Japanese	2052	7484	1.4	1.18-2.01	5.02x10^−09	Risk	[65]
rs11235604	C>T	Missense	Rheumatoid arthritis	Han Chinese	594	604	2.16*	1.24–3.79	6.11x10^−03	Risk	[74]
rs11235604	C>T	Missense	Susceptibility to Tuberculosis	Indonesian	1022	952	-	-	NS	NS	[44]
rs11235604	C>T	Missense	Coronary artery disease	Japanese	29,319	183,134	0.91	0.88-0.94	1.73x10^−08	Protective	[73]

*Only significant when stratified with ATG16L1 rs2241880 or rs6758317. NS=not significant

Table 2. ATG16L2 SNPs associated with cancer and efficacy of cancer treatments

SNP	Nucleotide change	Gene consequence	Association with cancer	Population	Cases	OR/HR	95% CI	P-value	Risk/ Protective	Reference
rs10751215	T>C	Intron variant	Risk of developing clear cell renal cell carcinoma	Italian	40	0.48	NR	0.024	Protective (decreased risk of developing the disease)	[50]
rs11235604	C>T	Missense	Overall survival of lung adenocarcinoma treated with gefitinib	Chinese	108	1.78*	1.07-2.96	0.028	Risk (decreased overall survival)	[58]
rs10898880	A>C	2-kb upstream variant	Overall survival after radiation in non–small cell lung cancer	North American	393	0.64*	0.48–0.86	0.003	Protective (increased overall survival)	[55]
rs10898880	A>C	2-kb upstream variant	Radiation pneumonitis after radiation in non–small cell lung cancer	North American	393	1.8*	1.04–3.12	0.037	Risk (increased risk of radiation pneumonitis)	[55]
rs10898880	A>C	2-kb upstream variant	Efficacy of radiotherapy in nasopharyngeal carcinoma	Chinese	468	1.84	1.32-2.56	<0.001	Protective (increased efficacy of radiotherapy)	[59]
rs10898880	A>C	2-kb upstream variant	Toxicity of radiotherapy in nasopharyngeal carcinoma	Chinese	468	1.51	1.1-2.06	0.01	Risk (increased toxicity of radiotherapy)	[59]
rs1126205	G>T	2-kb upstream variant	Efficacy of radiotherapy in nasopharyngeal carcinoma	Chinese	468	1	0.97–1.03	0.82	NS	[59]
rs1126205	G>T	2-kb upstream variant	Toxicity of Radiotherapy in nasopharyngeal carcinoma	Chinese	468	0.92	0.76–1.12	0.413	NS	[59]

*Indicates hazard ratios

NR=not reported. NS=not significant

Figure 3. Heat map illustrating significant upregulation or downregulation of ATG16L2 reported in different cancer and neurodegenerative diseases from published studies and/or Gene expression profiling interactive analysis (GEPIA) [84]. Color is indicative of significant upregulation (red) or downregulation (blue) not the magnitude of the fold-change. For the specified cancers and neurodegenerative diseases, no significant differences in ATG16L1 expression were reported in the published studies and/or GEPIA.

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

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

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

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 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

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

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

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

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

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

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

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

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

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

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