Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy

Abstract

The polymorphism ATG16L1 T300A, associated with increased risk of Crohn's disease, impairs pathogen defense mechanisms including selective autophagy, but specific pathway interactions altered by the risk allele remain unknown. Here, we use perturbational profiling of human peripheral blood cells to reveal that CLEC12A is regulated in an ATG16L1-T300A-dependent manner. Antibacterial autophagy is impaired in CLEC12A-deficient cells, and this effect is exacerbated in the presence of the ATG16L1(∗)300A risk allele. Clec12a(-/-) mice are more susceptible to Salmonella infection, supporting a role for CLEC12A in antibacterial defense pathways in vivo. CLEC12A is recruited to sites of bacterial entry, bacteria-autophagosome complexes, and sites of sterile membrane damage. Integrated genomics identified a functional interaction between CLEC12A and an E3-ubiquitin ligase complex that functions in antibacterial autophagy. These data identify CLEC12A as early adaptor molecule for antibacterial autophagy and highlight perturbational profiling as a method to elucidate defense pathways in complex genetic disease.

Graphical abstract

Figure 1

Perturbational Profiling Reveals Genotype-Specific Transcriptional Responses, Including Differentially Regulated Genes that Are Required for Autophagy (A) Gene expression analysis of PBMCs isolated from healthy individuals after infection or stimulation with Borrelia burgdorferi (Bor), MDP, or Pam₃Cys (Pam). Heatmap shows log₂ (fold change) relative to mock-treated control. (B) Heatmap identifying transcripts exhibiting response differences to infection or immune stimuli, stratified by ATG16L1 T300A polymorphism status. (C) HeLa GFP-LC3 cells were transfected with indicated siRNAs and infected with DsRed-labeled Salmonella. The percentage of GFP-LC3+ Salmonella at 1 hr post-infection is shown. Data are shown as means ± SD; n = 75 cells per condition from three biological replicates. Data are representative of three independent experiments. (D) Representative epifluorescent microscopy images of HeLa cells used to generate data shown in (C). The scale bars represent 10 μm. (E) Western blot of HeLa cells transfected with the indicated siRNAs and treated with Torin E64D/PepA. Data are representative of three independent experiments. (F) CLEC12A rescue constructs indicating positions of synonymous mutations and location of targeting siRNA. (G) HeLa GFP-LC3 cells were transfected with control siRNA, CLEC12A siRNA1, or CLEC12A siRNA2 as well as CLEC12A rescue constructs (R1 or R2) and infected for 1 hr with DsRed-labeled Salmonella. Data are shown as mean ± SD; n = 75 per condition. Data are representative of three independent experiments. (H) HeLa cells from (G) were lysed, and HA-CLEC12A expression levels were assessed by western blot. Data are representative of three independent experiments. See also Figure S1.

Figure 2

CLEC12A Knockdown and the ATG16L1 T300A SNP Act Additively to Impair LC3-Bacteria Colocalization (A) Representative epifluorescent images showing impaired antibacterial autophagy in ATG16L1 KO HeLa cells complemented with the indicated ATG16L1 protein in the presence of control siRNA or CLEC12A siRNA. The scale bars represent 10 μm. (B) Percentage of LC3-Salmonella colocalization in WT HeLa cells, ATG16L1 KO HeLa cells, and ATG16L1 KO HeLa cells stably expressing ATG16L1^∗300T or ^∗300A alleles in the presence of control siRNA or CLEC12A siRNA. Data are shown as means ± SD; n = 75. Data shown are representative of three independent experiments. See also Figure S2.

Figure 3

Clec12a^−/− Mice Are More Susceptible to Salmonella Infection In Vivo (A) Confocal micrographs of LC3-Listeria colocalization in WT and Clec12a^−/− BMDMs at 1 hr post-infection. The scale bars represent 10 μm. (B) Quantification of LC3-Listeria colocalization in WT and Clec12a^−/− BMDMs. Data shown represent mean ± SD of n = 3 independent experiments; unpaired t test. ^∗∗p < 0.01. (C and D) Salmonella cfus quantified per gram of stool (C) and per organ (D) at 4 days post-infection are displayed. Data are shown as mean ± SD; ^∗∗p ≤ 0.01. Data are representative of at least two independent experiments (n = 9 for WT; n = 7 or 8 for Clec12a^−/−). (E) Clinical score for infected mice at 4 days post-infection. Data are shown as mean ± SD. Data are representative of at least two independent experiments. ^∗∗∗∗p < 0.0001; unpaired t test. (n = 14 for WT; n = 13 for Clec12a^−/−). (F) Survival curve for infected WT and Clec12a^−/− mice (n = 9 mice per genotype). See also Figure S3.

Figure 4

CLEC12A Associates with Bacteria Early after Entry into Host Cells and Restricts Intracellular Bacterial Replication (A) Gentamicin protection assay in HeLa cells showing fold replication of Salmonella in cells treated with the indicated siRNAs. Data are shown as mean ± SD; n = 6. Data are representative of four independent experiments. (B) Quantitation of CLEC12A-bacteria and LC3-bacteria colocalization at indicated time points. Data are shown as mean ± SD; n = 3 independent experiments. (C) Representative confocal micrographs of HeLa cells showing association of intracellular bacteria with GFP-CLEC12A at 20, 40, 60, and 80 min post-infection. The scale bars represent 10 μm. See also Figure S4.

Figure 5

CLEC12A Colocalizes with Autophagosome Proteins and Plays a Role in Pathogen Defense (A–C) Representative epifluorescent images of HeLa cells showing colocalization of (A) CLEC12A (green) and galectin 8 or galectin 3 (red) around intracellular Salmonella (blue), (B) GFP-CLEC12A (green) and NDP52 (red) around Salmonella (blue), and (C) endogenous CLEC12A (red) and GFP-LC3 (green) around Salmonella (blue). (D) CLEC12A or GFP-CLEC12A (green) and GABARAPL2 or ATG16L1 (red) around intracellular Salmonella (blue). Images are representative of three or more independent experiments. (E) Representative epifluorescent images of HeLa cells transfected with a control siRNA or a siRNA against CLEC12A and infected with DsRed-labeled Salmonella for 1 hr. (F) Quantitation of ubiquitin-bacteria colocalization at 1 hr post-infection in cells shown in (E). Data are shown as means ± SEM from three independent experiments. (G) Representative epifluorescent images of HeLa cells transfected and infected as in (E). (H) Quantitation of NDP52-bacteria colocalization at 1 hr post-infection in cells shown in (G). Data are shown as means ± SEM from three independent experiments. (I) Representative confocal micrographs of HeLa cells expressing GFP-CLEC12A. Cells were untreated or exposed to hypertonic media containing PEG 1000, followed by hypotonic shock. All scale bars represent 10 μm. See also Figure S5.

Figure 6

Integrated Systems Analysis Identifies KLHL9, NEDD8, and KLHL13 as CLEC12A-Interacting Antibacterial Autophagy Molecules (A) Gene expression analysis of WT and Clec12a^−/− BMDMs infected with Listeria for the indicated times. Heatmap shows log₂ (fold change) relative to uninfected WT BMDMs at indicated time points. Shown are the top ten most-significant upregulated and downregulated genes in Clec12a^−/− BMDMs compared to WT BMDMs. (B) Cluster analysis of 674 differentially expressed genes in Clec12a^−/− BMDMs versus WT BMDMs. (C) Schematic of integrated proteomic and transcriptomic approach to identify functionally relevant CLEC12A-interacting proteins. (D) Interactome analysis shows network of proteins identified from quantitative iTRAQ proteomics. Red box highlights the KLHL9-KLHL13-CUL3-NEDD8 complex interaction within the CLEC12A interactome. (E) HeLa GFP-LC3 cells were transfected with indicated siRNAs for 48 hr and then infected with DsRed-labeled Salmonella for 1 hr. The fraction of GFP-positive intracellular Salmonella is shown. Data are mean ± SD and are representative of three independent experiments. (F) Gentamicin protection assay in HeLa cells showing increased intracellular bacterial replication after 48 hr of knockdown of ATG16L1, KLHL9, NEDD8, or KLHL13. Data shown as mean ± SD; n = 4. Data are representative of three independent experiments. See also Figure S6 and Tables S1, S2, and S3.