The role of ATG16L1 in bacterial-induced autophagy
Bibliographic record
Abstract
Recent genome wide association studies have implicated variants of the autophagy gene ATG16L1 in Crohn disease pathogenesis. However, few functional studies translating this risk association have been published to date. The aim of this study was to validate the role of ATG16L1 in autophagy induction in vitro in response to the intracellular pathogen Shigella flexneri and bacterial associated ligands. Epithelial cells (MDAMC) stably transformed to produce green fluorescent light chain 3 (GFP-LC3), a known marker of autophagy, were transduced with lentiviral short hairpin RNA (shRNA) constructs, interfering with ATG16L1 expression. Following transduction, cells were examined for their ability to control infection of wild-type (WT) or IcsB mutant (ΔIcsB) S. flexneri using gentamicin protection assays. WT S. flexneri is reported to evade autophagy whereas ΔIcsB S. flexneri is more susceptible to autophagy. Cells treated with rapamycin (15μg/1×106 cells) served as positive controls for autophagy. Lymphoblast cell lines (LCLs) from participants in the HapMap project who were homozygous for either risk (G) or protective (A) ATG16L1 alleles were transduced with a GFP-LC3 expressing lentivirus construct and subsequently treated with rapamycin, muramyl dipeptide (MDP) and peptidoglycan (PG). Autophagy induction was again assessed using confocal microscopy. Suppression of ATG16L1 using shRNA constructs was confirmed by immunofluorescence microscopy and ATG16L1 antibody by Western blotting. ATG16L1 suppression resulted in a profound reduction of autophagy induction following rapamycin treatment. Autophagosome formation around either WT or ΔIcsB S. flexneri was almost completely suppressed in shRNA transduced cells compared with control cells. Autophagosome formation in LCLs was also observed following both MDP and PG treatments. However, cells from a GG lineage had a mean 34% less autophagosomes/cell compared with AA cells, indicating a less efficient autophagy response to these bacterial ligands. This study demonstrates that ATG16L1 is essential to autophagosome formation in response to intracellular bacterial infection in epithelial cells. We also reveal a reduced autophagy response to NOD receptor ligands in myeloid cells homozygous for the Crohn disease associated (G) ATG16L1 allele, which may be of importance in disease pathogenesis. CAG/CIHR/CCFC
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".