Article | Published:

A Crohn’s disease variant in Atg16l1 enhances its degradation by caspase 3

Nature volume 506, pages 456462 (27 February 2014) | Download Citation



Crohn’s disease is a debilitating inflammatory bowel disease (IBD) that can involve the entire digestive tract. A single-nucleotide polymorphism (SNP) encoding a missense variant in the autophagy gene ATG16L1 (rs2241880, Thr300Ala) is strongly associated with the incidence of Crohn’s disease. Numerous studies have demonstrated the effect of ATG16L1 deletion or deficiency; however, the molecular consequences of the Thr300Ala (T300A) variant remains unknown. Here we show that amino acids 296–299 constitute a caspase cleavage motif in ATG16L1 and that the T300A variant (T316A in mice) significantly increases ATG16L1 sensitization to caspase-3-mediated processing. We observed that death-receptor activation or starvation-induced metabolic stress in human and murine macrophages increased degradation of the T300A or T316A variants of ATG16L1, respectively, resulting in diminished autophagy. Knock-in mice harbouring the T316A variant showed defective clearance of the ileal pathogen Yersinia enterocolitica and an elevated inflammatory cytokine response. In turn, deletion of the caspase-3-encoding gene, Casp3, or elimination of the caspase cleavage site by site-directed mutagenesis rescued starvation-induced autophagy and pathogen clearance, respectively. These findings demonstrate that caspase 3 activation in the presence of a common risk allele leads to accelerated degradation of ATG16L1, placing cellular stress, apoptotic stimuli and impaired autophagy in a unified pathway that predisposes to Crohn’s disease.

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The authors would like to thank M. Zepeda for coordinating human donors, R. A. Flavell for providing Casp3-knockout mice, J. E. Cupp, W. Ortmann, J. Borneo, J. Ruan, J. Ting and L. Rangell for technical assistance, D. Holmes, N. Kayagaki, C. J. Spooner, M. E. Keir, A. Ashkenazi and T. W. Behrens for critical evaluation of the manuscript.

Author information


  1. Department of Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA

    • Aditya Murthy
    • , Yun Li
    • , Ivan Peng
    • , Rajkumar Noubade
    • , Jason DeVoss
    •  & Menno van Lookeren Campagne
  2. Department of Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA

    • Mike Reichelt
    • , Anand Kumar Katakam
    •  & Lauri Diehl
  3. Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA

    • Merone Roose-Girma
  4. ITGR Human Genetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA

    • Robert R. Graham


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A.M. and M.v.L.C. conceptualized the study and designed experiments; A.M. and Y.L. conducted experiments; I.P. and J.D. performed in vivo administration of Y. enterocolitica; M.R. and A.K.K. performed electron microscopy; R.N. performed 35S pulse-chase assays on ATG16L1; M.R.-G. designed the T316A knock-in construct and coordinated generation of the mutant mouse; L.D. performed histological analysis; R.R.G. provided EBV-transformed cells, guided HapMap analysis and discussed the study; A.M. and M.v.L.C. wrote the manuscript.

Competing interests

All authors are employees of Genentech, Inc., a for-profit institution.

Corresponding author

Correspondence to Menno van Lookeren Campagne.

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    Supplementary Tables

    This file contains Supplementary Tables 1-5. The following is extra information for Supplementary Table 1: Comparison of the reference (A) and risk (G) allele frequency indicates that the Crohn’s disease risk associated G allele is the major allele in northern and western Europeans (CEU, frequency of 0.567), Tuscan Italians (TSI, frequency of 0.540) and near dominant in Gujarati Indians (GIH, frequency of 0.480).

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