NLRs (nucleotide-binding domain and leucine-rich repeats) belong to a large family of cytoplasmic sensors that regulate an extraordinarily diverse range of biological functions. One of these functions is to contribute to immunity against infectious diseases, but dysregulation of their functional activity leads to the development of inflammatory and autoimmune diseases1. Cytoplasmic innate immune sensors, including NLRs, are central regulators of intestinal homeostasis2,3,4,5,6,7,8,9. NLRC3 (also known as CLR16.2 or NOD3) is a poorly characterized member of the NLR family and was identified in a genomic screen for genes encoding proteins bearing leucine-rich repeats (LRRs) and nucleotide-binding domains10,11. Expression of NLRC3 is drastically reduced in the tumour tissue of patients with colorectal cancer compared to healthy tissues12, highlighting an undefined potential function for this sensor in the development of cancer. Here we show that mice lacking NLRC3 are hyper-susceptible to colitis and colorectal tumorigenesis. The effect of NLRC3 is most dominant in enterocytes, in which it suppresses activation of the mTOR signalling pathways and inhibits cellular proliferation and stem-cell-derived organoid formation. NLRC3 associates with PI3Ks and blocks activation of the PI3K-dependent kinase AKT following binding of growth factor receptors or Toll-like receptor 4. These findings reveal a key role for NLRC3 as an inhibitor of the mTOR pathways, mediating protection against colorectal cancer.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

    , & NLRs at the intersection of cell death and immunity. Nat. Rev. Immunol. 8, 372–379 (2008)

  2. 2.

    et al. The NLRP3 inflammasome protects against loss of epithelial integrity and mortality during experimental colitis. Immunity 32, 379–391 (2010)

  3. 3.

    , , , & IL-18 production downstream of the Nlrp3 inflammasome confers protection against colorectal tumor formation. J. Immunol. 185, 4912–4920 (2010)

  4. 4.

    et al. The NLRP3 inflammasome functions as a negative regulator of tumorigenesis during colitis-associated cancer. J. Exp. Med. 207, 1045–1056 (2010)

  5. 5.

    et al. NLRP12 suppresses colon inflammation and tumorigenesis through the negative regulation of noncanonical NF-κB signaling. Immunity 36, 742–754 (2012)

  6. 6.

    et al. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 145, 745–757 (2011)

  7. 7.

    et al. Critical role for the DNA sensor AIM2 in stem cell proliferation and cancer. Cell 162, 45–58 (2015)

  8. 8.

    et al. Inflammasome-independent role of AIM2 in suppressing colon tumorigenesis via DNA-PK and Akt. Nat. Med. 21, 906–913 (2015)

  9. 9.

    et al. The NOD-like receptor NLRP12 attenuates colon inflammation and tumorigenesis. Cancer Cell 20, 649–660 (2011)

  10. 10.

    , , & Cutting edge: CATERPILLER: a large family of mammalian genes containing CARD, pyrin, nucleotide-binding, and leucine-rich repeat domains. J. Immunol. 169, 4088–4093 (2002)

  11. 11.

    et al. CATERPILLER 16.2 (CLR16.2), a novel NBD/LRR family member that negatively regulates T cell function. J. Biol. Chem. 280, 18375–18385 (2005)

  12. 12.

    et al. Expression profile of innate immune receptors, NLRs and AIM2, in human colorectal cancer: correlation with cancer stages and inflammasome components. Oncotarget 6, 33456–33469 (2015)

  13. 13.

    et al. The innate immune sensor NLRC3 attenuates Toll-like receptor signaling via modification of the signaling adaptor TRAF6 and transcription factor NF-κB. Nat. Immunol. 13, 823–831 (2012)

  14. 14.

    et al. NLRC3, a member of the NLR family of proteins, is a negative regulator of innate immune signaling induced by the DNA sensor STING. Immunity 40, 329–341 (2014)

  15. 15.

    & Converging roles of caspases in inflammasome activation, cell death and innate immunity. Nat. Rev. Immunol. 16, 7–21 (2016)

  16. 16.

    & Making new contacts: the mTOR network in metabolism and signalling crosstalk. Nat. Rev. Mol. Cell Biol. 15, 155–162 (2014)

  17. 17.

    et al. Characterization of a 3-phosphoinositide-dependent protein kinase which phosphorylates and activates protein kinase Bα. Curr. Biol. 7, 261–269 (1997)

  18. 18.

    et al. Protein kinase B kinases that mediate phosphatidylinositol 3,4,5-trisphosphate-dependent activation of protein kinase B. Science 279, 710–714 (1998)

  19. 19.

    et al. Dual role of phosphatidylinositol-3,4,5-trisphosphate in the activation of protein kinase B. Science 277, 567–570 (1997)

  20. 20.

    et al. Ragulator–Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids. Cell 141, 290–303 (2010)

  21. 21.

    et al. mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H+-ATPase. Science 334, 678–683 (2011)

  22. 22.

    et al. Lipopolysaccharide activates Akt in human alveolar macrophages resulting in nuclear accumulation and transcriptional activity of β-catenin. J. Immunol. 166, 4713–4720 (2001)

  23. 23.

    , , , & Differential roles of Toll-like receptors in the elicitation of proinflammatory responses by macrophages. Ann. Rheum. Dis. 60 (Supp. 3), iii6–iii12 (2001)

  24. 24.

    et al. Phosphatidylinositol 3-kinase is involved in Toll-like receptor 4-mediated cytokine expression in mouse macrophages. Eur. J. Immunol. 33, 597–605 (2003)

  25. 25.

    et al. Molecular signatures of a disturbed nasal barrier function in the primary tissue of Wegener’s granulomatosis. Mucosal Immunol. 4, 564–573 (2011)

  26. 26.

    , , & An anti-inflammatory NOD-like receptor is required for microglia development. Cell Reports 5, 1342–1352 (2013)

  27. 27.

    , & Mouse genome engineering via CRISPR–Cas9 for study of immune function. Immunity 42, 18–27 (2015)

  28. 28.

    , & Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473–1475 (2014)

  29. 29.

    et al. Cutting edge: STING mediates protection against colorectal tumorigenesis by governing the magnitude of intestinal inflammation. J. Immunol. 193, 4779–4782 (2014)

  30. 30.

    et al. The transcription factor IRF1 and guanylate-binding proteins target activation of the AIM2 inflammasome by Francisella infection. Nat. Immunol. 16, 467–475 (2015)

  31. 31.

    et al. eIF4F is a nexus of resistance to anti-BRAF and anti-MEK cancer therapies. Nature 513, 105–109 (2014)

  32. 32.

    et al. Concerted activation of the AIM2 and NLRP3 inflammasomes orchestrates host protection against Aspergillus infection. Cell Host Microbe 17, 357–368 (2015)

Download references


We thank the Transgenic Gene Knockout Shared Resource at St. Jude Children’s Research Hospital (SJCRH) for assistance with knockout mouse generation. Images were acquired at the SJCRH Cell & Tissue Imaging Center, which is supported by SJCRH and NCI grant P30 CA021765-35. Work from our laboratory is supported by the US National Institutes of Health (grants AI101935, AI124346, AR056296 and CA163507 to T.-D.K.), ALSAC (to T.-D.K.), and the ExC306 Inflammation at Interfaces, the DFG SFB 877 B9 and DFG SFB1182 C2 projects (to P.R.). S.M.M. is supported by the R. G. Menzies Early Career Fellowship from the National Health and Medical Research Council of Australia.

Author information

Author notes

    • Rajendra Karki
    •  & Si Ming Man

    These authors contributed equally to this work.


  1. Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA

    • Rajendra Karki
    • , Si Ming Man
    • , R. K. Subbarao Malireddi
    • , Sannula Kesavardhana
    • , Qifan Zhu
    • , Amanda R. Burton
    • , Bhesh Raj Sharma
    • , Xiaopeng Qi
    • , Stephane Pelletier
    •  & Thirumala-Devi Kanneganti
  2. Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA

    • Qifan Zhu
  3. Embryonic Stem Cell Laboratory, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA

    • Stephane Pelletier
  4. Animal Resources Center and the Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA

    • Peter Vogel
  5. Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, D-24105 Kiel, Germany

    • Philip Rosenstiel


  1. Search for Rajendra Karki in:

  2. Search for Si Ming Man in:

  3. Search for R. K. Subbarao Malireddi in:

  4. Search for Sannula Kesavardhana in:

  5. Search for Qifan Zhu in:

  6. Search for Amanda R. Burton in:

  7. Search for Bhesh Raj Sharma in:

  8. Search for Xiaopeng Qi in:

  9. Search for Stephane Pelletier in:

  10. Search for Peter Vogel in:

  11. Search for Philip Rosenstiel in:

  12. Search for Thirumala-Devi Kanneganti in:


R.K., S.M.M. and T.-D.K. conceptualized the study; R.K., S.M.M., R.K.S.M. and S.K. designed the methodology; R.K., S.M.M., R.K.S.M., S.K., Q.Z., B.R.S., A.R.B., X.Q., S.P. and P.V. performed the experiments; R.K., S.M.M., R.K.S.M., S.K., Q.Z. and P.V. conducted the analysis; R.K., S.M.M. and T.-D.K. wrote the manuscript; P.R. and T.-D.K. provided resources; T.-D.K. provided overall supervision.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Thirumala-Devi Kanneganti.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains the uncropped gel source data.

Excel files

  1. 1.

    Supplementary Data

    This file contains a list of primer sequences.

About this article

Publication history






Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.