Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly

Abstract

Galloway–Mowat syndrome (GAMOS) is an autosomal-recessive disease characterized by the combination of early-onset nephrotic syndrome (SRNS) and microcephaly with brain anomalies. Here we identified recessive mutations in OSGEP, TP53RK, TPRKB, and LAGE3, genes encoding the four subunits of the KEOPS complex, in 37 individuals from 32 families with GAMOS. CRISPR–Cas9 knockout in zebrafish and mice recapitulated the human phenotype of primary microcephaly and resulted in early lethality. Knockdown of OSGEP, TP53RK, or TPRKB inhibited cell proliferation, which human mutations did not rescue. Furthermore, knockdown of these genes impaired protein translation, caused endoplasmic reticulum stress, activated DNA-damage-response signaling, and ultimately induced apoptosis. Knockdown of OSGEP or TP53RK induced defects in the actin cytoskeleton and decreased the migration rate of human podocytes, an established intermediate phenotype of SRNS. We thus identified four new monogenic causes of GAMOS, describe a link between KEOPS function and human disease, and delineate potential pathogenic mechanisms.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Whole-exome sequencing in 32 families with GAMOS identifies recessive mutations in four genes encoding KEOPS-complex subunits (LAGE3, OSGEP, TP53RK, and TPRKB).
Figure 2: TP53RK mutations abrogate interaction with TPRKB, and GAMOS mutations do not rescue the decrease in cell proliferation rate after knockdown of OSGEP or TP53RK.
Figure 3: Knockdown of OSGEP decreases t6A levels, and knockdown of OSGEP, TP53RK, or TPRKB inhibits nascent-protein synthesis and activates the UPR.
Figure 4: Knockdown of OSGEP, TP53RK, or TPRKB in human podocytes induces DDR signaling and subsequent apoptosis.
Figure 5: OSGEP and TP53RK colocalize with the ARP2/3 complex at the lamellipodia of podocytes, and knockdown disrupts the actin cytoskeleton and impairs cell migration.

Similar content being viewed by others

Accession codes

Accessions

NCBI Reference Sequence

Protein Data Bank

References

  1. Vodopiutz, J. et al. WDR73 mutations cause infantile neurodegeneration and variable glomerular kidney disease. Hum. Mutat. 36, 1021–1028 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Jinks, R.N. et al. Recessive nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum is caused by homozygous protein-truncating mutations of WDR73. Brain 138, 2173–2190 (2015).

    PubMed  PubMed Central  Google Scholar 

  3. Colin, E. et al. Loss-of-function mutations in WDR73 are responsible for microcephaly and steroid-resistant nephrotic syndrome: Galloway-Mowat syndrome. Am. J. Hum. Genet. 95, 637–648 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Hildebrandt, F. et al. A systematic approach to mapping recessive disease genes in individuals from outbred populations. PLoS Genet. 5, e1000353 (2009).

    PubMed  PubMed Central  Google Scholar 

  5. Chaki, M. et al. Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling. Cell 150, 533–548 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Wan, L.C. et al. Proteomic analysis of the human KEOPS complex identifies C14ORF142 as a core subunit homologous to yeast Gon7. Nucleic Acids Res. 45, 805–817 (2017).

    CAS  PubMed  Google Scholar 

  7. Daugeron, M.C. et al. Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs. Nucleic Acids Res. 39, 6148–6160 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. El Yacoubi, B. et al. A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J. 30, 882–893 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Srinivasan, M. et al. The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A. EMBO J. 30, 873–881 (2011).

    CAS  PubMed  Google Scholar 

  10. Yarian, C. et al. Accurate translation of the genetic code depends on tRNA modified nucleosides. J. Biol. Chem. 277, 16391–16395 (2002).

    CAS  PubMed  Google Scholar 

  11. Downey, M. et al. A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator. Cell 124, 1155–1168 (2006).

    CAS  PubMed  Google Scholar 

  12. Oberto, J. et al. Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance. Nucleic Acids Res. 37, 5343–5352 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Kisseleva-Romanova, E. et al. Yeast homolog of a cancer-testis antigen defines a new transcription complex. EMBO J. 25, 3576–3585 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Hecker, A. et al. The universal Kae1 protein and the associated Bud32 kinase (PRPK), a mysterious protein couple probably essential for genome maintenance in Archaea and Eukarya. Biochem. Soc. Trans. 37, 29–35 (2009).

    CAS  PubMed  Google Scholar 

  15. Peterson, D. et al. A chemosensitization screen identifies TP53RK, a kinase that restrains apoptosis after mitotic stress. Cancer Res. 70, 6325–6335 (2010).

    CAS  PubMed  Google Scholar 

  16. Sadowski, C.E. et al. A single-gene cause in 29.5% of cases of steroid-resistant nephrotic syndrome. J. Am. Soc. Nephrol. 26, 1279–1289 (2015).

    CAS  PubMed  Google Scholar 

  17. Halbritter, J. et al. Identification of 99 novel mutations in a worldwide cohort of 1,056 patients with a nephronophthisis-related ciliopathy. Hum. Genet. 132, 865–884 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Hildebrandt, F. & Heeringa, S.F. Specific podocin mutations determine age of onset of nephrotic syndrome all the way into adult life. Kidney Int. 75, 669–671 (2009).

    CAS  PubMed  Google Scholar 

  19. Edvarson, S. et al. tRNA N6-adenosine threonylcarbamoyltransferase defect due to KAE1/TCS3 (OSGEP) mutation manifest by neurodegeneration and renal tubulopathy. Eur. J. Hum. Genet. 25, 545–551 (2017).

    Google Scholar 

  20. Mao, D.Y. et al. Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine. Mol. Cell 32, 259–275 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Hecker, A. et al. Structure of the archaeal Kae1/Bud32 fusion protein MJ1130: a model for the eukaryotic EKC/KEOPS subcomplex. EMBO J. 27, 2340–2351 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Zhang, W. et al. Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex. Nucleic Acids Res. 43, 3358–3372 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Thiaville, P.C. et al. Global translational impacts of the loss of the tRNA modification t6A in yeast. Microb. Cell 3, 29–45 (2016).

    CAS  PubMed  Google Scholar 

  24. Nedialkova, D.D. & Leidel, S.A. Optimization of codon translation rates via tRNA modifications maintains proteome integrity. Cell 161, 1606–1618 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Laguesse, S. et al. A dynamic unfolded protein response contributes to the control of cortical neurogenesis. Dev. Cell 35, 553–567 (2015).

    CAS  PubMed  Google Scholar 

  26. Schröder, M. & Kaufman, R.J. Divergent roles of IRE1alpha and PERK in the unfolded protein response. Curr. Mol. Med. 6, 5–36 (2006).

    PubMed  Google Scholar 

  27. O'Driscoll, M. & Jeggo, P.A. The role of the DNA damage response pathways in brain development and microcephaly: insight from human disorders. DNA Repair (Amst.) 7, 1039–1050 (2008).

    CAS  Google Scholar 

  28. Griffith, E. et al. Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling. Nat. Genet. 40, 232–236 (2008).

    CAS  PubMed  Google Scholar 

  29. Ameziane, N. et al. A novel Fanconi anaemia subtype associated with a dominant-negative mutation in RAD51. Nat. Commun. 6, 8829 (2015).

    CAS  PubMed  Google Scholar 

  30. O'Driscoll, M., Ruiz-Perez, V.L., Woods, C.G., Jeggo, P.A. & Goodship, J.A. A splicing mutation affecting expression of ataxia-telangiectasia and Rad3-related protein (ATR) results in Seckel syndrome. Nat. Genet. 33, 497–501 (2003).

    CAS  PubMed  Google Scholar 

  31. Wharram, B.L. et al. Podocyte depletion causes glomerulosclerosis: diphtheria toxin-induced podocyte depletion in rats expressing human diphtheria toxin receptor transgene. J. Am. Soc. Nephrol. 16, 2941–2952 (2005).

    CAS  PubMed  Google Scholar 

  32. Costessi, A. et al. The human EKC/KEOPS complex is recruited to Cullin2 ubiquitin ligases by the human tumour antigen PRAME. PLoS One 7, e42822 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Kristensen, A.R., Gsponer, J. & Foster, L.J. A high-throughput approach for measuring temporal changes in the interactome. Nat. Methods 9, 907–909 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Suraneni, P. et al. The Arp2/3 complex is required for lamellipodia extension and directional fibroblast cell migration. J. Cell Biol. 197, 239–251 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Faul, C., Asanuma, K., Yanagida-Asanuma, E., Kim, K. & Mundel, P. Actin up: regulation of podocyte structure and function by components of the actin cytoskeleton. Trends Cell Biol. 17, 428–437 (2007).

    CAS  PubMed  Google Scholar 

  36. Gee, H.Y. et al. ARHGDIA mutations cause nephrotic syndrome via defective RHO GTPase signaling. J. Clin. Invest. 123, 3243–3253 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Gee, H.Y. et al. KANK deficiency leads to podocyte dysfunction and nephrotic syndrome. J. Clin. Invest. 125, 2375–2384 (2015).

    PubMed  PubMed Central  Google Scholar 

  38. Ashraf, S. et al. ADCK4 mutations promote steroid-resistant nephrotic syndrome through CoQ10 biosynthesis disruption. J. Clin. Invest. 123, 5179–5189 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Seelow, D., Schuelke, M., Hildebrandt, F. & Nürnberg, P. HomozygosityMapper: an interactive approach to homozygosity mapping. Nucleic Acids Res. 37, W593–W599 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. MacArthur, D.G. et al. Guidelines for investigating causality of sequence variants in human disease. Nature 508, 469–476 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Halbritter, J. et al. High-throughput mutation analysis in patients with a nephronophthisis-associated ciliopathy applying multiplexed barcoded array-based PCR amplification and next-generation sequencing. J. Med. Genet. 49, 756–767 (2012).

    CAS  PubMed  Google Scholar 

  43. Montague, T.G., Cruz, J.M., Gagnon, J.A., Church, G.M. & Valen, E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 42, W401–W407 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Gagnon, J.A. et al. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One 9, e98186 (2014).

    PubMed  PubMed Central  Google Scholar 

  45. Fu, Y., Sander, J.D., Reyon, D., Cascio, V.M. & Joung, J.K. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 32, 279–284 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Meeker, N.D., Hutchinson, S.A., Ho, L. & Trede, N.S. Method for isolation of PCR-ready genomic DNA from zebrafish tissues. Biotechniques 43, 610–614 (2007).

    CAS  PubMed  Google Scholar 

  47. Vouillot, L., Thélie, A. & Pollet, N. Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3 (Bethesda) 5, 407–415 (2015).

    CAS  PubMed Central  Google Scholar 

  48. Brinkman, E.K., Chen, T., Amendola, M. & van Steensel, B. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res. 42, e168 (2014).

    PubMed  PubMed Central  Google Scholar 

  49. Kelley, L.A., Mezulis, S., Yates, C.M., Wass, M.N. & Sternberg, M.J. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Lipecka, J. et al. Sensitivity of mass spectrometry analysis depends on the shape of the filtration unit used for filter aided sample preparation (FASP). Proteomics 16, 1852–1857 (2016).

    CAS  PubMed  Google Scholar 

  51. Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).

    CAS  PubMed  Google Scholar 

  52. Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016).

    CAS  PubMed  Google Scholar 

  53. Saleem, M.A. et al. A conditionally immortalized human podocyte cell line demonstrating nephrin and podocin expression. J. Am. Soc. Nephrol. 13, 630–638 (2002).

    CAS  PubMed  Google Scholar 

  54. Thüring, K., Schmid, K., Keller, P. & Helm, M. Analysis of RNA modifications by liquid chromatography-tandem mass spectrometry. Methods 107, 48–56 (2016).

    PubMed  Google Scholar 

  55. Touzot, F. et al. Function of Apollo (SNM1B) at telomere highlighted by a splice variant identified in a patient with Hoyeraal-Hreidarsson syndrome. Proc. Natl. Acad. Sci. USA 107, 10097–10102 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We are grateful to the families and participating individuals for their contribution. We thank the Yale Center for Mendelian Genomics (U54HG006504) and the Care4Rare Canada Consortium for WES. We acknowledge D. Ogino (Yamagata University) for providing the nephrology data for patient B60, H. Sartelet (Département de Pathologie, CHU-Sainte-Justine, Université de Montréal) for providing pathology pictures from the renal biopsy from patient B80, S. Blaser (Hospital for Sick Children, Department of Pediatrics, Division of Neuroradiology, University of Toronto) for providing cranial imaging for patient DC, and S. Ameli (Children's Medical Center, Tehran University of Medical Sciences) for providing DNA samples of family B50. We thank A. Reis and A. Ekici (Institute of Human Genetics, University of Erlangen-Nuremberg) for supporting the initial GAMOS mapping study conducted by M.Z. We thank D. Libri (Institut Jacques Monod) and M. Saleem (University of Bristol) for reagents. This research was supported by funding from the National Institutes of Health (DK076683) and the Howard Hughes Medical Institute to F.H. F.H. was also supported as the William E. Harmon Professor. W.T. was supported by the ASN Foundation for Kidney Research. B. Behnam was supported in part by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (Common Fund). N.D.R., S.V. and B. Callewaert were supported as a research fellow, a postdoctoral research fellow, and a senior clinical investigator, respectively, of the Fund for Scientific Research, Flanders. E.W. was supported by the German National Academy of Sciences Leopoldina (LPDS-2015-07). H.Y.G. was supported by the National Research Foundation of Korea, Ministry of Science, ICT and Future planning (2015R1D1A1A01056685) and by the Yonsei University College of Medicine (2015-32-0047). M.T.F.W. was supported by K08-DK095994-05 (NIH) and the Children′s Clinical Research Advisory Committee (CCRAC), Children′s Medical Center, Dallas. M.B. was supported by a Senior Research Scholar Award from Fonds de la Recherche du Québec-Santé (FRQS) and a grant from the Canadian Institutes for Health Research (MOP-84470). O.S.-F. was supported by a KRESCENT Post-Doctoral Fellowship and a McGill Integrated Cancer Research Training (MICRTP) fellowship. T.J.-S. was supported by grant Jo 1324/1-1 from the Deutsche Forschungsgemeinschaft (DFG). T.H. was supported by the German Research Foundation, DFG fellowship (HE 7456/1-1). C.A. was supported by grants from the Agence Nationale de la Recherche (GenPod project ANR-12- BSV1-0033.01), the European Union's Seventh Framework Programme (FP7/2007-2013/no 305608- EURenOmics), the Fondation Recherche Médicale (DEQ20150331682) and the 'Investissements d'avenir' program (ANR-10-IAHU-01). M.F. was supported by grants from the Spanish Society of Nephrology and the Catalan Society of Nephrology. M.D.S. acknowledges financial support from the Department of Health by the National Institute for Health Research (NIHR) comprehensive Biomedical Research Centre award to Guy's & St Thomas' NHS Foundation Trust in partnership with King's College London and King's College Hospital NHS Foundation Trust. M.Z. was supported by the Deutsche Forschungsgemeinschaft (SFB423). Work in the laboratory of P.C.D. was supported by the Singapore National Research Foundation under the Singapore–MIT Alliance for Research and Technology, the National Institute of Environmental Health Science (ES017010, ES022858, ES002109) and the National Science Foundation (MCB-1412379). F.O. was supported by the European Community's Seventh Framework Programme (FP7/2007-2013) (EURenOmics; grant 2012-305608). The Nephrogenetics Laboratory at Hacettepe University was established by the Hacettepe University Infrastructure Project (grant 06A101008). P.M.G. was supported by a COBRE Grant (P30 GM110766). C.A.H. was supported by the Dutch Kidney Foundation. S.A.L. was supported by the Max Planck Society and the European Research Council (ERC-2012-StG 310489-tRNAmodi). A. Poduri was supported by the Boston Children's Hospital Translational Research Program.

Author information

Authors and Affiliations

Authors

Contributions

J.R., G. Mollet, D. Schapiro, W.T., O.G., S.A., D. Schanze, N.B., G. Martin, S.L., M.F., B.M., S.V., N.D.R., M.A., T.H., S. Shril, E.W., H.Y.G., W.-I.C., C.E.S., W.L.P., J.K.W., A.D., V.M., A.B., R.E.S., P.M.G., S.M., R.P.L., M.Z., C.A., and F.H. generated total-genome linkage data, performed exome capture with massively parallel sequencing, and performed whole-exome evaluation and mutation analysis. D.A.B. generated knockdown cell lines, performed in vitro studies (proliferation, survival, ER stress, DDR, apoptosis, and migration) in immortalized human podocytes, and performed coimmunoprecipitation experiments. D.A.B. and J.A.L. performed immunofluorescence and subcellular localization studies in tissue sections and cell lines by confocal microscopy. J.R., W.T., J.K.W., D.A.B., O.B., B. Behnam, B. Beeson, M. Bruce, G.-S.C., J.-H.C., M.T.C., P.E.G., C.K.-B., Y.-Y.K., W.-m.L., E.L., S.-P.L., R.O.L., A.M., M.M., K.N., F.O., M.P., A. Prytula, C.P., P. Rump, T.S., M.D.S., N.A.S., K. Soulami, W.-H.T., J.-D.T., D.A.S., R.T., U.V., D.H.V., N.V., J.L.W., K.J.W., M.T.F.W., S.-N.W., P.K., D.C., D.M., C.-H.C., C.-H.H., J.A.K., E.R.R., B. Callewaert, M.Z., C.A., and F.H. recruited patients and gathered detailed clinical information for the study. M.-C.D., B. Collinet, D.L., T.B., and H.v.T. performed yeast complementation experiments and 3D modeling of the KEOPS complex. I.C.G. and G. Mollet performed proteomic studies in human podocyte cell lines P. Revy performed telomere restriction-fragment assays. T.J.-S., J.M.S., C.A.H., J.F.P.U., A. Poduri, and G.T. performed zebrafish experiments and data analysis. O.S.-F. and M. Bouchard performed CRISPR–Cas9 knockout in mouse embryos and subsequent embryonic phenotyping. M.-C.D., B. Collinet, D.L., T.B., A.-C.B., S. Sanquer, and H.v.T. performed t6A analysis in Δkae1 yeast strains. P.C.D. and J.F.H. performed t6A analysis in human podocytes. K. Scharmann, S.D.K., and S.A.L. contributed to the t6A analysis. All authors critically reviewed the paper. M.Z., C.A. and F.H. conceived and directed the project and wrote the paper, with the help of D.A.B., G. Mollet, and H.v.T.

Corresponding authors

Correspondence to Martin Zenker, Corinne Antignac or Friedhelm Hildebrandt.

Ethics declarations

Competing interests

M.T.C., A.B., and R.E.S. are employees of GeneDx. F.H. is a cofounder of Goldfinch Biopharma, Inc. and receives royalties from Claritas Genomics. The other authors declare that they have no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–28 and Supplementary Tables 1–3. (PDF 6522 kb)

Life Sciences Reporting Summary (PDF 193 kb)

Supplementary Data

Unedited western blots. (PDF 3090 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Braun, D., Rao, J., Mollet, G. et al. Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly. Nat Genet 49, 1529–1538 (2017). https://doi.org/10.1038/ng.3933

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.3933

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing