Abstract

Histidine phosphorylation, the so-called hidden phosphoproteome, is a poorly characterized post-translational modification of proteins1,2. Here we describe a role of histidine phosphorylation in tumorigenesis. Proteomic analysis of 12 tumours from an mTOR-driven hepatocellular carcinoma mouse model revealed that NME1 and NME2, the only known mammalian histidine kinases, were upregulated. Conversely, expression of the putative histidine phosphatase LHPP was downregulated specifically in the tumours. We demonstrate that LHPP is indeed a protein histidine phosphatase. Consistent with these observations, global histidine phosphorylation was significantly upregulated in the liver tumours. Sustained, hepatic expression of LHPP in the hepatocellular carcinoma mouse model reduced tumour burden and prevented the loss of liver function. Finally, in patients with hepatocellular carcinoma, low expression of LHPP correlated with increased tumour severity and reduced overall survival. Thus, LHPP is a protein histidine phosphatase and tumour suppressor, suggesting that deregulated histidine phosphorylation is oncogenic.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    & Chasing phosphohistidine, an elusive sibling in the phosphoamino acid family. ACS Chem. Biol. 7, 44–51 (2012)

  2. 2.

    et al. Monoclonal 1- and 3-phosphohistidine antibodies: new tools to study histidine phosphorylation. Cell 162, 198–210 (2015)

  3. 3.

    et al. Hepatocellular carcinoma. Nat. Rev. Dis. Primers 2, 16018–16023 (2016)

  4. 4.

    et al. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets. Nat. Genet. 47, 505–511 (2015)

  5. 5.

    et al. Akt and mTORC1 have different roles during liver tumorigenesis in mice. Gastroenterology 144, 1055–1065 (2013)

  6. 6.

    et al. mTORC2 promotes tumorigenesis via lipid synthesis. Cancer Cell 32, 807–823 (2017)

  7. 7.

    , & Molecular cloning of a cDNA for the human phospholysine phosphohistidine inorganic pyrophosphate phosphatase. J. Biochem. 133, 607–614 (2003)

  8. 8.

    , & 3-phosphohistidine and 6-phospholysine are substrates of a 56-kDa inorganic pyrophosphatase from bovine liver. Arch. Biochem. Biophys. 349, 381–387 (1998)

  9. 9.

    , , , & Purification and characterization of hepatic inorganic pyrophosphatase hydrolyzing imidodiphosphate. Arch. Biochem. Biophys. 341, 153–159 (1997)

  10. 10.

    et al. Identification and characterization of a mammalian 14-kDa phosphohistidine phosphatase. Eur. J. Biochem. 269, 5016–5023 (2002)

  11. 11.

    et al. Protein histidine phosphatase: a novel enzyme with potency for neuronal signaling. J. Cereb. Blood Flow Metab. 22, 1420–1424 (2002)

  12. 12.

    et al. Identification of PGAM5 as a mammalian protein histidine phosphatase that plays a central role to negatively regulate CD4+ T Cells. Mol. Cell 63, 457–469 (2016)

  13. 13.

    , , , & Regulation of the epithelial Ca2+ channel TRPV5 by reversible histidine phosphorylation mediated by NDPK-B and PHPT1. Mol. Biol. Cell 25, 1244–1250 (2014)

  14. 14.

    et al. Nm23-H1 metastasis suppressor phosphorylation of kinase suppressor of Ras via a histidine protein kinase pathway. J. Biol. Chem. 277, 32389–32399 (2002)

  15. 15.

    & Phosphorylation of ATP-citrate lyase by nucleoside diphosphate kinase. J. Biol. Chem. 270, 21758–21764 (1995)

  16. 16.

    & pHisphorylation: the emergence of histidine phosphorylation as a reversible regulatory modification. Curr. Opin. Cell Biol. 45, 8–16 (2017)

  17. 17.

    , , & Development of stable phosphohistidine analogues. J. Am. Chem. Soc. 132, 14327–14329 (2010)

  18. 18.

    & Phosphoproteomics in the age of rapid and deep proteome profiling. Anal. Chem. 88, 74–94 (2016)

  19. 19.

    , , & Focus on phosphohistidine. Amino Acids 32, 145–156 (2007)

  20. 20.

    & Detection and analysis of protein histidine phosphorylation. Mol. Cell. Biochem. 329, 93–106 (2009)

  21. 21.

    et al. Gene expression analysis of biopsy samples reveals critical limitations of transcriptome-based molecular classifications of hepatocellular carcinoma. J. Pathol. Clin. Res. 2, 80–92 (2016)

  22. 22.

    et al. Cancer genome landscapes. Science 339, 1546–1558 (2013)

  23. 23.

    et al. A genome-wide association study identifies risk loci for childhood acute lymphoblastic leukemia at 10q26.13 and 12q23.1. Leukemia 31, 573–579 (2017)

  24. 24.

    et al. Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer. Nat. Genet. 48, 1544–1550 (2016)

  25. 25.

    et al. Evidence for HTR1A and LHPP as interacting genetic risk factors in major depression. Mol. Psychiatry 14, 621–630 (2009)

  26. 26.

    CONVERGE consortium. Sparse whole-genome sequencing identifies two loci for major depressive disorder. Nature 523, 588–591 (2015)

  27. 27.

    , , & Regulation of ribosomal S6 kinase 2 by mammalian target of rapamycin. J. Biol. Chem. 277, 31423–31429 (2002)

  28. 28.

    et al. LEO1 is regulated by PRL-3 and mediates its oncogenic properties in acute myelogenous leukemia. Cancer Res. 74, 3043–3053 (2014)

  29. 29.

    et al. Induction of cancer cell stemness by depletion of macrohistone H2A1 in hepatocellular carcinoma. Hepatology 67, (2018)

  30. 30.

    et al. High-Mobility Group Box 1 promotes hepatocellular carcinoma progression through miR-21-mediated matrix metalloproteinase activity. Cancer Res. 75, 1645–1656 (2015)

  31. 31.

    et al. A mouse model of TSC1 reveals sex-dependent lethality from liver hemangiomas, and up-regulation of p70S6 kinase activity in Tsc1 null cells. Hum. Mol. Genet. 11, 525–534 (2002)

  32. 32.

    et al. Hepatocyte-specific Pten deficiency results in steatohepatitis and hepatocellular carcinomas. J. Clin. Invest. 113, 1774–1783 (2004)

  33. 33.

    & DNA excision in liver by an albumin-Cre transgene occurs progressively with age. Genesis 26, 149–150 (2000)

  34. 34.

    & A solid phase extraction-based platform for rapid phosphoproteomic analysis. Methods 54, 379–386 (2011)

  35. 35.

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

  36. 36.

    , & Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116–5121 (2001)

  37. 37.

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

  38. 38.

    et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci. Signal. 6, pl1 (2013)

  39. 39.

    et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401–404 (2012)

  40. 40.

    et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016)

Download references

Acknowledgements

M.N.H. acknowledges the Louis Jeantet Foundation, the Swiss National Science Foundation, SystemsX.ch, and the European Research Council (MERiC). T.H. acknowledges USPHS grants CA080100, CA082683 and CA194584 from the NCI. T.H. is an American Cancer Society Professor, and holds the Renato Dulbecco Chair in Cancer Research. S.P. acknowledges the Swiss National Science Foundation (Ambizione grant number PZ00P3_168165).

Author information

Affiliations

  1. Biozentrum, University of Basel, 4056 Basel, Switzerland

    • Sravanth K. Hindupur
    • , Marco Colombi
    • , Yakir Guri
    • , Marion Cornu
    • , Charles Betz
    • , Dritan Liko
    • , Suzette Moes
    • , Paul Jenoe
    •  & Michael N. Hall
  2. Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • Stephen R. Fuhs
    • , Kevin Adam
    •  & Tony Hunter
  3. Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland

    • Matthias S. Matter
    • , Salvatore Piscuoglio
    • , Charlotte K. Y. Ng
    • , Luca Quagliata
    •  & Luigi M. Terracciano
  4. Department of Biomedicine, University Hospital Basel, 4031 Basel, Switzerland

    • Markus H. Heim

Authors

  1. Search for Sravanth K. Hindupur in:

  2. Search for Marco Colombi in:

  3. Search for Stephen R. Fuhs in:

  4. Search for Matthias S. Matter in:

  5. Search for Yakir Guri in:

  6. Search for Kevin Adam in:

  7. Search for Marion Cornu in:

  8. Search for Salvatore Piscuoglio in:

  9. Search for Charlotte K. Y. Ng in:

  10. Search for Charles Betz in:

  11. Search for Dritan Liko in:

  12. Search for Luca Quagliata in:

  13. Search for Suzette Moes in:

  14. Search for Paul Jenoe in:

  15. Search for Luigi M. Terracciano in:

  16. Search for Markus H. Heim in:

  17. Search for Tony Hunter in:

  18. Search for Michael N. Hall in:

Contributions

S.K.H. and M.N.H. conceived and designed the experiments, and wrote the manuscript. M.Col. maintained the in-house proteome database. S.R.F., K.A. and T.H. prepared pHis antibodies. L.M.T., L.Q. and M.S.M. performed histological analysis on patient tissues. D.L., C.B. and Y.G. assisted with animal experimentation. M.Cor. generated the L-dKO mouse. S.P. and C.K.Y.N. analysed public databases for mutations, gene expression and patient survival. S.M. and P.J. assisted with mass spectrometry. M.H.H. provided HCC microarray data. All authors commented and agree on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Michael N. Hall.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Life Sciences Reporting Summary

  2. 2.

    Supplementary Figures

    This file contains supplementary figures 1-13.

Excel files

  1. 1.

    Supplementary Table

    This file contains Supplementary Table 1: Identification of proteins enriched with histidine phosphorylation in tumours. 1173 proteins were detected and enriched (min 2-fold) in 2 out of 2 tumours (100%), or 3 out of 3 tumours (100%), or 3/4 out of 4 tumours (75%, 100%).

  2. 2.

    Supplementary Table

    This file contains Supplementary Table 2: Identification of proteins enriched with histidine phosphorylation in control tissue. 823 proteins were detected and enriched (min 2-fold) in 2 out of 2 control tissues (100%), or 3 out of 3 control tissues (100%), or 3/4 out of 4 control tissues (75%, 100%).

  3. 3.

    Supplementary Table

    This file contains Supplementary Table 3: Differentially enriched proteins with histidine phosphorylation in tumours 236 proteins were detected and enriched (min 2-fold) in 2 out of 2 experiments (100%), or 3 out of 3 experiments (100%), or 3/4 out of 4 experiments (75%, 100%).

  4. 4.

    Supplementary Table

    This file contains Supplementary Table 4: Identification of proteins whose histidine phosphorylation decreased upon LHPP re-expression. Nine proteins (with a log fold change of 1.7) and 17 proteins (with a log fold change of 1.4) were more abundant in immunoprecipitates from CB1 cells lacking LHPP in at least 50% of the detections (out of 5 experiments).

  5. 5.

    Supplementary Table

    This file contains Supplementary Table 5: List of mutations detected in LHPP. It shows a list of LHPP mutations detected from TCGA and ICGC portal. Deleterious mutations are highlighted in red.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature26140

Comments

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.