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.

  • Original Article
  • Published:

Lymphoma

Epigenetic mechanisms of protein tyrosine phosphatase 6 suppression in diffuse large B-cell lymphoma: implications for epigenetic therapy

Leukemia volume 28, pages 147–154 (2014)Cite this article

Subjects

Abstract

Protein tyrosine phosphatases such as PTPN6 can be downregulated in various neoplasms. PTPN6 expression by immunohistochemistry in 40 diffuse large B-cell lymphoma (DLBCL) tumors was lost or suppressed in 53% (21/40). To elucidate the molecular mechanisms of PTPN6 suppression, we performed a comprehensive epigenetic analysis of PTPN6 promoter 2 (P2). None of the DLBCL primary tumors (0/37) had PTPN6 hypermethylation on the CpG1 island using methylation-specific PCR, pyrosequencing, and high-resolution melting assays. However, hypermethylation in 57% (21/37) of cases was found in a novel CpG island (CpG2) in P2. PTPN6 gene suppression was reversed by 5-aza-deoxycytidine (5-Aza), a DNA methyltransferase inhibitor, and the histone deacetylase inhibitor (HDACi) LBH589. LBH589 and 5-Aza in combination inhibited DLBCL survival and PTPN6 hypermethylation at CpG2. The role of histone modifications was investigated with a chromatin-immunoprecipitation assay demonstrating that PTPN6 P2 is associated with silencing histone marks H3K27me3 and H3K9me3 in DLBCL cells but not normal B cells. 3-Deazaneplanocin A, a histone methyltransferase inhibitor, decreased the H3K27me3 mark, whereas HDACi LBH589 increased the H3K9Ac mark within P2 resulting in re-expression of PTPN6. These studies have uncovered novel epigenetic mechanisms of PTPN6 suppression and suggest that PTPN6 may be a potential target of epigenetic therapy in DLBCL.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5

Similar content being viewed by others

References

  1. Habermann TM, Weller EA, Morrison VA, Gascoyne RD, Cassileth PA, Cohn JB et al. Rituximab-CHOP versus CHOP alone or with maintenance rituximab in older patients with diffuse large B-cell lymphoma. J Clin Oncol 2006; 24: 3121–3127.

    Article  CAS  PubMed  Google Scholar 

  2. Coiffier B, Lepage E, Briere J, Herbrecht R, Tilly H, Bouabdallah R et al. CHOP chemotherapy plus rituximab compared with CHOP alone in elderly patients with diffuse large-B-cell lymphoma. N Engl J Med 2002; 346: 235–242.

    Article  CAS  PubMed  Google Scholar 

  3. Witzig TE, Reeder CB, LaPlant BR, Gupta M, Johnston PB, Micallef IN et al. A phase II trial of the oral mTOR inhibitor everolimus in relapsed aggressive lymphoma. Leukemia 2011; 25: 341–347.

    Article  CAS  PubMed  Google Scholar 

  4. Lam LT, Wright G, Davis RE, Lenz G, Farinha P, Dang L et al. Cooperative signaling through the signal transducer and activator of transcription 3 and nuclear factor-{kappa}B pathways in subtypes of diffuse large B-cell lymphoma. Blood 2008; 111: 3701–3713.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Ding BB, Yu JJ, Yu RY, Mendez LM, Shaknovich R, Zhang Y et al. Constitutively activated STAT3 promotes cell proliferation and survival in the activated B-cell subtype of diffuse large B-cell lymphomas. Blood 2008; 111: 1515–1523.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Gupta M, Maurer MJ, Wellik LE, Law ME, Han JJ, Ozsan N et al. Expression of Myc, but not pSTAT3, is an adverse prognostic factor for diffuse large B-cell lymphoma treated with epratuzumab/R-CHOP. Blood 2012; 120: 4400–4406.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Gupta M, Han JJ, Stenson M, Wellik L, Witzig TE . Regulation of STAT3 by histone deacetylase-3 in diffuse large B-cell lymphoma: implications for therapy. Leukemia 2012; 26: 1356–1364.

    Article  CAS  PubMed  Google Scholar 

  8. O'Shea JJ, Gadina M, Schreiber RD . Cytokine signaling in 2002: new surprises in the Jak/Stat pathway. Cell 2002; 109 (Suppl): S121–S131.

    Article  CAS  PubMed  Google Scholar 

  9. Yoshida K, Kharbanda S, Kufe D . Functional interaction between SHPTP1 and the Lyn tyrosine kinase in the apoptotic response to DNA damage. J Biol Chem 1999; 274: 34663–34668.

    Article  CAS  PubMed  Google Scholar 

  10. Jiao H, Berrada K, Yang W, Tabrizi M, Platanias LC, Yi T . Direct association with and dephosphorylation of Jak2 kinase by the SH2-domain-containing protein tyrosine phosphatase SHP-1. Mol Cell Biol 1996; 16: 6985–6992.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Han Y, Amin HM, Frantz C, Franko B, Lee J, Lin Q et al. Restoration of shp1 expression by 5-AZA-2'-deoxycytidine is associated with downregulation of JAK3/STAT3 signaling in ALK-positive anaplastic large cell lymphoma. Leukemia 2006; 20: 1602–1609.

    Article  CAS  PubMed  Google Scholar 

  12. Banville D, Stocco R, Shen SH . Human protein tyrosine phosphatase 1C (PTPN6) gene structure: alternate promoter usage and exon skipping generate multiple transcripts. Genomics 1995; 27: 165–173.

    Article  CAS  PubMed  Google Scholar 

  13. Paling NR, Welham MJ . Tyrosine phosphatase SHP-1 acts at different stages of development to regulate hematopoiesis. Blood 2005; 105: 4290–4297.

    Article  CAS  PubMed  Google Scholar 

  14. Wu C, Sun M, Liu L, Zhou GW . The function of the protein tyrosine phosphatase SHP-1 in cancer. Gene 2003; 306: 1–12.

    Article  CAS  PubMed  Google Scholar 

  15. Tsui FW, Martin A, Wang J, Tsui HW . Investigations into the regulation and function of the SH2 domain-containing protein-tyrosine phosphatase, SHP-1. Immunologic Res 2006; 35: 127–136.

    Article  CAS  Google Scholar 

  16. Oka T, Yoshino T, Hayashi K, Ohara N, Nakanishi T, Yamaai Y et al. Reduction of hematopoietic cell-specific tyrosine phosphatase SHP-1 gene expression in natural killer cell lymphoma and various types of lymphomas/leukemias: combination analysis with cDNA expression array and tissue microarray. Am J Pathol 2001; 159: 1495–1505.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Oka T, Ouchida M, Koyama M, Ogama Y, Takada S, Nakatani Y et al. Gene silencing of the tyrosine phosphatase SHP1 gene by aberrant methylation in leukemias/lymphomas. Cancer Res 2002; 62: 6390–6394.

    CAS  PubMed  Google Scholar 

  18. Chim CS, Fung TK, Cheung WC, Liang R, Kwong YL . SOCS1 and SHP1 hypermethylation in multiple myeloma: implications for epigenetic activation of the Jak/STAT pathway. Blood 2004; 103: 4630–4635.

    Article  CAS  PubMed  Google Scholar 

  19. Chim CS, Wong AS, Kwong YL . Epigenetic dysregulation of the Jak/STAT pathway by frequent aberrant methylation of SHP1 but not SOCS1 in acute leukaemias. Ann Hematol 2004; 83: 527–532.

    Article  CAS  PubMed  Google Scholar 

  20. Micallef IN, Maurer MJ, Wiseman GA, Nikcevich DA, Kurtin PJ, Cannon MW et al. Epratuzumab with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone chemotherapy in patients with previously untreated diffuse large B-cell lymphoma. Blood 2011; 118: 4053–4061.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Li LC, Dahiya R . MethPrimer: designing primers for methylation PCRs. Bioinformatics 2002; 18: 1427–1431.

    Article  CAS  PubMed  Google Scholar 

  22. Ronaghi M . Pyrosequencing sheds light on DNA sequencing. Genome Res 2001; 11: 3–11.

    Article  CAS  PubMed  Google Scholar 

  23. Lynch M, Chen L, Ravitz MJ, Mehtani S, Korenblat K, Pazin MJ et al. hnRNP K binds a core polypyrimidine element in the eukaryotic translation initiation factor 4E (eIF4E) promoter, and its regulation of eIF4E contributes to neoplastic transformation. Mol Cell Biol 2005; 25: 6436–6453.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Gupta M, Dillon SR, Ziesmer SC, Feldman AL, Witzig TE, Ansell SM et al. A proliferation-inducing ligand mediates follicular lymphoma B-cell proliferation and cyclin D1 expression through phosphatidylinositol 3-kinase-regulated mammalian target of rapamycin activation. Blood 2009; 113: 5206–5216.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Koyama M, Oka T, Ouchida M, Nakatani Y, Nishiuchi R, Yoshino T et al. Activated proliferation of B-cell lymphomas/leukemias with the SHP1 gene silencing by aberrant CpG methylation. Lab Invest 2003; 83: 1849–1858.

    Article  CAS  PubMed  Google Scholar 

  26. Dupont JM, Tost J, Jammes H, Gut IG . De novo quantitative bisulfite sequencing using the pyrosequencing technology. Anal Biochem 2004; 333: 119–127.

    Article  CAS  PubMed  Google Scholar 

  27. Colella S, Shen L, Baggerly KA, Issa JP, Krahe R . Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites. Biotechniques 2003; 35: 146–150.

    Article  CAS  PubMed  Google Scholar 

  28. Candiloro IL, Mikeska T, Dobrovic A . Assessing combined methylation-sensitive high resolution melting and pyrosequencing for the analysis of heterogeneous DNA methylation. Epigenetics 2011; 6: 500–507.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Chou TC, Talalay P . Quantitative analysis of dose-effect relationships: the combined effects of multiple drugs or enzyme inhibitors. Adv Enzyme Regul 1984; 22: 27–55.

    Article  CAS  PubMed  Google Scholar 

  30. Tan J, Yang X, Zhuang L, Jiang X, Chen W, Lee PL et al. Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. Genes Dev 2007; 21: 1050–1063.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Zhang Q, Raghunath PN, Vonderheid E, Odum N, Wasik MA . Lack of phosphotyrosine phosphatase SHP-1 expression in malignant T-cell lymphoma cells results from methylation of the SHP-1 promoter. Am J Pathol 2000; 157: 1137–1146.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Migone TS, Cacalano NA, Taylor N, Yi T, Waldmann TA, Johnston JA . Recruitment of SH2-containing protein tyrosine phosphatase SHP-1 to the interleukin 2 receptor; loss of SHP-1 expression in human T-lymphotropic virus type I-transformed T cells. Proc Natl Acad Sci USA 1998; 95: 3845–3850.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Khoury JD, Rassidakis GZ, Medeiros LJ, Amin HM, Lai R . Methylation of SHP1 gene and loss of SHP1 protein expression are frequent in systemic anaplastic large cell lymphoma. Blood 2004; 104: 1580–1581.

    Article  CAS  PubMed  Google Scholar 

  34. Amara K, Trimeche M, Ziadi S, Laatiri A, Hachana M, Korbi S . Prognostic significance of aberrant promoter hypermethylation of CpG islands in patients with diffuse large B-cell lymphomas. Ann Oncol 2008; 19: 1774–1786.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported through Iowa/Mayo Lymphoma Specialized Program of Research Excellence (P50 CA097274) to MG; R01CA127433 to TEW and the Predolin Foundation.

AUTHOR CONTRIBUTIONS

TEW interpreted data, wrote the manuscript and provided clinical samples. GH performed the PTPN6 methylation (MSP-PCR and pyrosequencing for CpG1 and CpG2) and ChIP assay. SMO performed high-resolution methylation array. LEW performed PTPN6 IHC staining. MJS performed apoptosis. JJH performed PTPN6 western blotting and PTPN6 Q-PCR. AD scored and reviewed PTPN6 IHC slides. RBD edited the paper. MG designed and supervised the research, interpreted and analyzed the data, finalized the figures and wrote the manuscript.

Author information

Authors and Affiliations

  1. Division of Hematology, Department of Internal Medicine, Mayo Clinic, College of Medicine, Rochester, MN, USA

    T E Witzig, G Hu, L E Wellik, J J Han, M J Stenson & M Gupta

  2. Department of Molecular and Experimental Therapeutics, Mayo Clinic, College of Medicine, Rochester, MN, USA

    S M Offer & R B Diasio

  3. Department of Pathology, Memorial Sloan-Kettering Cancer, New York, NY, USA

    A Dogan

Authors
  1. T E Witzig
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. G Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S M Offer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. L E Wellik
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J J Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. M J Stenson
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. A Dogan
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. R B Diasio
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. M Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to M Gupta.

Ethics declarations

Competing interests

The authors declare no conflict of interest.

Additional information

Supplementary Information accompanies this paper on the Leukemia website

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Witzig, T., Hu, G., Offer, S. et al. Epigenetic mechanisms of protein tyrosine phosphatase 6 suppression in diffuse large B-cell lymphoma: implications for epigenetic therapy. Leukemia 28, 147–154 (2014). https://doi.org/10.1038/leu.2013.251

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/leu.2013.251

Keywords

This article is cited by

Search

Advanced search

Quick links