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The mutational landscape of cutaneous T cell lymphoma and Sézary syndrome

Abstract

Sézary syndrome is a leukemic and aggressive form of cutaneous T cell lymphoma (CTCL) resulting from the malignant transformation of skin-homing central memory CD4+ T cells. Here we performed whole-exome sequencing of tumor-normal sample pairs from 25 patients with Sézary syndrome and 17 patients with other CTCLs. These analyses identified a distinctive pattern of somatic copy number alterations in Sézary syndrome, including highly prevalent chromosomal deletions involving the TP53, RB1, PTEN, DNMT3A and CDKN1B tumor suppressors. Mutation analysis identified a broad spectrum of somatic mutations in key genes involved in epigenetic regulation (TET2, CREBBP, KMT2D (MLL2), KMT2C (MLL3), BRD9, SMARCA4 and CHD3) and signaling, including MAPK1, BRAF, CARD11 and PRKG1 mutations driving increased MAPK, NF-κB and NFAT activity upon T cell receptor stimulation. Collectively, our findings provide new insights into the genetics of Sézary syndrome and CTCL and support the development of personalized therapies targeting key oncogenically activated signaling pathways for the treatment of these diseases.

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Figure 1: Somatic copy number variants and mutations in Sézary syndrome and CTCL.
Figure 2: Somatic alterations in Sézary syndrome and CTCL.
Figure 3: Functional characterization of Sézary syndrome CARD11 linker domain alterations.
Figure 4: Functional characterization of Sézary syndrome cGKIβ alterations.

References

  1. Querfeld, C., Rosen, S.T., Guitart, J. & Kuzel, T.M. The spectrum of cutaneous T-cell lymphomas: new insights into biology and therapy. Curr. Opin. Hematol. 12, 273–278 (2005).

    Article  Google Scholar 

  2. Wilcox, R.A. Cutaneous T-cell lymphoma: 2014 update on diagnosis, risk-stratification, and management. Am. J. Hematol. 89, 837–851 (2014).

    Article  Google Scholar 

  3. Agar, N.S. et al. Survival outcomes and prognostic factors in mycosis fungoides/Sézary syndrome: validation of the revised International Society for Cutaneous Lymphomas/European Organisation for Research and Treatment of Cancer staging proposal. J. Clin. Oncol. 28, 4730–4739 (2010).

    Article  Google Scholar 

  4. Cristofoletti, C. et al. Comprehensive analysis of PTEN status in Sézary syndrome. Blood 122, 3511–3520 (2013).

    Article  CAS  Google Scholar 

  5. Mao, X. et al. Heterogeneous abnormalities of CCND1 and RB1 in primary cutaneous T-cell lymphomas suggesting impaired cell cycle control in disease pathogenesis. J. Invest. Dermatol. 126, 1388–1395 (2006).

    Article  CAS  Google Scholar 

  6. Brito-Babapulle, V. et al. p53 allele deletion and protein accumulation occurs in the absence of p53 gene mutation in T-prolymphocytic leukaemia and Sézary syndrome. Br. J. Haematol. 110, 180–187 (2000).

    Article  CAS  Google Scholar 

  7. Ungewickell, A. et al. Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2. Nat. Genet. 47, 1056–1060 (2015).

    Article  CAS  Google Scholar 

  8. Choi, J. et al. Genomic landscape of cutaneous T cell lymphoma. Nat. Genet. 47, 1011–1019 (2015).

    Article  CAS  Google Scholar 

  9. Alexandrov, T., Becker, M., Guntinas-Lichius, O., Ernst, G. & von Eggeling, F. MALDI–imaging segmentation is a powerful tool for spatial functional proteomic analysis of human larynx carcinoma. J. Cancer Res. Clin. Oncol. 139, 85–95 (2013).

    Article  CAS  Google Scholar 

  10. Solary, E., Bernard, O.A., Tefferi, A., Fuks, F. & Vainchenker, W. The Ten-Eleven Translocation-2 (TET2) gene in hematopoiesis and hematopoietic diseases. Leukemia 28, 485–496 (2014).

    Article  CAS  Google Scholar 

  11. Smith, A.E. et al. Next-generation sequencing of the TET2 gene in 355 MDS and CMML patients reveals low-abundance mutant clones with early origins, but indicates no definite prognostic value. Blood 116, 3923–3932 (2010).

    Article  CAS  Google Scholar 

  12. Palomero, T. et al. Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas. Nat. Genet. 46, 166–170 (2014).

    Article  CAS  Google Scholar 

  13. Hu, Y. et al. CHD3 protein recognizes and regulates methylated histone H3 lysines 4 and 27 over a subset of targets in the rice genome. Proc. Natl. Acad. Sci. USA 109, 5773–5778 (2012).

    Article  CAS  Google Scholar 

  14. Barollo, S. et al. Prevalence, tumorigenic role, and biochemical implications of rare BRAF alterations. Thyroid 24, 809–819 (2014).

    Article  CAS  Google Scholar 

  15. Van Allen, E.M. et al. Genomic correlate of exceptional erlotinib response in head and neck squamous cell carcinoma. JAMA Oncol. 1, 238–244 (2015).

    Article  Google Scholar 

  16. Bergmann, A.K. et al. Recurrent mutation of JAK3 in T-cell prolymphocytic leukemia. Genes Chromosom. Cancer 53, 309–316 (2014).

    Article  CAS  Google Scholar 

  17. Koskela, H.L. et al. Somatic STAT3 mutations in large granular lymphocytic leukemia. N. Engl. J. Med. 366, 1905–1913 (2012).

    Article  CAS  Google Scholar 

  18. Fine, B. et al. Activation of the PI3K pathway in cancer through inhibition of PTEN by exchange factor P-REX2a. Science 325, 1261–1265 (2009).

    Article  CAS  Google Scholar 

  19. Forbes, S.A. et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805–D811 (2015).

    Article  CAS  Google Scholar 

  20. Vaqué, J.P. et al. PLCG1 mutations in cutaneous T-cell lymphomas. Blood 123, 2034–2043 (2014).

    Article  Google Scholar 

  21. Sors, A. et al. Down-regulating constitutive activation of the NF-κB canonical pathway overcomes the resistance of cutaneous T-cell lymphoma to apoptosis. Blood 107, 2354–2363 (2006).

    Article  CAS  Google Scholar 

  22. Lenz, G. et al. Oncogenic CARD11 mutations in human diffuse large B cell lymphoma. Science 319, 1676–1679 (2008).

    Article  CAS  Google Scholar 

  23. Sommer, K. et al. Phosphorylation of the CARMA1 linker controls NF-κB activation. Immunity 23, 561–574 (2005).

    Article  CAS  Google Scholar 

  24. Hofmann, F. & Wegener, J.W. cGMP-dependent protein kinases (cGK). Methods Mol. Biol. 1020, 17–50 (2013).

    Article  CAS  Google Scholar 

  25. Francis, S.H., Busch, J.L., Corbin, J.D. & Sibley, D. cGMP-dependent protein kinases and cGMP phosphodiesterases in nitric oxide and cGMP action. Pharmacol. Rev. 62, 525–563 (2010).

    Article  CAS  Google Scholar 

  26. Fischer, T.A. et al. Activation of cGMP-dependent protein kinase Iβ inhibits interleukin 2 release and proliferation of T cell receptor–stimulated human peripheral T cells. J. Biol. Chem. 276, 5967–5974 (2001).

    Article  CAS  Google Scholar 

  27. Casteel, D.E. et al. A crystal structure of the cyclic GMP–dependent protein kinase Iβ dimerization/docking domain reveals molecular details of isoform-specific anchoring. J. Biol. Chem. 285, 32684–32688 (2010).

    Article  CAS  Google Scholar 

  28. Richie-Jannetta, R., Francis, S.H. & Corbin, J.D. Dimerization of cGMP-dependent protein kinase Iβ is mediated by an extensive amino-terminal leucine zipper motif, and dimerization modulates enzyme function. J. Biol. Chem. 278, 50070–50079 (2003).

    Article  CAS  Google Scholar 

  29. Lander, H.M., Jacovina, A.T., Davis, R.J. & Tauras, J.M. Differential activation of mitogen-activated protein kinases by nitric oxide–related species. J. Biol. Chem. 271, 19705–19709 (1996).

    Article  CAS  Google Scholar 

  30. Lang, P. et al. Protein kinase A phosphorylation of RhoA mediates the morphological and functional effects of cyclic AMP in cytotoxic lymphocytes. EMBO J. 15, 510–519 (1996).

    Article  CAS  Google Scholar 

  31. Trifonov, V., Pasqualucci, L., Tiacci, E., Falini, B. & Rabadan, R. SAVI: a statistical algorithm for variant frequency identification. BMC Syst. Biol. 7 (suppl. 2), S2 (2013).

    Article  Google Scholar 

  32. Pasqualucci, L. et al. Genetics of follicular lymphoma transformation. Cell Rep. 6, 130–140 (2014).

    Article  CAS  Google Scholar 

  33. Magi, A. et al. EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biol. 14, R120 (2013).

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by a Leukemia and Lymphoma Society Translational Research Grant (A.F.), a Herbert Irving Comprehensive Cancer Center interprogrammatic pilot project grant (A.F. and R.R.) and Dutch Cancer Society grant UL2013-6104 (C.P.T. and M.H.V.). A.C.d.S.A. is supported by a Lady Tata Memorial Trust fellowship.

Author information

Authors and Affiliations

Authors

Contributions

A.C.d.S.A. performed functional assays. F.A. and H.K. performed exome and copy number analyses. E.M.-E., J.G., C.P.T. and M.H.V. contributed clinical samples. R.R. directed sequencing analyses. A.F. and T.P. designed the study, directed and supervised research, and wrote the manuscript.

Corresponding authors

Correspondence to Raul Rabadan, Adolfo Ferrando or Teresa Palomero.

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Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 DNMT3A and TP53 expression analysis in samples from patients with Sézary syndrome.

(a,b) Quantitative RT-PCR analysis of CD4+ T cells isolated from the peripheral blood of individuals with benign erythroderma lesions and representative cases of Sézary syndrome harboring 2p23.3 deletions (a) or 17p13.1 deletions (b). The bar graphs in a and b show the mean values from three technical triplicates in the quantitative PCR reaction; error bars, s.d. P values were calculated using Student's t test. Gray boxes indicate heterozygous deletions; solid boxes indicate homozygous deletions. CNV, copy number variation.

Supplementary Figure 2 Signatures of mutational processes in Sézary syndrome.

Analysis of mutational processes showed the presence of a mutational signature characterized by C>T substitutions at NpCpG trinucleotides, as well as a high frequency of C>A substitutions at CpCpN trinucleotides and C>T substitutions at CpCpN and TpCpN trinucleotides.

Supplementary Figure 3 Functional characterization of CTCL MAPK1 mutations.

(a) Schematic of the structure of the MAPK1 (ERK2) protein. The positions of the MAPK1 alterations identified in CTCL samples are indicated with solid circles; the positions of recurrent alterations in COSMIC (p.Glu322Lys) identified in solid tumors are indicated with open circles. (b,c) Immunoblot analysis (b) and quantification (c) of ERK phosphorylation in HEK293T cells expressing wild-type V5-MAPK1, V5-MAPK1 E322K and V5-MAPK1 E322A. WT, wild type.

Supplementary Figure 4 Comparative functional analysis of Sézary syndrome CARD11 linker domain mutations and DLBCL CARD11 coiled-coil domain mutations.

(a) Schematic of the structure of the CARD11 protein. The positions of the CARD11 alterations identified in the linker domain are indicated with black circles, and the positions of three examples of CARD11 alterations identified in DLBCL are indicated with blue circles. (b) NF-κB luciferase reporter activity in HEK293T cells transfected with V5-CARD11 wild type, mutants (S615F, E626K, D230N, L215P, M183L) or empty vector. (c) NF-κB–dependent GFP reporter activity in non-stimulated Jurkat cells expressing CARD11 wild type, CARD11 mutants (S615F, E626K, D230N, L215P, M183L) or empty vector. Bar graphs indicate the percentage of GFP-positive cells analyzed by flow cytometry. Data are representative of three independent experiments. (d) NF-κB–dependent GFP reporter activity after stimulation for 6 h with 1 μg/ml ionomycin and 0.2 nM PMA in Jurkat cells expressing CARD11 wild type, CARD11 mutants (S615F, E626K, D230N, L215P, M183L) or empty vector. Bar graphs indicate mean GFP intensity measured by flow cytometry across three replicates. (e) Analysis of the levels of V5-CARD11 protein in a Jurkat NF-κB–GFP reporter cell line infected with lentiviruses driving the expression of CARD11 wild type, CARD11 mutants (S615F, E626K, D230N, L215P, M183L) or empty vector. The bar graphs in bd show mean values; error bars, s.d. P values were calculated using Student's t test. WT, wild type.

Supplementary Figure 5 Activated signaling pathways in CTCL cell lines.

(a) Immunoblot analysis of STAT3, ERK1/2 and JNK phosphorylation. (b) Analysis of nuclear NF-κB after subcellular fractionation in CTCL cell lines.

Supplementary Figure 6 Antitumor activity of signaling inhibitors in CTCL.

Proliferation analysis of CTCL cell lines (HH, HUT78, HUT102, SeAX) after treatment with the indicated compounds for 72 h.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 and Supplementary Tables 1, 2 and 8. (PDF 2339 kb)

Supplementary Table 3

CNVs in Sézary syndrome samples. (XLSX 201 kb)

Supplementary Table 4

CNVs in CTCL samples. (XLSX 29 kb)

Supplementary Table 5

Number of nonsynonymous somatic mutations per sample. (XLSX 14 kb)

Supplementary Table 6

SNVs in Sézary syndrome samples. (XLSX 154 kb)

Supplementary Table 7

SNVs in CTCL samples. (XLSX 99 kb)

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da Silva Almeida, A., Abate, F., Khiabanian, H. et al. The mutational landscape of cutaneous T cell lymphoma and Sézary syndrome. Nat Genet 47, 1465–1470 (2015). https://doi.org/10.1038/ng.3442

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