Abstract

Chromosomal translocations are critically involved in the molecular pathogenesis of B-cell lymphomas, and highly recurrent and specific rearrangements have defined distinct molecular subtypes linked to unique clinicopathological features1,2. In contrast, several well-characterized lymphoma entities still lack disease-defining translocation events. To identify novel fusion transcripts resulting from translocations, we investigated two Hodgkin lymphoma cell lines by whole-transcriptome paired-end sequencing (RNA-seq). Here we show a highly expressed gene fusion involving the major histocompatibility complex (MHC) class II transactivator CIITA (MHC2TA) in KM-H2 cells. In a subsequent evaluation of 263 B-cell lymphomas, we also demonstrate that genomic CIITA breaks are highly recurrent in primary mediastinal B-cell lymphoma (38%) and classical Hodgkin lymphoma (cHL) (15%). Furthermore, we find that CIITA is a promiscuous partner of various in-frame gene fusions, and we report that CIITA gene alterations impact survival in primary mediastinal B-cell lymphoma (PMBCL). As functional consequences of CIITA gene fusions, we identify downregulation of surface HLA class II expression and overexpression of ligands of the receptor molecule programmed cell death 1 (CD274/PDL1 and CD273/PDL2). These receptor–ligand interactions have been shown to impact anti-tumour immune responses in several cancers3, whereas decreased MHC class II expression has been linked to reduced tumour cell immunogenicity4. Thus, our findings suggest that recurrent rearrangements of CIITA may represent a novel genetic mechanism underlying tumour–microenvironment interactions across a spectrum of lymphoid cancers.

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Gene Expression Omnibus

Data deposits

Array data are deposited in NCBI Gene Expression Omnibus under accession number GSE25990.

References

  1. 1.

    The pathogenetic role of oncogenes deregulated by chromosomal translocation in B-cell malignancies. Int. J. Hematol. 77, 315–320 (2003)

  2. 2.

    et al. LAZ3, a novel zinc-finger encoding gene, is disrupted by recurring chromosome 3q27 translocations in human lymphomas. Nature Genet. 5, 66–70 (1993)

  3. 3.

    , & Interaction of PD-L1 on tumor cells with PD-1 on tumor-specific T cells as a mechanism of immune evasion: implications for tumor immunotherapy. Cancer Immunol. Immunother. 54, 307–314 (2005)

  4. 4.

    et al. Loss of MHC class II gene and protein expression in diffuse large B-cell lymphoma is related to decreased tumor immunosurveillance and poor patient survival regardless of other prognostic factors: a follow-up study from the Leukemia and Lymphoma Molecular Profiling Project. Blood 103, 4251–4258 (2004)

  5. 5.

    et al. Chromosomal breakpoints affecting immunoglobulin loci are recurrent in Hodgkin and Reed-Sternberg cells of classical Hodgkin lymphoma. Cancer Res. 66, 10332–10338 (2006)

  6. 6.

    , , , & Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621–628 (2008)

  7. 7.

    et al. Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nature Med. 16, 793–798 (2010)

  8. 8.

    & The bare lymphocyte syndrome and the regulation of MHC expression. Annu. Rev. Immunol. 19, 331–373 (2001)

  9. 9.

    , , , & Developmental extinction of major histocompatibility complex class II gene expression in plasmocytes is mediated by silencing of the transactivator gene CIITA. J. Exp. Med. 180, 1329–1336 (1994)

  10. 10.

    et al. CIITA is a transcriptional coactivator that is recruited to MHC class II promoters by multiple synergistic interactions with an enhanceosome complex. Genes Dev. 14, 1156–1166 (2000)

  11. 11.

    , , & A defect in the nuclear translocation of CIITA causes a form of type II bare lymphocyte syndrome. Immunity 10, 163–171 (1999)

  12. 12.

    et al. Hodgkin’s lymphoma cell lines are characterized by frequent aberrations on chromosomes 2p and 9p including REL and JAK2. Int. J. Cancer 103, 489–495 (2003)

  13. 13.

    , & Activation and transdominant suppression of MHC class II and HLA-DMB promoters by a series of C-terminal class II transactivator deletion mutants. J. Immunol. 159, 2789–2794 (1997)

  14. 14.

    , , , & CIITA-dependent and -independent class II MHC expression revealed by a dominant negative mutant. J. Immunol. 158, 4741–4749 (1997)

  15. 15.

    et al. Loss of major histocompatibility class II gene and protein expression in primary mediastinal large B-cell lymphoma is highly coordinated and related to poor patient survival. Blood 108, 311–318 (2006)

  16. 16.

    et al. HLA class II expression by Hodgkin Reed-Sternberg cells is an independent prognostic factor in classical Hodgkin’s lymphoma. J. Clin. Oncol. 25, 3101–3108 (2007)

  17. 17.

    et al. Favorable outcome of primary mediastinal large B-cell lymphoma in a single institution: the British Columbia experience. Ann. Oncol. 17, 123–130 (2006)

  18. 18.

    A predictive model for aggressive non-Hodgkin’s lymphoma. N. Engl. J. Med. 329, 987–994 (1993)

  19. 19.

    et al. Molecular diagnosis of primary mediastinal B cell lymphoma identifies a clinically favorable subgroup of diffuse large B cell lymphoma related to Hodgkin lymphoma. J. Exp. Med. 198, 851–862 (2003)

  20. 20.

    et al. PD-1-PD-1 ligand interaction contributes to immunosuppressive microenvironment of Hodgkin lymphoma. Blood 111, 3220–3224 (2008)

  21. 21.

    et al. Integrative analysis reveals selective 9p24.1 amplification, increased PD-1 ligand expression, and further induction via JAK2 in nodular sclerosing Hodgkin lymphoma and primary mediastinal large B-cell lymphoma. Blood 116, 3268–3277 (2010)

  22. 22.

    et al. Costimulatory B7–H1 in renal cell carcinoma patients: Indicator of tumor aggressiveness and potential therapeutic target. Proc. Natl Acad. Sci. USA 101, 17174–17179 (2004)

  23. 23.

    et al. Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways. Proc. Natl Acad. Sci. USA 105, 13520–13525 (2008)

  24. 24.

    et al. Isolation of a B-cell-specific promoter for the human class II transactivator. Immunogenetics 45, 266–273 (1997)

  25. 25.

    et al. U-2940, a human B-cell line derived from a diffuse large cell lymphoma sequential to Hodgkin lymphoma. Int. J. Cancer 118, 555–563 (2006)

  26. 26.

    et al. The molecular signature of mediastinal large B-cell lymphoma differs from that of other diffuse large B-cell lymphomas and shares features with classical Hodgkin lymphoma. Blood 102, 3871–3879 (2003)

  27. 27.

    et al. Biallelic deletion within 16p13.13 including SOCS-1 in Karpas1106P mediastinal B-cell lymphoma line is associated with delayed degradation of JAK2 protein. Int. J. Cancer 118, 1941–1944 (2006)

  28. 28.

    et al. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 45, 81–94 (2008)

  29. 29.

    et al. A distal single nucleotide polymorphism alters long-range regulation of the PU.1 gene in acute myeloid leukemia. J. Clin. Invest. 117, 2611–2620 (2007)

  30. 30.

    et al. A loss-of-function RNA interference screen for molecular targets in cancer. Nature 441, 106–110 (2006)

  31. 31.

    et al. A novel B-cell line (U-2932) established from a patient with diffuse large B-cell lymphoma following Hodgkin lymphoma. Leuk. Lymphoma 43, 2179–2189 (2002)

  32. 32.

    et al. Biology of the human malignant lymphomas. IV. Functional characterization of ten diffuse histiocytic lymphoma cell lines. Cancer 42, 2379–2391 (1978)

  33. 33.

    et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461, 809–813 (2009)

  34. 34.

    , , & Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009)

  35. 35.

    , & A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics 25, 2149–2156 (2009)

  36. 36.

    et al. Integrating copy number polymorphisms into array CGH analysis using a robust HMM. Bioinformatics 22, e431–e439 (2006)

  37. 37.

    et al. Multicolour fluorescence in situ hybridization analysis of t(14;18)-positive follicular lymphoma and correlation with gene expression data and clinical outcome. Br. J. Haematol. 122, 745–759 (2003)

  38. 38.

    et al. Tumor-associated macrophages and survival in classic Hodgkin’s lymphoma. N. Engl. J. Med. 362, 875–885 (2010)

  39. 39.

    et al. Correlations between BCL6 rearrangement and outcome in patients with diffuse large B-cell lymphoma treated with CHOP or R-CHOP. Haematologica 95, 96–101 (2010)

  40. 40.

    et al. Simultaneous detection of the immunophenotypic markers and genetic aberrations on routinely processed paraffin sections of lymphoma samples by means of the FICTION technique. Leukemia 18, 348–353 (2004)

  41. 41.

    et al. Transcriptional analysis of the B cell germinal center reaction. Proc. Natl Acad. Sci. USA 100, 2639–2644 (2003)

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Acknowledgements

This work is supported by a postdoctoral fellowship of the Cancer Research Society (Steven E. Drabin Fellowship) to C.S., the Michael Smith Foundation for Health Research to C.S. and S.P.S., the Lymphoma Research Foundation to C.S. and the Canadian Breast Cancer Foundation to S.P.S. Operational funds were available through the Canadian Institutes of Health Research, grant number 178536 to R.D.G. R.D.G., J.M.C., M.A.M. and D.E.H. are also supported by the Terry Fox Foundation (number 019001). This work was in part supported by an infrastructure grant of Genome Canada/Genome BC. U.S. is the recipient of a Howard Temin Award of the National Institutes of Health/National Cancer Institute (R00CA131503), a new investigator award of the Leukemia Research Foundation, and is the Diane and Arthur B. Belfer Faculty Scholar in Cancer Research of the Albert Einstein College of Medicine. We thank G. Simkin, C. Polumbo and T. Vogler for technical support. L.R. is the recipient of a CJ Martin Fellowship from the National Health and Medical Research Council of Australia.

Author information

Author notes

    • Christian Steidl
    •  & Sohrab P. Shah

    These authors contributed equally to this work.

Affiliations

  1. Department of Pathology and Laboratory Medicine, Centre for Lymphoid Cancers and the Centre for Translational and Applied Genomics (CTAG), Vancouver, British Columbia, V5Z4E6, Canada

    • Christian Steidl
    • , Sohrab P. Shah
    • , Bruce W. Woolcock
    • , Pedro Farinha
    • , Nathalie A. Johnson
    • , Adele Telenius
    • , Susana Ben Neriah
    • , Andrew McPherson
    • , Barbara Meissner
    • , Mark Sun
    • , Gillian Leung
    • , David G. Huntsman
    • , Douglas E. Horsman
    •  & Randy D. Gascoyne
  2. Metabolism Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892, USA

    • Lixin Rui
    •  & Louis M. Staudt
  3. Department of Cell Biology and Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, New York, 10461, USA

    • Masahiro Kawahara
    • , Ujunwa C. Okoye
    •  & Ulrich Steidl
  4. Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z4S6, Canada

    • Yongjun Zhao
    • , Steven J. Jones
    •  & Marco A. Marra
  5. Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700, The Netherlands

    • Arjan Diepstra
    •  & Anke van den Berg
  6. Division of Medical Oncology, BC Cancer Agency Centre for Lymphoid Cancer, Vancouver, British Columbia, V5Z4E6, Canada

    • Joseph M. Connors
    •  & Kerry J. Savage
  7. Department of Pathology, University of Arizona, Tucson, Arizona, 85724, USA

    • Lisa M. Rimsza
  8. Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6T1Z3, Canada

    • Marco A. Marra

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Contributions

C.S. designed the research, performed FISH, PCR and direct sequencing, interpreted results and wrote the paper. S.P.S. designed the research, analysed the transcriptome data and wrote the paper. B.W.W. performed PCR and interpreted results. M.K., U.C.O. and L.R. performed in vitro functional analyses. P.F. reviewed pathology and constructed the tissue microarrays. N.A.J. performed single nucleotide polymorphism analyses. Y.Z. performed library construction and RNA-seq. A.T. performed nucleic acid extraction and quantitative RT-PCR. B.M. and S.B.N. performed FISH. A.M., M.S., G.L. and S.J.J. analysed the transcriptome data. A.D., A.B., L.R. and D.E.H. interpreted results. J.M.C. and K.J.S. provided clinical data. D.G.H. designed the research. L.M.S. and U.S. designed the research and interpreted results. M.A.A. designed the research. R.D.G. designed the research, constructed the tissue microarrays, interpreted results and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Randy D. Gascoyne.

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    Supplementary Information

    The file contains Supplementary Tables 1-7, additional text and Supplementary Figures 1-10 with legends.

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https://doi.org/10.1038/nature09754

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