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Chronic Lymphocytic Leukemia

A B-cell epigenetic signature defines three biologic subgroups of chronic lymphocytic leukemia with clinical impact

Leukemia volume 29, pages 598–605 (2015)Cite this article

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Abstract

Prospective identification of patients with chronic lymphocytic leukemia (CLL) destined to progress would greatly facilitate their clinical management. Recently, whole-genome DNA methylation analyses identified three clinicobiologic CLL subgroups with an epigenetic signature related to different normal B-cell counterparts. Here, we developed a clinically applicable method to identify these subgroups and to study their clinical relevance. Using a support vector machine approach, we built a prediction model using five epigenetic biomarkers that was able to classify CLL patients accurately into the three subgroups, namely naive B-cell-like, intermediate and memory B-cell-like CLL. DNA methylation was quantified by highly reproducible bisulfite pyrosequencing assays in two independent CLL series. In the initial series (n=211), the three subgroups showed differential levels of IGHV (immunoglobulin heavy-chain locus) mutation (P<0.001) and VH usage (P<0.03), as well as different clinical features and outcome in terms of time to first treatment (TTT) and overall survival (P<0.001). A multivariate Cox model showed that epigenetic classification was the strongest predictor of TTT (P<0.001) along with Binet stage (P<0.001). These findings were corroborated in a validation series (n=97). In this study, we developed a simple and robust method using epigenetic biomarkers to categorize CLLs into three subgroups with different clinicobiologic features and outcome.

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Acknowledgements

We are grateful to S Guijarro, S Martín, C Capdevila, M Sánchez, L Plà, A Heydorn and G Riesen for excellent technical assistance, and to N Villahoz and C Muro for excellent work in the coordination of the Spanish CLL Genome Consortium. We are indebted to the Hospital Clínic de Barcelona–IDIBAPS Biobank-Tumor Bank and Hematopathology Collection for the sample procurement as well as to the technical and medical staff of all the laboratories involved in the study. We are also very grateful to the patients with CLL who have participated in this study. This work was funded by the Spanish Ministry of Economy and Competitiveness (MINECO) through the Instituto de Salud Carlos III (ISCIII) and the Red Temática de Investigación del Cáncer (RTICC) of the ISCIII (RD12/0036/0036 to EC, RD12/0036/0023 to AL-G, RD12/0036/0004 to DC and RD12/0036/0067 to CL-O) and project SAF2009-08663 (JIM-S), the UK Medical Research Council (AM, SJ and MJSD) as well as the European Union’s Seventh Framework Programme through the Blueprint Consortium (grant agreement 282510 to EC and RS). CL-O is a researcher of the Botín Foundation and EC an ICREA-Academia researcher. JIM-S is supported by a Ramon y Cajal contract of the MINECO, ACQ by the Portuguese Fundação para a Ciência e a Tecnologia, MK by the Agència de Gestió d’Ajuts Universitaris i de Recerca (Generalitat de Catalunya) and JR by a Junior Excellence Research Group of the Jackstädt foundation.

Author Contributions

ACQ, MK, AN, JR, AKB, JK, CR, NR and ML-G performed experiments. ACQ, NV, AM-T, G Clot, G Castellano, SB, IS, XSP, RS, CR, AL-G and JIM-S analyzed and interpreted data. EMM-P, MP and MA performed sample preparation and quality control. NV, AM-T, SJ, AM, DC, MA, MR, JD, EG, MG-D and MJSD reviewed the pathologic and clinical data and confirmed diagnosis. CL-O, EC and JIM-S designed the study. ACQ, NV, EC, AL-G and JIM-S wrote the manuscript. All authors read and approved the final version of the manuscript.

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Author notes

  1. A C Queirós and N Villamor: These authors contributed equally to this study as first authors.

  2. A López-Guillermo and J I Martín-Subero: These authors contributed equally to this study as senior authors.

Authors and Affiliations

  1. Departamento de Anatomía Patológica, Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Farmacología y Microbiología, Universitat de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain

    A C Queirós, N Villamor, G Clot, M Kulis, A Navarro, C Royo, N Russiñol, G Castellano, M Pinyol, S Bea, I Salaverria, M López-Guerra, D Colomer, M Aymerich, M Rozman, E Campo & J I Martín-Subero

  2. Servicio de Hematología, Hospital Clínic de Barcelona, IDIBAPS, Barcelona, Spain

    A Martinez-Trillos, J Delgado, E Giné & A López-Guillermo

  3. Institute of Human Genetics, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Campus Kiel, Germany

    E M M Penas, J Richter, A K Bergmann, J Kolarova & R Siebert

  4. MRC Toxicology Unit Leicester, Leicester, UK

    S Jayne & A Majid

  5. Servicio de Hematología, Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Universidad de Salamanca, Salamanca, Spain,

    M González-Díaz

  6. Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain

    X S Puente & C López-Otín

  7. Ernest and Helen Scott Haematological Research Institute, Leicester University, Leicester, UK

    M J S Dyer

  8. Josep Carreras Leukemia Research Institute, Barcelona, Spain

    C Rozman

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  1. A C Queirós
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Correspondence to A López-Guillermo or J I Martín-Subero.

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Queirós, A., Villamor, N., Clot, G. et al. A B-cell epigenetic signature defines three biologic subgroups of chronic lymphocytic leukemia with clinical impact. Leukemia 29, 598–605 (2015). https://doi.org/10.1038/leu.2014.252

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