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Edelmann J, Holzmann K, Tausch E, Saunderson EA, Jebaraj BMC, Steinbrecher D, Dolnik A, Blätte TJ, Landau DA, Saub J, Estenfelder S, Ibach S, Cymbalista F, Leblond V, Delmer A, Bahlo J, Robrecht S, Fischer K, Goede V, Bullinger L, Wu CJ, Mertens D, Ficz G, Gribben JG, Hallek M, Döhner H, Stilgenbauer S. Genomic alterations in high-risk chronic lymphocytic leukemia frequently affect cell cycle key regulators and NOTCH1-regulated transcription. Haematologica 2019; 105:1379-1390. [PMID: 31467127 PMCID: PMC7193490 DOI: 10.3324/haematol.2019.217307] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/23/2019] [Indexed: 12/14/2022] Open
Abstract
To identify genomic alterations contributing to the pathogenesis of high-risk chronic lymphocytic leukemia (CLL) beyond the well-established role of TP53 aberrations, we comprehensively analyzed 75 relapsed/refractory and 71 treatment-naïve high-risk cases from prospective clinical trials by single nucleotide polymorphism arrays and targeted next-generation sequencing. Increased genomic complexity was a hallmark of relapsed/refractory and treatment-naïve high-risk CLL. In relapsed/refractory cases previously exposed to the selective pressure of chemo(immuno)therapy, gain(8)(q24.21) and del(9)(p21.3) were particularly enriched. Both alterations affect key regulators of cell-cycle progression, namely MYC and CDKN2A/B. While homozygous CDKN2A/B loss has been directly associated with Richter transformation, we did not find this association for heterozygous loss of CDKN2A/B. Gains in 8q24.21 were either focal gains in a MYC enhancer region or large gains affecting the MYC locus, but only the latter type was highly enriched in relapsed/refractory CLL (17%). In addition to a high frequency of NOTCH1 mutations (23%), we found recurrent genetic alterations in SPEN (4% mutated), RBPJ (8% deleted) and SNW1 (8% deleted), all affecting a protein complex that represses transcription of NOTCH1 target genes. We investigated the functional impact of these alterations on HES1, DTX1 and MYC gene transcription and found derepression of these NOTCH1 target genes particularly with SPEN mutations. In summary, we provide new insights into the genomic architecture of high-risk CLL, define novel recurrent DNA copy number alterations and refine knowledge on del(9p), gain(8q) and alterations affecting NOTCH1 signaling. This study was registered at ClinicalTrials.gov with number NCT01392079.
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Affiliation(s)
- Jennifer Edelmann
- Department of Internal Medicine III, Ulm University, Ulm, Germany .,Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Emily A Saunderson
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | | | - Anna Dolnik
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Tamara J Blätte
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Dan A Landau
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.,New York Genome Center, New York, NY, USA
| | - Jenny Saub
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Sven Estenfelder
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Stefan Ibach
- Wissenschaftlicher Service Pharma GmbH (WiSP), Langenfeld, Germany
| | | | | | - Alain Delmer
- Service d'Hématologie Clinique, CHU de Reims, Reims, France
| | - Jasmin Bahlo
- Department of Internal Medicine I, University of Cologne, Cologne, Germany
| | - Sandra Robrecht
- Department of Internal Medicine I, University of Cologne, Cologne, Germany
| | - Kirsten Fischer
- Department of Internal Medicine I, University of Cologne, Cologne, Germany
| | - Valentin Goede
- Department of Internal Medicine I, University of Cologne, Cologne, Germany
| | - Lars Bullinger
- Department of Internal Medicine III, Ulm University, Ulm, Germany.,Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Catherine J Wu
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Daniel Mertens
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Gabriella Ficz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - John G Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Michael Hallek
- Department of Internal Medicine I, University of Cologne, Cologne, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University, Ulm, Germany
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