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Integrative genomic analysis reveals cancer-associated mutations at diagnosis of CML in patients with high-risk disease. Blood 2018; 132:948-961. [PMID: 29967129 DOI: 10.1182/blood-2018-02-832253] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 06/20/2018] [Indexed: 12/12/2022] Open
Abstract
Genomic events associated with poor outcome in chronic myeloid leukemia (CML) are poorly understood. We performed whole-exome sequencing, copy-number variation, and/or RNA sequencing for 65 patients to discover mutations at diagnosis and blast crisis (BC). Forty-six patients with chronic-phase disease with the extremes of outcome were studied at diagnosis. Cancer gene variants were detected in 15 (56%) of 27 patients with subsequent BC or poor outcome and in 3 (16%) of 19 optimal responders (P = .007). Frequently mutated genes at diagnosis were ASXL1, IKZF1, and RUNX1 The methyltransferase SETD1B was a novel recurrently mutated gene. A novel class of variant associated with the Philadelphia (Ph) translocation was detected at diagnosis in 11 (24%) of 46 patients comprising fusions and/or rearrangement of genes on the translocated chromosomes, with evidence of fragmentation, inversion, and imperfect sequence reassembly. These were more frequent at diagnosis in patients with poor outcome: 9 (33%) of 27 vs 2 (11%) of 19 optimal responders (P = .07). Thirty-nine patients were tested at BC, and all had cancer gene variants, including ABL1 kinase domain mutations in 58%. However, ABL1 mutations cooccurred with other mutated cancer genes in 89% of cases, and these predated ABL1 mutations in 62% of evaluable patients. Gene fusions not associated with the Ph translocation occurred in 42% of patients at BC and commonly involved fusion partners that were known cancer genes (78%). Genomic analysis revealed numerous relevant variants at diagnosis in patients with poor outcome and all patients at BC. Future refined biomarker testing of specific variants will likely provide prognostic information to facilitate a risk-adapted therapeutic approach.
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Lund HL, Hughesman CB, McNeil K, Clemens S, Hocken K, Pettersson R, Karsan A, Foster LJ, Haynes C. Initial diagnosis of chronic myelogenous leukemia based on quantification of M-BCR status using droplet digital PCR. Anal Bioanal Chem 2015; 408:1079-94. [DOI: 10.1007/s00216-015-9204-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/11/2015] [Accepted: 11/18/2015] [Indexed: 01/25/2023]
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Bennour A, Saad A, Sennana H. Chronic myeloid leukemia: Relevance of cytogenetic and molecular assays. Crit Rev Oncol Hematol 2015; 97:263-74. [PMID: 26412717 DOI: 10.1016/j.critrevonc.2015.08.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 07/07/2015] [Accepted: 08/24/2015] [Indexed: 12/12/2022] Open
Abstract
Chronic myeloid leukemia (CML) is the prototype cytogenetic malignancy. Even before the development of basic G- and R-banding techniques, CML was found to be associated with a persistent chromosomal abnormality, the Philadelphia (Ph) chromosome. Banding technology later showed the marker chromosome to be a translocation between the breakpoint cluster region (BCR) on chromosome 22q11.2 and the Abelson proto-oncogene (ABL) on chromosome 9q34. Further advances in cytogenetic and molecular biology have also contributed to the understanding, diagnosis, and treatment of CML. Fluorescent in situ hybridization (FISH) has revealed cryptic translocations in most cases of Ph-negative CML. Additional rare chromosomal variant translocations have been discovered as well. The understanding of cytogenetic and molecular physiopathology of CML has led to the use of tyrosine kinase inhibitors as treatment for this disease with spectacular success. Over the 40 years since being identified as the first cytogenetic disease, CML has become the greatest success in translating the basic science of oncology into the treatment of patients with cancer. In this review we will not only summarize the biology of CML, recent progress in the delineation of mechanisms and treatment strategies, but also we will discuss the laboratory tools used for diagnosing CML, for monitoring during treatment and for revealing point mutations and additional chromosomal abnormalities. In doing so, we will describe in detail our individual research on CML, identifying why and how these tests were performed to help to explain CML subgroups and clinical significance of additional chromosomal abnormalities.
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Affiliation(s)
- Ayda Bennour
- Department of Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Teaching Hospital, Sousse, Tunisia.
| | - Ali Saad
- Department of Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Teaching Hospital, Sousse, Tunisia
| | - Halima Sennana
- Department of Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Teaching Hospital, Sousse, Tunisia
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Cytogenetic and molecular characteristics of 25 Chilean patients with a variant Ph translocation. Cancer Genet 2011; 204:410-2. [PMID: 21872829 DOI: 10.1016/j.cancergen.2011.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 06/14/2011] [Accepted: 06/29/2011] [Indexed: 11/20/2022]
Abstract
Chronic myeloid leukemia (CML) is characterized by the presence of the Philadelphia chromosome (Ph), which results from a balanced translocation between chromosomes 9 and 22, the t(9;22)(q34;q11.2). In 5-10% of the cases, variants of the Ph (vPh) are detected, involving various breakpoints in addition to 9q34 and 22q11.2. Deletions on the der(9) and der(22) can be detected in approximately 10-15% of CML patients. The frequency of a deletion of the der(9) in vPh CML is variable. Most studies have shown high frequencies (30-45%) in this subgroup. We report the cytogenetic evaluation of 25 vPh cases, which represents 6.8% of the CML cases diagnosed at one institution in 20 years. The breakpoints of the partners of the vPh in our patients agree with those reported previously, except for a novel 18q23. We found a low incidence of deletions of the der(9) (10%) and der(22) (5%) in these patients, contrasting with several reports in the literature. This finding may reflect the extensive spectrum of aberrations in vPh, and the possibility that a considerable group of these aberrations may not affect the genetic stability of 5'ABL1 and 3'BCR. Epidemiologic differences may also exist and could explain our results. These differences would require further investigation.
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Bennour A, Ouahchi I, Ben Youssef Y, Zaier M, Laatiri MA, Harrabi I, Meddeb B, Elloumi M, Khelif A, Saad A, Sennana H. Molecular cytogenetic study of derivative chromosome 9 deletion in chronic myeloid leukemia patients. Med Oncol 2011; 29:1151-60. [DOI: 10.1007/s12032-011-9918-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 03/18/2011] [Indexed: 10/18/2022]
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Saito M, Morioka M. [An elderly case of chronic myeloid leukemia in which BCR/ABL decreased or disappeared, following imatinib therapy after each episode of blast crisis]. Nihon Ronen Igakkai Zasshi 2010; 47:86-91. [PMID: 20339212 DOI: 10.3143/geriatrics.47.86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An elderly woman with chronic myeloid leukemia-chronic phase (CML-CP) aged at 67 underwent imatinib therapy. Ph chromosomes gradually decreased, but imatinib was discontinued after 10 months because of aggravated skin eruptions. Three months later, myeloid blast crisis (MBC) occurred. DXR+VCR+PSL chemotherapy and imatinib therapy was administered, and return to CP (RTC) was achieved with the disappearance of Ph chromosomes and a marked decrease of BCR/ABL (FISH). Although imatinib therapy was continued, a second MBC was diagnosed, 13 months after RTC. Chemotherapy, using mainly VCR+PSL was performed and imatinib was discontinued. RTC was achieved, and Ph chromosomes and BCR/ABL again disappeared. One year later, a 3rd MBC developed, and chemotherapy using Ara-C+DNR was performed. A 3rd RTC was achieved, and BCR/ABL decreased. This CML case was resistant to imatinib, but chemotherapy was effective in all 3 episodes of MBC, and BCR/ABL decreased or disappeared.
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GHAITH F, ABDOU S, EL-BENDARY A, SHAHIN D, EID M, MEGEED WA, EL-SHEIKH I, FARRAG W, YOUSUF S. Prognostic relevance of 9q34 deletion and the suppressor of cytokine signalling-1 in CML patients. Int J Lab Hematol 2010; 32:103-12. [DOI: 10.1111/j.1751-553x.2009.01143.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Richebourg S, Eclache V, Perot C, Portnoi MF, Van den Akker J, Terré C, Maareck O, Soenen V, Viguié F, Laï JL, Andrieux J, Corm S, Roche-Lestienne C. Mechanisms of genesis of variant translocation in chronic myeloid leukemia are not correlated with ABL1 or BCR deletion status or response to imatinib therapy. ACTA ACUST UNITED AC 2008; 182:95-102. [PMID: 18406870 DOI: 10.1016/j.cancergencyto.2008.01.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 12/20/2007] [Accepted: 01/14/2008] [Indexed: 11/30/2022]
MESH Headings
- Benzamides
- Cytogenetic Analysis
- Female
- Gene Deletion
- Humans
- Imatinib Mesylate
- In Situ Hybridization, Fluorescence
- Karyotyping
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Male
- Piperazines/therapeutic use
- Prognosis
- Protein Kinase Inhibitors/therapeutic use
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Proto-Oncogene Proteins c-abl/genetics
- Proto-Oncogene Proteins c-bcr/genetics
- Pyrimidines/therapeutic use
- Retrospective Studies
- Survival Rate
- Translocation, Genetic
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Affiliation(s)
- Steven Richebourg
- Laboratory of Medical Genetics, Hospital Jeanne de Flandre, University Hospital Regional Center-CHRU, Avenue Eugène Avinée, 59037 Lille cedex, France
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Douet-Guilbert N, Morel F, Quemener S, Maguer A, Le Bris MJ, Morice P, Berthou C, De Braekeleer M. Deletion size characterization of der(9) deletions in Philadelphia-positive chronic myeloid leukemia. ACTA ACUST UNITED AC 2006; 170:89-92. [PMID: 17011977 DOI: 10.1016/j.cancergencyto.2006.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Accepted: 06/14/2006] [Indexed: 10/24/2022]
Abstract
About 95% of the CML patients with chronic myeloid leukemia (CML) have a Philadelphia chromosome resulting from a reciprocal translocation between bands 9q34 and 22q11.2 that juxtaposes the 3' region of the ABL gene to the 5' region of BCR. Over the past few years, submicroscopic deletions due to the loss of sequences proximal to chromosome 9 breakpoint or distal to chromosome 22 breakpoint have been found using fluorescence in situ hybridization (FISH). Among 150 CML bone marrow samples analyzed by molecular cytogenetics in our laboratory, 11 had a der(9) deletion detectable by FISH (deletion of the 5'ABL region and 3'BCR region in 10 samples and deletion of the 5'ABL region solely in 1 sample). To delineate the size of the deletions, FISH mapping was performed using 22 bacterial artificial chromosomes (BACs), 11 on either side of the breakpoints, the mean distance between BACs being 0.5 Mb. The deletion size of the 5'ABL region on the der(9) extended from 2 to 5 Mb, the minimal deletion size being localized between BACs RP11-101E3 and RP11-83J21. In two patients, the deletion size of the 3'BCR region was about 500 kb (between RP11-80O7 and RP11-681C06). The poor prognosis associated with these deletions was postulated by several workers to be explained by haploinsufficiency of a tumor suppressor gene. However, in our cases, the hypothetical deletion of one or more tumor suppressor genes is not sufficient to explain the poor response to interferon therapy, but the good response to imatinib treatment. We think that there could be one or more genes coding for interferon receptors or for proteins acting directly or indirectly with these receptors in the deleted regions.
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Affiliation(s)
- Nathalie Douet-Guilbert
- Laboratory of Histology, Embryology and Cytogenetics, Faculty of Medicine and Health Sciences, Université de Bretagne Occidentale (UBO), Brest, France
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