ASXL1, TP53 and IKZF3 mutations are present in the chronic phase and blast crisis of chronic myeloid leukemia

Abstract Targeted therapies against the BCR-ABL1 kinase have revolutionized treatment of chronic phase (CP) chronic myeloid leukemia (CML). In contrast, management of blast crisis (BC) CML remains challenging because BC cells acquire complex molecular alterations that confer stemness features to progenitor populations and resistance to BCR-ABL1 tyrosine kinase inhibitors. Comprehensive models of BC transformation have proved elusive because of the rarity and genetic heterogeneity of BC, but are important for developing biomarkers predicting BC progression and effective therapies. To better understand BC, we performed an integrated multiomics analysis of 74 CP and BC samples using whole-genome and exome sequencing, transcriptome and methylome profiling, and chromatin immunoprecipitation followed by high-throughput sequencing. Employing pathway-based analysis, we found the BC genome was significantly enriched for mutations affecting components of the polycomb repressive complex (PRC) pathway. While transcriptomically, BC progenitors were enriched and depleted for PRC1- and PRC2-related gene sets respectively. By integrating our data sets, we determined that BC progenitors undergo PRC-driven epigenetic reprogramming toward a convergent transcriptomic state. Specifically, PRC2 directs BC DNA hypermethylation, which in turn silences key genes involved in myeloid differentiation and tumor suppressor function via so-called epigenetic switching, whereas PRC1 represses an overlapping and distinct set of genes, including novel BC tumor suppressors. On the basis of these observations, we developed an integrated model of BC that facilitated the identification of combinatorial therapies capable of reversing BC reprogramming (decitabine+PRC1 inhibitors), novel PRC-silenced tumor suppressor genes (NR4A2), and gene expression signatures predictive of disease progression and drug resistance in CP.

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Homozygous deletions of the p16 tumor-suppressor gene are associated with lymphoid transformation of chronic myeloid leukemia

Blood ◽

10.1182/blood.v85.8.2013.bloodjournal8582013 ◽

1995 ◽

Vol 85 (8) ◽

pp. 2013-2016 ◽

Cited By ~ 136

Author(s):

H Sill ◽

JM Goldman ◽

NC Cross

Keyword(s):

Chronic Myeloid Leukemia ◽

Tumor Suppressor ◽

Myeloid Leukemia ◽

Lymphoblastic Leukemia ◽

Blast Crisis ◽

Chronic Phase ◽

P16 Gene ◽

Number Of Patients ◽

Wide Range ◽

Homozygous Deletions

The p16 gene, also referred to as MTS1, INK4, CDK4I, or CDKN2, at chromosome 9p21 has recently been described as a tumor suppressor that may be involved in a wide range of tumors. We have used a semiquantitative multiplex polymerase chain reaction assay to search for deletions of the p16 gene in 34 patients with chronic myeloid leukemia in blast crisis (CML BC), 19 patients with acute lymphoblastic leukemia (ALL), and 25 patients with acute myeloid leukemia (AML). Homozygous deletions of p16 exons were found in 5 of 10 (50%) patients with CML in lymphoid BC and in 5 (26%) ALL patients, but in only 1 (2%) case with AML. No deletions were found in CML BC of nonlymphoid phenotype. Comparison of chronic phase DNA or remission DNA with acute leukemia DNA in 5 individuals showed that the p16 deletions were acquired and not inherited, directly implicating these lesions in the pathogenesis of the disease. We conclude that functional elimination of the p16 gene, or a closely mapping gene, is involved in a significant number of patients with CML in lymphoid transformation.

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Adenosine deaminase and ecto-5'-nucleotidase activities in various leukemias with special reference to blast crisis: significance of ecto- 5'-nucleotidase in lymphoid blast crisis of chronic myeloid leukemia

Blood ◽

10.1182/blood.v58.6.1107.1107 ◽

1981 ◽

Vol 58 (6) ◽

pp. 1107-1111 ◽

Cited By ~ 18

Author(s):

M Koya ◽

T Kanoh ◽

H Sawada ◽

H Uchino ◽

K Ueda

Keyword(s):

Chronic Myeloid Leukemia ◽

Adenosine Deaminase ◽

Myeloid Leukemia ◽

Blast Crisis ◽

Chronic Phase ◽

Lymphocytic Leukemia ◽

Lymphoid Cells ◽

Leukemia Cells ◽

Terminal Deoxynucleotidyl Transferase ◽

Acute Myeloid Leukemia Cells

Abstract Adenosine deaminase (ADA) and ecto-5′-nucleotidase (5′-N) activities were examined in peripheral leukocytes from patients with leukemias, including nine patients with chronic myeloid leukemia (CML) in blast crisis. Four of none cases of CML in blast crisis were myeloid and the remaining lymphoid morphologically. The diagnosis of CML in lymphoid blast crisis was further contributed by the measurement of terminal deoxynucleotidyl transferase (TdT) activity. In all four cases of lymphoid blast crisis and one of myeloid blast crisis, leukemia cells had high 5′-N activity, while there was a little or no detectable activity in those from four cases of myeloid blast crisis and all of CML in chronic phase. ADA activity was high in seven of nine patients with blast crisis. Taken together, leukemia cells from two cases of lymphoid blast crisis had high ADA and 5′-N activities comparable to those in acute lymphocytic leukemia (ALL) cells. In contrast, the enzyme activities of leukemia cells from all but one patient in myeloid blast crisis were in a range similar to acute myeloid leukemia cells. The implications of these findings are as follows: (1) 5′-N may be used as a new biochemical marker of CML in lymphoid blast crisis. (2) Some lymphoid cells of CML in blast crisis have high ADA, 5′-N, and TdT activities and thus are very similar to ALL cells.

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Successful allogeneic bone marrow transplantation after reversion to chronic phase of blast crisis in chronic myeloid leukemia

American Journal of Hematology ◽

10.1002/ajh.2830110211 ◽

1981 ◽

Vol 11 (2) ◽

pp. 205-207 ◽

Cited By ~ 4

Author(s):

J. P. Vernant ◽

M. Rodet ◽

H. Rochant ◽

F. Feuilhade ◽

A. Thuran ◽

...

Keyword(s):

Bone Marrow ◽

Bone Marrow Transplantation ◽

Chronic Myeloid Leukemia ◽

Marrow Transplantation ◽

Myeloid Leukemia ◽

Blast Crisis ◽

Allogeneic Bone Marrow Transplantation ◽

Chronic Phase ◽

Allogeneic Bone Marrow ◽

Allogeneic Bone

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Molecular biology of bcr-abl1–positive chronic myeloid leukemia

Blood ◽

10.1182/blood-2008-03-144790 ◽

2009 ◽

Vol 113 (8) ◽

pp. 1619-1630 ◽

Cited By ~ 370

Author(s):

Alfonso Quintás-Cardama ◽

Jorge Cortes

Keyword(s):

Chronic Myeloid Leukemia ◽

Myeloid Leukemia ◽

Kinase Inhibitors ◽

Current Knowledge ◽

Blast Crisis ◽

Chronic Phase ◽

Oncogenic Signaling ◽

Stem Cell Quiescence ◽

Oncogenic Signaling Pathways

Abstract Chronic myeloid leukemia (CML) has been regarded as the paradigmatic example of a malignancy defined by a unique molecular event, the BCR-ABL1 oncogene. Decades of research zeroing in on the role of BCR-ABL1 kinase in the pathogenesis of CML have culminated in the development of highly efficacious therapeutics that, like imatinib mesylate, target the oncogenic kinase activity of BCR-ABL1. In recent years, most research efforts in CML have been devoted to developing novel tyrosine kinase inhibitors (TKIs) as well as to elucidating the mechanisms of resistance to imatinib and other TKIs. Nonetheless, primordial aspects of the pathogenesis of CML, such as the mechanisms responsible for the transition from chronic phase to blast crisis, the causes of genomic instability and faulty DNA repair, the phenomenon of stem cell quiescence, the role of tumor suppressors in TKI resistance and CML progression, or the cross-talk between BCR-ABL1 and other oncogenic signaling pathways, still remain poorly understood. Herein, we synthesize the most relevant and current knowledge on such areas of the pathogenesis of CML.

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Nilotinib for imatinib-resistant or -intolerant chronic myeloid leukemia in chronic phase, accelerated phase, or blast crisis: A single- and multiple-dose, open-label pharmacokinetic study in Chinese patients

Clinical Therapeutics ◽

10.1016/j.clinthera.2009.07.016 ◽

2009 ◽

Vol 31 (7) ◽

pp. 1568-1575 ◽

Cited By ~ 14

Author(s):

Li Zhou ◽

Fanyi Meng ◽

Ophelia Yin ◽

Jianxiang Wang ◽

Ying Wang ◽

...

Keyword(s):

Chronic Myeloid Leukemia ◽

Pharmacokinetic Study ◽

Myeloid Leukemia ◽

Multiple Dose ◽

Blast Crisis ◽

Chronic Phase ◽

Chinese Patients ◽

Open Label ◽

Imatinib Resistant

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Centrosome Aberrations in Chronic Myeloid Leukemia (CML) Are Correlated with Disease Progression and Chromosome Instability.

Blood ◽

10.1182/blood.v104.11.2949.2949 ◽

2004 ◽

Vol 104 (11) ◽

pp. 2949-2949

Author(s):

Michelle Giehl ◽

Alice Fabarius ◽

Chun Zheng ◽

Oliver Frank ◽

Andreas Hochhaus ◽

...

Keyword(s):

Chronic Myeloid Leukemia ◽

Disease Progression ◽

Myeloid Leukemia ◽

Blast Crisis ◽

Chromosome Instability ◽

Chronic Phase ◽

Normal Karyotype ◽

Benign Tumors ◽

Preneoplastic Lesions ◽

Cd34 Cells

Abstract Purpose: Numerical and structural centrosome abnormalities are hallmarks of a variety of cancers and have been implicated in chromosome missegregation, chromosomal instability, and aneuploidy. These phenomena already occur in preneoplastic lesions like oral leukoplakia, early cervical neoplasias, and small benign tumors of colon and breast. Moreover, deviations from normal karyotype seem to increase as tumors enlarge and become malignant. Genetic instability is a common feature in chronic myeloid leukemia (CML). We sought to establish a relationship between centrosome abnormalities and cytogenetic aberrations in CD34+ cells from CML patients at diagnosis (chronic phase - CP) and in blast crisis (BC). Methods: Diagnosis of CML was established by hematologic, cytogenetic and molecular parameters. Treatment was performed according to the protocols of the German CML study group (www.kompetenznetz-leukaemie.de). CD34+ cells from ten umbilical cord blood specimens served as negative controls. Centrosome number and morphology were analyzed by immunofluorescence microscopy. In brief, CD34+ cells from ficollized peripheral blood samples were concentrated by magnetic cell sorting (MACS) and cytospun onto coated slides. After methanol fixation cells were incubated with antibodies directed to centrosomal proteins Pericentrin and gamma-Tubulin. Antibody-antigen complexes were stained by incubation with FITC- and Cy3-conjugated secondary antibodies. Results: CML CP samples tested at initial diagnosis (n=20) already displayed numerical and structural centrosome aberrations (30.0% +/−2.3) as compared with corresponding normal control cells (n=10) (2.3% +/−1.1). In BC samples (n=10) an increase of centrosome aberrations was observed (58.0% +/−2.0). Conclusion: The findings suggest that centrosome defects in CML occur early and are already present at primary diagnosis. Centrosome defects may contribute to disease progression by generation of further chromosome instability leading to accumulation of alleles carrying pro-oncogenic mutations and loss of alleles containing normal tumor suppressor genes and thus accelerating complex genomic changes associated with CML BC.

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Cytogenetic Analysis of 1863 Chineses Patients with Chronic Myeloid Leukemia

Blood ◽

10.1182/blood.v118.21.4888.4888 ◽

2011 ◽

Vol 118 (21) ◽

pp. 4888-4888

Author(s):

Qitian Mu ◽

Qiuling Ma ◽

Yungui Wang ◽

Xiangmin Tong ◽

Zhimei Chen ◽

...

Keyword(s):

Chronic Myeloid Leukemia ◽

Disease Progression ◽

Myeloid Leukemia ◽

Conflicts Of Interest ◽

Blast Crisis ◽

Chronic Phase ◽

Newly Diagnosed ◽

Monocytic Differentiation ◽

Granulocytic Differentiation ◽

Monosomy 7

Abstract Abstract 4888 Background: Cytogenetic analyses of chronic myeloid leukemia (CML) have been performed previously in a large number of reports, but systematical research based on large sample sizes is seldom available. In order to further elucidate the cytogenetic nature of CML, we analyzed retrospectively the cytogenetic profiles of 1863 Ph/BCR-ABL-positive CML patients from a research center in China. Results: Of 1266 newly diagnosed CML patients, the median age was 41 years, which is younger than the median age of diagnosis in western populations. The incidence of additional chromosome abnormalities(ACAs) was 3.1% in newly-diagnosed chronic phase(CP), 9.1% in CP after therapy, 35.4% in accelerated phase(AP) and 52.9% in blast phase(BP), reflecting cytogenetic evolution with CML progression. 5.3% patients harbored a variant Ph translocation. A higher prevalence of ACAs was observed in variant Ph translocations than in classical t(9;22) in the disease progression, especially in BP(88.2% vs. 50%, p=0.002). Moreover, a hyperdiploid karyotype and trisomy 8 were closely correlated with myeloid blast crisis(BC) while a hypodiploid karyotype and monosomy 7 were associated with lymphoid-BC. Among subsets of myeloid-BC, compared with myeloid-BC with granulocytic differentiation or monocytic differentiation, myeloid-BC with minimal differentiation had higher ACAs rate (80% vs.46.8%, p=0.009 and 80% vs. 42.9%, p=0.006). Conclusion: CML tends to afflict younger population in China. In the disease progression, the incident of ACAs was higher in variant Ph translocations than in classical t(9;22). Among subsets of myeloid-BC, myeloid with minimal differentiation had distinct cytogenetic features. Disclosures: No relevant conflicts of interest to declare.

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B-Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL) Specific Copy Number Alterations Are Unique For Progressive Pediatric Chronic Myeloid Leukemia (CML): A Large Cohort Study

Blood ◽

10.1182/blood.v122.21.2715.2715 ◽

2013 ◽

Vol 122 (21) ◽

pp. 2715-2715

Author(s):

Naomi E van der Sligte ◽

Manuela Krumbholz ◽

Agata Pastorczak ◽

Blanca Scheijen ◽

Josephine T. Tauer ◽

...

Keyword(s):

Chronic Myeloid Leukemia ◽

B Cell ◽

Disease Progression ◽

Copy Number ◽

Myeloid Leukemia ◽

Blast Crisis ◽

Chronic Phase ◽

Copy Number Alterations ◽

Cell Precursor ◽

Predict Disease Progression

Abstract Chronic myeloid leukemia (CML) is a rare malignancy in children and is mostly diagnosed in the chronic phase (CP). In adults, the five-year overall survival rate is 89% for patients on Imatinib and disease progression occurs in 1-3% per year (Druker 2006). Once a blast crisis (BC) has occurred, treatment options are limited with a median survival of only a few months (Cortes 2008). Therefore, early recognition of patients at risk for developing a BC is desirable. Besides the translocation t(9;22)(q34;q11), IKZF1, PAX5, and CDKN2A deletions have been reported in CML lymphoid blast crisis (LyBC) of both adult and pediatric patients (Mullighan 2008, Alpár 2012). The aim of this study was to investigate the presence of IKZF1 deletions and other copy number alterations (CNAs) by MLPA analysis in a large cohort of pediatric CML patients at time of diagnosis in order to determine whether CNAs commonly found in pediatric ALL might predict disease progression and / or treatment response. Between October 1991 and October 2012 a total of 86 children with newly diagnosed CML were included. The median follow up was 31 months. Among the 86 patients, 82 patients were diagnosed in CP, 2 patients in accelerated phase (AP), and 2 patients in LyBC. Six patients experienced progression to a BC respectively a myeloid blast crisis (MyBC) (N=2) and LyBC (N=4). At time of diagnosis, an IKZF1 deletion was detected in one patient diagnosed with CML-AP (Table A, patient no 58). IKZF1 and EBF1 deletions were detected in one patient diagnosed with CML-LyBC (Table A, patient no 22). No CNAs were detected in the 82 patients diagnosed with CML-CP. At time of disease progression, new CNAs were detected at time of the LyBC (Table A, patient no 62, 64, and 67). Due to the absence of material no CNAs could be detected in both patients experiencing a MyBC. In conclusion, we were able to detect CNAs in progressive CML disease (CML-AP and CML-LyBC) and not in the samples at the time of chronic phase in this large pediatric cohort of CML patients. Therefore, the investigated CNAs could not be used to predict disease progression at time of diagnosis. The CNAs detected in patients with progressive CML were similar to specific CNAs detected in pediatric B-cell precursor ALL, indicating a similar disease development (Kuiper 2010). Additionally, our results are in accordance with existing literature, suggesting that mechanisms of disease progression in pediatric and adult CML might be similar (Brazma, 2007). Disclosures: No relevant conflicts of interest to declare.

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