Methylation Profiling of Three Homogenous Cancers: Chronic Myelogenous Leukemia (CML), Acute Promyelocytic Leukemia (APL) and Gastrointestinal Stromal Tumors (GIST).

Abstract Aberrant promoter DNA methylation is found in many cancers and is associated with aberrant gene silencing. Some abnormal cancer related methylation changes have been associated with a number of clinical features including pathologic features, prognosis, and treatment response. However, other DNA methylation changes do not appear to have phenotypic consequences and may reflect a stochastic event or a downstream event of tumorogenesis. In order to obtain a better understanding of DNA methylation changes in cancer we chose to study three very homogenous cancers: CML, APL and GIST. CML is a leukemia characterized by the Philadelphia chromosome, t(9:22), and is very sensitive to imatinib mesylate. APL is another leukemia characterized by a specific chromosomal translocation, t(15:17), and a high response to all-trans-retinoic acid. Lastly, GIST is a sarcoma with a high frequency of c-kit mutations and sensitivity to imatinib mesylate. In this study, we used bisulfite PCR/Pyrosequencing to accurately quantitate the absolute amount of DNA methylation of 15 genes (MDR, ID4, PROX1, ER, Jun B, p73, p15, ABL1, THBS1, p16, RASSF1A, RUNX3, SOCS1, RARA, and PML). We analyzed the blood and bone marrow of 58 patients with CML (chronic phase n=32, accelerated phase n=11, blast crisis n=13), and 23 patients with APL. We also analyzed tumors from 9 GIST patients. We show clearly that DNA methylation changes are not random events, but related to the biology of the cancer. We have identified at least four specific types of aberrant DNA methylation. Cancer specific hypermethylation of genes related to clinical phenotype. ID4 and PROX1 were hypermethylated in APL and CML, but not GIST. Methylation of these genes in CML was strongly associated with the development of blast crisis (P=0.0005), and the methylation of these two genes was also associated with an increase in the percentage of bone marrow blasts in APL (p<0.0001). DNA methylation related to geographic changes that are related to recombinatorial translocation events. ABL hypermethylation was isolated to CML patients who have the bcr-abl translocation. In contrast, RARalpha hypermethylation was unique to APL patients, who have the PML-RARalpha translocation. General DNA methylation changes associated with malignant transformation. Hypermethylation of MDR, ER, p16 and p15 was found in all three types of cancer. Interestingly, RUNX3 was hypermethylated in normal tissue, but became hypomethylated in all three cancers studied. Genes that are resistant to hypermethylation (p73 and RASSF1A). In conclusion, ID4 and PROX1 hypermethylation is a marker of disease progression in leukemia such as blast crisis in CML and higher percentage of bone marrow blasts in APL. Methylation of ABL and RARalpha are specific to CML and APL, respectively, and is likely related to specific chromosomal translocations. There are genes that are subject to small increases or decreases in DNA methylation that do not correlate with any obvious biology or clinical features. Finally, there are genes that are clearly resistant to DNA methylation changes. Our study shows that DNA methylation changes are clearly non-random events, and suggests there are several mechanisms that drive DNA methylation changes.

Download Full-text

CNS blast crisis of chronic myelogenous leukemia in a patient with a major cytogenetic response in bone marrow associated with low levels of imatinib mesylate and its N-desmethylated metabolite in cerebral spinal fluid

Annals of Hematology ◽

10.1007/s00277-003-0829-4 ◽

2004 ◽

Vol 83 (6) ◽

pp. 401-402 ◽

Cited By ~ 32

Author(s):

Martin Bornhauser ◽

Andreas Jenke ◽

Jens Freiberg-Richter ◽

J�rgen Radke ◽

Ulrich S. Schuler ◽

...

Keyword(s):

Bone Marrow ◽

Imatinib Mesylate ◽

Chronic Myelogenous Leukemia ◽

Cerebral Spinal Fluid ◽

Blast Crisis ◽

Cytogenetic Response ◽

Spinal Fluid ◽

Myelogenous Leukemia ◽

Low Levels

Download Full-text

Activation of a novel Bcr/Abl destruction pathway by WP1130 induces apoptosis of chronic myelogenous leukemia cells

Blood ◽

10.1182/blood-2006-02-005579 ◽

2007 ◽

Vol 109 (8) ◽

pp. 3470-3478 ◽

Cited By ~ 56

Author(s):

Geoffrey A. Bartholomeusz ◽

Moshe Talpaz ◽

Vaibhav Kapuria ◽

Ling Yuan Kong ◽

Shimei Wang ◽

...

Keyword(s):

Imatinib Mesylate ◽

Chronic Myelogenous Leukemia ◽

Colony Formation ◽

Blast Crisis ◽

Philadelphia Chromosome ◽

Point Mutations ◽

Myelogenous Leukemia ◽

Wild Type ◽

Protein Levels ◽

Kinase Inhibitory Activity

Abstract Imatinib mesylate (Gleevec) is effective therapy against Philadelphia chromosome–positive leukemia, but resistance develops in all phases of the disease. Bcr/Abl point mutations and other alterations reduce the kinase inhibitory activity of imatinib mesylate; thus, agents that target Bcr/Abl through unique mechanisms may be needed. Here we describe the activity of WP1130, a small molecule that specifically and rapidly down-regulates both wild-type and mutant Bcr/Abl protein without affecting bcr/abl gene expression in chronic myelogenous leukemia (CML) cells. Loss of Bcr/Abl protein correlated with the onset of apoptosis and reduced phosphorylation of Bcr/Abl substrates. WP1130 did not affect Hsp90/Hsp70 ratios within the cells and did not require the participation of the proteasomal pathway for loss of Bcr/Abl protein. WP1130 was more effective in reducing leukemic versus normal hematopoietic colony formation and strongly inhibited colony formation of cells derived from patients with T315I mutant Bcr/Abl–expressing CML in blast crisis. WP1130 suppressed the growth of K562 heterotransplanted tumors as well as both wild-type Bcr/Abl and T315I mutant Bcr/Abl–expressing BaF/3 cells transplanted into nude mice. Collectively, our results demonstrate that WP1130 reduces wild-type and T315I mutant Bcr/Abl protein levels in CML cells through a unique mechanism and may be useful in treating CML.

Download Full-text

Dasatinib (BMS-354825) in Patients with Chronic Myeloid Leukemia (CML) and Philadelphia-Chromosome Positive Acute Lymphoblastic Leukemia (Ph+ ALL) Who Are Resistant or Intolerant to Imatinib: Update of a Phase I Study.

Blood ◽

10.1182/blood.v106.11.38.38 ◽

2005 ◽

Vol 106 (11) ◽

pp. 38-38 ◽

Cited By ~ 8

Author(s):

Charles L. Sawyers ◽

H. Kantarjian ◽

N. Shah ◽

J. Cortes ◽

R. Paquette ◽

...

Keyword(s):

Bone Marrow ◽

Phase I ◽

Advanced Disease ◽

Lymphoblastic Leukemia ◽

Blast Crisis ◽

Philadelphia Chromosome ◽

Imatinib Treatment ◽

Hematologic Response ◽

Imatinib Resistant ◽

Bone Marrow Blasts

Abstract Imatinib mesylate resistance in CML and Ph+ ALL is frequently associated with BCR-ABL mutations that interfere with the ability of imatinib to inhibit BCR-ABL. Dasatinib (BMS-354825) is a novel, oral, multi-targeted kinase inhibitor, which targets BCR-ABL and SRC kinases. Dasatinib is 325-fold more potent versus imatinib in cells transduced with wild-type BCR-ABL, and has demonstrated preclinical activity against 18 of 19 imatinib-resistant BCR-ABL mutants (O’Hare, et al. Cancer Res65(11):4500–5, 2005; Shah et al, Science, 305:399–401, 2004). Here we present an update of a Phase I dose-escalating study, initiated in November 2003, of dasatinib in imatinib-resistant/intolerant patients with CML in late chronic phase (CP) or advanced disease (accelerated phase [AP], myeloid blast crisis [MBC] or lymphoid blast crisis [LBC]) or with Ph+ ALL. Data are available for 84 patients (40 CP, 10 AP, 23 MBC, 11 LBC/Ph+ ALL). As of this writing, 40 CP patients, with 8 years’ median duration of CML (range: 1–17 yrs), have been treated with dasatinib (15–180 mg/day, once-daily [QD] or twice daily [BID]) for a median of 13 months. The rate of complete hematologic response (CHR) in CP is 88% (35/40). Major cytogenetic responses (MCyR) were observed in 40% (16/40), with complete CyR (CCyR) in 33% (13/40). In advanced disease, 44 patients have been treated with dasatinib (70–240 mg/day, BID) for a median of 3–7 months, depending on the cohort (see Table); 2 patients (1 MBC and 1 LBC) are not evaluable for response, but are included in the analysis of time to progression. The rate of major hematologic response (MHR) (bone marrow blasts <5%) is 80% (8/10) in AP, 77% (17/22) in MBC and 60% (6/10) in LBC/Ph+ ALL. The CHR rate (<5% bone marrow blasts, with recovery of peripheral blood counts) is 50% (5/10) in AP, 18% (4/22) in MBC and 50% (5/10) in LBC/Ph+ ALL. The overall rates of MCyR and CCyR in advanced disease were 36% (15/42) and 21% (9/42), respectively. Cytogenetic responses were seen in patients with a wide spectrum of BCR-ABL mutations, as well as in patients with minimal or no prior CyR with imatinib. Treatment was well tolerated. Reversible grade 3–4 myelosuppression was observed in all cohorts [CP (38%); AP (70%); MBC and LBC/Ph+ ALL (91%)]. 8 patients developed unexplained pleural effusions (2 CP; 6 BC), which were easily managed without treatment discontinuation. No patients have gone off study for toxicity. Responses are durable in CP and AP patients, but relapses have occurred in the MBC and LBC/Ph+ ALL cohorts, often due to dasatinib-resistant BCR-ABL mutations. These data support the therapeutic potential of dasatinib in patients with imatinib-resistant or -intolerant CML/Ph+ ALL. Phase II studies (the ‘START’ [SRC/ABL Tyrosine kinase inhibition Activity: Research Trials of dasatinib] program) are currently ongoing in imatinib-resistant/intolerant patients with all phases of CML and Ph+ ALL. Phase of CML/ALL Patients remaining in response at July 31, 2005 Follow-up, median (range) days CP (N=40) 36 (90%) 392 (95–588) AP (N=10) 8 (80%) 200 (39–365) MBC (N=23) 9 (39%) 144 (2–364) LBC/Ph+ ALL (N=11) 1 (9%) 77 (8–233)

Download Full-text

Prognostic factors associated with complete cytogenetic response in patients with chronic myelogenous leukemia on imatinib mesylate therapy

Srpski arhiv za celokupno lekarstvo ◽

10.2298/sarh1006305c ◽

2010 ◽

Vol 138 (5-6) ◽

pp. 305-308 ◽

Cited By ~ 2

Author(s):

Irena Cojbasic ◽

Lana Macukanovic-Golubovic

Keyword(s):

Bone Marrow ◽

Prognostic Factors ◽

Imatinib Mesylate ◽

Chronic Myelogenous Leukemia ◽

Philadelphia Chromosome ◽

Cytogenetic Response ◽

Myelogenous Leukemia ◽

Base Line ◽

Complete Cytogenetic Response ◽

Pre Treatment

Introduction Imatinib mesylate, a selective Bcr-Abl tyrosine kinase inhibitor, has proved to be most effective therapy of Philadelphia chromosome-positive chronic myelogenous leukemia. Imatinib induces complete haematological and cytogenetic response in high percentage of patients. Objective The aim of this study was to identify potential prognostic factors before beginning treatment with imatinib associated with complete cytogenetic response. Methods We analyzed 20 patients with newly diagnosed Philadelphia positive chronic myelogenous leukemia treated at our institution from June 2006 until May 2009. These patients were treated with imatinib mesylate in oral dose of 400 to 800 mg daily. Complete blood counts were performed every month, while serum chemistry evaluations and bone marrow evaluations including morphology and cytogenetics were performed every 6 months. Results Of the 20 patients analyzed in this study, 19 (95%) achieved complete haematologic response within three months. In all patients cytogenetic analyses were done and all have achieved absolute cytogenetic response. The best cytogenetic response rate at any time during study treatment among 20 patients was: complete cytogenetic response in 15, partial cytogenetic response in three and minor cytogenetic response in two patients. Among 11 observed base-line patients' characteristics five were independent predictors of a high rate of complete cytogenetic response; the absence of blasts and basophils in peripheral blood, the presence of less than 5 percent of bone marrow blasts, white blood cell count less than 10x109/L and the absence of splenomegaly (p<0.01). Conclusion Our results showed that some pre-treatment characteristics of patients might be the cause of differences in treatment outcome. On the basis of this analysis, we identified several pre-treatment patients' characteristics to be independent prognostic factors for achievement of complete cytogenetic response. .

Download Full-text

Philadelphia chromosome and terminal transferase-positive acute leukemia: similarity of terminal phase of chronic myelogenous leukemia and de novo acute presentation.

Journal of Clinical Oncology ◽

10.1200/jco.1983.1.11.669 ◽

1983 ◽

Vol 1 (11) ◽

pp. 669-676 ◽

Cited By ~ 28

Author(s):

K Jain ◽

Z Arlin ◽

R Mertelsmann ◽

T Gee ◽

S Kempin ◽

...

Keyword(s):

Bone Marrow ◽

Acute Leukemia ◽

Chronic Myelogenous Leukemia ◽

Lymphoblastic Leukemia ◽

Allogeneic Bone Marrow Transplantation ◽

Philadelphia Chromosome ◽

Myelogenous Leukemia ◽

Allogeneic Bone ◽

Leukocyte Antigen ◽

Terminal Transferase

Twenty-eight patients with Philadelphia chromosome (Ph1)--positive and terminal transferase (TdT)--positive acute leukemia (AL) were treated with intensive chemotherapy used for adult acute lymphoblastic leukemia (L-10 and L-10M protocols). Fifteen patients had a documented chronic phase of Ph1-positive chronic myelogenous leukemia preceding the acute transformation (TdT + BLCML) while the remaining 13 patients did not (TdT + Ph1 + AL). An overall complete remission (CR) rate of 71% was obtained with a median survival of 13 months in the responders. Clinical presentation, laboratory data, cytogenetics, response to treatment, and survivals of the two groups of patients are compared. These results appear to be similar, suggesting a common or closely related origin. Since the overall survival of those receiving chemotherapy maintenance is poor, three patients underwent allogeneic bone marrow transplantation (BMT) from histocompatibility leukocyte antigen--matched siblings after they achieved CR. One of them is a long-term survivor (35 + months) with a Ph1-negative bone marrow. New techniques such as BMT should be considered in young patients with a histocompatibility leukocyte antigen--compatible sibling once a CR has been achieved.

Download Full-text

Congenital Juvenile Chronic Myelogenous Leukemia: Case Report and Review

PEDIATRICS ◽

10.1542/peds.73.3.324 ◽

1984 ◽

Vol 73 (3) ◽

pp. 324-326

Author(s):

Reese H. Clark ◽

Leslie L. Taylor ◽

Robert J. Wells

Keyword(s):

Bone Marrow ◽

Case Report ◽

Chronic Myelogenous Leukemia ◽

Peripheral Blood ◽

Blast Crisis ◽

Myelogenous Leukemia ◽

Juvenile Form

The case of a patient with ecchymosis, hepatomegaly, leukocytosis, thrombocytopenia, and anemia at birth is presented. Throughout his course, thrombocytopenia, anemia, and leukocytosis without a marked increase in the number of blast forms in either peripheral blood or bone marrow persisted until the patient developed a blast crisis shortly before his death at age 4 months. This patient is the youngest reported to have the juvenile form of chronic myelogenous leukemia and the first that in the present era can be considered congenital in origin.

Download Full-text

Imatinib mesylate (STI571) therapy for Philadelphia chromosome–positive chronic myelogenous leukemia in blast phase

Blood ◽

10.1182/blood.v99.10.3547 ◽

2002 ◽

Vol 99 (10) ◽

pp. 3547-3553 ◽

Cited By ~ 207

Author(s):

Hagop M. Kantarjian ◽

Jorge Cortes ◽

Susan O'Brien ◽

Francis J. Giles ◽

Maher Albitar ◽

...

Keyword(s):

Imatinib Mesylate ◽

Chronic Myelogenous Leukemia ◽

Response Rate ◽

Philadelphia Chromosome ◽

Response To Therapy ◽

Myelogenous Leukemia ◽

Control Group ◽

Blast Phase ◽

Molecular Abnormalities ◽

Philadelphia Chromosome Positive

Molecular abnormalities caused by the hybrid Bcr-Abl gene are causally associated with the development and progression of Philadelphia chromosome–positive (Ph+) chronic myelogenous leukemia (CML). Imatinib mesylate (STI571), a specific Bcr-Abl tyrosine-kinase signal-transduction inhibitor, has shown encouraging activity in phase I and II studies of CML. Here, we describe the use of imatinib mesylate to treat 75 patients in blast-phase CML (median age, 53 years; 65 with nonlymphoid and 10 with lymphoid blasts), and compare the results with those of a historical control group treated with standard cytarabine-based therapy. Imatinib mesylate was given as oral doses at 300 to 1000 mg per day and was the first salvage therapy for 47 patients. The objective response rate was 52% (39 of 75 patients: 16 had complete and 3 had partial hematologic response; 12 had hematologic improvement; 7 returned to second chronic phase; and 1 had a complete response in extramedullary blastic disease). Response rates were not different between nonlymphoid and lymphoid groups. The cytogenetic response rate was 16% (12 patients: 5 complete, 3 partial [Ph+ below 35%], and 4 minor [Ph+, 34% to 90%]). The estimated median overall survival was 6.5 months; the estimated 1-year survival was 22%. Response to therapy (landmark analysis at 8 weeks) was associated with survival prolongation. Compared with standard cytarabine combinations, imatinib mesylate therapy was less toxic and produced a higher response rate (55% versus 29%, P = .001), longer median survival (7 versus 4 months, P = .04), and lower 4-week induction mortality (4% versus 15%, P = .07). Imatinib mesylate is currently being tested in combination with other drugs to improve the prognosis for blast-phase CML.

Download Full-text

Several Bcr-Abl kinase domain mutants associated with imatinib mesylate resistance remain sensitive to imatinib

Blood ◽

10.1182/blood-2002-12-3659 ◽

2003 ◽

Vol 101 (11) ◽

pp. 4611-4614 ◽

Cited By ~ 236

Author(s):

Amie S. Corbin ◽

Paul La Rosée ◽

Eric P. Stoffregen ◽

Brian J. Druker ◽

Michael W. Deininger

Keyword(s):

Imatinib Mesylate ◽

Kinase Inhibitor ◽

Blast Crisis ◽

Chronic Phase ◽

Kinase Domain ◽

Myelogenous Leukemia ◽

Imatinib Resistance ◽

Abl Kinase ◽

Cellular Assays ◽

Kinase Domain Mutations

Abstract Imatinib mesylate is a selective Bcr-Abl kinase inhibitor, effective in the treatment of chronic myelogenous leukemia. Most patients in chronic phase maintain durable responses; however, many in blast crisis fail to respond, or relapse quickly. Kinase domain mutations are the most commonly identified mechanism associated with relapse. Many of these mutations decrease the sensitivity of the Abl kinase to imatinib, thus accounting for resistance to imatinib. The role of other mutations in the emergence of resistance has not been established. Using biochemical and cellular assays, we analyzed the sensitivity of several mutants (Met244Val, Phe311Leu, Phe317Leu, Glu355Gly, Phe359Val, Val379Ile, Leu387Met, and His396Pro/Arg) to imatinib mesylate to better understand their role in mediating resistance.While some Abl mutations lead to imatinib resistance, many others are significantly, and some fully, inhibited. This study highlights the need for biochemical and biologic characterization, before a resistant phenotype can be ascribed to a mutant.

Download Full-text