1
|
Ip A, Della Pia A, Kim GY(G, Lofters J, Behrmann J, Patel D, Kats S, Estella JJ, De Dios I, Ma W, Pecora AL, Goy AH, Koprivnikar J, McCloskey JK, Albitar M. Reliability of Cell-Free DNA and Targeted NGS in Predicting Chromosomal Abnormalities of Patients With Myeloid Neoplasms. Front Oncol 2022; 12:923809. [PMID: 35774119 PMCID: PMC9238409 DOI: 10.3389/fonc.2022.923809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction Cytogenetic analysis is important for stratifying patients with various neoplasms. We explored the use of targeted next generation sequencing (NGS) in detecting chromosomal structural abnormalities or copy number variations (CNVs) in patients with myeloid neoplasms. Methods Plasma cell-free DNA (cfDNA) from 2821 myeloid or lymphoid neoplasm patients were collected. cfDNA was sequenced using a 275 gene panel. CNVkit software was used for analyzing and visualizing CNVs. Cytogenetic data from corresponding bone marrow (BM) samples was available on 89 myeloid samples. Results Of the 2821 samples, 1539 (54.5%) showed evidence of mutations consistent with the presence of neoplastic clones in circulation. Of these 1539 samples, 906 (59%) showed abnormalities associated with myeloid neoplasms and 633 (41%) with lymphoid neoplasms. Chromosomal structural abnormalities in cfDNA were detected in 146 (16%) myeloid samples and 76 (12%) lymphoid samples. Upon comparison of the myeloid samples with 89 BM patients, NGS testing was able to reliably detect chromosomal gain or loss, except for fusion abnormalities. When cytogenetic abnormalities were classified according to prognostic classes, there was a complete (100%) concordance between cfDNA NGS data and cytogenetic data. Conclusions This data shows that liquid biopsy using targeted NGS is reliable in detecting chromosomal structural abnormalities in myeloid neoplasms. In specific circumstances, targeted NGS may be reliable and efficient to provide adequate information without the need for BM biopsy considering broad mutation profiling can be obtained through adequate sequencing within the same test. Overall, this study supports the use of liquid biopsy for early diagnosis and monitoring of patients with myeloid neoplasms.
Collapse
Affiliation(s)
- Andrew Ip
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Alexandra Della Pia
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- Ernest Mario School of Pharmacy at Rutgers University, Department of Pharmacy Practice and Administration, Piscataway, NJ, United States
| | - Gee Youn (Geeny) Kim
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- Ernest Mario School of Pharmacy at Rutgers University, Department of Pharmacy Practice and Administration, Piscataway, NJ, United States
| | - Jason Lofters
- Englewood Health Internal Medicine Residency Program, Englewood, NJ, United States
| | - James Behrmann
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Dylon Patel
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Simone Kats
- Ernest Mario School of Pharmacy at Rutgers University, Department of Pharmacy Practice and Administration, Piscataway, NJ, United States
| | | | - Ivan De Dios
- Genomic Testing Cooperative, Hematology, Irvine, CA, United States
| | - Wanlong Ma
- Genomic Testing Cooperative, Hematology, Irvine, CA, United States
| | - Andrew L. Pecora
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Andre H. Goy
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Jamie Koprivnikar
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
| | - James K. McCloskey
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
| | - Maher Albitar
- Genomic Testing Cooperative, Hematology, Irvine, CA, United States
- *Correspondence: Maher Albitar,
| |
Collapse
|
2
|
Eyal E, Tohami T, Amir A, Cesarkas K, Jacob-Hirsch J, Volchek Y, Nagler A, Rechavi G, Amariglio N. Detection ofBCR-ABL1mutations in chronic myeloid leukaemia by massive parallel sequencing. Br J Haematol 2012; 160:477-86. [DOI: 10.1111/bjh.12171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/29/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Eran Eyal
- Cancer Research Centre; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
| | - Tali Tohami
- Division of Haematology; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
| | - Amnon Amir
- Cancer Research Centre; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
| | - Karen Cesarkas
- Cancer Research Centre; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
| | | | - Yuliya Volchek
- Division of Haematology; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
| | | | | | - Ninette Amariglio
- Division of Haematology; Chaim Sheba Medical Centre; Tel-Hashomer; Israel
| |
Collapse
|
3
|
Elias MH, Baba AA, Husin A, Abdullah AD, Hassan R, Sim GA, Wahid SFA, Ankathil R. Contribution of BCR-ABL kinase domain mutations to imatinib mesylate resistance in Philadelphia chromosome positive Malaysian chronic myeloid leukemia patients. Hematol Rep 2012; 4:e23. [PMID: 23355941 PMCID: PMC3555211 DOI: 10.4081/hr.2012.e23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/23/2012] [Accepted: 10/31/2012] [Indexed: 01/26/2023] Open
Abstract
Development of resistance to imatinib mesylate (IM) in chronic myeloid leukemia (CML) patients is mediated by different mechanisms that can be classified as BCR-ABL dependent or BCR-ABL independent pathways. BCR-ABL dependent mechanisms are most frequently associated with point mutations in tyrosine kinase domain (TKD) of BCR-ABL1 and also with BCR-ABL gene amplification. Many different types and frequencies of mutations have been reported in different studies, probably due to the different composition of study cohorts. Since no reports are available from Malaysia, this study was undertaken to investigate the frequency and pattern of BCR-ABL kinase domain mutations using dHPLC followed by sequencing, and also status of BCR-ABL gene amplification using fluorescence in situ hybridization (FISH) on 40 IM resistant Malaysian CML patients. Mutations were detected in 13 patients (32.5%). Five different types of mutations (T315I, E255K, Y253H, M351T, V289F) were identified in these patients. In the remaining 27 IM resistant CML patients, we investigated the contribution made by BCR-ABL gene amplification, but none of these patients showed amplification. It is presumed that the mechanisms of resistance in these 27 patients might be due to BCR-ABL independent pathways. Different mutations confer different levels of resistance and, therefore, detection and characterization of TKD mutations is highly important in order to guide therapy in CML patients.
Collapse
|
4
|
Ubiquitin-proteasome system profiling in acute leukemias and its clinical relevance. Leuk Res 2010; 35:526-33. [PMID: 20951430 DOI: 10.1016/j.leukres.2010.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 09/06/2010] [Accepted: 09/10/2010] [Indexed: 11/24/2022]
Abstract
The ubiquitin-proteasome system (UPS) plays a major role in the homeostasis of cellular protein. We demonstrate that each of the major hematologic diseases (AML, ALL, and MDS) has a specific and different plasma profile of UPS protein and enzymatic activities. While high levels of proteasome and ubiquitin proteins and enzymatic activities are detected in the plasma samples from patients, normalizing enzymatic activities, show that each proteasome has lower enzymatic activities in these diseases as compared with normal controls. Proteasome protein levels in AML are strong predictor of survival independently of cytogenetics, performance status and age. The Ch-L activity when normalized to the level of proteasome protein show significant negative correlation with survival in ALL.
Collapse
|
5
|
Ma W, Kantarjian H, Bekele B, Donahue AC, Zhang X, Zhang ZJ, O'Brien S, Estey E, Estrov Z, Cortes J, Keating M, Giles F, Albitar M. Proteasome enzymatic activities in plasma as risk stratification of patients with acute myeloid leukemia and advanced-stage myelodysplastic syndrome. Clin Cancer Res 2009; 15:3820-6. [PMID: 19458051 DOI: 10.1158/1078-0432.ccr-08-3034] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Cytogenetic abnormalities are currently the most important predictors of response and clinical outcome for patients with acute myeloid leukemia (AML) or advanced-stage myelodysplastic syndrome (MDS). Because clinical outcomes vary markedly within cytogenetic subgroups, additional biological markers are needed for risk stratification. EXPERIMENTAL DESIGN We assessed the utility of measuring pretreatment proteasome chymotrypsin-like, caspase-like, and trypsin-like activities in plasma to predict response and survival of patients with AML (n = 174) or advanced-stage MDS (n = 52). RESULTS All three enzymatic activities were significantly (P < 0.001) increased in the plasma of patients with AML and MDS compared with normal controls. Both chymotrypsin-like and caspase-like activities, but not trypsin-like activity, correlated with outcome. Chymotrypsin-like and caspase-like activities, but not trypsin-like activity, predicted response in univariate analysis (P = 0.002). However, only chymotrypsin-like activity was independent predictor of response from age grouping (<70 versus > or =70 years), cytogenetics, and blood urea nitrogen in multivariate analysis. Similarly, both chymotrypsin-like and caspase-like activities, but not trypsin-like activity, were predictors of overall survival in univariate analysis (P < 0.0001), but only chymotrypsin-like activity was independent of cytogenetics, age, performance status, blood urea nitrogen, and beta(2)-microglobulin in multivariate Cox regression models. Chymotrypsin-like activity was also a strong independent predictor of survival in patients with intermediate karyotype (n = 124). CONCLUSIONS Measuring plasma chymotrypsin-like activity may provide a powerful biomarker for risk stratification in patients with AML and advanced-stage MDS, including those with normal karyotype.
Collapse
Affiliation(s)
- Wanlong Ma
- Department of Hematopathology, Quest Diagnostics Nichols Institute, San Juan Capistrano, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Lee TS, Ma W, Zhang X, Giles F, Cortes J, Kantarjian H, Albitar M. BCR-ABL alternative splicing as a common mechanism for imatinib resistance: evidence from molecular dynamics simulations. Mol Cancer Ther 2008; 7:3834-41. [PMID: 19056677 DOI: 10.1158/1535-7163.mct-08-0482] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Rare cases of chronic myelogenous leukemia (CML) express high levels of alternatively spliced BCR-ABL mRNA with a 35-bp insertion (35INS) between ABL kinase domain exons 8 and 9. This insertion results in a frameshift leading to the addition of 10 residues and truncation of 653 residues due to early termination. Sensitive PCR-based testing showed that 32 of 52 (62%) imatinib-resistant CML patients in chronic phase and 8 of 38 (21%) in accelerated or blast crisis expressed varying levels of the alternatively spliced BCR-ABL mRNA. A three-dimensional structural model of the 35INS ABL kinase domain complexed with imatinib was built using homology modeling, followed by molecular dynamics simulations. Simulation results showed that the new residues cause a significant global conformational change, altering imatinib binding in a way similar to that of the T315I mutation and, therefore, providing resistance to imatinib that depends on the level of expression.
Collapse
Affiliation(s)
- Tai-Sung Lee
- Consortium for Bioinformatics and Computational Biology and Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, MN 55455, USA.
| | | | | | | | | | | | | |
Collapse
|
8
|
Targeting survival cascades induced by activation of Ras/Raf/MEK/ERK, PI3K/PTEN/Akt/mTOR and Jak/STAT pathways for effective leukemia therapy. Leukemia 2008; 22:708-22. [PMID: 18337766 DOI: 10.1038/leu.2008.27] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Raf/MEK/ERK, PI3K/PTEN/Akt/mTOR and Jak/STAT pathways are frequently activated in leukemia and other hematopoietic disorders by upstream mutations in cytokine receptors, aberrant chromosomal translocations as well as other genetic mechanisms. The Jak2 kinase is frequently mutated in many myeloproliferative disorders. Effective targeting of these pathways may result in suppression of cell growth and death of leukemic cells. Furthermore it may be possible to combine various chemotherapeutic and antibody-based therapies with low molecular weight, cell membrane-permeable inhibitors which target the Raf/MEK/ERK, PI3K/PTEN/Akt/mTOR and Jak/STAT pathways to ultimately suppress the survival pathways, induce apoptosis and inhibit leukemic growth. In this review, we summarize how suppression of these pathways may inhibit key survival networks important in leukemogenesis and leukemia therapy as well as the treatment of other hematopoietic disorders. Targeting of these and additional cascades may also improve the therapy of chronic myelogenous leukemia, which are resistant to BCR-ABL inhibitors. Furthermore, we discuss how targeting of the leukemia microenvironment and the leukemia stem cell are emerging fields and challenges in targeted therapies.
Collapse
|
9
|
Giles FJ, Albitar M. Plasma-based testing as a new paradigm for clinical testing in hematologic diseases. Expert Rev Mol Diagn 2007; 7:615-23. [PMID: 17892367 DOI: 10.1586/14737159.7.5.615] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent advances in molecular biology have paved the way for the detection of minute quantities of cellular components with robust assays that are amenable for use in clinical laboratories. This review discusses the recently developed series of plasma-based assays that are changing the testing paradigm for hematologic diseases. These tests are based on the concept that a high turnover of neoplastic hematologic cells, relative to normal cells, enriches plasma with tumor-specific DNA, RNA and protein. Plasma-based testing promises to reduce the need for bone marrow biopsy, allow for more frequent and accurate monitoring of changes in bone marrow, allow the detection of more aggressive subclones of the malignant cells and provide a more quantitative means to measure the load of the malignant clone. We present data demonstrating that plasma, in some situations, allows even more sensitive detection than bone marrow cells. Moreover, the lessened impact of dilution by normal cells in plasma permits a distinction between homozygous and hemizygous abnormalities. Unlike solid tumors, currently available data suggest that in hematologic diseases, plasma is superior to cells in detecting molecular abnormalities.
Collapse
Affiliation(s)
- Francis J Giles
- University of Texas Health Science Center, Division of Hematology & Medical Oncology, San Antonio, TX 78229, USA.
| | | |
Collapse
|
10
|
Jilani I, Kantarjian H, Gorre M, Cortes J, Ottmann O, Bhalla K, Giles FJ, Albitar M. Phosphorylation levels of BCR-ABL, CrkL, AKT and STAT5 in imatinib-resistant chronic myeloid leukemia cells implicate alternative pathway usage as a survival strategy. Leuk Res 2007; 32:643-9. [PMID: 17900686 DOI: 10.1016/j.leukres.2007.08.009] [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: 04/18/2007] [Revised: 07/17/2007] [Accepted: 08/07/2007] [Indexed: 10/22/2022]
Abstract
Ex-vivo studies have suggested that imatinib-resistance in chronic myeloid leukemia (CML) patients occurs despite adequate suppression of BCR-ABL activity. Whether BCR-ABL phosphorylation levels differ between imatinib-sensitive and -resistant patients is not known. We compared the phosphorylation of BCR-ABL in 54 previously untreated CML patients and 62 imatinib-resistant CML patients with progressive disease. Resistant patients had significantly lower levels of BCR-ABL, CrkL and AKT phosphorylation than previously untreated patients, but STAT5 phosphorylation showed no difference. These observations suggest that imatinib- resistance is not necessarily dependent on higher activity in BCR-ABL-dependent pathways, but is likely due to the activation of other pathways.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing/metabolism
- Antineoplastic Agents/therapeutic use
- Apoptosis/drug effects
- Benzamides
- Drug Resistance, Neoplasm
- Flow Cytometry
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Gene Expression Regulation, Neoplastic/physiology
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Nuclear Proteins/metabolism
- Phosphorylation
- Piperazines/therapeutic use
- Prognosis
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Proto-Oncogene Proteins c-akt/metabolism
- Pyrimidines/therapeutic use
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- STAT5 Transcription Factor/metabolism
- Signal Transduction/drug effects
- Survival Rate
Collapse
Affiliation(s)
- Iman Jilani
- Department of Hematopathology, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92675, USA
| | | | | | | | | | | | | | | |
Collapse
|