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Pawlyn C, Loehr A, Ashby C, Tytarenko R, Deshpande S, Sun J, Fedorchak K, Mughal T, Davies FE, Walker BA, Morgan GJ. Loss of heterozygosity as a marker of homologous repair deficiency in multiple myeloma: a role for PARP inhibition? Leukemia 2018; 32:1561-1566. [PMID: 29467487 PMCID: PMC6035152 DOI: 10.1038/s41375-018-0017-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 10/31/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023]
Abstract
PARP inhibitors can induce synthetic lethality in tumors characterized by homologous recombination deficiency (HRD), which can be detected by evaluating genome-wide loss of heterozygosity (LOH). Multiple myeloma (MM) is a genetically unstable tumor and we hypothesized that HRD-related LOH (HRD-LOH) could be detected in patient samples, supporting a potential role for PARP inhibition in MM. Using results from targeted next-generation sequencing studies (FoundationOne® Heme), we analyzed HRD-LOH in patients at all disease stages (MGUS (n = 7), smoldering MM (SMM, n = 30), newly diagnosed MM (NDMM, n = 71), treated MM (TRMM, n = 64), and relapsed MM (RLMM, n = 234)) using an algorithm to identify HRD-LOH segments. We demonstrated HRD-LOH in MM samples, increasing as disease progresses. The extent of genomic HRD-LOH correlated with high-risk disease markers. Outcome of RLMM patients, the biggest clinical group, was analyzed and patients with HRD-LOH above the third quartile (≥5% HRD-LOH) had significantly worse progression-free and overall survival than those with lower levels (p < 0.001). Mutations in key homologous recombination genes account for some, but not all, of the cases with an excess of HRD-LOH. These data support the further evaluation of PARP inhibitors in MM patients, particularly in the relapsed setting with a high unmet need for new treatments.
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Affiliation(s)
| | | | - Cody Ashby
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ruslana Tytarenko
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Shayu Deshpande
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - James Sun
- Foundation Medicine, Cambridge, MA, USA
| | | | | | - Faith E Davies
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian A Walker
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Gareth J Morgan
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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Albitar F, Ma W, Diep K, De Dios I, Agersborg S, Thangavelu M, Brodie S, Albitar M. Deep Sequencing of Cell-Free Peripheral Blood DNA as a Reliable Method for Confirming the Diagnosis of Myelodysplastic Syndrome. Genet Test Mol Biomarkers 2016; 20:341-5. [PMID: 27248906 DOI: 10.1089/gtmb.2015.0278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Demonstrating the presence of myelodysplastic syndrome (MDS)-specific molecular abnormalities can aid in diagnosis and patient management. We explored the potential of using peripheral blood (PB) cell-free DNA (cf-DNA) and next-generation sequencing (NGS). MATERIALS AND METHODS We performed NGS on a panel of 14 target genes using total nucleic acid extracted from the plasma of 16 patients, all of whom had confirmed diagnoses for early MDS with blasts <5%. PB cellular DNA from the same patients was sequenced using conventional Sanger sequencing and NGS. RESULTS Deep sequencing of the cf-DNA identified one or more mutated gene(s), confirming the diagnosis of MDS in all cases. Five samples (31%) showed abnormalities in cf-DNA by NGS that were not detected by Sanger sequencing on cellular PB DNA. NGS of PB cell DNA showed the same findings as those of cf-DNA in four of five patients, but failed to show a mutation in the RUNX1 gene that was detected in one patient's cf-DNA. Mutant allele frequency was significantly higher in cf-DNA compared with cellular DNA (p = 0.008). CONCLUSION These data suggest that cf-DNA when analyzed using NGS is a reliable approach for detecting molecular abnormalities in MDS and should be used to determine if bone marrow aspiration and biopsy are necessary.
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Affiliation(s)
- Ferras Albitar
- NeoGenomics Laboratories , Department of Hematology and Cytogenetics, Irvine, California
| | - Wanlong Ma
- NeoGenomics Laboratories , Department of Hematology and Cytogenetics, Irvine, California
| | - Kevin Diep
- NeoGenomics Laboratories , Department of Hematology and Cytogenetics, Irvine, California
| | - Ivan De Dios
- NeoGenomics Laboratories , Department of Hematology and Cytogenetics, Irvine, California
| | - Sally Agersborg
- NeoGenomics Laboratories , Department of Hematology and Cytogenetics, Irvine, California
| | - Maya Thangavelu
- NeoGenomics Laboratories , Department of Hematology and Cytogenetics, Irvine, California
| | - Steve Brodie
- NeoGenomics Laboratories , Department of Hematology and Cytogenetics, Irvine, California
| | - Maher Albitar
- NeoGenomics Laboratories , Department of Hematology and Cytogenetics, Irvine, California
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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.
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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: 40] [Impact Index Per Article: 2.7] [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.
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Affiliation(s)
- Wanlong Ma
- Department of Hematopathology, Quest Diagnostics Nichols Institute, San Juan Capistrano, California, USA
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Abstract
OBJECTIVES Plasma has been found to be enriched with tumor-specific DNA, RNA, and protein in patients with hematologic disease. We assessed the utility of plasma as a DNA source for detection of genetic abnormalities in patients with suspected B- or T-cell lymphoproliferative disorders. METHODS DNA was extracted from paired peripheral blood (PB) cells and plasma for polymerase chain reaction (PCR)-based detection of immunoglobulin heavy chain (IgH) and T-cell receptor gamma chain (TCR-gamma) rearrangements, and B-cell leukemia/lymphoma (BCL)-1/IgH and BCL-2/IgH translocations. RESULTS Concordance between plasma and PB cell analysis was 100% for IgH (n = 57), TCR-gamma (n = 57), and BCL-1/IgH (n = 37) rearrangements, and 94% (60/64) for BCL-2/IgH; four of 11 plasma samples positive for BCL-2/IgH tested negative in paired cells. No plasma or PB cell samples from 195 healthy donors showed genetic abnormalities. CONCLUSIONS These findings indicate that plasma is a reliable sample type for detection of abnormalities associated with B- and T-cell lymphoproliferative disorders, providing sensitivity equal to or greater than that of PB cells.
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Affiliation(s)
- Chen-Hsiung Yeh
- Department of Hematopathology R&D, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
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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.
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Affiliation(s)
- Francis J Giles
- University of Texas Health Science Center, Division of Hematology & Medical Oncology, San Antonio, TX 78229, USA.
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Cheng SH, Ng MHL, Lau KM, Liu HSY, Chan JCW, Hui ABY, Lo KW, Jiang H, Hou J, Chu RW, Wong WS, Chan NPH, Ng HK. 4q loss is potentially an important genetic event in MM tumorigenesis: identification of a tumor suppressor gene regulated by promoter methylation at 4q13.3, platelet factor 4. Blood 2006; 109:2089-99. [PMID: 17077331 DOI: 10.1182/blood-2006-04-018770] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
In this study, we have elucidated the chromosomal imbalances in the multistep pathogenesis and delineated several critical tumor suppressor gene (TSG) loci in multiple myeloma (MM). By using comparative genomic hybridization, allelotyping, and multicolor interphase fluorescence in situ hybridization, 5 MM cell lines and bone marrow CD138+ plasma cells from 88 Chinese patients with monoclonal gammopathy of undetermined significance (MGUS) and early and advanced stages of MM were investigated. In all MGUS and MM samples, chromosome copy number abnormalities were detected. A higher number of chromosomal imbalances and specific genetic alterations are involved in MGUS to MM transition (−6q, +3p, and +1p) and MM progression (+2p and +9q). In addition to −13q, we first found high frequencies (42% to 46%) of −4q involving high percentages (70% to 74%) of clonal plasma cells in both MGUS and MM, suggesting that inactivation of TSG in this region is also a potentially critical genetic event in MM tumorigenesis. By high-resolution allelotyping, we defined a common deletion region on 4q13.3 and found that a candidate TSG, platelet factor 4, was frequently silenced by promoter hypermethylation in MM (15 of 28) and MM cell lines (5 of 5). These data have opened up a new approach in the molecular targeting therapy and provide novel insights into MM tumorigenesis.
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MESH Headings
- Aged
- Aged, 80 and over
- Alleles
- Cell Line, Tumor
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 4/genetics
- DNA Methylation
- Disease Progression
- Female
- Gene Deletion
- Gene Expression Regulation, Neoplastic
- Humans
- In Situ Hybridization
- Male
- Middle Aged
- Multiple Myeloma/genetics
- Multiple Myeloma/pathology
- Platelet Factor 4/genetics
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- Transcription, Genetic/genetics
- Tumor Suppressor Proteins/genetics
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Affiliation(s)
- Suk Hang Cheng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China
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8
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Fleischhacker M, Schmidt B. Circulating nucleic acids (CNAs) and cancer--a survey. Biochim Biophys Acta Rev Cancer 2006; 1775:181-232. [PMID: 17137717 DOI: 10.1016/j.bbcan.2006.10.001] [Citation(s) in RCA: 418] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 10/04/2006] [Accepted: 10/04/2006] [Indexed: 12/23/2022]
Abstract
It has been known for decades that it is possible to detect small amounts of extracellular nucleic acids in plasma and serum of healthy and diseased human beings. The unequivocal proof that part of these circulating nucleic acids (CNAs) is of tumor origin, initiated a surge of studies which confirmed and extended the original observations. In the past few years many experiments showed that tumor-associated alterations can be detected at the DNA and RNA level. At the DNA level the detection of point mutations, microsatellite alterations, chromosomal alterations, i.e. inversion and deletion, and hypermethylation of promoter sequences were demonstrated. At the RNA level the overexpression of tumor-associated genes was shown. These observations laid the foundation for the development of assays for an early detection of cancer as well as for other clinical means.
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Affiliation(s)
- M Fleischhacker
- Charité, Universitätsmedizin Berlin, Medizinische Klinik mS Onkologie u Hämatologie, CCM, Charitéplatz 1, 10117 Berlin, Germany.
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Ma W, Kantarjian H, Jilani I, Gorre M, Bhalla K, Ottmann O, Giles F, Albitar M. Heterogeneity in detecting Abl kinase mutations and better sensitivity using circulating plasma RNA. Leukemia 2006; 20:1989-91. [PMID: 16932346 DOI: 10.1038/sj.leu.2404355] [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: 11/09/2022]
Abstract
Most studies test for mutations in the kinase domain of the abl gene in chronic myeloid leukemia (CML) using peripheral blood (PB) cells. Frequently, progression of the disease manifests with increased blasts in bone marrow (BM) and not in PB. Simultaneous analysis of plasma, PB cells and BM cells from 41 imatinib-resistant CML patients showed mutations in 63% of PB cells and 68% of plasma or BM cells (P = 0.04). In discordant patients, 13 mutations were detected in plasma, 11 in BM cells and 9 in PB cells. The T315I mutation was detected in plasma and BM but not PB cells in one patient. We detected no mutations in the plasma of 45 previously untreated CML patients, but two of these patients showed mutations in plasma and not cells by 9 months on therapy. Circulating plasma mRNA is a reliable alternative to BM mRNA for detecting ABL mutations.
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MESH Headings
- Antineoplastic Agents/therapeutic use
- Benzamides
- Drug Monitoring/methods
- Drug Resistance, Neoplasm
- Fusion Proteins, bcr-abl/genetics
- Genetic Heterogeneity
- Genetic Testing/methods
- Genetic Testing/standards
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/blood
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Mutation
- Piperazines/therapeutic use
- Plasma
- Pyrimidines/therapeutic use
- RNA, Messenger/blood
- RNA, Messenger/isolation & purification
- Reproducibility of Results
- Sensitivity and Specificity
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Affiliation(s)
- W Ma
- Department of Hematology, Nichols Institute, Quest Diagnostics, San Juan Capistrano, CA 92690-6130, USA
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Woenckhaus M, Grepmeier U, Werner B, Schulz C, Rockmann F, Wild PJ, Röckelein G, Blaszyk H, Schuierer M, Hofstaedter F, Hartmann A, Dietmaier W. Microsatellite analysis of pleural supernatants could increase sensitivity of pleural fluid cytology. J Mol Diagn 2005; 7:517-24. [PMID: 16237222 PMCID: PMC1888495 DOI: 10.1016/s1525-1578(10)60583-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pleural effusions may result from various inflammatory, hemodynamic, or neoplastic conditions. A common diagnostic problem lies in distinguishing malignant from benign pleural effusions using routine cytological evaluation. We studied pleural fluid samples obtained from 14 patients with histologically confirmed malignancy and from 6 patients with benign pleural effusions using 12 microsatellite markers from 8 different chromosomal regions. Supernatants and cellular sediments of all 20 pleural fluid samples were analyzed. Routine cytological examination was 100% specific for malignancy but was only 57% sensitive. Microsatellite analyses of pleural fluid supernatants showed genetic alterations in tumor patients only. However, 50% of pleural effusions that were considered negative for malignancy by routine cytological analysis showed either loss of heterozygosity or microsatellite instability. The sensitivity of pleural fluid examination rose to 79% when routine cytological assessment was supplemented by molecular studies. Our data suggest that microsatellite analysis increases the sensitivity of cytological pleural fluid examination in assessing potential malignancy and that combining cytological and molecular methods may improve yield and certainty in diagnostically challenging cases.
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Affiliation(s)
- Matthias Woenckhaus
- Department of Pathology, University of Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany.
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