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Luskin MR, Gimotty PA, Smith C, Loren AW, Figueroa ME, Harrison J, Sun Z, Tallman MS, Paietta EM, Litzow MR, Melnick AM, Levine RL, Fernandez HF, Luger SM, Carroll M, Master SR, Wertheim GBW. A clinical measure of DNA methylation predicts outcome in de novo acute myeloid leukemia. JCI Insight 2016; 1. [PMID: 27446991 DOI: 10.1172/jci.insight.87323] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Variable response to chemotherapy in acute myeloid leukemia (AML) represents a major treatment challenge. Clinical and genetic features incompletely predict outcome. The value of clinical epigenetic assays for risk classification has not been extensively explored. We assess the prognostic implications of a clinical assay for multilocus DNA methylation on adult patients with de novo AML. METHODS We performed multilocus DNA methylation assessment using xMELP on samples and calculated a methylation statistic (M-score) for 166 patients from UPENN with de novo AML who received induction chemotherapy. The association of M-score with complete remission (CR) and overall survival (OS) was evaluated. The optimal M-score cut-point for identifying groups with differing survival was used to define a binary M-score classifier. This classifier was validated in an independent cohort of 383 patients from the Eastern Cooperative Oncology Group Trial 1900 (E1900; NCT00049517). RESULTS A higher mean M-score was associated with death and failure to achieve CR. Multivariable analysis confirmed that a higher M-score was associated with death (P = 0.011) and failure to achieve CR (P = 0.034). Median survival was 26.6 months versus 10.6 months for low and high M-score groups. The ability of the M-score to perform as a classifier was confirmed in patients ≤ 60 years with intermediate cytogenetics and patients who achieved CR, as well as in the E1900 validation cohort. CONCLUSION The M-score represents a valid binary prognostic classifier for patients with de novo AML. The xMELP assay and associated M-score can be used for prognosis and should be further investigated for clinical decision making in AML patients.
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Affiliation(s)
- Marlise R Luskin
- Division of Hematology and Oncology, Abramson Cancer Center at the University of Pennsylvania (UPENN), Philadelphia, Pennsylvania, USA
| | - Phyllis A Gimotty
- Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania (UPENN), Philadelphia, Pennsylvania, USA
| | - Catherine Smith
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Alison W Loren
- Division of Hematology and Oncology, Abramson Cancer Center at the University of Pennsylvania (UPENN), Philadelphia, Pennsylvania, USA
| | | | - Jenna Harrison
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zhuoxin Sun
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | | | | | - Ari M Melnick
- Hematology and Oncology Division, Weill Cornell Medical College, New York, New York, USA
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Selina M Luger
- Division of Hematology and Oncology, Abramson Cancer Center at the University of Pennsylvania (UPENN), Philadelphia, Pennsylvania, USA
| | - Martin Carroll
- Division of Hematology and Oncology, Abramson Cancer Center at the University of Pennsylvania (UPENN), Philadelphia, Pennsylvania, USA; Philadelphia Veterans Administration Medical Center, Philadelphia, Pennsylvania, USA
| | - Stephen R Master
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Gerald B W Wertheim
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Wertheim GBW, Smith C, Luskin M, Rager A, Figueroa ME, Carroll M, Master SR. Validation of DNA methylation to predict outcome in acute myeloid leukemia by use of xMELP. Clin Chem 2014; 61:249-58. [PMID: 25348669 DOI: 10.1373/clinchem.2014.229781] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Epigenetic dysregulation involving alterations in DNA methylation is a hallmark of various types of cancer, including acute myeloid leukemia (AML). Although specific cancer types and clinical aggressiveness of tumors can be determined by DNA methylation status, the assessment of DNA methylation at multiple loci is not routinely performed in the clinical laboratory. METHODS We recently described a novel microsphere-based assay for multiplex evaluation of DNA methylation. In the current study, we validated and used an improved assay [termed expedited microsphere HpaII small fragment Enrichment by Ligation-mediated PCR (xMELP)] that can be performed with appropriate clinical turnaround time. RESULTS Using the xMELP assay in conjunction with a new 17-locus random forest classifier that has been trained using 344 AML samples, we were able to segregate an independent cohort of 70 primary AML patients into methylation-determined subgroups with significantly distinct mortality risk (P = 0.009). We also evaluated precision, QC parameters, and preanalytic variables of the xMELP assay and determined the sensitivity of the random forest classifier score to failure at 1 or more loci. CONCLUSIONS Our results demonstrate that xMELP performance is suitable for implementation in the clinical laboratory and predicts AML outcome in an independent patient cohort.
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Affiliation(s)
- Gerald B W Wertheim
- Department of Pathology, Children's Hospital of Philadelphia; Department of Pathology and Laboratory Medicine
| | - Catherine Smith
- Department of Pathology, Children's Hospital of Philadelphia
| | | | | | - Maria E Figueroa
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Martin Carroll
- Division of Hematology and Oncology, and Abramson Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Wertheim GBW, Smith C, Figueroa ME, Kalos M, Bagg A, Carroll M, Master SR. Microsphere-based multiplex analysis of DNA methylation in acute myeloid leukemia. J Mol Diagn 2013; 16:207-15. [PMID: 24373919 DOI: 10.1016/j.jmoldx.2013.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 01/19/2023] Open
Abstract
Aberrant regulation of DNA methylation is characteristic of cancer cells and clearly influences phenotypes of various malignancies. Despite clear correlations between DNA methylation and patient outcome, tests that directly measure multiple-locus DNA methylation are typically expensive and technically challenging. Previous studies have demonstrated that the prognosis of patients with acute myeloid leukemia can be predicted by the DNA methylation pattern of 18 loci. We have developed a novel strategy, termed microsphere HpaII tiny fragment enrichment by ligation-mediated PCR (MELP), to simultaneously analyze the DNA methylation pattern at these loci using methylation-specific DNA digestion, fluorescently labeled microspheres, and branched DNA hybridization. The method uses techniques that are inexpensive and easily performed in a molecular laboratory. MELP accurately reflects the methylation levels at each locus analyzed and segregates patients with acute myeloid leukemia into prognostic subgroups. Our results demonstrate the usefulness of MELP as a platform for simultaneous evaluation of DNA methylation of multiple loci.
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Affiliation(s)
- Gerald B W Wertheim
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Catherine Smith
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Maria E Figueroa
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Michael Kalos
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Abramson Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Martin Carroll
- Division of Hematology and Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephen R Master
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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Wertheim GBW, Hexner E, Bagg A. Molecular-based classification of acute myeloid leukemia and its role in directing rational therapy: personalized medicine for profoundly promiscuous proliferations. Mol Diagn Ther 2013. [PMID: 23184342 DOI: 10.1007/s40291-012-0009-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Acute myeloid leukemia (AML) is not a single pathologic entity but represents a heterogeneous group of malignancies. This heterogeneity is exemplified by the variable clinical outcomes that are observed in patients with AML, and it is largely the result of diverse mutations within the leukemic cells. These mutations range from relatively large genetic alterations, such as gains, losses, and translocations of chromosomes, to single nucleotide changes. Detection of many of these mutations is required for accurate diagnosis, prognosis, and treatment of patients with AML. As such, many testing modalities have been developed and are currently employed in clinical laboratories to ascertain mutational status at prognostically and therapeutically critical loci. The assays include those that specifically identify large chromosomal alterations, such as conventional metaphase analysis and fluorescence in situ hybridization, and methods that are geared more toward analysis of small mutations, such as PCR with allele-specific oligonucleotide primers. Furthermore, newer tests, including array analysis and next-generation sequencing, which can simultaneously probe numerous molecular aberrancies within tumor cells, are likely to become commonplace in AML diagnostics. Each testing method clearly has advantages and disadvantages, an understanding of which should influence the choice of test in various clinical circumstances. To aid such understanding, this review discusses both genetic mutations in AML and the clinical tests-including their pros and cons-that may be used to probe these abnormalities. Additionally, we highlight the significance of genetic testing by describing cases in which results of genetic testing significantly influence clinical management of patients with AML.
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Affiliation(s)
- Gerald B W Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Wertheim GBW, Daber R, Bagg A. Molecular diagnostics of acute myeloid leukemia: it's a (next) generational thing. J Mol Diagn 2012; 15:27-30. [PMID: 23159532 DOI: 10.1016/j.jmoldx.2012.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 08/14/2012] [Indexed: 12/28/2022] Open
Abstract
This commentary highlights the article by Spencer et al that outlines a novel next-generation sequencing-based method for the detection of FLT3 mutations.
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Affiliation(s)
- Gerald B W Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19014, USA.
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Gunther EJ, Belka GK, Wertheim GBW, Wang J, Hartman JL, Boxer RB, Chodosh LA. A novel doxycycline-inducible system for the transgenic analysis of mammary gland biology. FASEB J 2002; 16:283-92. [PMID: 11874978 DOI: 10.1096/fj.01-0551com] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Normal developmental events such as puberty, pregnancy, and parity influence the susceptibility of the mammary gland to tumorigenesis in both humans and rodent model systems. Unfortunately, constitutive transgenic mouse models that rely on mammary-specific promoters to control transgene expression have limited utility for studying the effect of developmental events on breast cancer risk since the hormonal signals governing these events also markedly influence transgene expression levels. A novel transgenic mouse system is described that uses the MMTV-LTR to drive expression of the reverse tetracycline-dependent transactivator rtTA. Transgenic mice expressing rtTA in the mammary epithelium were crossed with reporter lines bearing tet operator-controlled transgenes. We tested the ability to spatially, temporally, and quantitatively control reporter gene expression after administration of doxycycline to bitransgenic mice. Transgene expression using this system can be rapidly induced and deinduced, is highly mammary specific, can be reproducibly titrated over a wide range of expression levels, and is essentially undetectable in the uninduced state. Homogeneous transgene expression throughout the mammary epithelium can be achieved. This system permits transgene expression to be restricted to any desired stage of postnatal mammary gland development. We have developed a mammary-specific, doxycycline-inducible transgenic mouse model for studying the effect of mammary gland development on transgene-mediated phenotypes. Unlike other mammary-specific, transgenic systems that have been described, this system combines spatially homogeneous transgene expression in the mammary epithelium during puberty, pregnancy, lactation, and involution with the use of an orally administered, inexpensive, and widely available inducing agent. This system offers new opportunities for the transgenic analysis of mammary gland biology in vivo.
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Affiliation(s)
- Edward J Gunther
- Department of Cancer Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6160, USA
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