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Zimran E, Tripodi J, Rampal R, Rappoport F, Zirkiev S, Hoffman R, Najfeld V. Genomic characterization of spleens in patients with myelofibrosis. Haematologica 2018; 103:e446-e449. [PMID: 29748436 DOI: 10.3324/haematol.2018.193763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Eran Zimran
- Myeloproliferative Neoplasms Research Program, Department of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, Rockefeller University, New York, NY, USA
| | - Joseph Tripodi
- Myeloproliferative Neoplasms Research Program, Department of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, Rockefeller University, New York, NY, USA.,Tumor Cytogenomics Laboratory, Department of Pathology, Icahn School of Medicine at Mount Sinai, Rockefeller University, New York, NY, USA
| | - Raajit Rampal
- Human Oncology and Pathogenesis Program, Leukemia Service, Memorial Sloan-Kettering Cancer Center, Rockefeller University, New York, NY, USA
| | - Franck Rappoport
- Human Oncology and Pathogenesis Program, Leukemia Service, Memorial Sloan-Kettering Cancer Center, Rockefeller University, New York, NY, USA.,Center for Clinical and Translational Science, Rockefeller University, New York, NY, USA
| | - Sharon Zirkiev
- Tumor Cytogenomics Laboratory, Department of Pathology, Icahn School of Medicine at Mount Sinai, Rockefeller University, New York, NY, USA
| | - Ronald Hoffman
- Myeloproliferative Neoplasms Research Program, Department of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, Rockefeller University, New York, NY, USA
| | - Vesna Najfeld
- Myeloproliferative Neoplasms Research Program, Department of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, Rockefeller University, New York, NY, USA .,Tumor Cytogenomics Laboratory, Department of Pathology, Icahn School of Medicine at Mount Sinai, Rockefeller University, New York, NY, USA
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52
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The spatial and developmental expression of mouse Vwa8 (von Willebrand domain-containing protein 8). Gene Expr Patterns 2018; 29:39-46. [PMID: 29660410 DOI: 10.1016/j.gep.2018.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 04/06/2018] [Indexed: 01/07/2023]
Abstract
The Drosophila gene c12.2 was isolated in a screen examining mRNA binding proteins. Drosophila c12.2 is the mouse Vwa8 homolog. Various genome-wide associated studies have linked human Vwa8 to both neurological and oncological pathologies, which include autism, bipolar disorder, comorbid migraine, and acute myeloid leukemia, however, the function and role of the VWA8 protein remain poorly understood. To further analyze the Vwa8 gene in mouse, gene structure, protein homology modeling, and gene expression patterns were examined throughout mouse development. Our analyses indicate that the mouse Vwa8 gene produces two transcripts; the full-length Vwa8a is highly expressed relative to the truncated Vwa8b transcript across all developmental time points and tissues analyzed. Protein homology modeling indicates that VWA8a belongs to a novel protein superfamily containing both the midasin and cytoplasmic dynein 1 heavy chain 1 proteins. These data establish the development timeline and expression profile for both Vwa8a and Vwa8b, paving the way for future studies to determine the cellular role(s) of this highly conserved protein family.
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53
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Chi HC, Tsai CY, Tsai MM, Lin KH. Impact of DNA and RNA Methylation on Radiobiology and Cancer Progression. Int J Mol Sci 2018; 19:ijms19020555. [PMID: 29439529 PMCID: PMC5855777 DOI: 10.3390/ijms19020555] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/09/2018] [Accepted: 02/10/2018] [Indexed: 12/24/2022] Open
Abstract
Radiotherapy is a well-established regimen for nearly half the cancer patients worldwide. However, not all cancer patients respond to irradiation treatment, and radioresistance is highly associated with poor prognosis and risk of recurrence. Elucidation of the biological characteristics of radioresistance and development of effective prognostic markers to guide clinical decision making clearly remain an urgent medical requirement. In tumorigenic and radioresistant cancer cell populations, phenotypic switch is observed during the course of irradiation treatment, which is associated with both stable genetic and epigenetic changes. While the importance of epigenetic changes is widely accepted, the irradiation-triggered specific epigenetic alterations at the molecular level are incompletely defined. The present review provides a summary of current studies on the molecular functions of DNA and RNA m6A methylation, the key epigenetic mechanisms involved in regulating the expression of genetic information, in resistance to irradiation and cancer progression. We additionally discuss the effects of DNA methylation and RNA N6-methyladenosine (m6A) of specific genes in cancer progression, recurrence, and radioresistance. As epigenetic alterations could be reversed by drug treatment or inhibition of specific genes, they are also considered potential targets for anticancer therapy and/or radiotherapy sensitizers. The mechanisms of irradiation-induced alterations in DNA and RNA m6A methylation, and ways in which this understanding can be applied clinically, including utilization of methylation patterns as prognostic markers for cancer radiotherapy and their manipulation for anticancer therapy or use as radiotherapy sensitizers, have been further discussed.
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Affiliation(s)
- Hsiang-Cheng Chi
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University/Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan.
| | - Chung-Ying Tsai
- Kidney Research Center and Department of Nephrology, Chang Gung Immunology Consortium, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 333, Taiwan.
| | - Ming-Ming Tsai
- Department of Nursing, Chang-Gung University of Science and Technology, Taoyuan 333, Taiwan.
- Department of General Surgery, Chang Gung Memorial Hospital, Chiayi 613, Taiwan.
| | - Kwang-Huei Lin
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan.
- Department of Biochemistry, College of Medicine, Chang-Gung University, Taoyuan 333, Taiwan.
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan.
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54
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WDR5 high expression and its effect on tumorigenesis in leukemia. Oncotarget 2018; 7:37740-37754. [PMID: 27192115 PMCID: PMC5122345 DOI: 10.18632/oncotarget.9312] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/27/2016] [Indexed: 01/21/2023] Open
Abstract
WD repeat domain 5 (WDR5) plays an important role in various biological functions through the epigenetic regulation of gene transcription. However, the oncogenic effect of WDR5 in leukemia remains largely unknown. Here, we found WDR5 expression is increased in leukemia patients. High expression of WDR5 is associated with high risk leukemia; Patients with WDR5 and MLL1 high expression have poor complete remission rate. We further identified the global genomic binding of WDR5 in leukemic cells and found the genomic co-localization of WDR5 binding with H3K4me3 enrichment. Moreover, WDR5 knockdown by shRNA suppresses cell proliferation, induces apoptosis, inhibits the expression of WDR5 targets, and blocks the H3K4me3 enrichment on the promoter of its targets. We also observed the positive correlation of WDR5 expression with these targets in the cohort study of leukemia patients. Our data reveal that WDR5 may have oncogenic effect and WDR5-mediated H3K4 methylation plays an important role in leukemogenesis.
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55
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Castelli G, Pelosi E, Testa U. Targeting histone methyltransferase and demethylase in acute myeloid leukemia therapy. Onco Targets Ther 2017; 11:131-155. [PMID: 29343972 PMCID: PMC5749389 DOI: 10.2147/ott.s145971] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clonal disorder of myeloid progenitors characterized by the acquisition of chromosomal abnormalities, somatic mutations, and epigenetic changes that determine a consistent degree of biological and clinical heterogeneity. Advances in genomic technologies have increasingly shown the complexity and heterogeneity of genetic and epigenetic alterations in AML. Among the genetic alterations occurring in AML, frequent are the genetic alterations at the level of various genes involved in the epigenetic control of the DNA methylome and histone methylome. In fact, genes involved in DNA demethylation (such as DNMT3A, TET2, IDH1, and IDH2) or histone methylation and demethylation (EZH2, MLL, DOT1L) are frequently mutated in primary and secondary AML. Furthermore, some histone demethylases, such as LSD1, are frequently overexpressed in AML. These observations have strongly supported a major role of dysregulated epigenetic regulatory processes in leukemia onset and development. This conclusion was further supported by the observation that mutations in genes encoding epigenetic modifiers, such as DMT3A, ASXL1, TET2, IDH1, and IDH2, are usually acquired early and are present in the founding leukemic clone. These observations have contributed to development of the idea that targeting epigenetic abnormalities could represent a potentially promising strategy for the development of innovative treatments of AML. In this review, we analyze those proteins and their inhibitors that have already reached the first stages of clinical trials in AML, namely the histone methyltransferase DOT1L, the demethylase LSD1, and the MLL-interacting protein menin.
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Affiliation(s)
- Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
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56
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Aoki H, Yamamoto E, Takasawa A, Niinuma T, Yamano HO, Harada T, Matsushita HO, Yoshikawa K, Takagi R, Harada E, Tanaka Y, Yoshida Y, Aoyama T, Eizuka M, Yorozu A, Kitajima H, Kai M, Sawada N, Sugai T, Nakase H, Suzuki H. Epigenetic silencing of SMOC1 in traditional serrated adenoma and colorectal cancer. Oncotarget 2017; 9:4707-4721. [PMID: 29435136 PMCID: PMC5797007 DOI: 10.18632/oncotarget.23523] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/30/2017] [Indexed: 02/07/2023] Open
Abstract
Colorectal sessile serrated adenoma/polyps (SSA/Ps) are well-known precursors of colorectal cancer (CRC) characterized by BRAF mutation and microsatellite instability. By contrast, the molecular characteristics of traditional serrated adenoma (TSAs) are not fully understood. We analyzed genome-wide DNA methylation in TSAs having both protruding and flat components. We identified 11 genes, including SMOC1, methylation of which progressively increased during the development of TSAs. SMOC1 was prevalently methylated in TSAs, but was rarely methylated in SSA/Ps (p < 0.001). RT-PCR and immunohistochemistry revealed that SMOC1 was expressed in normal colon and SSA/Ps, but its expression was decreased in TSAs. Ectopic expression of SMOC1 suppressed proliferation, colony formation and in vivo tumor formation by CRC cells. Analysis of colorectal lesions (n = 847) revealed that SMOC1 is frequently methylated in TSAs, high-grade adenomas and CRCs. Among these, SMOC1 methylation was strongly associated with KRAS mutation and CpG island methylator phenotype (CIMP)-low. These results demonstrate that epigenetic silencing of SMOC1 is associated with TSA development but is rarely observed in SSA/Ps. SMOC1 expression could thus be a diagnostic marker of serrated lesions, and SMOC1 methylation could play a role in neoplastic pathways in TSAs and conventional adenomas.
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Affiliation(s)
- Hironori Aoki
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Eiichiro Yamamoto
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Akira Takasawa
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takeshi Niinuma
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiro-O Yamano
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Taku Harada
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiro-O Matsushita
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Kenjiro Yoshikawa
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Ryo Takagi
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Eiji Harada
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Yoshihito Tanaka
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Yuko Yoshida
- Department of Digestive Disease Center, Akita Red Cross Hospital, Akita, Japan
| | - Tomoyuki Aoyama
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Makoto Eizuka
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Akira Yorozu
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Kitajima
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masahiro Kai
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Norimasa Sawada
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
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57
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Li Y, Zhao H, Xu Q, Lv N, Jing Y, Wang L, Wang X, Guo J, Zhou L, Liu J, Chen G, Chen C, Li Y, Yu L. Detection of prognostic methylation markers by methylC-capture sequencing in acute myeloid leukemia. Oncotarget 2017; 8:110444-110459. [PMID: 29299160 PMCID: PMC5746395 DOI: 10.18632/oncotarget.22789] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/15/2017] [Indexed: 12/11/2022] Open
Abstract
Clinical and genetic features incompletely predict outcome in acute myeloid leukemia (AML). The value of clinical methylation assays for prognostic markers has not been extensively explored. We assess the prognostic implications of methylC-capture sequencing (MCC-Seq) in patients with de novo AML by integrating DNA methylation and genetic risk stratification. MCC-Seq assessed DNA methylation level in 44 samples. The differentially methylated regions associated with prognostic genetic information were identified. The selected prognostic DNA methylation markers were independently validated in two sets. MCC-Seq exhibited good performance in AML patients. A panel of 12 differentially methylated genes was identified with promoter hyper-differentially methylated regions associated with the outcome. Compared with a low M-value, a high M-value was associated with failure to achieve complete remission (p = 0.024), increased hazard for disease-free survival in the study set (p = 0.039) and poor overall survival in The Cancer Genome Atlas set (p = 0.038). Hematopoietic stem cell transplantation and survival outcomes were not adversely affected by a high M-value (p = 0.271). Our study establishes that MCC-Seq is a stable, reproducible, and cost-effective methylation assay in AML. A 12-gene M-value encompassing epigenetic and genetic prognostic information represented a valid prognostic marker for patients with AML.
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Affiliation(s)
- Yan Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, China
| | - Hongmei Zhao
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Qingyu Xu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Medical School of Nankai University, Tianjin 300071, China
| | - Na Lv
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
| | - Yu Jing
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Lili Wang
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiaowen Wang
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Jing Guo
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Lei Zhou
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Jing Liu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Guofeng Chen
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Medical School of Nankai University, Tianjin 300071, China
| | - Chongjian Chen
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Yonghui Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Li Yu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
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58
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Pogosova-Agadjanyan EL, Moseley A, Othus M, Appelbaum FR, Chauncey TR, Chen IML, Erba HP, Godwin JE, Fang M, Kopecky KJ, List AF, Pogosov GL, Radich JP, Willman CL, Wood BL, Meshinchi S, Stirewalt DL. Impact of Specimen Heterogeneity on Biomarkers in Repository Samples from Patients with Acute Myeloid Leukemia: A SWOG Report. Biopreserv Biobank 2017; 16:42-52. [PMID: 29172682 DOI: 10.1089/bio.2017.0079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Current prognostic models for acute myeloid leukemia (AML) are inconsistent at predicting clinical outcomes for individual patients. Variability in the quality of specimens utilized for biomarker discovery and validation may contribute to this prognostic inconsistency. METHODS We evaluated the impact of sample heterogeneity on prognostic biomarkers and methods to mitigate any adverse effects of this heterogeneity in 240 cryopreserved bone marrow and peripheral blood specimens from AML patients enrolled on SWOG (Southwest Oncology Group) trials. RESULTS Cryopreserved samples displayed a broad range in viability (37% with viabilities ≤60%) and nonleukemic cell contamination (13% with lymphocyte percentages >20%). Specimen viability was impacted by transport time, AML immunophenotype, and, potentially, patients' age. The viability and cellular heterogeneity in unsorted samples significantly altered biomarker results. Enriching for viable AML blasts improved the RNA quality from specimens with poor viability and refined results for both DNA and RNA biomarkers. For example, FLT3-ITD allelic ratio, which is currently utilized to risk-stratify AML patients, was on average 1.49-fold higher in the viable AML blasts than in the unsorted specimens. CONCLUSION To our knowledge, this is the first study to provide evidence that using cryopreserved specimens can introduce uncontrollable variables that may impact biomarker results and enrichment for viable AML blasts may mitigate this impact.
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Affiliation(s)
| | - Anna Moseley
- 2 SWOG Statistical Center , Fred Hutch, Seattle, Washington
| | - Megan Othus
- 2 SWOG Statistical Center , Fred Hutch, Seattle, Washington
| | - Frederick R Appelbaum
- 1 Clinical Research Division , Fred Hutch, Seattle, Washington.,3 Departments of Oncology and Hematology, University of Washington , Seattle, Washington
| | - Thomas R Chauncey
- 1 Clinical Research Division , Fred Hutch, Seattle, Washington.,3 Departments of Oncology and Hematology, University of Washington , Seattle, Washington.,4 VA Puget Sound Health Care System , Seattle, Washington
| | - I-Ming L Chen
- 5 Department of Pathology, University of New Mexico , UNM Comprehensive Cancer Center, Albuquerque, New Mexico
| | - Harry P Erba
- 6 Division of Hematology and Oncology, University of Alabama at Birmingham , Birmingham, Alabama
| | - John E Godwin
- 7 Providence Cancer Center, Earle A. Chiles Research Institute , Portland, Oregon
| | - Min Fang
- 8 Departments of Laboratory Medicine and Pathology, University of Washington , Seattle, Washington
| | | | - Alan F List
- 9 Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute , Tampa, Florida
| | | | - Jerald P Radich
- 1 Clinical Research Division , Fred Hutch, Seattle, Washington.,3 Departments of Oncology and Hematology, University of Washington , Seattle, Washington
| | - Cheryl L Willman
- 5 Department of Pathology, University of New Mexico , UNM Comprehensive Cancer Center, Albuquerque, New Mexico
| | - Brent L Wood
- 8 Departments of Laboratory Medicine and Pathology, University of Washington , Seattle, Washington
| | - Soheil Meshinchi
- 1 Clinical Research Division , Fred Hutch, Seattle, Washington.,10 Department of Pediatrics, University of Washington , Seattle, Washington
| | - Derek L Stirewalt
- 1 Clinical Research Division , Fred Hutch, Seattle, Washington.,3 Departments of Oncology and Hematology, University of Washington , Seattle, Washington
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59
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Xavier-Ferrucio J, Ricon L, Vieira K, Longhini AL, Lazarini M, Bigarella CL, Franchi G, Krause DS, Saad STO. Hematopoietic defects in response to reduced Arhgap21. Stem Cell Res 2017; 26:17-27. [PMID: 29212046 PMCID: PMC6084430 DOI: 10.1016/j.scr.2017.11.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 11/13/2017] [Accepted: 11/20/2017] [Indexed: 12/28/2022] Open
Abstract
Arhgap21 is a member of the Rho GTPase activating protein (RhoGAP) family, which function as negative regulators of Rho GTPases. Arhgap21 has been implicated in adhesion and migration of cancer cells. However, the role of Arhgap21 has never been investigated in hematopoietic cells. Herein, we evaluated functional aspects of hematopoietic stem and progenitor cells (HSPC) using a haploinsufficient (Arhgap21+/-) mouse. Our results show that Arhgap21+/- mice have an increased frequency of phenotypic HSC, impaired ability to form progenitor colonies in vitro and decreased hematopoietic engraftment in vivo, along with a decrease in LSK cell frequency during serial bone marrow transplantation. Arhgap21+/- hematopoietic progenitor cells have impaired adhesion and enhanced mobilization of immature LSK and myeloid progenitors. Arhgap21+/- mice also exhibit reduced erythroid commitment and differentiation, which was recapitulated in human primary cells, in which knockdown of ARHGAP21 in CMP and MEP resulted in decreased erythroid commitment. Finally, we observed enhanced RhoC activity in the bone marrow cells of Arhgap21+/- mice, indicating that Arhgap21 functions in hematopoiesis may be at least partially mediated by RhoC inactivation.
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Affiliation(s)
- Juliana Xavier-Ferrucio
- Hematology and Blood Transfusion Center University of Campinas/Hemocentro-UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, SP, Brazil; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Lauremília Ricon
- Hematology and Blood Transfusion Center University of Campinas/Hemocentro-UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, SP, Brazil
| | - Karla Vieira
- Hematology and Blood Transfusion Center University of Campinas/Hemocentro-UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, SP, Brazil
| | - Ana Leda Longhini
- Hematology and Blood Transfusion Center University of Campinas/Hemocentro-UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, SP, Brazil
| | - Mariana Lazarini
- Hematology and Blood Transfusion Center University of Campinas/Hemocentro-UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, SP, Brazil; Department of Biological Sciences, Federal University of São Paulo, Diadema, Brazil
| | - Carolina Louzão Bigarella
- Hematology and Blood Transfusion Center University of Campinas/Hemocentro-UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, SP, Brazil
| | - Gilberto Franchi
- Onco-Hematological Child Research Center (CIPOI), Faculty of Medical Sciences, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | - Diane S Krause
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Sara T O Saad
- Hematology and Blood Transfusion Center University of Campinas/Hemocentro-UNICAMP, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, SP, Brazil.
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60
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Sobieszkoda D, Czech J, Gablo N, Kopanska M, Tabarkiewicz J, Kolacinska A, Robak T, Zawlik I. MGMT promoter methylation as a potential prognostic marker for acute leukemia. Arch Med Sci 2017; 13:1433-1441. [PMID: 29181075 PMCID: PMC5701700 DOI: 10.5114/aoms.2017.71067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/14/2016] [Indexed: 01/14/2023] Open
Abstract
INTRODUCTION It has been proved that genetic and epigenetic changes play a significant role in the development and progression of acute leukemia. The aim of our study was to evaluate the frequency and prognostic implications of genetic and epigenetic alterations in p15, MGMT, DNMT3A and TP53 genes in acute leukemias. MATERIAL AND METHODS We included in the study 59 patients with acute leukemia. Evaluation of TP53 and DNMT3A mutations was performed using sequencing analysis and PCR-RFLP, respectively. Methylation status of MGMT and p15 genes was evaluated using MSP and COBRA, respectively. For assessment of global DNA methylation ELISA-based kit was used. RESULTS We found that overall survival was higher for ALL patients. MGMT promoter methylation was significantly associated with patients age at the time of diagnosis (p = 0.03). TP53 and DNMT3A mutations were observed only in AML patients (16.67% and 8.8%, respectively). Patients with acute leukemia and p15 promoter methylation had significantly more frequently mutated TP53 gene (p = 0.04) and AML patients with p15 promoter methylation had significantly more frequently detected global hypomethylation of DNA (p = 0.009). In the group of ALL patients we noted an opposite trend: only patients negative for p15 promoter methylation were characterized by global DNA hypomethylation. CONCLUSIONS Our findings demonstrate that MGMT promoter methylation can have a considerable impact on the development of acute leukemia in older patients. DNMT3A and TP53 mutations may play a significant role in AML development. However, further studies conducted in a larger cohort of patients are needed to determine its clinical utility.
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Affiliation(s)
- Dominika Sobieszkoda
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Joanna Czech
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Natalia Gablo
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Marta Kopanska
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Jacek Tabarkiewicz
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Department of Immunology, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Agnieszka Kolacinska
- Department of Head and Neck Cancer Surgery, Medical University of Lodz, Lodz, Poland
- Department of Surgical Oncology, Cancer Center, Copernicus Memorial Hospital, Lodz, Poland
| | - Tadeusz Robak
- Department of Hematology, Medical University of Lodz, Copernicus Memorial Hospital, Lodz, Poland
| | - Izabela Zawlik
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
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61
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Lee SH, Chiu YC, Li YH, Lin CC, Hou HA, Chou WC, Tien HF. High expression of dedicator of cytokinesis 1 ( DOCK1) confers poor prognosis in acute myeloid leukemia. Oncotarget 2017; 8:72250-72259. [PMID: 29069784 PMCID: PMC5641127 DOI: 10.18632/oncotarget.19706] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022] Open
Abstract
DOCK family genes encode evolutionarily conserved guanine nucleotide exchange factors for Rho GTPase involving multiple biological functions. Yet the patterns and prognostic significance of their expression in acute myeloid leukemia (AML) remain unexplored. Here we analyzed the expression patterns of 11 DOCK family genes in AML cells based on the array data of 347 patients from our cohort and several other published datasets. We further focused on the implications of the expression of DOCK1 since it was the only one in DOCK family to be associated with survival. Physiological functions and biological pathways associated with DOCK1 were identified using bioinformatics approaches. With a median follow up of 57 months, higher DOCK1 expression was associated with shorter disease free and overall survival. The finding could be validated by two independent cohorts. Multivariate analysis showed higher DOCK1 expression as a strong independent unfavorable prognostic factor. Higher DOCK1 expression was closely associated with older age, higher platelet and peripheral blast counts, intermediate-risk cytogenetics, FLT3-ITD, MLL-PTD and mutations in PTPN11, NPM1, RUNX1, ASXL1 and DNMT3A. Functional enrichment analysis suggested the association of DOCK1 overexpression with several key physiological pathways including cell proliferation, motility, and chemotaxis. Therefore, we suggested that AML with higher DOCK1 expression showed characteristic clinical and biological features. DOCK1 expression is an important prognostic marker and a potential therapeutic target for the treatment of AML. Studies in large prospective cohorts are necessary to confirm our findings. Further mechanistic studies to delineate the role of DOCK1 in the leukemogenesis are warranted.
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Affiliation(s)
- Sze-Hwei Lee
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Chiao Chiu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Yi-Hung Li
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Chin Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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62
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Fu L, Fu H, Qiao J, Pang Y, Xu K, Zhou L, Wu Q, Li Z, Ke X, Xu K, Shi J. High expression of CPNE3 predicts adverse prognosis in acute myeloid leukemia. Cancer Sci 2017; 108:1850-1857. [PMID: 28670859 PMCID: PMC5581509 DOI: 10.1111/cas.13311] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 01/17/2023] Open
Abstract
CPNE3, a member of a Ca2+‐dependent phospholipid‐binding protein family, was identified as a ligand of ERBB2 and has a more general role in carcinogenesis. Here, we identified the prognostic significance of CPNE3 expression in acute myeloid leukemia (AML) patients based on two datasets. In the first microarray dataset (n = 272), compared to low CPNE3 expression (CPNE3low), high CPNE3 expression (CPNE3high) was associated with adverse overall survival (OS, P < 0.001) and event‐free survival (EFS, P < 0.001). In the second independent group of AML patients (TCGA dataset, n = 179), CPNE3high was also associated with adverse OS and EFS (OS, P = 0.01; EFS, P = 0.036). Notably, among CPNE3high patients, those received allogenic hematopoietic cell transplantation (HCT) had longer OS and EFS than those with chemotherapy alone (allogeneic HCT, n = 40 vs chemotherapy, n = 46), but treatment modules played an insignificant role in the survival of CPNE3low patients (allogeneic HCT, n = 32 vs chemotherapy, n = 54). These results indicated that CPNE3high is an independent, adverse prognostic factor in AML and might guide treatment decisions towards allogeneic HCT. To understand its inherent mechanisms, we investigated genome‐wide gene/microRNA expression signatures and cell signaling pathways associated with CPNE3 expression. In conclusion, CPNE3high is an adverse prognostic biomarker for AML. Its effect may be attributed to the distinctive genome‐wide gene/microRNA expression and related cell signaling pathways.
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Affiliation(s)
- Lin Fu
- Department of Hematology and Lymphoma Research Center, Third Hospital, Peking University, Beijing, China.,Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, China
| | - Huaping Fu
- Departments of Nuclear Medicine, Chinese PLA General Hospital, Beijing, China
| | - Jianlin Qiao
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yifan Pang
- Department of Medicine, William Beaumont Hospital, Royal Oak, MI, USA
| | - Keman Xu
- Northeastern University, Boston, MA, USA
| | - Lei Zhou
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Qingyun Wu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Zhenyu Li
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Xiaoyan Ke
- Department of Hematology and Lymphoma Research Center, Third Hospital, Peking University, Beijing, China
| | - Kailin Xu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Jinlong Shi
- Departments of Biomedical Engineering, Chinese PLA General Hospital, Beijing, China.,Departments of Medical Big Data, Chinese PLA General Hospital, Beijing, China.,Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, China
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63
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Luo M, Mengos AE, Ma W, Finlayson J, Bustos RZ, Xiao Zhu Y, Shi CX, Stubblefield TM, Willis WT, Mandarino LJ. Characterization of the novel protein KIAA0564 (Von Willebrand Domain-containing Protein 8). Biochem Biophys Res Commun 2017; 487:545-551. [PMID: 28414126 PMCID: PMC5824621 DOI: 10.1016/j.bbrc.2017.04.067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/13/2017] [Indexed: 11/28/2022]
Abstract
The VWA8 gene was first identified by the Kazusa cDNA project and named KIAA0564. Based on the observation, by similarity, that the protein encoded by KIAA0564 contains a Von Willebrand Factor 8 domain, KIAA0564 was named Von Willebrand Domain-containing Protein 8 (VWA8). The function of VWA8 protein is almost unknown. The purpose of this study was to characterize the tissue distribution, cellular location, and function of VWA8. In mice VWA8 protein was mostly distributed in liver, kidney, heart, pancreas and skeletal muscle, and is present as a long isoform and a shorter splice variant (VWA8a and VWA8b). VWA8 protein and mRNA were elevated in mouse liver in response to high fat feeding. Sequence analysis suggests that VWA8 has a mitochondrial targeting sequence and domains responsible for ATPase activity. VWA8 protein was targeted exclusively to mitochondria in mouse AML12 liver cells, and this was prevented by deletion of the targeting sequence. Moreover, the VWA8 short isoform overexpressed in insect cells using a baculovirus construct had in vitro ATPase activity. Deletion of the Walker A motif or Walker B motif in VWA8 mostly blocked ATPase activity, suggesting Walker A motif or Walker B motif are essential to the ATPase activity of VWA8. Finally, homology modeling suggested that VWA8 may have a structure most confidently similar to dynein motor proteins.
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Affiliation(s)
- Moulun Luo
- Division of Endocrinology, University of Arizona, Tucson, AZ, United States
| | - April E Mengos
- Division of Laboratory Medicine, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Wuqiong Ma
- Division of Endocrinology, University of Arizona, Tucson, AZ, United States
| | - Jean Finlayson
- Division of Endocrinology, University of Arizona, Tucson, AZ, United States
| | | | - Yuan Xiao Zhu
- Division of Hematology-Oncology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Chang-Xin Shi
- Division of Hematology-Oncology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Tianna M Stubblefield
- Mouse Metabolic Phenotyping Laboratory, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Wayne T Willis
- Division of Endocrinology, University of Arizona, Tucson, AZ, United States
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64
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Papaioannou D, Nicolet D, Volinia S, Mrózek K, Yan P, Bundschuh R, Carroll AJ, Kohlschmidt J, Blum W, Powell BL, Uy GL, Kolitz JE, Wang ES, Eisfeld AK, Orwick SJ, Lucas DM, Caligiuri MA, Stone RM, Byrd JC, Garzon R, Bloomfield CD. Prognostic and biologic significance of long non-coding RNA profiling in younger adults with cytogenetically normal acute myeloid leukemia. Haematologica 2017; 102:1391-1400. [PMID: 28473620 PMCID: PMC5541873 DOI: 10.3324/haematol.2017.166215] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Long non-coding ribonucleic acids (RNAs) are a novel class of RNA molecules, which are increasingly recognized as important molecular players in solid and hematologic malignancies. Herein we investigated whether long non-coding RNA expression is associated with clinical and molecular features, as well as outcome of younger adults (aged <60 years) with de novo cytogenetically normal acute myeloid leukemia. Whole transcriptome profiling was performed in a training (n=263) and a validation set (n=114). Using the training set, we identified 24 long non-coding RNAs associated with event-free survival. Linear combination of the weighted expression values of these transcripts yielded a prognostic score. In the validation set, patients with high scores had shorter disease-free (P<0.001), overall (P=0.002) and event-free survival (P<0.001) than patients with low scores. In multivariable analyses, long non-coding RNA score status was an independent prognostic marker for disease-free (P=0.01) and event-free survival (P=0.002), and showed a trend for overall survival (P=0.06). Among multiple molecular alterations tested, which are prognostic in cytogenetically normal acute myeloid leukemia, only double CEBPA mutations, NPM1 mutations and FLT3-ITD associated with distinct long non-coding RNA signatures. Correlation of the long non-coding RNA scores with messenger RNA and microRNA expression identified enrichment of genes involved in lymphocyte/leukocyte activation, inflammation and apoptosis in patients with high scores. We conclude that long non-coding RNA profiling provides meaningful prognostic information in younger adults with cytogenetically normal acute myeloid leukemia. In addition, expression of prognostic long non-coding RNAs associates with oncogenic molecular pathways in this disease. clinicaltrials.gov Identifier: 00048958 (CALGB-8461), 00899223 (CALGB-9665), and 00900224 (CALGB-20202).
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Affiliation(s)
| | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.,The Alliance for Clinical Trials in Oncology Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - Stefano Volinia
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Italy
| | - Krzysztof Mrózek
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Pearlly Yan
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Ralf Bundschuh
- Department of Physics, Department of Chemistry & Biochemistry, Division of Hematology, Department of Internal Medicine, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, AL, USA
| | - Jessica Kohlschmidt
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.,The Alliance for Clinical Trials in Oncology Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - William Blum
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Bayard L Powell
- The Comprehensive Cancer Center of Wake Forest University, Winston-Salem, NC, USA
| | - Geoffrey L Uy
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Jonathan E Kolitz
- Hofstra North Shore-Long Island Jewish School of Medicine, Lake Success, NY, USA
| | | | | | - Shelley J Orwick
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - David M Lucas
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Richard M Stone
- Dana-Farber Cancer Institute, Harvard University, Boston, MA, USA
| | - John C Byrd
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Ramiro Garzon
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Clara D Bloomfield
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
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65
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66
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Lester J, Stout R, Crosthwaite K, Andersen B. Self-Reported Distress: Adult Acute Leukemia Survivors During and After Induction Therapy. Clin J Oncol Nurs 2017; 21:211-218. [DOI: 10.1188/17.cjon.211-218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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67
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Lin CC, Hsu YC, Li YH, Kuo YY, Hou HA, Lan KH, Chen TC, Tzeng YS, Kuo YY, Kao CJ, Chuang PH, Tseng MH, Chiu YC, Chou WC, Tien HF. Higher HOPX expression is associated with distinct clinical and biological features and predicts poor prognosis in de novo acute myeloid leukemia. Haematologica 2017; 102:1044-1053. [PMID: 28341738 PMCID: PMC5451336 DOI: 10.3324/haematol.2016.161257] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/17/2017] [Indexed: 01/29/2023] Open
Abstract
Homeodomain-only protein homeobox (HOPX) is the smallest homeodomain protein. It was regarded as a stem cell marker in several non-hematopoietic systems. While the prototypic homeobox genes such as the HOX family have been well characterized in acute myeloid leukemia (AML), the clinical and biological implications of HOPX in the disease remain unknown. Thus we analyzed HOPX and global gene expression patterns in 347 newly diagnosed de novo AML patients in our institute. We found that higher HOPX expression was closely associated with older age, higher platelet counts, lower white blood cell counts, lower lactate dehydrogenase levels, and mutations in RUNX1, IDH2, ASXL1, and DNMT3A, but negatively associated with acute promyelocytic leukemia, favorable karyotypes, CEBPA double mutations and NPM1 mutation. Patients with higher HOPX expression had a lower complete remission rate and shorter survival. The finding was validated in two independent cohorts. Multivariate analysis revealed that higher HOPX expression was an independent unfavorable prognostic factor irrespective of other known prognostic parameters and gene signatures derived from multiple cohorts. Gene set enrichment analysis showed higher HOPX expression was associated with both hematopoietic and leukemia stem cell signatures. While HOPX and HOX family genes showed concordant expression patterns in normal hematopoietic stem/progenitor cells, their expression patterns and associated clinical and biological features were distinctive in AML settings, demonstrating HOPX to be a unique homeobox gene. Therefore, HOPX is a distinctive homeobox gene with characteristic clinical and biological implications and its expression is a powerful predictor of prognosis in AML patients.
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Affiliation(s)
- Chien-Chin Lin
- Department of Laboratory Medicine, National Taiwan University, Taipei, Taiwan.,Division of Hematology and Department of Internal Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
| | - Yueh-Chwen Hsu
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Hung Li
- Division of Hematology and Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
| | - Yuan-Yeh Kuo
- Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology and Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
| | - Keng-Hsueh Lan
- Division of Radiation Oncology and Department of Oncology, National Taiwan University, Taipei, Taiwan
| | - Tsung-Chih Chen
- Division of Hematology and Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Shiuan Tzeng
- Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Yi Kuo
- Division of Hematology and Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
| | - Chein-Jun Kao
- Division of Hematology and Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
| | - Po-Han Chuang
- Division of Hematology and Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
| | - Mei-Hsuan Tseng
- Division of Hematology and Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Chiao Chiu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Wen-Chien Chou
- Department of Laboratory Medicine, National Taiwan University, Taipei, Taiwan .,Division of Hematology and Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology and Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
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68
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Qu X, Othus M, Davison J, Wu Y, Yan L, Meshinchi S, Ostronoff F, Estey EH, Radich JP, Erba HP, Appelbaum FR, Fang M. Prognostic methylation markers for overall survival in cytogenetically normal patients with acute myeloid leukemia treated on SWOG trials. Cancer 2017; 123:2472-2481. [PMID: 28222251 DOI: 10.1002/cncr.30626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND Aberrant DNA methylation is known to occur in patients with acute myeloid leukemia (AML), whereas methylation signatures and prognostic markers have been proposed. The objective of the current study was to evaluate all CpG sites of the genome and identify prognostic methylation markers for overall survival in patients with AML with normal karyotype (AML-NK). METHODS AML-NK samples from 7 SWOG trials were analyzed using a novel genome-wide approach called "CHARMcox" (comprehensive high-throughput array-based relative methylation analysis combined with the Cox proportional hazards model) controlling for known clinical covariates. CHARMcox was applied to a phase 1 discovery cohort (72 patients) to identify survival-associated methylation regions (SAMRs). Subsequently, using bisulfite pyrosequencing, SAMRs were studied in phase 2 model-building (65 patients) and phase 3 validation (65 patients) cohorts. An independent external cohort from The Cancer Genome Atlas (TCGA) AML study (LAML) was used for further validation (93 patients). RESULTS Two SAMRs, located at the CpG island shores of leucine zipper tumor suppressor 2 (LZTS2) and nuclear receptor subfamily 6 group a member 1 (NR6A1), respectively, were identified. Multivariable analyses demonstrated that hypomethylation of either LZTS2 or NR6A1 was associated with worse overall survival in the SWOG cohort (P<.001). The prognosis was validated in patients with AML-NK from the TCGA-LAML cohort. Methylation values below the median at both markers predicted worse overall survival (SWOG: hazard ratio, 1.89 [P<.001]; and TCGA-LAML: hazard ratio, 2.08 [P=.006]). The C-statistic was 0.71 for both cohorts, and the impact was independent of the Fms-related tyrosine kinase 3 internal tandem duplication (FLT3-ITD) status. CONCLUSIONS The 2 methylation markers, measurable by clinically applicable assays such as bisulfite pyrosequencing, are promising for risk stratification among patients with AML-NK. Cancer 2017;123:2472-81. © 2017 American Cancer Society.
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Affiliation(s)
- Xiaoyu Qu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Megan Othus
- Public Health Sciences Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,SWOG Leukemia Committee, Portland, Oregon
| | - Jerry Davison
- Public Health Sciences Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Yu Wu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Fabiana Ostronoff
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Elihu H Estey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington
| | - Jerry P Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Harry P Erba
- SWOG Leukemia Committee, Portland, Oregon.,Division of Hematology & Oncology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Frederick R Appelbaum
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington.,SWOG Leukemia Committee, Portland, Oregon.,Department of Medicine, University of Washington, Seattle, Washington
| | - Min Fang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington.,SWOG Leukemia Committee, Portland, Oregon.,Department of Pathology, University of Washington, Seattle, Washington
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69
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Ozer B, Sezerman U. An integrative study on the impact of highly differentially methylated genes on expression and cancer etiology. PLoS One 2017; 12:e0171694. [PMID: 28178311 PMCID: PMC5298317 DOI: 10.1371/journal.pone.0171694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/24/2017] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an important epigenetic phenomenon that plays a key role in the regulation of expression. Most of the studies on the topic of methylation's role in cancer mechanisms include analyses based on differential methylation, with the integration of expression information as supporting evidence. In the present study, we sought to identify methylation-driven patterns by also integrating protein-protein interaction information. We performed integrative analyses of DNA methylation, expression, SNP and copy number data on paired samples from six different cancer types. As a result, we found that genes that show a methylation change larger than 32.2% may influence cancer-related genes via fewer interaction steps and with much higher percentages compared with genes showing a methylation change less than 32.2%. Additionally, we investigated whether there were shared cancer mechanisms among different cancer types. Specifically, five cancer types shared a change in AGTR1 and IGF1 genes, which implies that there may be similar underlying disease mechanisms among these cancers. Additionally, when the focus was placed on distinctly altered genes within each cancer type, we identified various cancer-specific genes that are also supported in the literature and may play crucial roles as therapeutic targets. Overall, our novel graph-based approach for identifying methylation-driven patterns will improve our understanding of the effects of methylation on cancer progression and lead to improved knowledge of cancer etiology.
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Affiliation(s)
- Bugra Ozer
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- * E-mail:
| | - Ugur Sezerman
- Department of Biostatistics and Medical Informatics, Acibadem University, Istanbul, Turkey
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70
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Validation of risk stratification models in acute myeloid leukemia using sequencing-based molecular profiling. Leukemia 2017; 31:2029-2036. [PMID: 28167833 PMCID: PMC5629364 DOI: 10.1038/leu.2017.48] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/17/2017] [Accepted: 01/20/2017] [Indexed: 12/24/2022]
Abstract
Risk stratification of acute myeloid leukemia (AML) patients needs improvement. Several AML risk classification models based on somatic mutations or gene-expression profiling have been proposed. However, systematic and independent validation of these models is required for future clinical implementation. We performed whole-transcriptome RNA-sequencing and panel-based deep DNA sequencing of 23 genes in 274 intensively treated AML patients (Clinseq-AML). We also utilized the The Cancer Genome Atlas (TCGA)-AML study (N=142) as a second validation cohort. We evaluated six previously proposed molecular-based models for AML risk stratification and two revised risk classification systems combining molecular- and clinical data. Risk groups stratified by five out of six models showed different overall survival in cytogenetic normal-AML patients in the Clinseq-AML cohort (P-value<0.05; concordance index >0.5). Risk classification systems integrating mutational or gene-expression data were found to add prognostic value to the current European Leukemia Net (ELN) risk classification. The prognostic value varied between models and across cohorts, highlighting the importance of independent validation to establish evidence of efficacy and general applicability. All but one model replicated in the Clinseq-AML cohort, indicating the potential for molecular-based AML risk models. Risk classification based on a combination of molecular and clinical data holds promise for improved AML patient stratification in the future.
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71
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Li Y, Xu Q, Lv N, Wang L, Zhao H, Wang X, Guo J, Chen C, Li Y, Yu L. Clinical implications of genome-wide DNA methylation studies in acute myeloid leukemia. J Hematol Oncol 2017; 10:41. [PMID: 28153026 PMCID: PMC5290606 DOI: 10.1186/s13045-017-0409-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/27/2017] [Indexed: 01/01/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults. AML is a heterogeneous malignancy characterized by distinct genetic and epigenetic abnormalities. Recent genome-wide DNA methylation studies have highlighted an important role of dysregulated methylation signature in AML from biological and clinical standpoint. In this review, we will outline the recent advances in the methylome study of AML and overview the impacts of DNA methylation on AML diagnosis, treatment, and prognosis.
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Affiliation(s)
- Yan Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya, 572013, Hainan Province, China
| | - Qingyu Xu
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.,Medical school of Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Na Lv
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Lili Wang
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Hongmei Zhao
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Xiuli Wang
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Jing Guo
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Chongjian Chen
- Annoroad Gene Technology Co. Ltd, Beijing, 100176, China
| | - Yonghui Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Li Yu
- Department of Hematology and BMT center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.
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Kamps R, Brandão RD, Bosch BJVD, Paulussen ADC, Xanthoulea S, Blok MJ, Romano A. Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. Int J Mol Sci 2017; 18:ijms18020308. [PMID: 28146134 PMCID: PMC5343844 DOI: 10.3390/ijms18020308] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/19/2017] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.
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Affiliation(s)
- Rick Kamps
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Rita D Brandão
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Bianca J van den Bosch
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Aimee D C Paulussen
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Sofia Xanthoulea
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Marinus J Blok
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Andrea Romano
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
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73
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Yuan X, Chen J, Lin Y, Li Y, Xu L, Chen L, Hua H, Shen B. Network Biomarkers Constructed from Gene Expression and Protein-Protein Interaction Data for Accurate Prediction of Leukemia. J Cancer 2017; 8:278-286. [PMID: 28243332 PMCID: PMC5327377 DOI: 10.7150/jca.17302] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/29/2016] [Indexed: 12/14/2022] Open
Abstract
Leukemia is a leading cause of cancer deaths in the developed countries. Great efforts have been undertaken in search of diagnostic biomarkers of leukemia. However, leukemia is highly complex and heterogeneous, involving interaction among multiple molecular components. Individual molecules are not necessarily sensitive diagnostic indicators. Network biomarkers are considered to outperform individual molecules in disease characterization. We applied an integrative approach that identifies active network modules as putative biomarkers for leukemia diagnosis. We first reconstructed the leukemia-specific PPI network using protein-protein interactions from the Protein Interaction Network Analysis (PINA) and protein annotations from GeneGo. The network was further integrated with gene expression profiles to identify active modules with leukemia relevance. Finally, the candidate network-based biomarker was evaluated for the diagnosing performance. A network of 97 genes and 400 interactions was identified for accurate diagnosis of leukemia. Functional enrichment analysis revealed that the network biomarkers were enriched in pathways in cancer. The network biomarkers could discriminate leukemia samples from the normal controls more effectively than the known biomarkers. The network biomarkers provide a useful tool to diagnose leukemia and also aids in further understanding the molecular basis of leukemia.
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Affiliation(s)
- Xuye Yuan
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Jiajia Chen
- School of Chemistry and Biological Engineering, Suzhou University of Science and Technology, Suzhou, 215011, China
| | - Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Yin Li
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
| | - Lihua Xu
- Department of Pediatrics, The First People's Hospital of Lianyungang, Lianyungang, 222002, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Haiying Hua
- Department of Hematology, The Third Hospital Affiliated to Nantong University, No. 585 North Xingyuan Road, Wuxi, Jiangsu214041, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou, 215006, China
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A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome. Leukemia 2017; 31:2011-2019. [PMID: 28074068 PMCID: PMC5537054 DOI: 10.1038/leu.2017.12] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/12/2022]
Abstract
Genetic changes are infrequent in acute myeloid leukemia (AML) compared to other malignancies and often involve epigenetic regulators, suggesting that an altered epigenome may underlie AML biology and outcomes. In 96 AML cases including 65 pilot samples selected for cured/not-cured, we found higher CpG island (CGI) promoter methylation in cured patients. Expanded genome-wide digital restriction enzyme analysis of methylation (DREAM) data revealed a CGI methylator phenotype independent of IDH1/2 mutations we term AML-CIMP (A-CIMP+). A-CIMP was associated with longer overall survival (OS) in this dataset (median OS, years: A-CIMP+ = Not reached, A-CIMP− =1.17; P=0.08). For validation we used 194 samples from The Cancer Genome Atlas interrogated with Illumina 450k methylation arrays where we confirmed longer OS in A-CIMP (median OS, years: A-CIMP+ =2.34, A-CIMP− =1.00; P=0.01). Hypermethylation in A-CIMP favored CGIs (OR: CGI/non-CGI=5.21), and while A-CIMP was enriched in CEBPA (P=0.002) and WT1 mutations (P=0.02), 70% of cases lacked either mutation. Hypermethylated genes in A-CIMP function in pluripotency maintenance, and a gene expression signature of A-CIMP was associated with outcomes in multiple datasets. We conclude that CIMP in AML cannot be explained solely by gene mutations (e.g. IDH1/2, TET2), and that curability in A-CIMP+ AML should be validated prospectively.
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75
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An mRNA expression signature for prognostication in de novo acute myeloid leukemia patients with normal karyotype. Oncotarget 2016; 6:39098-110. [PMID: 26517675 PMCID: PMC4770759 DOI: 10.18632/oncotarget.5390] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 08/30/2015] [Indexed: 12/28/2022] Open
Abstract
Although clinical features, cytogenetics, and mutations are widely used to predict prognosis in patients with acute myeloid leukemia (AML), further refinement of risk stratification is necessary for optimal treatment, especially in cytogenetically normal (CN) patients. We sought to generate a simple gene expression signature as a predictor of clinical outcome through analyzing the mRNA arrays of 158 de novo CN AML patients. We compared the gene expression profiles of patients with poor response to induction chemotherapy with those who responded well. Forty-six genes expressed differentially between the two groups. Among them, expression of 11 genes was significantly associated with overall survival (OS) in univariate Cox regression analysis in 104 patients who received standard intensive chemotherapy. We integrated the z-transformed expression levels of these 11 genes to generate a risk scoring system. Higher risk scores were significantly associated with shorter OS (median 17.0 months vs. not reached, P < 0.001) in ours and another 3 validation cohorts. In addition, it was an independent unfavorable prognostic factor by multivariate analysis (HR 1.116, 95% CI 1.035~1.204, P = 0.004). In conclusion, we developed a simple mRNA expression signature for prognostication in CN-AML patients. This prognostic biomarker will help refine the treatment strategies for this group of patients.
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76
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Frontline treatment of acute myeloid leukemia in adults. Crit Rev Oncol Hematol 2016; 110:20-34. [PMID: 28109402 DOI: 10.1016/j.critrevonc.2016.12.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 11/01/2016] [Accepted: 12/07/2016] [Indexed: 01/13/2023] Open
Abstract
Recent years have highlighted significant progress in understanding the underlying genetic and epigenetic signatures of acute myeloid leukemia(AML). Most importantly, novel chemotherapy and targeted strategies have led to improved outcomes in selected genetic subsets. AML is a remarkably heterogeneous disease, and individualized therapies for disease-specific characteristics (considering patients' age, cytogenetics, and mutations) could yield better outcomes. Compared with the historical 5-to 10-year survival rate of 10%, the survival of patients who undergo modern treatment approaches reaches up to 40-50%, and for specific subsets, the improvements are even more dramatic; for example, in acute promyelocytic leukemia, the use of all-trans retinoic acid and arsenic trioxide improved survival from 30 to 40% up to 80 to 90%. Similar progress has been documented in core-binding-factor-AML, with an increase in survival from 30% to 80% upon the use of high-dose cytarabine/fludarabine/granulocyte colony-stimulating factor combination regimens. AML treatment was also recently influenced by the discovery of the superiority of regimens with higher dose Ara-C and nucleoside analogues compared with the "7+3"regimen, with about a 20% improvement in overall survival. Despite these significant differences, most centers continue to use the "7+3" regimen, and greater awareness will improve the outcome. The discovery of targetable molecular abnormalities and recent studies of targeted therapies (gemtuzumab ozagomycin, FLT3 inhibitors, isocitrate dehydrogenase inhibitors, and epigenetic therapies), future use of checkpoint inhibitors and other immune therapies such as chimeric antigen receptor T-cells, and maintenance strategies based on the minimal residual disease evaluation represent novel, exciting clinical leads aimed to improve AML outcomes in the near future.
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77
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Aberrant DNA methylation of acute myeloid leukemia and colorectal cancer in a Chinese pedigree with a MLL3 germline mutation. Tumour Biol 2016; 37:12609-12618. [PMID: 27405564 DOI: 10.1007/s13277-016-5130-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/29/2016] [Indexed: 12/14/2022] Open
Abstract
Unlike genetic aberrations, epigenetic alterations do not modify the deoxyribonucleic acid (DNA) coding sequence and can be reversed pharmacologically. Identifying a particular epigenetic alteration such as abnormal DNA methylation may provide better understanding of cancers and improve current therapy. In a Chinese pedigree with colorectal carcinoma and acute myeloid leukemia, we examined the genome-wide DNA methylation level of cases and explored the role of methylation in pathogenesis and progression. DNA methylation status in the four cases, which all harbor a MLL3 germline mutation, differed from that of the normal control, and hypermethylation was more prevalent. Also, more CpG sites were hypermethylated in the acute-phase AML patient than in the AML patient in remission. Fifty-nine hyper- or hypomethylated genes were identified as common to all four cases. Genome-wide DNA methylation analysis demonstrated that differentially methylated sites among acute myeloid leukemia and colorectal carcinoma cases and the control were in both promoters (CpG island) and gene body regions (shelf/shore areas). Hypermethylation was more prevalent in cancer cases. The study supports the suggestion that the level of DNA methylation changes in AML progression.
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78
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Yang IV, Pedersen BS, Liu AH, O'Connor GT, Pillai D, Kattan M, Misiak RT, Gruchalla R, Szefler SJ, Khurana Hershey GK, Kercsmar C, Richards A, Stevens AD, Kolakowski CA, Makhija M, Sorkness CA, Krouse RZ, Visness C, Davidson EJ, Hennessy CE, Martin RJ, Togias A, Busse WW, Schwartz DA. The nasal methylome and childhood atopic asthma. J Allergy Clin Immunol 2016; 139:1478-1488. [PMID: 27745942 DOI: 10.1016/j.jaci.2016.07.036] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 06/24/2016] [Accepted: 07/14/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Given the strong environmental influence on both epigenetic marks and allergic asthma in children, the epigenetic alterations in respiratory epithelia might provide insight into allergic asthma. OBJECTIVE We sought to identify DNA methylation and gene expression changes associated with childhood allergic persistent asthma. METHODS We compared genomic DNA methylation patterns and gene expression in African American children with persistent atopic asthma (n = 36) versus healthy control subjects (n = 36). Results were validated in an independent population of asthmatic children (n = 30) by using a shared healthy control population (n = 36) and in an independent population of white adult atopic asthmatic patients (n = 12) and control subjects (n = 12). RESULTS We identified 186 genes with significant methylation changes, differentially methylated regions or differentially methylated probes, after adjustment for age, sex, race/ethnicity, batch effects, inflation, and multiple comparisons. Genes differentially methylated included those with established roles in asthma and atopy and genes related to extracellular matrix, immunity, cell adhesion, epigenetic regulation, and airflow obstruction. The methylation changes were substantial (median, 9.5%; range, 2.6% to 29.5%). Hypomethylated and hypermethylated genes were associated with increased and decreased gene expression, respectively (P < 2.8 × 10-6 for differentially methylated regions and P < 7.8 × 10-10 for differentially methylated probes). Quantitative analysis in 53 differentially expressed genes demonstrated that 32 (60%) have significant methylation-expression relationships within 5 kb of the gene. Ten loci selected based on the relevance to asthma, magnitude of methylation change, and methylation-expression relationships were validated in an independent cohort of children with atopic asthma. Sixty-seven of 186 genes also have significant asthma-associated methylation changes in nasal epithelia of adult white asthmatic patients. CONCLUSIONS Epigenetic marks in respiratory epithelia are associated with allergic asthma and gene expression changes in inner-city children.
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Affiliation(s)
- Ivana V Yang
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo; National Jewish Health, Denver, Colo; Department of Epidemiology, Colorado School of Public Health, Aurora, Colo.
| | - Brent S Pedersen
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | | | - George T O'Connor
- Department of Medicine, Boston University School of Medicine, Boston, Mass
| | | | - Meyer Kattan
- Columbia University Medical Center, New York, NY
| | | | | | - Stanley J Szefler
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado, School of Medicine, Aurora, Colo
| | | | | | - Adam Richards
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | | | | | | | - Christine A Sorkness
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | | | | | - Elizabeth J Davidson
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | - Corinne E Hennessy
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | | | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md; and University of Colorado, Aurora, CO
| | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - David A Schwartz
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo; National Jewish Health, Denver, Colo; Department of Immunology, University of Colorado, Aurora, Colo.
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79
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Podoltsev NA, Stahl M, Zeidan AM, Gore SD. Selecting initial treatment of acute myeloid leukaemia in older adults. Blood Rev 2016; 31:43-62. [PMID: 27745715 DOI: 10.1016/j.blre.2016.09.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 08/05/2016] [Accepted: 09/30/2016] [Indexed: 11/30/2022]
Abstract
More than half of the patients with acute myeloid leukaemia (AML) are older than 60years. The treatment outcomes in this group remain poor with a median overall survival of <1year. Selecting initial treatment for these patients involves an assessment of 'fitness' for induction chemotherapy. This is done based on patient and disease-related characteristics which help to estimate treatment-related mortality and chance of complete remission with induction chemotherapy. If the risk of treatment-related mortality is high and/or the likelihood of a patient achieving a complete remission is low, lower-intensity treatment (low-dose cytarabine, decitabine and azacitidine) should be discussed. As outcomes in both groups of patients remain poor, enrolment into clinical trials of novel agents with varying mechanisms of action should be considered for all older adults with AML. Novel agents in Phase III development include CPX-351, guadecitabine (SGI-110), quizartinib, crenolanib, sapacitabine, vosaroxin and volasertib.
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Affiliation(s)
- Nikolai A Podoltsev
- Department of Internal Medicine, Hematology Section, Yale University School of Medicine, New Haven, CT, USA.
| | - Maximilian Stahl
- Yale Traditional Internal Medicine Program, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.
| | - Amer M Zeidan
- Department of Internal Medicine, Hematology Section, Yale University School of Medicine, New Haven, CT, USA.
| | - Steven D Gore
- Department of Internal Medicine, Hematology Section, Yale University School of Medicine, New Haven, CT, USA.
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80
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Prada-Arismendy J, Arroyave JC, Röthlisberger S. Molecular biomarkers in acute myeloid leukemia. Blood Rev 2016; 31:63-76. [PMID: 27639498 DOI: 10.1016/j.blre.2016.08.005] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022]
Abstract
Acute myeloid leukemia (AML) is the most common acute leukemia in adults. The pathophysiology of this disease is just beginning to be understood at the cellular and molecular level, and currently cytogenetic markers are the most important for risk stratification and treatment of AML patients. However, with the advent of new technologies, the detection of other molecular markers such as point mutations and characterization of epigenetic and proteomic profiles, have begun to play an important role in how the disease is approached. Recent evidence shows that the identification of new AML biomarkers contributes to a better understanding of the molecular basis of the disease, is significantly useful in screening, diagnosis, prognosis and monitoring of AML, as well as the possibility of predicting each individual's response to treatment. This review summarizes the most relevant molecular (genetic, epigenetic, and protein) biomarkers associated with acute myeloid leukemia and discusses their clinical importance in terms of risk prediction, diagnosis and prognosis.
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MESH Headings
- Biomarkers, Tumor
- DNA Methylation
- Disease Susceptibility
- Epigenesis, Genetic
- Genetic Variation
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Mutation
- Prognosis
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Affiliation(s)
- Jeanette Prada-Arismendy
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Medellín, Colombia.
| | - Johanna C Arroyave
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Medellín, Colombia
| | - Sarah Röthlisberger
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Medellín, Colombia
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81
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Wilop S, Chou WC, Jost E, Crysandt M, Panse J, Chuang MK, Brümmendorf TH, Wagner W, Tien HF, Kharabi Masouleh B. A three-gene expression-based risk score can refine the European LeukemiaNet AML classification. J Hematol Oncol 2016; 9:78. [PMID: 27585840 PMCID: PMC5009640 DOI: 10.1186/s13045-016-0308-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/24/2016] [Indexed: 12/18/2022] Open
Abstract
Background Risk stratification based on cytogenetics of acute myeloid leukemia (AML) remains imprecise. The introduction of novel genetic and epigenetic markers has helped to close this gap and increased the specificity of risk stratification, although most studies have been conducted in specific AML subpopulations. In order to overcome this limitation, we used a genome-wide approach in multiple AML populations to develop a robust prediction model for AML survival. Methods We conducted a genome-wide expression analysis of two data sets from AML patients enrolled into the AMLCG-1999 trial and from the Tumor Cancer Genome Atlas (TCGA) to develop a prognostic score to refine current risk classification and performed a validation on two data sets of the National Taiwan University Hospital (NTUH) and an independent AMLCG cohort. Results In our training set, using a stringent multi-step approach, we identified a small three-gene prognostic scoring system, named Tri-AML score (TriAS) which highly correlated with overall survival (OS). Multivariate analysis revealed TriAS to be an independent prognostic factor in all tested training and additional validation sets, even including age, current cytogenetic-based risk stratification, and three other recently developed expression-based scoring models for AML. Conclusions The Tri-AML score allows robust and clinically practical risk stratification for the outcome of AML patients. TriAS substantially refined current ELN risk stratification assigning 44.5 % of the patients into a different risk category. Electronic supplementary material The online version of this article (doi:10.1186/s13045-016-0308-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Wilop
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Wen-Chien Chou
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Edgar Jost
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Martina Crysandt
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Jens Panse
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ming-Kai Chuang
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular, Engineering, University Hospital of the RWTH Aachen, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of the RWTH, Aachen, Germany
| | - Hwei-Fang Tien
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Behzad Kharabi Masouleh
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany.
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82
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Estey E. Acute myeloid leukemia: 2016 Update on risk-stratification and management. Am J Hematol 2016; 91:824-46. [PMID: 27417880 DOI: 10.1002/ajh.24439] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 11/09/2022]
Abstract
Evidence suggest that even patients aged 70 or above benefit from specific AML therapy. The fundamental decision in AML then becomes whether to recommend standard or investigational treatment. This decision must rest on the likely outcome of standard treatment. Hence we review factors that predict treatment related mortality and resistance to therapy, the latter the principal cause of failure even in patients aged 70 or above. We emphasize the limitations of prediction of resistance based only on pre- treatment factors and stress the need to incorporate post-treatment factors, for example indicators of minimal residual disease. We review various newer therapeutic options and considerations that underlie the decision to recommend allogeneic hematopoietic cell transplant. Am. J. Hematol. 91:825-846, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Elihu Estey
- Division of Hematology, University of Washington School of Medicine, Seattle, WA, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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83
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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: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [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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84
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Fu L, Shi J, Hu K, Wang J, Wang W, Ke X. Mitogen-activated protein kinase binding protein 1 (MAPKBP1) is an unfavorable prognostic biomarker in cytogenetically normal acute myeloid leukemia. Oncotarget 2016; 6:8144-54. [PMID: 25924238 PMCID: PMC4480741 DOI: 10.18632/oncotarget.3519] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/03/2015] [Indexed: 11/25/2022] Open
Abstract
Mitogen-activated protein kinase binding protein 1 (MAPKBP1) is a key transcription factor in the NF-κB signalling pathway. In this study, associations between MAPKBP1 expression and molecular and clinical characteristics were evaluated by several microarray datasets. We found that MAPKBP1 was over-expressed in cytogenetically normal AML (CN-AML) patients compared to normal bone marrow. High MAPKBP1 expression (MAPKBP1high) was associated with significantly shorter event-free survival (EFS; P = 0.0004) and overall survival (OS; P = 0.0006) than low MAPKBP1 expression (MAPKBP1low) in a cohort of 157 CN-AML patients. In multivariable analyses, MAPKBP1high remained associated with shorter EFS (P = 0.003) and OS (P = 0.01). Validation in an independent cohort of 162 CN-AML patients further confirmed the prognostic value of MAPKBP1 (OS, P = 0.00172). Gene-expression profiling revealed that some important oncogenes, including MYCN, MYB, CDK6 and CCND2, etc, were up-regulated, while cell signalling pathways leading to apoptosis, antigen processing, and natural killer cell-mediated cytotoxicity were down-regulated in MAPKBP1high patients with CN-AML. MicroRNA expression profiling revealed thatsome oncogenic microRNAsincluding miR-155 and miR-126 were up-regulated, whilst anti-oncogenic microRNAsincluding miR-148a and miR-193a were down-regulated in MAPKBP1high patients with CN-AML, which may underlie the pathological processes in this malignancy. Taken together, these findings suggest MAPKBP1highis a novel, unfavourably prognostic biomarker for CN-AML risk-stratification.
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Affiliation(s)
- Lin Fu
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, China
| | - Jinlong Shi
- Medical Engineering Support Center, Chinese PLA General Hospital, Beijing, China
| | - Kai Hu
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, China
| | - Jijun Wang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, China
| | - Weidong Wang
- Medical Engineering Support Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaoyan Ke
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing, China
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85
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Yuan XQ, Peng L, Zeng WJ, Jiang BY, Li GC, Chen XP. DNMT3A R882 Mutations Predict a Poor Prognosis in AML: A Meta-Analysis From 4474 Patients. Medicine (Baltimore) 2016; 95:e3519. [PMID: 27149454 PMCID: PMC4863771 DOI: 10.1097/md.0000000000003519] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
DNA (cytosine-5)-methyltransferase 3 alpha (DNMT3A) mutations were widely believed to be independently associated with inferior prognosis in acute myeloid leukemia (AML) patients. As dominant missense alterations in DNMT3A mutations, R882 mutations cause the focal hypomethylation phenotype. However, there remains debate on the influence of R882 mutations on AML prognosis. Thus, this meta-analysis aimed at further illustrating the prognostic power of DNMT3A R882 mutations in AML patients.Eligible studies were identified from 5 databases containing PubMed, Embase, Web of Science, Clinical Trials, and the Cochrane Library (up to October 25, 2015). Effects (hazard ratios [HRs] with 95% confidence interval [CI]) of relapse-free survival (RFS) and overall survival (OS) were pooled to estimate the prognostic power of mutant DNMT3A R882 in overall patients and subgroups of AML patients.Eight competent studies with 4474 AML patients including 694 with DNMT3A R882 mutations were included. AML patients with DNMT3A R882 mutations showed significant shorter RFS (HR = 1.40, 95% CI = 1.24-1.59, P < 0.001) and OS (HR = 1.47, 95% CI = 1.17-1.86, P = 0.001) in the overall population. DNMT3A R882 mutations predicted worse RFS and OS among the subgroups of patients under age 60 (RFS: HR = 1.44, 95% CI = 1.25-1.66, P < 0.001; OS: HR = 1.48, 95% CI = 1.15-1.90, P = 0.002), over age 60 (RFS: HR = 2.03, 95% CI = 1.40-2.93, P < 0.001; OS: HR = 1.85, 95% CI = 1.36-2.53, P < 0.001), cytogenetically normal (CN)-AML (RFS: HR = 1.52, 95% CI = 1.26-1.83, P < 0.001; OS: HR = 1.67, 95% CI = 1.16-2.41, P = 0.006), and non-CN-AML (RFS: HR = 1.96, 95% CI = 1.20-3.21, P = 0.006; OS: HR = 2.51, 95% CI = 1.52-4.15, P = 0.0038).DNMT3A R882 mutations possessed significant unfavorable prognostic influence on RFS and OS in AML patients.
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Affiliation(s)
- Xiao-Qing Yuan
- From the Department of Clinical Pharmacology, Xiangya Hospital; Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics (X-QY, W-JZ, X-PC); Cancer Research Institute, Central South University; Key Laboratory of Carcinogenesis, National Health and Family Planning Commission; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha (LP, B-YJ, G-CL); and Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, P.R. China (X-PC)
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86
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Niavarani A, Herold T, Reyal Y, Sauerland MC, Buchner T, Hiddemann W, Bohlander SK, Valk PJM, Bonnet D. A 4-gene expression score associated with high levels of Wilms Tumor-1 (WT1) expression is an adverse prognostic factor in acute myeloid leukaemia. Br J Haematol 2016; 172:401-11. [PMID: 26597595 PMCID: PMC4833185 DOI: 10.1111/bjh.13836] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 09/22/2015] [Indexed: 11/29/2022]
Abstract
Wilms Tumor-1 (WT1) expression level is implicated in the prognosis of acute myeloid leukaemia (AML). We hypothesized that a gene expression profile associated with WT1 expression levels might be a good surrogate marker. We identified high WT1 gene sets by comparing the gene expression profiles in the highest and lowest quartiles of WT1 expression in two large AML studies. Two high WT1 gene sets were found to be highly correlated in terms of the altered genes and expression profiles. We identified a 17-probe set signature of the high WT1 set as the optimal prognostic predictor in the first AML set, and showed that it was able to predict prognosis in the second AML series after adjustment for European LeukaemiaNet genetic groups. The gene signature also proved to be of prognostic value in a third AML series of 163 samples assessed by RNA sequencing, demonstrating its cross-platform consistency. This led us to derive a 4-gene expression score, which faithfully predicted adverse outcome. In conclusion, a short gene signature associated with high WT1 expression levels and the resultant 4-gene expression score were found to be predictive of adverse prognosis in AML. This study provides new clues to the molecular pathways underlying high WT1 states in leukaemia.
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Affiliation(s)
- Ahmadreza Niavarani
- Digestive Oncology Research CenterDigestive Disease Research Institute (DDRI)Shariati HospitalTehran University of Medical SciencesTehranIran
- Haematopoietic Stem Cell LaboratoryLondon Research InstituteCancer Research UKLondonUnited Kingdom
| | - Tobias Herold
- Department of Internal Medicine 3University Hospital GrosshadernLudwig‐Maximilians‐UniversitätMunichGermany
| | - Yasmin Reyal
- Department of HaematologyUniversity College London Hospitals NHS TrustLondonUK
| | - Maria C. Sauerland
- Institute of Biostatistics and Clinical ResearchUniversity of MünsterMünsterGermany
- Department of Medicine A ‐ Haematology, Oncology and PneumologyUniversity of MünsterMünsterGermany
| | - Thomas Buchner
- Department of Molecular Medicine and PathologyThe University of AucklandAucklandNew Zealand
| | - Wolfgang Hiddemann
- Department of Internal Medicine 3University Hospital GrosshadernLudwig‐Maximilians‐UniversitätMunichGermany
| | - Stefan K. Bohlander
- Department of Molecular Medicine and PathologyThe University of AucklandAucklandNew Zealand
| | - Peter J. M. Valk
- Department of HaematologyErasmus University Medical Centre Cancer InstituteRotterdamthe Netherlands
| | - Dominique Bonnet
- Haematopoietic Stem Cell LaboratoryLondon Research InstituteCancer Research UKLondonUnited Kingdom
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87
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Walker AR, Wang H, Walsh K, Bhatnagar B, Vasu S, Garzon R, Canning R, Geyer S, Wu YZ, Devine SM, Klisovic R, Blum W, Marcucci G. Midostaurin, bortezomib and MEC in relapsed/refractory acute myeloid leukemia. Leuk Lymphoma 2016; 57:2100-8. [PMID: 26784138 DOI: 10.3109/10428194.2015.1135435] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Targeting aberrant tyrosine kinase activity may impact clinical outcome in acute myeloid leukemia (AML). We conducted a phase I study of the tyrosine kinase inhibitor midostaurin with bortezomib alone and in combination with chemotherapy in patients with AML. Patients on dose levels 1 and 2 (DL1 & 2) received midostaurin 50 mg bid and escalating doses of bortezomib (1 to 1.3 mg/m2). Patients on DL3 or higher received midostaurin and bortezomib following chemotherapy with mitoxantrone, etoposide, cytarabine (MEC). None of the patients enrolled to DL1 & 2 had dose-limiting toxicities (DLTs) or a clinical response. Among patients enrolled to DL3 or higher, DLTs were peripheral neuropathy, decrease in ejection fraction and diarrhea. A 56.5% CR rate and 82.5% overall response rate (CR + CR with incomplete neutrophil or platelet count recovery) were observed. The midostaurin/bortezomib/MEC combination is active in refractory/relapsed AML, but is associated with expected drug-related toxicities (NCT01174888).
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Affiliation(s)
- Alison R Walker
- a Division of Hematology, Department of Medicine , The Ohio State University and the Comprehensive Cancer Center , Columbus , OH , USA
| | - Hongyan Wang
- a Division of Hematology, Department of Medicine , The Ohio State University and the Comprehensive Cancer Center , Columbus , OH , USA
| | - Katherine Walsh
- a Division of Hematology, Department of Medicine , The Ohio State University and the Comprehensive Cancer Center , Columbus , OH , USA
| | - Bhavana Bhatnagar
- a Division of Hematology, Department of Medicine , The Ohio State University and the Comprehensive Cancer Center , Columbus , OH , USA
| | - Sumithira Vasu
- a Division of Hematology, Department of Medicine , The Ohio State University and the Comprehensive Cancer Center , Columbus , OH , USA
| | - Ramiro Garzon
- a Division of Hematology, Department of Medicine , The Ohio State University and the Comprehensive Cancer Center , Columbus , OH , USA
| | - Renee Canning
- a Division of Hematology, Department of Medicine , The Ohio State University and the Comprehensive Cancer Center , Columbus , OH , USA
| | - Susan Geyer
- b Health Informatics Institute, University of South Florida , Tampa , FL , USA
| | - Yue-Zhong Wu
- a Division of Hematology, Department of Medicine , The Ohio State University and the Comprehensive Cancer Center , Columbus , OH , USA
| | - Steven M Devine
- a Division of Hematology, Department of Medicine , The Ohio State University and the Comprehensive Cancer Center , Columbus , OH , USA
| | - Rebecca Klisovic
- a Division of Hematology, Department of Medicine , The Ohio State University and the Comprehensive Cancer Center , Columbus , OH , USA
| | - William Blum
- a Division of Hematology, Department of Medicine , The Ohio State University and the Comprehensive Cancer Center , Columbus , OH , USA
| | - Guido Marcucci
- c City of Hope Comprehensive Cancer Center , Gehr Family Center for Leukemia , Duarte , CA , USA
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88
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Graubert TA, Brunner AM, Fathi AT. New molecular abnormalities and clonal architecture in AML: from reciprocal translocations to whole-genome sequencing. Am Soc Clin Oncol Educ Book 2015:e334-40. [PMID: 24857122 DOI: 10.14694/edbook_am.2014.34.e334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Acute myeloid leukemia (AML) is characterized by recurrent genetic alterations, including amplifications, deletions, rearrangements, and point mutations. Clinically, these lesions can be used to stratify patients into categories of risk, which directs further clinical management and prognostication. Patient risk categories were first described based on recurrent karyotypic abnormalities; most patients with AML, however, fall into intermediate cytogenetic risk, the majority harboring a normal karyotype. Subsequently, identification of recurrently mutated genes, including FLT3, NPM1, and CEBPA, allowed further stratification of patients with a normal karyotype. More extensive genomic and epigenomic analysis of AML samples has expanded the number of known molecular alterations present in this disease. The further understanding of this mutational landscape has shed light into the pathogenesis of AML. AML arises in a founding clone that often gives rise to subclones. Clonal evolution is a feature of the natural history of the disease but may also be influenced by the selective pressure of chemotherapy. The complex network of genetic and epigenetic alterations in this disease has yielded numerous new targets for intervention. In the future, further understanding of this mutational framework, along with the development of novel therapeutic targets, may lead to improved outcomes for patients with AML.
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Affiliation(s)
| | | | - Amir T Fathi
- From the Massachusetts General Hospital, Boston, MA
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89
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Yamazaki J, Taby R, Jelinek J, Raynal NJM, Cesaroni M, Pierce SA, Kornblau SM, Bueso-Ramos CE, Ravandi F, Kantarjian HM, Issa JPJ. Hypomethylation of TET2 Target Genes Identifies a Curable Subset of Acute Myeloid Leukemia. J Natl Cancer Inst 2015; 108:djv323. [PMID: 26568194 DOI: 10.1093/jnci/djv323] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 10/08/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is curable in a subset of cases. The DNA methylation regulator TET2 is frequently mutated in AML, and we hypothesized that studying TET2-specific differentially methylated CpGs (tet2-DMCs) improves AML classification. METHODS We used bisulfite pyrosequencing to analyze the methylation status of four tet2-DMCs (SP140, MCCC1, EHMT1, and MTSS1) in a test group of 94 consecutive patients and a validation group of 92 consecutive patients treated with cytarabine-based chemotherapy. Data were analyzed with hierarchical clustering, Cox proportional hazards regression, and Kaplan-Meier analyses. All statistical tests were two-sided. RESULTS In the test cohort, hierarchical clustering analysis identified low levels of tet2-DMC methylation in 31 of 94 (33%) cases, and these had markedly longer overall survival (median survival 72+ vs 14 months, P = .002). Similar results were seen in the validation cohort. tet2-DMC-low status was shown to be an independent predictor of overall survival (hazard ratio = 0.29, P = .0002). In The Cancer Genome Atlas (TCGA) dataset where DNA methylation was analyzed by a different platform, tet2-DMC-low methylation was also associated with improved outcome (median survival = 55 vs 15 months, P = .0003) and was a better predictor of survival than mutations in TET2, IDH1, or IDH2, individually or combined. CONCLUSIONS Low levels of tet2-DMC methylation define a subgroup of AML that is highly curable and cannot be identified solely by genetic and cytogenetic analyses.
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Affiliation(s)
- Jumpei Yamazaki
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rodolphe Taby
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Noel J M Raynal
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Matteo Cesaroni
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sherry A Pierce
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Steven M Kornblau
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carlos E Bueso-Ramos
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Farhad Ravandi
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hagop M Kantarjian
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA (JY, JJ, NJMR, MC, JPJI); Department of Leukemia (JY, RT, JJ, NJMR, SAP, SMK, FR, HMK, JPJI) and Department of Hematopathology (CEBR), The University of Texas MD Anderson Cancer Center, Houston, TX.
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90
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The dual epigenetic role of PRMT5 in acute myeloid leukemia: gene activation and repression via histone arginine methylation. Leukemia 2015; 30:789-99. [PMID: 26536822 DOI: 10.1038/leu.2015.308] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 10/05/2015] [Accepted: 10/20/2015] [Indexed: 01/13/2023]
Abstract
Changes in the enzymatic activity of protein arginine methyltransferase (PRMT) 5 have been associated with cancer; however, the protein's role in acute myeloid leukemia (AML) has not been fully evaluated. Here, we show that increased PRMT5 activity enhanced AML growth in vitro and in vivo while PRMT5 downregulation reduced it. In AML cells, PRMT5 interacted with Sp1 in a transcription repressor complex and silenced miR-29b preferentially via dimethylation of histone 4 arginine residue H4R3. As Sp1 is also a bona fide target of miR-29b, the miR silencing resulted in increased Sp1. This event in turn led to transcription activation of FLT3, a gene that encodes a receptor tyrosine kinase. Inhibition of PRMT5 via sh/siRNA or a first-in-class small-molecule inhibitor (HLCL-61) resulted in significantly increased expression of miR-29b and consequent suppression of Sp1 and FLT3 in AML cells. As a result, significant antileukemic activity was achieved. Collectively, our data support a novel leukemogenic mechanism in AML where PRMT5 mediates both silencing and transcription of genes that participate in a 'yin-yang' functional network supporting leukemia growth. As FLT3 is often mutated in AML and pharmacologic inhibition of PRMT5 appears feasible, the PRMT5-miR-29b-FLT3 network should be further explored as a novel therapeutic target for AML.
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91
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DNA-methylation in C1R is a prognostic biomarker for acute myeloid leukemia. Clin Epigenetics 2015; 7:116. [PMID: 26539253 PMCID: PMC4632269 DOI: 10.1186/s13148-015-0153-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/29/2015] [Indexed: 02/02/2023] Open
Abstract
Background Epigenetic aberrations play a central role in the pathophysiology of acute myeloid leukemia (AML). It has been shown that molecular signatures based on DNA-methylation (DNAm) patterns can be used for classification of the disease. In this study, we followed the hypothesis that DNAm at a single CpG site might support risk stratification in AML. Findings Using DNAm profiles of 194 patients from The Cancer Genome Atlas (TCGA), we identified a CpG site in complement component 1 subcomponent R (C1R) as best suited biomarker: patients with higher methylation at this CpG site (>27 % DNAm) reveal significantly longer overall survival (53 versus 11 months; P < 0.0001). This finding was validated in an independent set of 62 DNAm profiles of cytogenetically normal AML patients (P = 0.009) and with a region-specific pyrosequencing assay in 84 AML samples (P = 0.012). DNAm of C1R correlated with genomic DNAm and gene expression patterns, whereas there was only moderate association with gene expression levels of C1R. These results indicate that DNAm of C1R is a biomarker reflecting chromatin reorganization rather than being of pathophysiological relevance per se. Notably, DNAm of C1R was associated with occurrence of specific genomic mutations that are traditionally used for risk stratification in AML. Furthermore, DNAm of C1R correlates also with overall survival in several other types of cancer, but the prognostic relevance was less pronounced than in AML. Conclusions Analysis of DNAm at C1R provides a simple, robust, and cost-effective biomarker to further complement risk assessment in AML. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0153-6) contains supplementary material, which is available to authorized users.
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92
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Ciccone M, Calin GA. MicroRNAs in Myeloid Hematological Malignancies. Curr Genomics 2015; 16:336-48. [PMID: 27047254 PMCID: PMC4763972 DOI: 10.2174/138920291605150710122815] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs are 19-24 nucleotides noncoding RNAs which silence modulate the expression of target genes by binding to the messenger RNAs. Myeloid malignancies include a broad spectrum of acute and chronic disorders originating from from the clonal transformation of a hematopoietic stem cell. Specific genetic abnormalities may define myeloid malignancies, such as translocation t(9;22) that represent the hallmark of chronic myeloid leukemia. Although next-generation sequencing pro-vided new insights in the genetic characterization and pathogenesis of myeloid neoplasms, the molecular mechanisms underlying myeloid neoplasms are lacking in most cases. Recently, several studies have demonstrated that the expression levels of specific miRNAs may vary among patients with myeloid malignancies compared with healthy individuals and partially unveiled how miRNAs participate in the leukemic transformation process. Finally, in vitro experiments and pre-clinical model provided preliminary data of the safety and efficacy of miRNA inhibitory molecules, opening new avenue in the treatment of myeloid hematological malignancies.
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Affiliation(s)
- Maria Ciccone
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George Adrian Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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93
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Prognostic significance of NPM1 mutation-modulated microRNA−mRNA regulation in acute myeloid leukemia. Leukemia 2015; 30:274-84. [DOI: 10.1038/leu.2015.253] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/19/2015] [Accepted: 09/04/2015] [Indexed: 02/08/2023]
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94
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Rocca A, Andreis D, Fedeli A, Maltoni R, Sarti S, Cecconetto L, Pietri E, Schirone A, Bravaccini S, Serra P, Farolfi A, Amadori D. Pharmacokinetics, pharmacodynamics and clinical efficacy of pertuzumab in breast cancer therapy. Expert Opin Drug Metab Toxicol 2015; 11:1647-63. [DOI: 10.1517/17425255.2015.1078311] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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95
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Yang IV, Pedersen BS, Liu A, O'Connor GT, Teach SJ, Kattan M, Misiak RT, Gruchalla R, Steinbach SF, Szefler SJ, Gill MA, Calatroni A, David G, Hennessy CE, Davidson EJ, Zhang W, Gergen P, Togias A, Busse WW, Schwartz DA. DNA methylation and childhood asthma in the inner city. J Allergy Clin Immunol 2015; 136:69-80. [PMID: 25769910 PMCID: PMC4494877 DOI: 10.1016/j.jaci.2015.01.025] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 01/21/2015] [Accepted: 01/23/2015] [Indexed: 01/15/2023]
Abstract
BACKGROUND Epigenetic marks are heritable, influenced by the environment, direct the maturation of T lymphocytes, and in mice enhance the development of allergic airway disease. Thus it is important to define epigenetic alterations in asthmatic populations. OBJECTIVE We hypothesize that epigenetic alterations in circulating PBMCs are associated with allergic asthma. METHODS We compared DNA methylation patterns and gene expression in inner-city children with persistent atopic asthma versus healthy control subjects by using DNA and RNA from PBMCs. Results were validated in an independent population of asthmatic patients. RESULTS Comparing asthmatic patients (n = 97) with control subjects (n = 97), we identified 81 regions that were differentially methylated. Several immune genes were hypomethylated in asthma, including IL13, RUNX3, and specific genes relevant to T lymphocytes (TIGIT). Among asthmatic patients, 11 differentially methylated regions were associated with higher serum IgE concentrations, and 16 were associated with percent predicted FEV1. Hypomethylated and hypermethylated regions were associated with increased and decreased gene expression, respectively (P < 6 × 10(-12) for asthma and P < .01 for IgE). We further explored the relationship between DNA methylation and gene expression using an integrative analysis and identified additional candidates relevant to asthma (IL4 and ST2). Methylation marks involved in T-cell maturation (RUNX3), TH2 immunity (IL4), and oxidative stress (catalase) were validated in an independent asthmatic cohort of children living in the inner city. CONCLUSIONS Our results demonstrate that DNA methylation marks in specific gene loci are associated with asthma and suggest that epigenetic changes might play a role in establishing the immune phenotype associated with asthma.
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Affiliation(s)
- Ivana V Yang
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo; Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo
| | - Brent S Pedersen
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Andrew Liu
- Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo
| | - George T O'Connor
- Department of Medicine, Boston University School of Medicine, Boston, Mass
| | | | - Meyer Kattan
- Columbia University Medical Center, New York, NY
| | | | | | | | - Stanley J Szefler
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado, School of Medicine, Aurora, Colo
| | - Michelle A Gill
- University of Texas, Southwestern Medical Center, Dallas, Tex
| | | | | | - Corinne E Hennessy
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Elizabeth J Davidson
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Weiming Zhang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Colo
| | - Peter Gergen
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - David A Schwartz
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo; Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo; Department of Immunology, University of Colorado, Aurora, Colo.
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96
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Eriksson A, Lennartsson A, Lehmann S. Epigenetic aberrations in acute myeloid leukemia: Early key events during leukemogenesis. Exp Hematol 2015; 43:609-24. [PMID: 26118500 DOI: 10.1016/j.exphem.2015.05.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 05/23/2015] [Indexed: 12/17/2022]
Abstract
As a result of the introduction of new sequencing technologies, the molecular landscape of acute myeloid leukemia (AML) is rapidly evolving. From karyotyping, which detects only large genomic aberrations of metaphase chromosomes, we have moved into an era when sequencing of each base pair allows us to define the AML genome at highest resolution. This has revealed a new complex landscape of genetic aberrations where addition of mutations in epigenetic regulators has been one of the most important contributions to the understanding of the pathogenesis of AML. These findings, together with new insights into epigenetic mechanisms, have placed dysregulated epigenetic mechanisms at the forefront of AML development. Not only have several new mutations in genes directly involved in epigenetic regulatory mechanisms been discovered, but also previously well-known gene fusions have been found to exert aberrant effects through epigenetic mechanisms. In addition, mutations in epigenetic regulators such as DNMT3A, TET2, and ASXL1 have recently been found to be the earliest known events during AML evolution and to be present as preleukemic lesions before the onset of AML. In this article, we review epigenetic changes in AML also in relation to what is known about their mechanism of action and their prognostic role.
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Affiliation(s)
- Anna Eriksson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Stockholm, Sweden
| | - Sören Lehmann
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Centre of Hematology, HERM, Department of Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.
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97
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Christopeit M, Bartholdy B. Epigenetic signatures as prognostic tools in acute myeloid leukemia and myelodysplastic syndromes. Epigenomics 2015; 6:371-4. [PMID: 25333846 DOI: 10.2217/epi.14.32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Maximilian Christopeit
- Department of Stem Cell Transplantation, University Hospital Hamburg-Eppendorf, Martinistraße 52, D-20246 Hamburg, Germany
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98
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Dorrance AM, Neviani P, Ferenchak GJ, Huang X, Nicolet D, Maharry KS, Ozer HG, Hoellarbauer P, Khalife J, Hill EB, Yadav M, Bolon BN, Lee RJ, Lee LJ, Croce CM, Garzon R, Caligiuri MA, Bloomfield CD, Marcucci G. Targeting leukemia stem cells in vivo with antagomiR-126 nanoparticles in acute myeloid leukemia. Leukemia 2015; 29:2143-53. [PMID: 26055302 PMCID: PMC4633325 DOI: 10.1038/leu.2015.139] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/15/2015] [Accepted: 05/06/2015] [Indexed: 12/31/2022]
Abstract
Current treatments for acute myeloid leukemia (AML) are designed to target rapidly dividing blast populations with limited success in eradicating the functionally distinct leukemia stem cell (LSC) population, which is postulated to be responsible for disease resistance and relapse. We have previously reported high miR-126 expression levels to be associated with a LSC-gene expression profile. Therefore, we hypothesized that miR-126 contributes to “stemness” and is a viable target for eliminating the LSC in AML. Here we first validate the clinical relevance of miR-126 expression in AML by showing that higher expression of this microRNA (miR) is associated with worse outcome in a large cohort of older (≥60 years) cytogenetically normal AML patients treated with conventional chemotherapy. We then show that miR-126 overexpression characterizes AML LSC-enriched cell subpopulations and contributes to LSC long-term maintenance and self-renewal. Finally, we demonstrate the feasibility of therapeutic targeting of miR-126 in LSCs with novel targeting nanoparticles (NP) containing antagomiR-126 resulting in in vivo reduction of LSCs likely by depletion of the quiescent cell subpopulation. Our findings suggest that by targeting a single miR, i.e., miR-126, it is possible to interfere with LSC activity, thereby opening potentially novel therapeutic approaches to treat AML patients.
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Affiliation(s)
- A M Dorrance
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - P Neviani
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - G J Ferenchak
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - X Huang
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Nanoscale Science and Engineering Center for Affordable Nanoengineering of Polymeric Biomedical Devices, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Department of Biomedical Informatics, Ohio State University, Columbus, OH, USA
| | - D Nicolet
- Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Alliance for Clinical Trials in Oncology Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - K S Maharry
- Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Alliance for Clinical Trials in Oncology Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - H G Ozer
- Department of Biomedical Informatics, Ohio State University, Columbus, OH, USA
| | - P Hoellarbauer
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - J Khalife
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - E B Hill
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - M Yadav
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - B N Bolon
- Comparative Pathology and Mouse Phenotyping Shared Resource, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - R J Lee
- Nanoscale Science and Engineering Center for Affordable Nanoengineering of Polymeric Biomedical Devices, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Department of Biomedical Informatics, Ohio State University, Columbus, OH, USA
| | - L J Lee
- Nanoscale Science and Engineering Center for Affordable Nanoengineering of Polymeric Biomedical Devices, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Department of Biomedical Informatics, Ohio State University, Columbus, OH, USA
| | - C M Croce
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA
| | - R Garzon
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA
| | - M A Caligiuri
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - C D Bloomfield
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - G Marcucci
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA
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99
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Al-Kateb H, Nguyen TT, Steger-May K, Pfeifer JD. Identification of major factors associated with failed clinical molecular oncology testing performed by next generation sequencing (NGS). Mol Oncol 2015; 9:1737-43. [PMID: 26071350 DOI: 10.1016/j.molonc.2015.05.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/05/2015] [Accepted: 05/07/2015] [Indexed: 12/21/2022] Open
Abstract
PURPOSE DNA analysis by NGS has become important to direct the clinical care of cancer patients. However, NGS is not successful in all cases, and the factors responsible for test failures have not been systematically evaluated. MATERIALS AND METHODS A series of 1528 solid and hematolymphoid tumor specimens was tested by an NGS comprehensive cancer panel during 2012-2014. DNA was extracted and 2×101 bp paired-end sequence reads were generated on cancer-related genes utilizing Illumina HiSeq and MiSeq platforms. RESULTS Testing was unsuccessful in 343 (22.5%) specimens. The failure was due to insufficient tissue (INST) in 223/343 (65%) cases, insufficient DNA (INS-DNA) in 99/343 (28.9%) cases, and failed library (FL) in 21/343 (6.1%) cases. 87/99 (88%) of the INS-DNA cases had below 10 ng DNA available for testing. Factors associated with INST and INS-DNA failures were site of biopsy (SOB) and type of biopsy (TOB) (both p < 0.0001), and clinical setting of biopsy (CSB, initial diagnosis or recurrence) (p < 0.0001). Factors common to INST and FL were age of specimen (p ≤ 0.006) and tumor viability (p ≤ 0.05). Factors common to INS-DNA and FL were DNA purity and DNA degradation (all p ≤ 0.005). In multivariate analysis, common predictors for INST and INS-DNA included CSB (p = 0.048 and p < 0.0001) and TOB (both p ≤ 0.003), respectively. SOB (p = 0.004) and number of cores (p = 0.001) were specific for INS-DNA, whereas TOB and DNA degradation were associated with FL (p = 0.04 and 0.02, respectively). CONCLUSIONS Pre-analytical causes (INST and INS-DNA) accounted for about 90% of all failed cases; independent of test design. Clinical setting; site and type of biopsy; and number of cores used for testing all correlated with failure. Accounting for these factors at the time of tissue biopsy acquisition could improve the analytic success rate.
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Affiliation(s)
- Hussam Al-Kateb
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, USA.
| | - TuDung T Nguyen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, USA
| | - Karen Steger-May
- Division of Biostatistics, Washington University School of Medicine, St. Louis, USA
| | - John D Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, USA
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100
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Zhou JD, Yao DM, Zhang YY, Ma JC, Wen XM, Yang J, Guo H, Chen Q, Lin J, Qian J. GPX3 hypermethylation serves as an independent prognostic biomarker in non-M3 acute myeloid leukemia. Am J Cancer Res 2015; 5:2047-2055. [PMID: 26269763 PMCID: PMC4529623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 05/10/2015] [Indexed: 06/04/2023] Open
Abstract
Hypermethylation of GPX3 (glutathione peroxidase 3) promoter has been identified in various solid tumors. However, the pattern of GPX3 promoter methylation in acute myeloid leukemia (AML) remains unknown. The current study was intended to investigate the clinical significance of GPX3 promoter methylation in de novo AML patients and further determine its role in regulating GPX3 expression. GPX3 promoter methylation status was detected in 181 de novo AML patients and 44 normal controls by real-time quantitative methylation-specific PCR and bisulfite sequencing PCR. Real-time quantitative PCR was carried out to assess GPX3 expression. GPX3 promoter was significantly methylated in AML patients compared with normal controls (P=0.022). The patients with GPX3 methylation presented significantly older age than those with GPX3 unmethylation (P=0.011). GPX3 methylated patients had significantly lower frequency of C/EBPA mutation and higher incidence of FLT3-ITD mutation (P=0.037 and 0.030, respectively). The non-M3 patients with GPX3 methylation had significantly lower overall survival than those with GPX3 unmethylation (P=0.036). No significant correlation was observed between GPX3 expression and its promoter methylation (R=0.110, P=0.284). However, GPX3 mRNA level was significantly increased after 5-aza-2'-deoxycytidine treatment in leukemic cell line THP1. Our data suggest that GPX3 methylation predicts adverse clinical outcome in non-M3 AML patients. Moreover, GPX3 expression is regulated by its promoter methylation in leukemic cell line THP1.
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Affiliation(s)
- Jing-Dong Zhou
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
| | - Dong-Ming Yao
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
| | - Ying-Ying Zhang
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
| | - Ji-Chun Ma
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
| | - Xiang-Mei Wen
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
| | - Jing Yang
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
| | - Hong Guo
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
| | - Qin Chen
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
| | - Jiang Lin
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
| | - Jun Qian
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
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