51
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Krzanowski J, Madzio J, Pastorczak A, Tracz A, Braun M, Tabarkiewicz J, Pluta A, Młynarski W, Zawlik I. Selected miRNA levels are associated with IKZF1 microdeletions in pediatric acute lymphoblastic leukemia. Oncol Lett 2017; 14:3853-3861. [PMID: 28927157 DOI: 10.3892/ol.2017.6599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/28/2017] [Indexed: 01/19/2023] Open
Abstract
The clinical outcome of children with high-risk relapsed B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is poor. The present study assessed the utility and prognostic value of selected microRNA (miRNA/miR) in BCP-ALL. The changes in the expression levels of these miRNAs regarding known gene lesions affecting lymphoid development [early B-cell factor 1 (EBF1), ETS variant 6 (ETV6), IKAROS family zinc finger 1 (IKZF1), paired box 5 (PAX5), cyclin dependent kinase inhibitor (CDKN) 2A/CDKN2B, retinoblastoma 1 (RB1), pseudoautosomal region 1 (PAR1), B-cell translocation gene 1 protein (BTG1)] were analyzed. The following miRNAs were analyzed: miR-24, miR-31, miR-128, miR-542, and miR-708. The present study focused on patients with deletions of the IKAROS transcriptional factor gene IKZF1, which is currently considered to be an independent negative prognostic factor for ALL outcome. It was demonstrated that the expression level of miR-128 was significantly lower in patients with IKZF1 deletion compared with patients without IKZF1 deletion. Additionally, low expression of miR-542 was associated with CDKN2A/B and miR-31deletions, and low expression of miR-24 was associated with miR-31 deletion. Low expression of miR-31, miR-24, miR-708 and miR-128 was associated with PAX5 deletion, high expression of miR-24 and miR-542 was associated with PAR1 deletion and high expression of miR-708 was associated with ETV6 deletion. The expression of the selected miRNAs was not associated with deletions of BTG1, EBF1 and RB1. These data, by emphasizing the association of miRNAs expression level with microdeletions, may assist to elucidate ALL biology and contribute to future studies on the possible applications of the miRNA profile for diagnosis.
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Affiliation(s)
- J Krzanowski
- Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszów, 35-959 Rzeszów, Poland
| | - J Madzio
- Department of Pediatrics, Hematology, Oncology and Diabetology, Medical University of Łódź, 91-738 Łódź, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - A Pastorczak
- Department of Pediatrics, Hematology, Oncology and Diabetology, Medical University of Łódź, 91-738 Łódź, Poland
| | - A Tracz
- Department of Pediatrics, Hematology, Oncology and Diabetology, Medical University of Łódź, 91-738 Łódź, Poland
| | - M Braun
- Department of Pediatrics, Hematology, Oncology and Diabetology, Medical University of Łódź, 91-738 Łódź, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland.,Department of Pathology, Chair of Oncology, Medical University of Łódź, 92-213 Łódź, Poland
| | - J Tabarkiewicz
- Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszów, 35-959 Rzeszów, Poland.,Department of Immunology, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszów, 35-959 Rzeszów, Poland
| | - A Pluta
- Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszów, 35-959 Rzeszów, Poland
| | - W Młynarski
- Department of Pediatrics, Hematology, Oncology and Diabetology, Medical University of Łódź, 91-738 Łódź, Poland
| | - I Zawlik
- Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszów, 35-959 Rzeszów, Poland.,Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszów, 35-959 Rzeszów, Poland
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52
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Navarrete-Meneses MDP, Pérez-Vera P. Alteraciones epigenéticas en leucemia linfoblástica aguda. BOLETIN MEDICO DEL HOSPITAL INFANTIL DE MEXICO 2017; 74:243-264. [DOI: 10.1016/j.bmhimx.2017.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/04/2017] [Accepted: 02/08/2017] [Indexed: 12/22/2022] Open
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Quagliano A, Gopalakrishnapillai A, Barwe SP. Epigenetic drug combination overcomes osteoblast-induced chemoprotection in pediatric acute lymphoid leukemia. Leuk Res 2017; 56:36-43. [PMID: 28171800 PMCID: PMC5366080 DOI: 10.1016/j.leukres.2017.01.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/23/2017] [Accepted: 01/25/2017] [Indexed: 01/06/2023]
Abstract
Although there has been much progress in the treatment of acute lymphoblastic leukemia (ALL), decreased sensitivity to chemotherapy remains a significant issue. Recent studies have shown how interactions with the bone marrow microenvironment can protect ALL cells from chemotherapy and allow for the persistence of the disease. Epigenetic drugs have been used for the treatment of ALL, but there are no reports on whether these drugs can overcome bone marrow-induced chemoprotection. Our study investigates the ability of the DNA methyltransferase inhibitor azacitidine and the histone deacetylase inhibitor panobinostat to overcome chemoprotective effects mediated by osteoblasts. We show that the combination of azacitidine and panobinostat has a synergistic killing effect and that this combination is more effective than cytarabine in inducing ALL cell death in co-culture with osteoblasts. We also show that this combination can be used to sensitize ALL cells to chemotherapeutics in the presence of osteoblasts. Finally, we demonstrate that these effects can be replicated ex vivo in a number of mouse passaged xenograft lines from both B-ALL and T-ALL patients with varying cytogenetics. Thus, our data provides evidence that azacitidine and panobinostat can successfully overcome osteoblast-induced chemoprotection in vitro and ex vivo in both B-ALL and T-ALL cells.
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Affiliation(s)
- Anthony Quagliano
- Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, United States; Department of Biological Sciences, University of Delaware, Wilmington, DE 19716, United States
| | - Anilkumar Gopalakrishnapillai
- Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, United States.
| | - Sonali P Barwe
- Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, United States; Department of Biological Sciences, University of Delaware, Wilmington, DE 19716, United States.
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55
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McGinn OJ, Krishnan S, Bourquin JP, Sapra P, Dempsey C, Saha V, Stern PL. Targeting the 5T4 oncofetal glycoprotein with an antibody drug conjugate (A1mcMMAF) improves survival in patient-derived xenograft models of acute lymphoblastic leukemia. Haematologica 2017; 102:1075-1084. [PMID: 28341731 PMCID: PMC5451339 DOI: 10.3324/haematol.2016.158485] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/15/2017] [Indexed: 12/29/2022] Open
Abstract
Outcome in childhood acute lymphoblastic leukemia is prognosticated from levels of minimal residual disease after remission induction therapy. Higher levels of minimal residual disease are associated with inferior results even with intensification of therapy, thus suggesting that identification and targeting of minimal residual disease cells could be a therapeutic strategy. Here we identify high expression of 5T4 in subclonal populations of patient-derived xenografts from patients with high, post-induction levels of minimal residual disease. 5T4-positive cells showed preferential ability to overcome the NOD-scidIL2Rγnull mouse xenograft barrier, migrated in vitro on a CXCL12 gradient, preferentially localized to bone marrow in vivo and displayed the ability to reconstitute the original clonal composition on limited dilution engraftment. Treatment with A1mcMMAF (a 5T4-antibody drug conjugate) significantly improved survival without overt toxicity in mice engrafted with a 5T4-positive acute lymphoblastic leukemia cell line. Mice engrafted with 5T4-positive patient-derived xenograft cells were treated with combination chemotherapy or dexamethasone alone and then given A1mcMMAF in the minimal residual disease setting. Combination chemotherapy was toxic to NOD-scidIL2Rγnull mice. While dexamethasone or A1mcMMAF alone improved outcomes, the sequential administration of dexamethasone and A1mcMMAF significantly improved survival (P=0.0006) over either monotherapy. These data show that specifically targeting minimal residual disease cells improved outcomes and support further investigation of A1mcMMAF in patients with high-risk B-cell precursor acute lymphoblastic leukemia identified by 5T4 expression at diagnosis.
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Affiliation(s)
- Owen J McGinn
- Immunology, Division of Molecular & Clinical Cancer Sciences, University of Manchester, UK
| | - Shekhar Krishnan
- Paediatric Oncology, Division of Molecular & Clinical Cancer Sciences, University of Manchester, UK.,Tata Translational Cancer Research Center, Tata Medical Center, Kolkata, India
| | - Jean-Pierre Bourquin
- Division of Oncology & Children's Research Center, University Children's Hospital, University of Zurich, Switzerland
| | - Puja Sapra
- Pfizer Inc. Pearl River, NY10965-1299, USA
| | - Clare Dempsey
- Paediatric Oncology, Division of Molecular & Clinical Cancer Sciences, University of Manchester, UK
| | - Vaskar Saha
- Paediatric Oncology, Division of Molecular & Clinical Cancer Sciences, University of Manchester, UK .,Tata Translational Cancer Research Center, Tata Medical Center, Kolkata, India
| | - Peter L Stern
- Immunology, Division of Molecular & Clinical Cancer Sciences, University of Manchester, UK
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56
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Abdullah M, Choo CW, Alias H, Abdul Rahman EJ, Mohd Ibrahim H, Jamal R, Hussin NH. ADAMTSL5 and CDH11: putative epigenetic markers for therapeutic resistance in acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2017; 22:386-391. [PMID: 28292214 DOI: 10.1080/10245332.2017.1299417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND OBJECTIVES DNA hypermethylation has been linked to poor treatment outcome in childhood acute lymphoblastic leukemia (ALL). Genes differentially methylated in the chemoresponsive pre-B-ALL compared to chemoresistant pre-B-ALL cases provide potential prognostic markers. METHODS DNA methylation profiles of five B-ALL childhood patients who achieved morphological complete remission (chemoresponsive) and five B-ALL patients who did not (chemoresistant) after induction treatments as well as four normal controls were compared on 27 000 CpG sites microarray chips. Subsequently, methylation-specific polymerase chain reaction (MSP) on selected hypermethylated genes was conducted on an additional 37 chemoresponsive and 9 chemoresistant B-ALL samples and 2 normal controls. RESULTS Both methods were found to be highly correlated. Unsupervised principal component analysis showed that the chemotherapy-responsive and -resistant B-ALL patients could be segregated from one another. Selection of segregated genes at high stringency identified two potential genes (CDH11 and ADAMTSL5). MSP analysis on the larger cohort of samples (42 chemoresponsive, 14 chemoresistant B-ALL samples and 6 normal controls) revealed significantly higher rates of hypermethylation in chemoresistant samples for ADAMTSL5 (93 vs. 38%; p = 0.0001) and CDH11 (79% vs. 40%, p < 0.01). All control cases remained unmethylated. CONCLUSION Chemoresistant B-ALL patients are associated with increased methylation in ADAMTSL5 and CDH11. These findings need to be validated in a larger group of patients, and the functional biological and prognostic significance of differential methylation needs to be studied further.
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Affiliation(s)
- Maha Abdullah
- a Immunology Unit, Department of Pathology , UPM, Serdang , Selangor , Malaysia
| | - Chee Wei Choo
- b Department of Pathology, Faculty of Medicine , UKM Medical Centre , Kuala Lumpur , Malaysia
| | - Hamidah Alias
- c Department of Paediatrics, Faculty of Medicine , UKM Medical Centre , Kuala Lumpur , Malaysia
| | | | | | - Rahman Jamal
- e UKM Medical Molecular Biology Institute , Kuala Lumpur , Malaysia
| | - Noor Hamidah Hussin
- b Department of Pathology, Faculty of Medicine , UKM Medical Centre , Kuala Lumpur , Malaysia
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57
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Bergmann AK, Castellano G, Alten J, Ammerpohl O, Kolarova J, Nordlund J, Martin-Subero JI, Schrappe M, Siebert R. DNA methylation profiling of pediatric B-cell lymphoblastic leukemia with KMT2A rearrangement identifies hypomethylation at enhancer sites. Pediatr Blood Cancer 2017; 64. [PMID: 27786413 DOI: 10.1002/pbc.26251] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 07/15/2016] [Accepted: 08/01/2016] [Indexed: 02/03/2023]
Abstract
Deregulation of the epigenome is an important pathogenetic mechanism in acute lymphoblastic leukemia (ALL) with lysine (K)-specific methyltransferase 2A rearrangement (KMT2Ar). We performed array-based DNA methylation profiling of KMT2Ar ALL cells from 26 children in comparison to normal B-cell precursors. Significant changes in DNA methylation in KMT2Ar ALL were identified in 2,545 CpG loci, influenced by age and the translocation partners AFF1 and MLLT1. In KMT2Ar ALL, DNA methylation loss was enriched at enhancers and for certain transcription factor binding sites such as BCL11A, EBF, and MEF2A. In summary, DNA methylation changes in KMT2Ar ALL target enhancers, genes involved in leukemogenesis and normal hematopoiesis, as well as transcription factor networks.
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Affiliation(s)
- Anke K Bergmann
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Department of Pediatrics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Giancarlo Castellano
- Departamento de Anatomía Patológica, Farmacología y Microbiología, Institutd'Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Julia Alten
- Department of Pediatrics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Human Genetics, University of Ulm & University Medical Center Ulm, Ulm, Germany
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Jose Ignacio Martin-Subero
- Departamento de Anatomía Patológica, Farmacología y Microbiología, Institutd'Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Martin Schrappe
- Department of Pediatrics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Human Genetics, University of Ulm & University Medical Center Ulm, Ulm, Germany
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58
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Uyen TN, Sakashita K, Al-Kzayer LFY, Nakazawa Y, Kurata T, Koike K. Aberrant methylation of protocadherin 17 and its prognostic value in pediatric acute lymphoblastic leukemia. Pediatr Blood Cancer 2017; 64. [PMID: 27643535 DOI: 10.1002/pbc.26259] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 11/12/2022]
Abstract
BACKGROUND The outcome of approximately 20% of patients with acute lymphoblastic leukemia (ALL) remains poor because of disease recurrence. We examined whether DNA methylation of cadherin superfamily genes is a useful biomarker for ALL relapse. PROCEDURE We used Infinium Methylation 450K Arrays to assess genome-wide DNA methylation status. The methylation status of each individual gene was then determined by a combination of bisulfite restriction analysis and genome bisulfite sequencing. mRNA expression was evaluated by reverse-transcriptase PCR (RT-PCR) and quantitative real-time PCR. RESULTS Cadherin superfamily genes including cadherin (CDH) 1, protocadherin (PCDH) 8, and PCDH17 were selected for analysis of methylation status. In 40 patient samples with B-cell precursor (BCP) ALL at diagnosis, the methylation frequencies of CDH1, PCDH8, and PCDH17 were 62.5, 55, and 30%, respectively. CDH1 and PCDH8 methylation was also detected in 80 and 20% of control bone marrow (BM) samples, respectively. On the contrary, PCDH17 was unmethylated in all control BM samples. There was a significant correlation between the methylation status of PCDH17 (but not CDH1 and PCDH8) and event-free survival or overall survival. Univariate and multivariate analyses showed that only PCDH17 methylation was associated with an increased risk for relapse and mortality in patients with BCP ALL. CONCLUSION PCDH17 methylation at diagnosis was closely related to poor prognosis and thus could be used as a new biomarker to predict relapse in patients with BCP ALL.
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Affiliation(s)
- Thanh Nha Uyen
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Kazuo Sakashita
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan.,Department of Pediatric Hematology and Oncology, Nagano Children's Hospital, Azumino, Nagano, Japan
| | | | - Yozo Nakazawa
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Takashi Kurata
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Kenichi Koike
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
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[Acute lymphoblastic leukemia: a genomic perspective]. BOLETIN MEDICO DEL HOSPITAL INFANTIL DE MEXICO 2017; 74:13-26. [PMID: 29364809 DOI: 10.1016/j.bmhimx.2016.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/14/2016] [Accepted: 07/07/2016] [Indexed: 11/22/2022] Open
Abstract
In parallel to the human genome sequencing project, several technological platforms have been developed that let us gain insight into the genome structure of human entities, as well as evaluate their usefulness in the clinical approach of the patient. Thus, in acute lymphoblastic leukemia (ALL), the most common pediatric malignancy, genomic tools promise to be useful to detect patients at high risk of relapse, either at diagnosis or during treatment (minimal residual disease), and they also increase the possibility to identify cases at risk of adverse reactions to chemotherapy. Therefore, the physician could offer patient-tailored therapeutic schemes. A clear example of the useful genomic tools is the identification of single nucleotide polymorphisms (SNPs) in the thiopurine methyl transferase (TPMT) gene, where the presence of two null alleles (homozygous or compound heterozygous) indicates the need to reduce the dose of mercaptopurine by up to 90% to avoid toxic effects which could lead to the death of the patient. In this review, we provide an overview of the genomic perspective of ALL, describing some strategies that contribute to the identification of biomarkers with potential clinical application.
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60
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Arthur G, Almamun M, Taylor K. Hypermethylation of antisense long noncoding RNAs in acute lymphoblastic leukemia. Epigenomics 2017; 9:635-645. [PMID: 28093925 DOI: 10.2217/epi-2016-0156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AIM Long noncoding RNAs serve critical regulatory functions highly specific for a tissue and its developmental stage. Antisense long ncRNA (AS-lncRNA) methylation changes in acute lymphoblastic leukemia (ALL) versus normal pre-B-cell lymphoblasts were evaluated to identify potential differential methylation in this group of genes. MATERIALS & METHODS The methylome of ALL and normal lymphoblasts was examined by the methylated CpG island recovery assay followed by NGS. CONCLUSION The potential effect of trans regulation by AS-lncRNA through DNA/RNA binding is significant as sequence alignment analysis of the 25 most differentially methylated AS-lncRNAs revealed 368 genes containing highly similar sequences with a median nucleotide identity of 90.8% and binding span of 122 base pairs. Regulation of biological processes and anatomical structure development were over represented. ALL classification schemes based on AS-lncRNA methylation can provide new insights into its pathogenesis and treatment.
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Affiliation(s)
- Gerald Arthur
- Department of Pathology & Anatomical Sciences, University of Missouri-Columbia, Columbia, MO 65212, USA.,MU Informatics Institute, University of Missouri-Columbia, Columbia, MO 65212, USA
| | - Md Almamun
- Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kristen Taylor
- Department of Pathology & Anatomical Sciences, University of Missouri-Columbia, Columbia, MO 65212, USA
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61
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Almamun M, Kholod O, Stuckel AJ, Levinson BT, Johnson NT, Arthur GL, Davis JW, Taylor KH. Inferring a role for methylation of intergenic DNA in the regulation of genes aberrantly expressed in precursor B-cell acute lymphoblastic leukemia. Leuk Lymphoma 2017; 58:1-12. [PMID: 28094574 DOI: 10.1080/10428194.2016.1272683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A complete understanding of the mechanisms involved in the development of pre-B ALL is lacking. In this study, we integrated DNA methylation data and gene expression data to elucidate the impact of aberrant intergenic DNA methylation on gene expression in pre-B ALL. We found a subset of differentially methylated intergenic loci that were associated with altered gene expression in pre-B ALL patients. Notably, 84% of these regions were also bound by transcription factors (TF) known to play roles in differentiation and B-cell development in a lymphoblastoid cell line. Further, an overall downregulation of eRNA transcripts was observed in pre-B ALL patients and these transcripts were associated with the downregulation of putative target genes involved in B-cell migration, proliferation, and apoptosis. The identification of novel putative regulatory regions highlights the significance of intergenic DNA sequences and may contribute to the identification of new therapeutic targets for the treatment of pre-B ALL.
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Olha Kholod
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Alexei J Stuckel
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Benjamin T Levinson
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Nathan T Johnson
- b Bioinformatics and Computational Biology , Worcester Polytechnic Institute , Worcester , MA , USA
| | - Gerald L Arthur
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - J Wade Davis
- c Department of Health Management and Informatics , University of Missouri-Columbia , Columbia , MO , USA
| | - Kristen H Taylor
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
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The Role of Histone Protein Modifications and Mutations in Histone Modifiers in Pediatric B-Cell Progenitor Acute Lymphoblastic Leukemia. Cancers (Basel) 2017; 9:cancers9010002. [PMID: 28054944 PMCID: PMC5295773 DOI: 10.3390/cancers9010002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/14/2016] [Accepted: 12/23/2016] [Indexed: 12/18/2022] Open
Abstract
While cancer has been long recognized as a disease of the genome, the importance of epigenetic mechanisms in neoplasia was acknowledged more recently. The most active epigenetic marks are DNA methylation and histone protein modifications and they are involved in basic biological phenomena in every cell. Their role in tumorigenesis is stressed by recent unbiased large-scale studies providing evidence that several epigenetic modifiers are recurrently mutated or frequently dysregulated in multiple cancers. The interest in epigenetic marks is especially due to the fact that they are potentially reversible and thus druggable. In B-cell progenitor acute lymphoblastic leukemia (BCP-ALL) there is a relative paucity of reports on the role of histone protein modifications (acetylation, methylation, phosphorylation) as compared to acute myeloid leukemia, T-cell ALL, or other hematologic cancers, and in this setting chromatin modifications are relatively less well studied and reviewed than DNA methylation. In this paper, we discuss the biomarker associations and evidence for a driver role of dysregulated global and loci-specific histone marks, as well as mutations in epigenetic modifiers in BCP-ALL. Examples of chromatin modifiers recurrently mutated/disrupted in BCP-ALL and associated with disease outcomes include MLL1, CREBBP, NSD2, and SETD2. Altered histone marks and histone modifiers and readers may play a particular role in disease chemoresistance and relapse. We also suggest that epigenetic regulation of B-cell differentiation may have parallel roles in leukemogenesis.
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63
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Godfrey L, Kerry J, Thorne R, Repapi E, Davies JOJ, Tapia M, Ballabio E, Hughes JR, Geng H, Konopleva M, Milne TA. MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation. Exp Hematol 2016; 47:64-75. [PMID: 27856324 PMCID: PMC5333536 DOI: 10.1016/j.exphem.2016.11.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/21/2016] [Accepted: 11/02/2016] [Indexed: 11/15/2022]
Abstract
Survival rates for children and adults carrying mutations in the Mixed Lineage Leukemia (MLL) gene continue to have a very poor prognosis. The most common MLL mutation in acute lymphoblastic leukemia is the t(4;11)(q21;q23) chromosome translocation that fuses MLL in-frame with the AF4 gene producing MLL-AF4 and AF4-MLL fusion proteins. Previously, we found that MLL-AF4 binds to the BCL-2 gene and directly activates it through DOT1L recruitment and increased H3K79me2/3 levels. In the study described here, we performed a detailed analysis of MLL-AF4 regulation of the entire BCL-2 family. By measuring nascent RNA production in MLL-AF4 knockdowns, we found that of all the BCL-2 family genes, MLL-AF4 directly controls the active transcription of both BCL-2 and MCL-1 and also represses BIM via binding of the polycomb group repressor 1 (PRC1) complex component CBX8. We further analyzed MLL-AF4 activation of the BCL-2 gene using Capture-C and identified a BCL-2-specific enhancer, consisting of two clusters of H3K27Ac at the 3' end of the gene. Loss of MLL-AF4 activity results in a reduction of H3K79me3 levels in the gene body and H3K27Ac levels at the 3' BCL-2 enhancer, revealing a novel regulatory link between these two histone marks and MLL-AF4-mediated activation of BCL-2.
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Affiliation(s)
- Laura Godfrey
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Jon Kerry
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Ross Thorne
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Emmanouela Repapi
- Weatherall Institute of Molecular Medicine, Computational Biology Research Group, University of Oxford, Headington, Oxford, UK
| | - James O J Davies
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Marta Tapia
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Erica Ballabio
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Jim R Hughes
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Huimin Geng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Marina Konopleva
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Thomas A Milne
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK.
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Chen D, Zheng J, Gerasimcik N, Lagerstedt K, Sjögren H, Abrahamsson J, Fogelstrand L, Mårtensson IL. The Expression Pattern of the Pre-B Cell Receptor Components Correlates with Cellular Stage and Clinical Outcome in Acute Lymphoblastic Leukemia. PLoS One 2016; 11:e0162638. [PMID: 27611867 PMCID: PMC5017602 DOI: 10.1371/journal.pone.0162638] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/25/2016] [Indexed: 12/20/2022] Open
Abstract
Precursor-B cell receptor (pre-BCR) signaling represents a crucial checkpoint at the pre-B cell stage. Aberrant pre-BCR signaling is considered as a key factor for B-cell precursor acute lymphoblastic leukemia (BCP-ALL) development. BCP-ALL are believed to be arrested at the pre-BCR checkpoint independent of pre-BCR expression. However, the cellular stage at which BCP-ALL are arrested and whether this relates to expression of the pre-BCR components (IGHM, IGLL1 and VPREB1) is still unclear. Here, we show differential protein expression and copy number variation (CNV) patterns of the pre-BCR components in pediatric BCP-ALL. Moreover, analyzing six BCP-ALL data sets (n = 733), we demonstrate that TCF3-PBX1 ALL express high levels of IGHM, IGLL1 and VPREB1, and are arrested at the pre-B stage. By contrast, ETV6-RUNX1 ALL express low levels of IGHM or VPREB1, and are arrested at the pro-B stage. Irrespective of subtype, ALL with high levels of IGHM, IGLL1 and VPREB1 are arrested at the pre-B stage and correlate with good prognosis in high-risk pediatric BCP-ALL (n = 207). Our findings suggest that BCP-ALL are arrested at different cellular stages, which relates to the expression pattern of the pre-BCR components that could serve as prognostic markers for high-risk pediatric BCP-ALL patients.
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Affiliation(s)
- Dongfeng Chen
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Junxiong Zheng
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Natalija Gerasimcik
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Kristina Lagerstedt
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Helene Sjögren
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Linda Fogelstrand
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Inga-Lill Mårtensson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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Wahlberg P, Lundmark A, Nordlund J, Busche S, Raine A, Tandre K, Rönnblom L, Sinnett D, Forestier E, Pastinen T, Lönnerholm G, Syvänen AC. DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands. Epigenomics 2016; 8:1367-1387. [PMID: 27552300 DOI: 10.2217/epi-2016-0052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of different subtypes on a genome-wide scale. MATERIALS & METHODS Whole-genome bisulfite sequencing (WGBS) was used to determine the DNA methylation levels in cells from four pediatric ALL patients of different subtypes. The findings were confirmed by 450k DNA methylation arrays in a large patient set. RESULTS Compared with mature B or T cells WGBS detected on average 82,000 differentially methylated regions per patient. Differentially methylated regions are enriched to CpG poor regions, active enhancers and transcriptional start sites. We also identified approximately 8000 CpG islands with variable intermediate DNA methylation that seems to occur as a result of stochastic de novo methylation. CONCLUSION WGBS provides an unbiased view and novel insights into the DNA methylome of ALL cells.
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Affiliation(s)
- Per Wahlberg
- Department of Medical Sciences, Molecular Medicine & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- Department of Medical Sciences, Molecular Medicine & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stephan Busche
- Department of Human Genetics, McGill University & Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Amanda Raine
- Department of Medical Sciences, Molecular Medicine & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karolina Tandre
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Daniel Sinnett
- Research Center, Sainte-Justine University Health Center; Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Erik Forestier
- Department of Medical Biosciences, University of Umeå, Umeå, Sweden
| | - Tomi Pastinen
- Department of Human Genetics, McGill University & Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Gudmar Lönnerholm
- Department of Women's & Children's Health, Pediatric Oncology, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Potuckova E, Zuna J, Hovorkova L, Starkova J, Stary J, Trka J, Zaliova M. Intragenic ERG Deletions Do Not Explain the Biology of ERG-Related Acute Lymphoblastic Leukemia. PLoS One 2016; 11:e0160385. [PMID: 27494621 PMCID: PMC4975502 DOI: 10.1371/journal.pone.0160385] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/18/2016] [Indexed: 11/18/2022] Open
Abstract
Intragenic ERG deletions occur in 3-5% of B-cell precursor acute lymphoblastic leukemia, specifically in B-other subtype lacking the classifying genetic lesions. They represent the only genetic lesion described so far present in the majority of cases clustering into a subgroup of B-other subtype characterized by a unique gene expression profile, probably sharing a common, however, not yet fully described, biological background. We aimed to elucidate whether ERG deletions could drive the specific biology of this ERG-related leukemia subgroup through expression of aberrant or decreased expression of wild type ERG isoforms. We showed that leukemic cells with endogenous ERG deletion express an aberrant transcript translated into two proteins in transfected cell lines and that one of these proteins colocalizes with wild type ERG. However, we did not confirm expression of the proteins in acute lymphoblastic leukemia cases with endogenous ERG deletion. ERG deletions resulted in significantly lower expression of wild type ERG transcripts compared to B-other cases without ERG deletion. However, cases with subclonal ERG deletion, clustering to the same ERG deletion associated subgroup, presented similar levels of wild type ERG as cases without ERG deletion. In conclusion, our data suggest that neither the expression of aberrant proteins from internally deleted allele nor the reduced expression of wild type ERG seem to provide a plausible explanation of the specific biology of ERG -related leukemia subgroup.
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Affiliation(s)
- Eliska Potuckova
- Childhood Leukaemia Investigation Prague (CLIP), Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Zuna
- Childhood Leukaemia Investigation Prague (CLIP), Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Lenka Hovorkova
- Childhood Leukaemia Investigation Prague (CLIP), Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Julia Starkova
- Childhood Leukaemia Investigation Prague (CLIP), Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Stary
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Trka
- Childhood Leukaemia Investigation Prague (CLIP), Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Marketa Zaliova
- Childhood Leukaemia Investigation Prague (CLIP), Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- * E-mail:
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Borssén M, Haider Z, Landfors M, Norén-Nyström U, Schmiegelow K, Åsberg AE, Kanerva J, Madsen HO, Marquart H, Heyman M, Hultdin M, Roos G, Forestier E, Degerman S. DNA Methylation Adds Prognostic Value to Minimal Residual Disease Status in Pediatric T-Cell Acute Lymphoblastic Leukemia. Pediatr Blood Cancer 2016; 63:1185-92. [PMID: 26928953 DOI: 10.1002/pbc.25958] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND Despite increased knowledge about genetic aberrations in pediatric T-cell acute lymphoblastic leukemia (T-ALL), no clinically feasible treatment-stratifying marker exists at diagnosis. Instead patients are enrolled in intensive induction therapies with substantial side effects. In modern protocols, therapy response is monitored by minimal residual disease (MRD) analysis and used for postinduction risk group stratification. DNA methylation profiling is a candidate for subtype discrimination at diagnosis and we investigated its role as a prognostic marker in pediatric T-ALL. PROCEDURE Sixty-five diagnostic T-ALL samples from Nordic pediatric patients treated according to the Nordic Society of Pediatric Hematology and Oncology ALL 2008 (NOPHO ALL 2008) protocol were analyzed by HumMeth450K genome wide DNA methylation arrays. Methylation status was analyzed in relation to clinical data and early T-cell precursor (ETP) phenotype. RESULTS Two distinct CpG island methylator phenotype (CIMP) groups were identified. Patients with a CIMP-negative profile had an inferior response to treatment compared to CIMP-positive patients (3-year cumulative incidence of relapse (CIR3y ) rate: 29% vs. 6%, P = 0.01). Most importantly, CIMP classification at diagnosis allowed subgrouping of high-risk T-ALL patients (MRD ≥0.1% at day 29) into two groups with significant differences in outcome (CIR3y rates: CIMP negative 50% vs. CIMP positive 12%; P = 0.02). These groups did not differ regarding ETP phenotype, but the CIMP-negative group was younger (P = 0.02) and had higher white blood cell count at diagnosis (P = 0.004) compared with the CIMP-positive group. CONCLUSIONS CIMP classification at diagnosis in combination with MRD during induction therapy is a strong candidate for further risk classification and could confer important information in treatment decision making.
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Affiliation(s)
- Magnus Borssén
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Zahra Haider
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Mattias Landfors
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Ann E Åsberg
- Department of Paediatrics, University Hospital of Trondheim, Norway
| | - Jukka Kanerva
- Hospital for Children and Adolescents, University of Helsinki, Helsinki, Finland
| | - Hans O Madsen
- Department of Clinical Immunology, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Hanne Marquart
- Department of Clinical Immunology, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Mats Heyman
- Department of Woman and Child health, Karolinska Institute, Stockholm, Sweden
| | - Magnus Hultdin
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Göran Roos
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Erik Forestier
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Umeå University, Umeå, Sweden.,Department of Paediatrics, University Hospital of Trondheim, Norway
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Almamun M, Levinson BT, van Swaay AC, Johnson NT, McKay SD, Arthur GL, Davis JW, Taylor KH. Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia. Epigenetics 2016; 10:882-90. [PMID: 26308964 PMCID: PMC4622668 DOI: 10.1080/15592294.2015.1078050] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children under the age of 15. In addition to genetic aberrations, epigenetic modifications such as DNA methylation are altered in cancer and impact gene expression. To identify epigenetic alterations in ALL, genome-wide methylation profiles were generated using the methylated CpG island recovery assay followed by next-generation sequencing. More than 25,000 differentially methylated regions (DMR) were observed in ALL patients with ∼90% present within intronic or intergenic regions. To determine the regulatory potential of the DMR, whole-transcriptome analysis was performed and integrated with methylation data. Aberrant promoter methylation was associated with the altered expression of genes involved in transcriptional regulation, apoptosis, and proliferation. Novel enhancer-like sequences were identified within intronic and intergenic DMR. Aberrant methylation in these regions was associated with the altered expression of neighboring genes involved in cell cycle processes, lymphocyte activation and apoptosis. These genes include potential epi-driver genes, such as SYNE1, PTPRS, PAWR, HDAC9, RGCC, MCOLN2, LYN, TRAF3, FLT1, and MELK, which may provide a selective advantage to leukemic cells. In addition, the differential expression of epigenetic modifier genes, pseudogenes, and non-coding RNAs was also observed accentuating the role of erroneous epigenetic gene regulation in ALL.
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences ; University of Missouri-Columbia ; Columbia , MO USA
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69
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Zhao MY, Yu Y, Xie M, Yang MH, Zhu S, Yang LC, Kang R, Tang DL, Zhao LL, Cao LZ. Digital gene expression profiling analysis of childhood acute lymphoblastic leukemia. Mol Med Rep 2016; 13:4321-8. [PMID: 27053012 DOI: 10.3892/mmr.2016.5089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/07/2016] [Indexed: 11/06/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most commonly diagnosed malignancy in children. It is a heterogeneous disease, and is determined by multiple gene alterations and chromosomal rearrangements. To improve current understanding of the underlying molecular mechanisms of ALL, the present study profiled genome‑wide digital gene expression (DGE) in a population of children with ALL in China. Using second‑generation sequencing technology, the profiling revealed that 2,825 genes were upregulated and 1,952 were downregulated in the ALL group. Based on the DGE profiling data, the present study further investigated seven genes (WT1, RPS26, MSX1, CD70, HOXC4, HOXA5 and HOXC6) using reverse transcription‑quantitative polymerase chain reaction analysis. Gene Ontology analysis suggested that the differentially expressed genes were predominantly involved in immune cell differentiation, metabolic processes and programmed cell death. The results of the present study provided novel insights into the gene expression patterns in children with ALL.
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Affiliation(s)
- Ming-Yi Zhao
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yan Yu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Min Xie
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Ming-Hua Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Shan Zhu
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410006, P.R. China
| | - Liang-Chun Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Rui Kang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Dao-Lin Tang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Ling-Ling Zhao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410006, P.R. China
| | - Li-Zhi Cao
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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Timms JA, Relton CL, Rankin J, Strathdee G, McKay JA. DNA methylation as a potential mediator of environmental risks in the development of childhood acute lymphoblastic leukemia. Epigenomics 2016; 8:519-36. [PMID: 27035209 PMCID: PMC4928498 DOI: 10.2217/epi-2015-0011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/22/2016] [Indexed: 11/21/2022] Open
Abstract
5-year survival rate for childhood acute lymphoblastic leukemia (ALL) has risen to approximately 90%, yet the causal disease pathway is still poorly understood. Evidence suggests multiple 'hits' are required for disease progression; an initial genetic abnormality followed by additional secondary 'hits'. It is plausible that environmental influences may trigger these secondary hits, and with the peak incidence of diagnosis between 2 and 5 years of age, early life exposures are likely to be key. DNA methylation can be modified by many environmental exposures and is dramatically altered in cancers, including childhood ALL. Here we explore the potential that DNA methylation may be involved in the causal pathway toward disease by acting as a mediator between established environmental factors and childhood ALL development.
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Affiliation(s)
- Jessica A Timms
- Institute of Health & Society, Newcastle University, Newcastle, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, UK
| | - Judith Rankin
- Institute of Health & Society, Newcastle University, Newcastle, UK
| | - Gordon Strathdee
- Northern Institute for Cancer Research, Newcastle University, UK
| | - Jill A McKay
- Institute of Health & Society, Newcastle University, Newcastle, UK
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Abstract
AXIN2, an important regulator in Wnt/β-catenin signaling pathway, takes part in regulating cell proliferation, cytometaplasia, migration, apoptosis and other important functions, has showed close relations with the development of liver cancer, colon cancer, lung cancer, breast cancer and so on. The epigenetic regulation provides new insights for further exploring the pathogenesis of tumor. In this paper, the roles of AXIN2 in tumorigenesis, AXIN2 methylation, ubiquitination and siRNA/RNA regulation will be reviewed.
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72
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Thingholm LB, Andersen L, Makalic E, Southey MC, Thomassen M, Hansen LL. Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges. Front Genet 2016; 7:2. [PMID: 26870081 PMCID: PMC4740898 DOI: 10.3389/fgene.2016.00002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 01/11/2016] [Indexed: 12/15/2022] Open
Abstract
The development and progression of cancer, a collection of diseases with complex genetic architectures, is facilitated by the interplay of multiple etiological factors. This complexity challenges the traditional single-platform study design and calls for an integrated approach to data analysis. However, integration of heterogeneous measurements of biological variation is a non-trivial exercise due to the diversity of the human genome and the variety of output data formats and genome coverage obtained from the commonly used molecular platforms. This review article will provide an introduction to integration strategies used for analyzing genetic risk factors for cancer. We critically examine the ability of these strategies to handle the complexity of the human genome and also accommodate information about the biological and functional interactions between the elements that have been measured-making the assessment of disease risk against a composite genomic factor possible. The focus of this review is to provide an overview and introduction to the main strategies and to discuss where there is a need for further development.
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Affiliation(s)
- Louise B Thingholm
- Department of Pathology, The University of MelbourneMelbourne, VIC, Australia; Department of Biomedicine, The University of AarhusAarhus, Denmark
| | - Lars Andersen
- Department of Clinical Genetics, Odense University Hospital Odense, Denmark
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, The University of Melbourne Melbourne, VIC, Australia
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne Melbourne, VIC, Australia
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital Odense, Denmark
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Oliveira LH, Schiavinato JL, Fráguas MS, Lucena-Araujo AR, Haddad R, Araújo AG, Dalmazzo LF, Rego EM, Covas DT, Zago MA, Panepucci RA. Potential roles of microRNA-29a in the molecular pathophysiology of T-cell acute lymphoblastic leukemia. Cancer Sci 2015; 106:1264-77. [PMID: 26251039 PMCID: PMC4637998 DOI: 10.1111/cas.12766] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 07/08/2015] [Accepted: 08/03/2015] [Indexed: 12/26/2022] Open
Abstract
Recent evidence has shown that deregulated expression of members of the microRNA-29 (miR-29) family may play a critical role in human cancer, including hematological malignancies. However, the roles of miR-29 in the molecular pathophysiology of T-cell acute lymphoblastic leukemia (T-ALL) has not been investigated. Here, we show that lower levels of miR-29a were significantly associated with higher blast counts in the bone marrow and with increased disease-free survival in T-ALL patients. Furthermore, miR-29a levels are extremely reduced in T-ALL cells compared to normal T cells. Microarray analysis following introduction of synthetic miR-29a mimics into Jurkat cells revealed the downregulation of several predicted targets (CDK6, PXDN, MCL1, PIK3R1, and CXXC6), including targets with roles in active and passive DNA demethylation (such as DNMT3a, DNMT3b, and members of the TET family and TDG). Restoring miR-29a levels in Jurkat and Molt-4 T-ALL cells led to the demethylation of many genes commonly methylated in T-ALL. Overall, our results suggest that reduced miR-29a levels may contribute to the altered epigenetic status of T-ALL, highlighting its relevance in the physiopathology of this disease.
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Affiliation(s)
- Lucila H Oliveira
- Department of Internal Medicine, Medical School of Ribeirão Preto, University of São PauloSão Paulo, Brazil
- Center for Cell Based Therapy, Regional Blood CenterRibeirão Preto, Brazil
| | - Josiane L Schiavinato
- Department of Genetics, Medical School of Ribeirão Preto, University of São PauloSão Paulo, Brazil
- Center for Cell Based Therapy, Regional Blood CenterRibeirão Preto, Brazil
| | - Mariane S Fráguas
- Department of Internal Medicine, Medical School of Ribeirão Preto, University of São PauloSão Paulo, Brazil
- Center for Cell Based Therapy, Regional Blood CenterRibeirão Preto, Brazil
| | | | - Rodrigo Haddad
- School of Ceilandia, University of BrasiliaBrasilia, Brazil
| | - Amélia G Araújo
- Department of Internal Medicine, Medical School of Ribeirão Preto, University of São PauloSão Paulo, Brazil
- Center for Cell Based Therapy, Regional Blood CenterRibeirão Preto, Brazil
| | - Leandro F Dalmazzo
- Department of Internal Medicine, Medical School of Ribeirão Preto, University of São PauloSão Paulo, Brazil
| | - Eduardo M Rego
- Department of Internal Medicine, Medical School of Ribeirão Preto, University of São PauloSão Paulo, Brazil
- Center for Cell Based Therapy, Regional Blood CenterRibeirão Preto, Brazil
| | - Dimas T Covas
- Department of Internal Medicine, Medical School of Ribeirão Preto, University of São PauloSão Paulo, Brazil
- Center for Cell Based Therapy, Regional Blood CenterRibeirão Preto, Brazil
| | - Marco A Zago
- Department of Internal Medicine, Medical School of Ribeirão Preto, University of São PauloSão Paulo, Brazil
- Center for Cell Based Therapy, Regional Blood CenterRibeirão Preto, Brazil
| | - Rodrigo A Panepucci
- Department of Internal Medicine, Medical School of Ribeirão Preto, University of São PauloSão Paulo, Brazil
- Department of Genetics, Medical School of Ribeirão Preto, University of São PauloSão Paulo, Brazil
- Center for Cell Based Therapy, Regional Blood CenterRibeirão Preto, Brazil
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Peirs S, Van der Meulen J, Van de Walle I, Taghon T, Speleman F, Poppe B, Van Vlierberghe P. Epigenetics in T-cell acute lymphoblastic leukemia. Immunol Rev 2015; 263:50-67. [PMID: 25510271 DOI: 10.1111/imr.12237] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Normal T-cell development is a strictly regulated process in which hematopoietic progenitor cells migrate from the bone marrow to the thymus and differentiate from early T-cell progenitors toward mature and functional T cells. During this maturation process, cooperation between a variety of oncogenes and tumor suppressors can drive immature thymocytes into uncontrolled clonal expansion and cause T-cell acute lymphoblastic leukemia (T-ALL). Despite improved insights in T-ALL disease biology and comprehensive characterization of its genetic landscape, clinical care remained largely similar over the past decades and still consists of high-dose multi-agent chemotherapy potentially followed by hematopoietic stem cell transplantation. Even with such aggressive treatment regimens, which are often associated with considerable side effects, clinical outcome is still extremely poor in a significant subset of T-ALL patients as a result of therapy resistance or hematological relapses. Recent genetic studies have identified recurrent somatic alterations in genes involved in DNA methylation and post-translational histone modifications in T-ALL, suggesting that epigenetic homeostasis is critically required in restraining tumor development in the T-cell lineage. In this review, we provide an overview of the epigenetic regulators that could be implicated in T-ALL disease biology and speculate how the epigenetic landscape of T-ALL could trigger the development of epigenetic-based therapies to further improve the treatment of human T-ALL.
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Affiliation(s)
- Sofie Peirs
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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75
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Redefining ALL classification: toward detecting high-risk ALL and implementing precision medicine. Blood 2015; 125:3977-87. [PMID: 25999453 DOI: 10.1182/blood-2015-02-580043] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/24/2015] [Indexed: 02/07/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the commonest childhood tumor and remains a leading cause of cancer death in the young. In the last decade, microarray and sequencing analysis of large ALL cohorts has revolutionized our understanding of the genetic basis of this disease. These studies have identified new ALL subtypes, each characterized by constellations of structural and sequence alterations that perturb key cellular pathways, including lymphoid development, cell-cycle regulation, and tumor suppression; cytokine receptor, kinase, and Ras signaling; and chromatin modifications. Several of these pathways, particularly kinase-activating lesions and epigenetic alterations, are logical targets for new precision medicine therapies. Genomic profiling has also identified important interactions between inherited genetic variants that influence the risk of leukemia development and the somatic genetic alterations that are required to establish the leukemic clone. Moreover, sequential sequencing studies at diagnosis, remission, and relapse have provided important insights into the relationship among genetic variants, clonal heterogeneity, and the risk of relapse. Ongoing studies are extending our understanding of coding and noncoding genetic alterations in B-progenitor and T-lineage ALL and using these insights to inform the development of faithful experimental models to test the efficacy of new treatment approaches.
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76
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Meldi K, Qin T, Buchi F, Droin N, Sotzen J, Micol JB, Selimoglu-Buet D, Masala E, Allione B, Gioia D, Poloni A, Lunghi M, Solary E, Abdel-Wahab O, Santini V, Figueroa ME. Specific molecular signatures predict decitabine response in chronic myelomonocytic leukemia. J Clin Invest 2015; 125:1857-72. [PMID: 25822018 DOI: 10.1172/jci78752] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 02/09/2015] [Indexed: 12/22/2022] Open
Abstract
Myelodysplastic syndromes and chronic myelomonocytic leukemia (CMML) are characterized by mutations in genes encoding epigenetic modifiers and aberrant DNA methylation. DNA methyltransferase inhibitors (DMTis) are used to treat these disorders, but response is highly variable, with few means to predict which patients will benefit. Here, we examined baseline differences in mutations, DNA methylation, and gene expression in 40 CMML patients who were responsive or resistant to decitabine (DAC) in order to develop a molecular means of predicting response at diagnosis. While somatic mutations did not differentiate responders from nonresponders, we identified 167 differentially methylated regions (DMRs) of DNA at baseline that distinguished responders from nonresponders using next-generation sequencing. These DMRs were primarily localized to nonpromoter regions and overlapped with distal regulatory enhancers. Using the methylation profiles, we developed an epigenetic classifier that accurately predicted DAC response at the time of diagnosis. Transcriptional analysis revealed differences in gene expression at diagnosis between responders and nonresponders. In responders, the upregulated genes included those that are associated with the cell cycle, potentially contributing to effective DAC incorporation. Treatment with CXCL4 and CXCL7, which were overexpressed in nonresponders, blocked DAC effects in isolated normal CD34+ and primary CMML cells, suggesting that their upregulation contributes to primary DAC resistance.
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MESH Headings
- Aged
- Aged, 80 and over
- Antimetabolites, Antineoplastic/pharmacology
- Antimetabolites, Antineoplastic/therapeutic use
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- Azacitidine/therapeutic use
- Bone Marrow/pathology
- DNA Methylation/drug effects
- DNA Mutational Analysis
- DNA, Intergenic/genetics
- Decitabine
- Drug Resistance, Neoplasm/genetics
- Enhancer Elements, Genetic/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/genetics
- Genes, Neoplasm
- Humans
- Leukemia, Myelomonocytic, Chronic/drug therapy
- Leukemia, Myelomonocytic, Chronic/genetics
- Leukemia, Myelomonocytic, Chronic/metabolism
- Male
- Middle Aged
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Platelet Factor 4/biosynthesis
- Platelet Factor 4/genetics
- Platelet Factor 4/physiology
- Treatment Outcome
- beta-Thromboglobulin/biosynthesis
- beta-Thromboglobulin/genetics
- beta-Thromboglobulin/physiology
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77
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Li J, Ching T, Huang S, Garmire LX. Using epigenomics data to predict gene expression in lung cancer. BMC Bioinformatics 2015; 16 Suppl 5:S10. [PMID: 25861082 PMCID: PMC4402699 DOI: 10.1186/1471-2105-16-s5-s10] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Epigenetic alterations are known to correlate with changes in gene expression among various diseases including cancers. However, quantitative models that accurately predict the up or down regulation of gene expression are currently lacking. Methods A new machine learning-based method of gene expression prediction is developed in the context of lung cancer. This method uses the Illumina Infinium HumanMethylation450K Beadchip CpG methylation array data from paired lung cancer and adjacent normal tissues in The Cancer Genome Atlas (TCGA) and histone modification marker CHIP-Seq data from the ENCODE project, to predict the differential expression of RNA-Seq data in TCGA lung cancers. It considers a comprehensive list of 1424 features spanning the four categories of CpG methylation, histone H3 methylation modification, nucleotide composition, and conservation. Various feature selection and classification methods are compared to select the best model over 10-fold cross-validation in the training data set. Results A best model comprising 67 features is chosen by ReliefF based feature selection and random forest classification method, with AUC = 0.864 from the 10-fold cross-validation of the training set and AUC = 0.836 from the testing set. The selected features cover all four data types, with histone H3 methylation modification (32 features) and CpG methylation (15 features) being most abundant. Among the dropping-off tests of individual data-type based features, removal of CpG methylation feature leads to the most reduction in model performance. In the best model, 19 selected features are from the promoter regions (TSS200 and TSS1500), highest among all locations relative to transcripts. Sequential dropping-off of CpG methylation features relative to different regions on the protein coding transcripts shows that promoter regions contribute most significantly to the accurate prediction of gene expression. Conclusions By considering a comprehensive list of epigenomic and genomic features, we have constructed an accurate model to predict transcriptomic differential expression, exemplified in lung cancer.
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78
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Roberts KG, Mullighan CG. Genomics in acute lymphoblastic leukaemia: insights and treatment implications. Nat Rev Clin Oncol 2015; 12:344-57. [PMID: 25781572 DOI: 10.1038/nrclinonc.2015.38] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Acute lymphoblastic leukaemia (ALL) is the commonest childhood cancer and an important cause of morbidity from haematological malignancies in adults. In the past several years, we have witnessed major advances in the understanding of the genetic basis of ALL. Genome-wide profiling studies, including microarray analysis and genome sequencing, have helped identify multiple key cellular pathways that are frequently mutated in ALL such as lymphoid development, tumour suppression, cytokine receptors, kinase and Ras signalling, and chromatin remodeling. These studies have characterized new subtypes of ALL, notably Philadelphia chromosome-like ALL, which is a high-risk subtype characterized by a diverse range of alterations that activate cytokine receptors or tyrosine kinases amenable to inhibition with approved tyrosine kinase inhibitors. Genomic profiling has also enabled the identification of inherited genetic variants of ALL that influence the risk of leukaemia development, and characterization of the relationship between genetic variants, clonal heterogeneity and the risk of relapse. Many of these findings are of direct clinical relevance and ongoing studies implementing clinical sequencing in leukaemia diagnosis and management have great potential to improve the outcome of patients with high-risk ALL.
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Affiliation(s)
- Kathryn G Roberts
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN 38105, USA
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79
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Nordlund J, Bäcklin CL, Zachariadis V, Cavelier L, Dahlberg J, Öfverholm I, Barbany G, Nordgren A, Övernäs E, Abrahamsson J, Flaegstad T, Heyman MM, Jónsson ÓG, Kanerva J, Larsson R, Palle J, Schmiegelow K, Gustafsson MG, Lönnerholm G, Forestier E, Syvänen AC. DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia. Clin Epigenetics 2015; 7:11. [PMID: 25729447 PMCID: PMC4343276 DOI: 10.1186/s13148-014-0039-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/18/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND We present a method that utilizes DNA methylation profiling for prediction of the cytogenetic subtypes of acute lymphoblastic leukemia (ALL) cells from pediatric ALL patients. The primary aim of our study was to improve risk stratification of ALL patients into treatment groups using DNA methylation as a complement to current diagnostic methods. A secondary aim was to gain insight into the functional role of DNA methylation in ALL. RESULTS We used the methylation status of ~450,000 CpG sites in 546 well-characterized patients with T-ALL or seven recurrent B-cell precursor ALL subtypes to design and validate sensitive and accurate DNA methylation classifiers. After repeated cross-validation, a final classifier was derived that consisted of only 246 CpG sites. The mean sensitivity and specificity of the classifier across the known subtypes was 0.90 and 0.99, respectively. We then used DNA methylation classification to screen for subtype membership of 210 patients with undefined karyotype (normal or no result) or non-recurrent cytogenetic aberrations ('other' subtype). Nearly half (n = 106) of the patients lacking cytogenetic subgrouping displayed highly similar methylation profiles as the patients in the known recurrent groups. We verified the subtype of 20% of the newly classified patients by examination of diagnostic karyotypes, array-based copy number analysis, and detection of fusion genes by quantitative polymerase chain reaction (PCR) and RNA-sequencing (RNA-seq). Using RNA-seq data from ALL patients where cytogenetic subtype and DNA methylation classification did not agree, we discovered several novel fusion genes involving ETV6, RUNX1, and PAX5. CONCLUSIONS Our findings indicate that DNA methylation profiling contributes to the clarification of the heterogeneity in cytogenetically undefined ALL patient groups and could be implemented as a complementary method for diagnosis of ALL. The results of our study provide clues to the origin and development of leukemic transformation. The methylation status of the CpG sites constituting the classifiers also highlight relevant biological characteristics in otherwise unclassified ALL patients.
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Affiliation(s)
- Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Box 1432, BMC, SE-751 44 Uppsala, Sweden
| | - Christofer L Bäcklin
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, Uppsala University Hospital, Entrance 40, SE-751 85 Uppsala, Sweden
| | - Vasilios Zachariadis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbecklaboratoriet, SE-751 85 Uppsala, Sweden
| | - Johan Dahlberg
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Box 1432, BMC, SE-751 44 Uppsala, Sweden
| | - Ingegerd Öfverholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Elin Övernäs
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Box 1432, BMC, SE-751 44 Uppsala, Sweden
| | - Jonas Abrahamsson
- Department of Pediatrics, Queen Silvia Children's Hospital, Rondvägen 10, SE-416 85 Gothenburg, Sweden
| | - Trond Flaegstad
- Department of Pediatrics, Tromsø University and University Hospital, Sykehusveien 38, N-9038 Tromsø, Norway
| | - Mats M Heyman
- Childhood Cancer Research Unit, Karolinska Institutet, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Q6:05, SE-171 76, Stockholm, Sweden
| | - Ólafur G Jónsson
- Pediatric Hematology-Oncology, Children's Hospital, Barnaspitali Hringsins, Landspitali University Hospital, Norðurmýri, 101, Reykjavik, Iceland
| | - Jukka Kanerva
- Division of Hematology-Oncology and Stem Cell Transplantation, Children's Hospital, Helsinki University Central Hospital and University of Helsinki, Box 281, FIN-00029 Helsinki, Finland
| | - Rolf Larsson
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, Uppsala University Hospital, Entrance 40, SE-751 85 Uppsala, Sweden
| | - Josefine Palle
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Box 1432, BMC, SE-751 44 Uppsala, Sweden.,Department of Women's and Children's Health, Pediatric Oncology, Uppsala University, Uppsala University Hospital, Entrance 95, SE-751 85 Uppsala, Sweden
| | - Kjeld Schmiegelow
- Pediatrics and Adolescent Medicine, Rigshospitalet, and the Medical Faculty, Institute of Clinical Medicine, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Mats G Gustafsson
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, Uppsala University Hospital, Entrance 40, SE-751 85 Uppsala, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Pediatric Oncology, Uppsala University, Uppsala University Hospital, Entrance 95, SE-751 85 Uppsala, Sweden
| | - Erik Forestier
- Department of Medical Biosciences, University of Umeå, SE-901 85 Umeå, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Box 1432, BMC, SE-751 44 Uppsala, Sweden
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80
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Abstract
Giant strides have been made in the management of childhood acute lymphoblastic leukemia (ALL) over previous decades. Extensive collaborative efforts internationally have played a vital role in the remarkable progress made in not only improving therapeutic outcomes but also deciphering the complex biology of childhood ALL. This review summarizes various insights gained from biological studies of childhood ALL, with a focus on recent studies, and also discusses genomic lesions and epigenetic regulatory mechanisms associated with leukemic transformation. The importance of studying the biology of the host so as to understand additional heterogeneity in treatment response and toxicities is highlighted.
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Affiliation(s)
- Deepa Bhojwani
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Jun J. Yang
- Department of Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA,Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA,Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis, TN, USA
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81
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Gabriel AS, Lafta FM, Schwalbe EC, Nakjang S, Cockell SJ, Iliasova A, Enshaei A, Schwab C, Rand V, Clifford SC, Kinsey SE, Mitchell CD, Vora A, Harrison CJ, Moorman AV, Strathdee G. Epigenetic landscape correlates with genetic subtype but does not predict outcome in childhood acute lymphoblastic leukemia. Epigenetics 2015; 10:717-26. [PMID: 26237075 PMCID: PMC4622588 DOI: 10.1080/15592294.2015.1061174] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 05/29/2015] [Accepted: 06/05/2015] [Indexed: 11/19/2022] Open
Abstract
Although children with acute lymphoblastic leukemia (ALL) generally have a good outcome, some patients do relapse and survival following relapse is poor. Altered DNA methylation is highly prevalent in ALL and raises the possibility that DNA methylation-based biomarkers could predict patient outcome. In this study, genome-wide methylation analysis, using the Illumina Infinium HumanMethylation450 BeadChip platform, was carried out on 52 diagnostic patient samples from 4 genetic subtypes [ETV6-RUNX1, high hyperdiploidy (HeH), TCF3-PBX1 and dic(9;20)(p11-13;q11)] in a 1:1 case-control design with patients who went on to relapse (as cases) and patients achieving long-term remission (as controls). Pyrosequencing assays for selected loci were used to confirm the array-generated data. Non-negative matrix factorization consensus clustering readily clustered samples according to genetic subgroups and gene enrichment pathway analysis suggested that this is in part driven by epigenetic disruption of subtype specific signaling pathways. Multiple bioinformatics approaches (including bump hunting and individual locus analysis) were used to identify CpG sites or regions associated with outcome. However, no associations with relapse were identified. Our data revealed that ETV6-RUNX1 and dic(9;20) subtypes were mostly associated with hypermethylation; conversely, TCF3-PBX1 and HeH were associated with hypomethylation. We observed significant enrichment of the neuroactive ligand-receptor interaction pathway in TCF3-PBX1 as well as an enrichment of genes involved in immunity and infection pathways in ETV6-RUNX1 subtype. Taken together, our results suggest that altered DNA methylation may have differential impacts in distinct ALL genetic subtypes.
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Affiliation(s)
- Alem S Gabriel
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
| | - Fadhel M Lafta
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
| | - Edward C Schwalbe
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
- Department of Applied Sciences; Northumbria University; Newcastle upon Tyne, UK
| | - Sirintra Nakjang
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
- Bioinformatics Support Unit; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
| | - Simon J Cockell
- Bioinformatics Support Unit; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
| | - Alice Iliasova
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
- Department of Applied Sciences; Northumbria University; Newcastle upon Tyne, UK
| | - Amir Enshaei
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
| | - Claire Schwab
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
| | - Vikki Rand
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
| | - Steven C Clifford
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
| | - Sally E Kinsey
- Department of Pediatric Haematology and Oncology; Leeds General Infirmary; Leeds, UK
| | - Chris D Mitchell
- Department of Pediatric Oncology; John Radcliffe Hospital; Oxford, UK
| | - Ajay Vora
- Department of Pediatric Oncology; John Radcliffe Hospital; Oxford, UK
| | - Christine J Harrison
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
| | - Anthony V Moorman
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
| | - Gordon Strathdee
- Northern Institute for Cancer Research; Faculty of Medical Sciences; Newcastle University; Newcastle upon Tyne, UK
- Department of Haematology; Great Ormond Street Hospital; London, UK
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82
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Epigenetic deregulation in myeloid malignancies. Transl Res 2015; 165:102-14. [PMID: 24813528 DOI: 10.1016/j.trsl.2014.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/14/2014] [Accepted: 04/17/2014] [Indexed: 11/20/2022]
Abstract
Abnormal epigenetic patterning commonly is observed in cancer, including the myeloid malignancies acute myeloid leukemia and myelodysplastic syndromes. However, despite the universal nature of epigenetic deregulation, specific subtypes of myeloid disorders are associated with distinct epigenetic profiles, which accurately reflect the biologic heterogeneity of these disorders. In addition, mutations and genetic alterations of epigenetic-modifying enzymes frequently have been reported in these myeloid malignancies, emphasizing the importance of epigenetic deregulation in the initiation, progression, and outcome of these disorders. These aberrant epigenetic modifiers have become new targets for drug design, because their inhibition can potentially reverse the altered epigenetic landscapes that contribute to the development of the leukemia. In this review, we provide an overview of the role of epigenetic deregulation in leukemic transformation and their potential for therapeutic targeting.
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83
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Pui CH. Genomic and pharmacogenetic studies of childhood acute lymphoblastic leukemia. Front Med 2014; 9:1-9. [DOI: 10.1007/s11684-015-0381-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 10/15/2014] [Indexed: 11/30/2022]
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84
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Mullighan CG. The genomic landscape of acute lymphoblastic leukemia in children and young adults. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2014; 2014:174-80. [PMID: 25696852 DOI: 10.1182/asheducation-2014.1.174] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Our understanding of the genetic basis of childhood acute lymphoblastic leukemia (ALL) has been greatly advanced by genomic profiling and sequencing studies. These efforts have characterized the genetic basis of recently described and poorly understood subtypes of ALL, including early T-cell precursor ALL, Philadelphia chromosome-like (Ph-like) ALL, and ALL with intrachromosomal amplification of chromosome 21, and have identified several rational therapeutic targets in high-risk ALL, notably ABL1-class and JAK-STAT inhibitors in Ph-like ALL. Deep sequencing studies are also refining our understanding of the genetic basis of clonal heterogeneity and relapse. These studies have elucidated the nature of clonal evolution during disease progression and identified genetic changes that confer resistance to specific therapeutic agents, including CREBBP and NT5C2. Genomic profiling has also identified common and rare inherited genetic variants that influence the risk of developing leukemia. These efforts are now being extended to ALL in adolescents and adults with the goal of fully defining the genetic landscape of ALL to further improve treatment outcomes in high-risk populations.
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Affiliation(s)
- Charles G Mullighan
- Department of Pathology and Hematological Malignancies Program, St Jude Children's Research Hospital, Memphis, TN
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85
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Burke MJ, Lamba JK, Pounds S, Cao X, Ghodke-Puranaik Y, Lindgren BR, Weigel BJ, Verneris MR, Miller JS. A therapeutic trial of decitabine and vorinostat in combination with chemotherapy for relapsed/refractory acute lymphoblastic leukemia. Am J Hematol 2014; 89:889-95. [PMID: 24891274 PMCID: PMC4134715 DOI: 10.1002/ajh.23778] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/28/2014] [Indexed: 02/01/2023]
Abstract
DNA hypermethylation and histone deacetylation are pathways of leukemia resistance. We investigated the tolerability and efficacy of decitabine and vorinostat plus chemotherapy in relapse/refractory acute lymphoblastic leukemia (ALL). Decitabine (15 mg/m(2) iv) and vorinostat (230 mg/m(2) PO div BID) were given days 1-4 followed by vincristine, prednisone, PEG-asparaginase, and doxorubicin. Genome wide methylation profiles were performed in 8 matched patient bone marrow (BM) samples taken at day 0 and day 5 (postdecitabine). The median age was 16 (range, 3-54) years. All patients had a prior BM relapse, with five relapsing after allogeneic transplant. The most common nonhematological toxicities possibly related to decitabine or vorinostat were infection with neutropenia (grade 3; n = 4) and fever/neutropenia (grade 3, n = 4; grade 4, n = 1). Of the 13 eligible patients, four achieved complete remission without platelet recovery (CRp), two partial response (PR), one stable disease (SD), one progressive disease (PD), two deaths on study and three patients who did not have end of therapy disease evaluations for an overall response rate of 46.2% (CRp + PR). Following decitabine, significant genome-wide hypo-methylation was observed. Comparison of clinical responders with nonresponders identified methylation profiles of clinical and biological relevance. Decitabine and vorinostat followed by re-Induction chemotherapy was tolerable and demonstrated clinical benefit in relapsed patients with ALL. Methylation differences were identified between responders and nonresponders indicating interpatient variation, which could impact clinical outcome. This study was registered at www.clinicaltrials.gov as NCT00882206.
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Affiliation(s)
- Michael J. Burke
- Division of Pediatric Hematology-Oncology, Medical College of Wisconsin, Milwaukee, WI
| | - Jatinder K Lamba
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Xueyuan Cao
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Yogita Ghodke-Puranaik
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN
| | | | - Brenda J. Weigel
- Division of Pediatric Hematology-Oncology University of Minnesota Amplatz Children's Hospital, Minneapolis, MN
| | - Michael R. Verneris
- Division of Pediatric Blood and Marrow Transplantation, University of Minnesota Amplatz Children's Hospital, Minneapolis, MN
| | - Jeffrey S. Miller
- Division of Hematology/Oncology and Transplantation in the Department of Medicine, Minneapolis, MN
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86
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Abstract
Although great strides have been made in the improvement of outcome for newly diagnosed pediatric acute lymphoblastic leukemia because of refinements in risk stratification and selective intensification of therapy, the prognosis for relapsed leukemia has lagged behind significantly. Understanding the underlying biological pathways responsible for drug resistance is essential to develop novel approaches for the prevention of recurrence and treatment of relapsed disease. High throughput genomic technologies have the potential to revolutionize cancer care in this era of personalized medicine. Using such advanced technologies, we and others have shown that a diverse assortment of cooperative genetic and epigenetic events drive the resistant phenotype. Herein, we summarize results using a variety of genomic technologies to highlight the power of this methodology in providing insight into the biological mechanisms that impart resistant disease.
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87
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Zuckerman T, Rowe JM. Pathogenesis and prognostication in acute lymphoblastic leukemia. F1000PRIME REPORTS 2014; 6:59. [PMID: 25184049 PMCID: PMC4108947 DOI: 10.12703/p6-59] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The process of lymphoid maturation is tightly controlled by the hierarchical activation of transcription factors and selection through functional signal transduction. Acute lymphoblastic leukemia (ALL) represents a group of B/T-precursor-stage lymphoid cell malignancies arising from genetic alterations that block lymphoid differentiation and drive aberrant cell proliferation and survival. With recent advances in next-generation sequencing, we are discovering new mutations affecting normal lymphopoiesis and the significance of cooperating mutations, as well as epigenetic alterations. The data obtained in this way aids in the evaluation of prognosis in the individual patient but, importantly, also in incorporating targeted therapy appropriate for the mutational abnormality.
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Affiliation(s)
- Tsila Zuckerman
- Department of Hematology and Bone Marrow Transplantation, Rambam Health Care Campus8 Ha'Aliya Street, Haifa 31096Israel
- Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of TechnologyEfron Street, Haifa 31096Israel
| | - Jacob M. Rowe
- Department of Hematology, Shaare Zedek Medical Center12 Bayit Street, Jerusalem 91031Israel
- Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of TechnologyEfron Street, Haifa 31096Israel
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88
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Olinski R, Styczynski J, Olinska E, Gackowski D. Viral infection-oxidative stress/DNA damage-aberrant DNA methylation: separate or interrelated events responsible for genetic instability and childhood ALL development? Biochim Biophys Acta Rev Cancer 2014; 1846:226-31. [PMID: 25003587 DOI: 10.1016/j.bbcan.2014.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/11/2014] [Accepted: 06/28/2014] [Indexed: 12/11/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a malignant disorder that originates in a single B- or T-lymphocyte progenitor and is characterized by a range of numeric and structural chromosomal aberrations. Although, so far no clear cause can be found for ALL the most commonly recognized and strongest causal factor is infection. However, an interesting question is how viral infection may be responsible for genetic changes that lead to lymphoid cell transformation. A plausible mechanism by which infection might impact the process of leukemogenesis via genetic alteration is through: oxidative stress/DNA damage which is closely linked with inflammation, aberrant expression of AID/ABOBEC family enzymes which may be responsible for massive mutation introduction and alteration of DNA methylation, leading to changes in the expression of hematopoietic genes. In this review we propose several specific molecular mechanisms which link infection with all the above-mentioned processes. The most likely event which links common virus infection with ALL pathogenesis is aberrant expression of AID/APOBEC. This event may be directly responsible for the introduction of point mutations (as the result of cytosine or 5-methylcytosine deamination and formation of G:U or G:T misspairs) as well as changes in DNA methylation status.
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Affiliation(s)
- Ryszard Olinski
- Department of Clinical Biochemistry, Nicolaus Copernicus University in Torun, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Poland.
| | - Jan Styczynski
- Department of Paediatrics, Haematology and Oncology, Nicolaus Copernicus University in Torun, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Poland
| | | | - Daniel Gackowski
- Department of Clinical Biochemistry, Nicolaus Copernicus University in Torun, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Poland
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89
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Woo JS, Alberti MO, Tirado CA. Childhood B-acute lymphoblastic leukemia: a genetic update. Exp Hematol Oncol 2014; 3:16. [PMID: 24949228 PMCID: PMC4063430 DOI: 10.1186/2162-3619-3-16] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 06/03/2014] [Indexed: 01/06/2023] Open
Abstract
In the pediatric population, B-acute lymphoblastic leukemia (B-ALL) is the most prevalent childhood hematological malignancy, as well as the leading cause of childhood cancer-related mortality. Advances in cytogenetics utilizing array-based technologies and next-generation sequencing (NGS) techniques have revealed exciting insights into the genetic basis of this disease, with the hopes of developing individualized treatment plans for affected children. In this comprehensive review, we discuss our current understanding of childhood (pediatric) B-ALL and highlight the most recent genetic advances and their therapeutic implications.
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Affiliation(s)
- Jennifer S Woo
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, 1010 Veteran Ave, 2nd Floor, room 2212 F, Los Angeles, CA 90024, USA
| | - Michael O Alberti
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, 1010 Veteran Ave, 2nd Floor, room 2212 F, Los Angeles, CA 90024, USA
| | - Carlos A Tirado
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, 1010 Veteran Ave, 2nd Floor, room 2212 F, Los Angeles, CA 90024, USA
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90
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Sharma NL, Massie CE, Butter F, Mann M, Bon H, Ramos-Montoya A, Menon S, Stark R, Lamb AD, Scott HE, Warren AY, Neal DE, Mills IG. The ETS family member GABPα modulates androgen receptor signalling and mediates an aggressive phenotype in prostate cancer. Nucleic Acids Res 2014; 42:6256-69. [PMID: 24753418 PMCID: PMC4041454 DOI: 10.1093/nar/gku281] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 03/21/2014] [Accepted: 03/26/2014] [Indexed: 12/31/2022] Open
Abstract
In prostate cancer (PC), the androgen receptor (AR) is a key transcription factor at all disease stages, including the advanced stage of castrate-resistant prostate cancer (CRPC). In the present study, we show that GABPα, an ETS factor that is up-regulated in PC, is an AR-interacting transcription factor. Expression of GABPα enables PC cell lines to acquire some of the molecular and cellular characteristics of CRPC tissues as well as more aggressive growth phenotypes. GABPα has a transcriptional role that dissects the overlapping cistromes of the two most common ETS gene fusions in PC: overlapping significantly with ETV1 but not with ERG target genes. GABPα bound predominantly to gene promoters, regulated the expression of one-third of AR target genes and modulated sensitivity to AR antagonists in hormone responsive and castrate resistant PC models. This study supports a critical role for GABPα in CRPC and reveals potential targets for therapeutic intervention.
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Affiliation(s)
- Naomi L Sharma
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK Department of Urology, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Charlie E Massie
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Falk Butter
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Helene Bon
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Antonio Ramos-Montoya
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Suraj Menon
- Department of Bioinformatics, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Rory Stark
- Department of Bioinformatics, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Alastair D Lamb
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Helen E Scott
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Anne Y Warren
- Department of Pathology, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - David E Neal
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK Department of Urology, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Ian G Mills
- Uro-oncology Research Group, CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK Prostate Cancer Research Group, Centre for Molecular Medicine (Norway), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Gaustadalleen 21, Oslo N-0349, Norway Department of Cancer Prevention and Department of Urology, Oslo University Hospital, Oslo N-0349, Norway
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91
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Bartholdy B, Christopeit M, Will B, Mo Y, Barreyro L, Yu Y, Bhagat TD, Okoye-Okafor UC, Todorova TI, Greally JM, Levine RL, Melnick A, Verma A, Steidl U. HSC commitment-associated epigenetic signature is prognostic in acute myeloid leukemia. J Clin Invest 2014; 124:1158-67. [PMID: 24487588 DOI: 10.1172/jci71264] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 11/14/2013] [Indexed: 12/15/2022] Open
Abstract
Acute myeloid leukemia (AML) is characterized by disruption of HSC and progenitor cell differentiation. Frequently, AML is associated with mutations in genes encoding epigenetic modifiers. We hypothesized that analysis of alterations in DNA methylation patterns during healthy HSC commitment and differentiation would yield epigenetic signatures that could be used to identify stage-specific prognostic subgroups of AML. We performed a nano HpaII-tiny-fragment-enrichment-by-ligation-mediated-PCR (nanoHELP) assay to compare genome-wide cytosine methylation profiles between highly purified human long-term HSC, short-term HSC, common myeloid progenitors, and megakaryocyte-erythrocyte progenitors. We observed that the most striking epigenetic changes occurred during the commitment of short-term HSC to common myeloid progenitors and these alterations were predominantly characterized by loss of methylation. We developed a metric of the HSC commitment–associated methylation pattern that proved to be highly prognostic of overall survival in 3 independent large AML patient cohorts, regardless of patient treatment and epigenetic mutations. Application of the epigenetic signature metric for AML prognosis was superior to evaluation of commitment-based gene expression signatures. Together, our data define a stem cell commitment–associated methylome that is independently prognostic of poorer overall survival in AML.
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92
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Bernt KM, Hunger SP. Current concepts in pediatric Philadelphia chromosome-positive acute lymphoblastic leukemia. Front Oncol 2014; 4:54. [PMID: 24724051 PMCID: PMC3971203 DOI: 10.3389/fonc.2014.00054] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/06/2014] [Indexed: 12/22/2022] Open
Abstract
The t(9;22)(q34;q11) or Philadelphia chromosome creates a BCR-ABL1 fusion gene encoding for a chimeric BCR-ABL1 protein. It is present in 3-4% of pediatric acute lymphoblastic leukemia (Ph(+) ALL), and about 25% of adult ALL cases. Prior to the advent of tyrosine kinase inhibitors (TKI), Ph(+) ALL was associated with a very poor prognosis despite the use of intensive chemotherapy and frequently hematopoietic stem-cell transplantation (HSCT) in first remission. The development of TKIs revolutionized the therapy of Ph(+) ALL. Addition of the first generation ABL1 class TKI imatinib to intensive chemotherapy dramatically increased the survival for children with Ph(+) ALL and established that many patients can be cured without HSCT. In parallel, the mechanistic understanding of Ph(+) ALL expanded exponentially through careful mapping of pathways downstream of BCR-ABL1, the discovery of mutations in master regulators of B-cell development such as IKZF1 (Ikaros), PAX5, and early B-cell factor (EBF), the recognition of the complex clonal architecture of Ph(+) ALL, and the delineation of genomic, epigenetic, and signaling abnormalities contributing to relapse and resistance. Still, many important basic and clinical questions remain unanswered. Current clinical trials are testing second generation TKIs in patients with newly diagnosed Ph(+) ALL. Neither the optimal duration of therapy nor the optimal chemotherapy backbone are currently defined. The role of HSCT in first remission and post-transplant TKI therapy also require further study. In addition, it will be crucial to continue to dig deeper into understanding Ph(+) ALL at a mechanistic level, and translate findings into complementary targeted approaches. Expanding targeted therapies hold great promise to decrease toxicity and improve survival in this high-risk disease, which provides a paradigm for how targeted therapies can be incorporated into treatment of other high-risk leukemias.
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Affiliation(s)
- Kathrin M Bernt
- Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado , Aurora, CO , USA
| | - Stephen P Hunger
- Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado , Aurora, CO , USA
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93
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Chromatin modifiers and the promise of epigenetic therapy in acute leukemia. Leukemia 2014; 28:1396-406. [PMID: 24609046 DOI: 10.1038/leu.2014.94] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 02/04/2014] [Accepted: 02/14/2014] [Indexed: 12/31/2022]
Abstract
Hematopoiesis is a tightly regulated process involving the control of gene expression that directs the transition from hematopoietic stem and progenitor cells to terminally differentiated blood cells. In leukemia, the processes directing self-renewal, differentiation and progenitor cell expansion are disrupted, leading to the accumulation of immature, non-functioning malignant cells. Insights into these processes have come in stages, based on technological advances in genetic analyses, bioinformatics and biological sciences. The first cytogenetic studies of leukemic cells identified chromosomal translocations that generate oncogenic fusion proteins and most commonly affect regulators of transcription. This was followed by the discovery of recurrent somatic mutations in genes encoding regulators of the signal transduction pathways that control cell proliferation and survival. Recently, studies of global changes in methylation and gene expression have led to the understanding that the output of transcriptional regulators and the proliferative signaling pathways are ultimately influenced by chromatin structure. Candidate gene, whole-genome and whole-exome sequencing studies have identified recurrent somatic mutations in genes encoding epigenetic modifiers in both acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL). In contrast to the two-hit model of leukemogenesis, emerging evidence suggests that these epigenetic modifiers represent a class of mutations that are critical to the development of leukemia and affect the regulation of various other oncogenic pathways. In this review, we discuss the range of recurrent, somatic mutations in epigenetic modifiers found in leukemia and how these modifiers relate to the classical leukemogenic pathways that lead to impaired cell differentiation and aberrant self-renewal and proliferation.
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94
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Newton TP, Cummings CT, Graham DK, Bernt KM. Epigenetics and chemoresistance in childhood acute lymphoblastic leukemia. Int J Hematol Oncol 2014. [DOI: 10.2217/ijh.13.68] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
SUMMARY For children with acute lymphoblastic leukemia (ALL) who relapse, prognosis is poor and novel therapeutic strategies are needed. In the last decade, it has become apparent that ALL exhibits unique epigenetic patterns in addition to the well known cytogenetic findings. Furthermore, whole genome sequencing efforts are revealing recurrent mutations in epigenetic modifiers in ALL. Aberrant epigenetic modulation may be involved in leukemic transformation and resistance to chemotherapy. Consequently, compounds that specifically modulate the maintenance of such epigenetic programs may offer new approaches to therapy, including the modulation or prevention of chemoresistance in ALL. In this article, we review some of the most recent findings with regard to epigenetic aberrations in ALL, and discuss therapeutic strategies that are currently in development.
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Affiliation(s)
- Timothy P Newton
- Center for Cancer & Blood Disorders, Children’s Hospital Colorado & Department of Pediatrics, Section of Hematology, Oncology & Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, RC1N, Mail Stop 8302, Aurora, CO 80045, USA
| | - Christopher T Cummings
- Center for Cancer & Blood Disorders, Children’s Hospital Colorado & Department of Pediatrics, Section of Hematology, Oncology & Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, RC1N, Mail Stop 8302, Aurora, CO 80045, USA
| | - Douglas K Graham
- Center for Cancer & Blood Disorders, Children’s Hospital Colorado & Department of Pediatrics, Section of Hematology, Oncology & Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, RC1N, Mail Stop 8302, Aurora, CO 80045, USA
| | - Kathrin M Bernt
- Center for Cancer & Blood Disorders, Children’s Hospital Colorado & Department of Pediatrics, Section of Hematology, Oncology & Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, RC1N, Mail Stop 8302, Aurora, CO 80045, USA.
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95
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Chatterton Z, Morenos L, Mechinaud F, Ashley DM, Craig JM, Sexton-Oates A, Halemba MS, Parkinson-Bates M, Ng J, Morrison D, Carroll WL, Saffery R, Wong NC. Epigenetic deregulation in pediatric acute lymphoblastic leukemia. Epigenetics 2014; 9:459-67. [PMID: 24394348 DOI: 10.4161/epi.27585] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Similar to most cancers, genome-wide DNA methylation profiles are commonly altered in pediatric acute lymphoblastic leukemia (ALL); however, recent observations highlight that a large portion of malignancy-associated DNA methylation alterations are not accompanied by related gene expression changes. By analyzing and integrating the methylome and transcriptome profiles of pediatric B-cell ALL cases and primary tissue controls, we report 325 genes hypermethylated and downregulated and 45 genes hypomethylated and upregulated in pediatric B-cell ALL, irrespective of subtype. Repressed cation channel subunits and cAMP signaling activators and transducers are overrepresented, potentially indicating a reduced cellular potential to receive and propagate apoptotic signals. Furthermore, we report specific DNA methylation alterations with concurrent gene expression changes within individual ALL subtypes. The ETV6-RUNX1 translocation was associated with downregulation of ASNS and upregulation of the EPO-receptor, while Hyperdiploid patients (> 50 chr) displayed upregulation of B-cell lymphoma (BCL) members and repression of PTPRG and FHIT. In combination, these data indicate genetically distinct B-cell ALL subtypes contain cooperative epimutations and genome-wide epigenetic deregulation is common across all B-cell ALL subtypes.
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Affiliation(s)
- Zac Chatterton
- Murdoch Childrens Research Institute; The University of Melbourne Department of Paediatrics at the Royal Children's Hospital; Victoria, VIC Australia
| | - Leah Morenos
- Murdoch Childrens Research Institute; The University of Melbourne Department of Paediatrics at the Royal Children's Hospital; Victoria, VIC Australia
| | | | - David M Ashley
- Andrew Love Cancer Centre; Deakin University; Victoria, VIC Australia
| | - Jeffrey M Craig
- Murdoch Childrens Research Institute; The University of Melbourne Department of Paediatrics at the Royal Children's Hospital; Victoria, VIC Australia
| | - Alexandra Sexton-Oates
- Murdoch Childrens Research Institute; The University of Melbourne Department of Paediatrics at the Royal Children's Hospital; Victoria, VIC Australia
| | - Minhee S Halemba
- Murdoch Childrens Research Institute; The University of Melbourne Department of Paediatrics at the Royal Children's Hospital; Victoria, VIC Australia
| | - Mandy Parkinson-Bates
- Murdoch Childrens Research Institute; The University of Melbourne Department of Paediatrics at the Royal Children's Hospital; Victoria, VIC Australia
| | - Jane Ng
- Murdoch Childrens Research Institute; The University of Melbourne Department of Paediatrics at the Royal Children's Hospital; Victoria, VIC Australia
| | | | | | - Richard Saffery
- Murdoch Childrens Research Institute; The University of Melbourne Department of Paediatrics at the Royal Children's Hospital; Victoria, VIC Australia
| | - Nicholas C Wong
- Murdoch Childrens Research Institute; The University of Melbourne Department of Paediatrics at the Royal Children's Hospital; Victoria, VIC Australia
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96
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Burke MJ, Bhatla T. Epigenetic modifications in pediatric acute lymphoblastic leukemia. Front Pediatr 2014; 2:42. [PMID: 24860797 PMCID: PMC4030177 DOI: 10.3389/fped.2014.00042] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/29/2014] [Indexed: 12/22/2022] Open
Abstract
Aberrant epigenetic modifications are well-recognized drivers for oncogenesis. Pediatric acute lymphoblastic leukemia (ALL) is no exception and serves as a model toward the significant impact these heritable alterations can have in leukemogenesis. In this brief review, we will focus on the main aspects of epigenetics, which control leukemogenesis in pediatric ALL, mainly DNA methylation, histone modification, and microRNA alterations. As we continue to gain better understanding of the driving mechanisms for pediatric ALL at both diagnosis and relapse, therapeutic interventions directed toward these pathways and mechanisms can be harnessed and introduced into clinical trials for pediatric ALL.
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Affiliation(s)
- Michael J Burke
- Division of Pediatric Hematology-Oncology, Medical College of Wisconsin , Milwaukee, WI , USA
| | - Teena Bhatla
- Division of Pediatric Hematology-Oncology, New York University Langone Medical Center , New York, NY , USA
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97
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Lim JYS, Bhatia S, Robison LL, Yang JJ. Genomics of racial and ethnic disparities in childhood acute lymphoblastic leukemia. Cancer 2013; 120:955-62. [PMID: 24382716 DOI: 10.1002/cncr.28531] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/01/2013] [Accepted: 11/20/2013] [Indexed: 12/23/2022]
Abstract
Although the cure rates of childhood acute lymphoblastic leukemia (ALL) have improved dramatically in the past 40 years, not all children have benefited equally from this impressive progress. Racial and ethnic disparities in the incidence and treatment outcome of childhood ALL persist, with Hispanic children having an elevated risk of developing ALL and one of the lowest survival rates after ALL therapy. A critical barrier to progress is the lack of an understanding of the causes of ALL disparities, particularly racial and ethnic differences in ALL biology. In this review, the authors summarize the current knowledge on population variation in childhood ALL incidence and treatment outcome, discuss the contributing genetic and nongenetic variables, and highlight possible therapeutic interventions to mitigate disparities in ALL.
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Affiliation(s)
- Joshua Yew-Suang Lim
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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98
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Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy and a leading case of childhood cancer death. The last decade has witnessed a transformation in our understanding of the genetic basis of ALL due to detailed integrative genomic profiling of large cohorts of childhood ALL. Initially using microarray based approaches, and more recently with next-generation sequencing, these studies have enabled more precise subclassification of ALL, and have shown that each ALL entity is characterized by constellations of structural and sequence mutations that typically perturb key cellular pathways including lymphoid development, cell cycle regulation, tumor suppression, Ras- and tyrosine kinase-driven signaling, and epigenetic regulation. Importantly, several of the newly identified genetic alterations have entered the clinic to improve diagnosis and risk stratification, and are being pursued as new targets for therapeutic intervention. Studies of ALL have also led the way in dissecting the subclonal heterogeneity of cancer, and have shown that individual patients commonly harbor multiple related but genetically distinct subclones, and that this genetically determined clonal heterogeneity is an important determinant of relapse. In addition, genome-wide profiling has identified inherited genetic variants that influence ALL risk. Ongoing studies are deploying detailed integrative genetic transcriptomic and epigenetic sequencing to comprehensively define the genomic landscape of ALL. This review describes the recent advances in our understanding of the genetics of ALL, with an emphasis on those alterations of key pathogenic or therapeutic importance.
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Affiliation(s)
- Charles G Mullighan
- Department of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN.
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99
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Nordlund J, Bäcklin CL, Wahlberg P, Busche S, Berglund EC, Eloranta ML, Flaegstad T, Forestier E, Frost BM, Harila-Saari A, Heyman M, Jónsson OG, Larsson R, Palle J, Rönnblom L, Schmiegelow K, Sinnett D, Söderhäll S, Pastinen T, Gustafsson MG, Lönnerholm G, Syvänen AC. Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia. Genome Biol 2013; 14:r105. [PMID: 24063430 PMCID: PMC4014804 DOI: 10.1186/gb-2013-14-9-r105] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 09/24/2013] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic background, drug resistance and relapse in ALL is poorly understood. RESULTS We surveyed the DNA methylation levels of 435,941 CpG sites in samples from 764 children at diagnosis of ALL and from 27 children at relapse. This survey uncovered four characteristic methylation signatures. First, compared with control blood cells, the methylomes of ALL cells shared 9,406 predominantly hypermethylated CpG sites, independent of cytogenetic background. Second, each cytogenetic subtype of ALL displayed a unique set of hyper- and hypomethylated CpG sites. The CpG sites that constituted these two signatures differed in their functional genomic enrichment to regions with marks of active or repressed chromatin. Third, we identified subtype-specific differential methylation in promoter and enhancer regions that were strongly correlated with gene expression. Fourth, a set of 6,612 CpG sites was predominantly hypermethylated in ALL cells at relapse, compared with matched samples at diagnosis. Analysis of relapse-free survival identified CpG sites with subtype-specific differential methylation that divided the patients into different risk groups, depending on their methylation status. CONCLUSIONS Our results suggest an important biological role for DNA methylation in the differences between ALL subtypes and in their clinical outcome after treatment.
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