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Torres-Llanos Y, Zabaleta J, Cruz-Rodriguez N, Quijano S, Guzmán PC, de los Reyes I, Poveda-Garavito N, Infante A, Lopez-Kleine L, Combita AL. MIR4435-2HG as a possible novel predictive biomarker of chemotherapy response and death in pediatric B-cell ALL. Front Mol Biosci 2024; 11:1385140. [PMID: 38745909 PMCID: PMC11091394 DOI: 10.3389/fmolb.2024.1385140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 02/28/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction: Although B-cell acute lymphoblastic leukemia (B-cell ALL) survival rates have improved in recent years, Hispanic children continue to have poorer survival rates. There are few tools available to identify at the time of diagnosis whether the patient will respond to induction therapy. Our goal was to identify predictive biomarkers of treatment response, which could also serve as prognostic biomarkers of death, by identifying methylated and differentially expressed genes between patients with positive minimal residual disease (MRD+) and negative minimal residual disease (MRD-). Methods: DNA and RNA were extracted from tumor blasts separated by immunomagnetic columns. Illumina MethlationEPIC and mRNA sequencing assays were performed on 13 bone marrows from Hispanic children with B-cell ALL. Partek Flow was used for transcript mapping and quantification, followed by differential expression analysis using DEseq2. DNA methylation analyses were performed with Partek Genomic Suite and Genome Studio. Gene expression and differential methylation were compared between patients with MRD-/- and MRD+/+ at the end of induction chemotherapy. Overexpressed and hypomethylated genes were selected and validated by RT-qPCR in samples of an independent validation cohort. The predictive ability of the genes was assessed by logistic regression. Survival and Cox regression analyses were performed to determine the association of genes with death. Results: DAPK1, BOC, CNKSR3, MIR4435-2HG, CTHRC1, NPDC1, SLC45A3, ITGA6, and ASCL2 were overexpressed and hypomethylated in MRD+/+ patients. Overexpression was also validated by RT-qPCR. DAPK1, BOC, ASCL2, and CNKSR3 can predict refractoriness, but MIR4435-2HG is the best predictor. Additionally, higher expression of MIR4435-2HG increases the probability of non-response, death, and the risk of death. Finally, MIR4435-2HG overexpression, together with MRD+, are associated with poorer survival, and together with overexpression of DAPK1 and ASCL2, it could improve the risk classification of patients with normal karyotype. Conclusion: MIR4435-2HG is a potential predictive biomarker of treatment response and death in children with B-cell ALL.
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Affiliation(s)
| | - Jovanny Zabaleta
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | | | - Sandra Quijano
- Department of Microbiology, Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | | | | | - Ana Infante
- Department of Pediatrics, Hospital Universitario San Ignacio, Bogotá, Colombia
| | | | - Alba Lucía Combita
- Cancer Biology Group, Instituto Nacional de Cancerología, Bogotá, Colombia
- Department of Microbiology, School of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
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2
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IRF8 is a transcriptional activator of CD37 expression in diffuse large B-cell lymphoma. Blood Adv 2022; 6:2254-2266. [PMID: 35086136 PMCID: PMC9006271 DOI: 10.1182/bloodadvances.2021004366] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 01/20/2022] [Indexed: 11/20/2022] Open
Abstract
IRF8 is a transcriptional regulator of CD37 expression in DLBCL, which may have implications for anti-CD37 therapies. Patients with poor prognostic CD37-negative DLBCL show significantly lower IRF8 expression compared with patients with CD37-positive DLBCL.
Diffuse large B-cell lymphoma (DLBCL) represents the most common form of non-Hodgkin lymphoma (NHL) that is still incurable in a large fraction of patients. Tetraspanin CD37 is highly expressed on mature B lymphocytes, and multiple CD37-targeting therapies are under clinical development for NHL. However, CD37 expression is nondetectable in ∼50% of DLBCL patients, which correlates with inferior treatment outcome, but the underlying mechanisms for differential CD37 expression in DLBCL are still unknown. Here, we investigated the regulation of the CD37 gene in human DLBCL at the (epi-)genetic and transcriptional level. No differences were observed in DNA methylation within the CD37 promoter region between CD37-positive and CD37-negative primary DLBCL patient samples. On the contrary, CD37-negative DLBCL cells specifically lacked CD37 promoter activity, suggesting differential regulation of CD37 gene expression. Using an unbiased quantitative proteomic approach, we identified transcription factor IRF8 to be significantly higher expressed in nuclear extracts of CD37-positive as compared with CD37-negative DLBCL. Direct binding of IRF8 to the CD37 promoter region was confirmed by DNA pulldown assay combined with mass spectrometry and targeted chromatin immunoprecipitation (ChIP). Functional analysis indicated that IRF8 overexpression enhanced CD37 protein expression, while CRISPR/Cas9 knockout of IRF8 decreased CD37 levels in DLBCL cell lines. Immunohistochemical analysis in a large cohort of primary DLBCL (n = 206) revealed a significant correlation of IRF8 expression with detectable CD37 levels. Together, this study provides new insight into the molecular mechanisms underlying differential CD37 expression in human DLBCL and reveals IRF8 as a transcriptional regulator of CD37 in B-cell lymphoma.
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Gİrgİn B, KaradaĞ-Alpaslan M, KocabaŞ F. Oncogenic and tumor suppressor function of MEIS and associated factors. ACTA ACUST UNITED AC 2021; 44:328-355. [PMID: 33402862 PMCID: PMC7759197 DOI: 10.3906/biy-2006-25] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Abstract
MEIS proteins are historically associated with tumorigenesis, metastasis, and invasion in cancer. MEIS and associated PBX-HOX proteins may act as tumor suppressors or oncogenes in different cellular settings. Their expressions tend to be misregulated in various cancers. Bioinformatic analyses have suggested their upregulation in leukemia/lymphoma, thymoma, pancreas, glioma, and glioblastoma, and downregulation in cervical, uterine, rectum, and colon cancers. However, every cancer type includes, at least, a subtype with high MEIS expression. In addition, studies have highlighted that MEIS proteins and associated factors may function as diagnostic or therapeutic biomarkers for various diseases. Herein, MEIS proteins and associated factors in tumorigenesis are discussed with recent discoveries in addition to how they could be modulated by noncoding RNAs or newly developed small-molecule MEIS inhibitors.
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Affiliation(s)
- Birkan Gİrgİn
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbul Turkey.,Graduate School of Natural and Applied Sciences, Yeditepe University, İstanbul Turkey.,Meinox Pharma Technologies, İstanbul Turkey
| | - Medine KaradaĞ-Alpaslan
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun Turkey
| | - Fatih KocabaŞ
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbul Turkey.,Graduate School of Natural and Applied Sciences, Yeditepe University, İstanbul Turkey.,Meinox Pharma Technologies, İstanbul Turkey
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4
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Broto GE, Corrêa S, Trigo FC, Dos Santos EC, Tomiotto-Pelissier F, Pavanelli WR, Silveira GF, Abdelhay E, Panis C. Comparative Analysis of Systemic and Tumor Microenvironment Proteomes From Children With B-Cell Acute Lymphocytic Leukemia at Diagnosis and After Induction Treatment. Front Oncol 2021; 10:550213. [PMID: 33381445 PMCID: PMC7769010 DOI: 10.3389/fonc.2020.550213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/06/2020] [Indexed: 12/03/2022] Open
Abstract
Among the childhood diseases, B-cell acute lymphocytic leukemia (B-ALL) is the most frequent type of cancer. Despite recent advances concerning disease treatment, cytotoxic chemotherapy remains the first line of treatment in several countries, and the modifications induced by such drugs in the organism are still poorly understood. In this context, the present study provided a comparative high-throughput proteomic analysis of the cumulative changes induced by chemotherapeutic drugs used in the induction phase of B-ALL treatment in both peripheral blood (PB) and bone marrow compartment (BM) samples. To reach this goal, PB and BM plasma samples were comparatively analyzed by using label-free proteomics at two endpoints: at diagnosis (D0) and the end of the cumulative induction phase treatment (D28). Proteomic data was available via ProteomeXchange with identifier PXD021584. The resulting differentially expressed proteins were explored by bioinformatics approaches aiming to identify the main gene ontology processes, pathways, and transcription factors altered by chemotherapy, as well as to understand B-ALL biology in each compartment at D0. At D0, PB was characterized as a pro-inflammatory environment, with the involvement of several downregulated coagulation proteins as KNG, plasmin, and plasminogen. D28 was characterized predominantly by immune response-related processes and the super expression of the transcription factor IRF3 and transthyretin. RUNX1 was pointed out as a common transcription factor found in both D0 and D28. We chose to validate the proteins transthyretin and interferon-gamma (IFN-γ) by commercial kits and expressed the results as PB/BM ratios. Transthyretin ratio was augmented after induction chemotherapy, while IFN-γ was reduced at the end of the treatment. Considering that most of these proteins were not yet described in B-ALL literature, these findings added to understanding disease biology at diagnosis and highlighted a possible role for transthyretin and IFN-γ as mechanisms related to disease resolution.
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Affiliation(s)
- Geise Ellen Broto
- Programa de Pós-graduação em Patologia Clínica e Laboratorial, Universidade Estadual de Londrina, Londrina, Brazil.,Laboratório de Biologia de Tumores, Universidade Estadual do Oeste do Paraná, UNIOESTE, Francisco Beltrão, Brazil
| | - Stephany Corrêa
- Laboratório de Células-Tronco, Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | - Everton Cruz Dos Santos
- Laboratório de Células-Tronco, Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | - Wander Rogério Pavanelli
- Programa de Pós-graduação em Patologia Experimental Universidade Estadual de Londrina, Londrina, Brazil
| | | | - Eliana Abdelhay
- Laboratório de Células-Tronco, Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Carolina Panis
- Programa de Pós-graduação em Patologia Clínica e Laboratorial, Universidade Estadual de Londrina, Londrina, Brazil.,Laboratório de Biologia de Tumores, Universidade Estadual do Oeste do Paraná, UNIOESTE, Francisco Beltrão, Brazil.,Programa de Pós-graduação em Patologia Experimental Universidade Estadual de Londrina, Londrina, Brazil.,Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Universidade Estadual do Oeste do Paraná, UNIOESTE, Francisco Beltrão, Brazil
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5
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Zsigrai S, Kalmár A, Nagy ZB, Barták BK, Valcz G, Szigeti KA, Galamb O, Dankó T, Sebestyén A, Barna G, Szabó V, Pipek O, Medgyes-Horváth A, Csabai I, Tulassay Z, Igaz P, Takács I, Molnár B. S-Adenosylmethionine Treatment of Colorectal Cancer Cell Lines Alters DNA Methylation, DNA Repair and Tumor Progression-Related Gene Expression. Cells 2020; 9:cells9081864. [PMID: 32784836 PMCID: PMC7464653 DOI: 10.3390/cells9081864] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/03/2020] [Accepted: 08/07/2020] [Indexed: 12/24/2022] Open
Abstract
Global DNA hypomethylation is a characteristic feature of colorectal carcinoma (CRC). The tumor inhibitory effect of S-adenosylmethionine (SAM) methyl donor has been described in certain cancers including CRC. However, the molecular impact of SAM treatment on CRC cell lines with distinct genetic features has not been evaluated comprehensively. HT-29 and SW480 cells were treated with 0.5 and 1 mmol/L SAM for 48 h followed by cell proliferation measurements, whole-genome transcriptome and methylome analyses, DNA stability assessments and exome sequencing. SAM reduced cell number and increased senescence by causing S phase arrest, besides, multiple EMT-related genes (e.g., TGFB1) were downregulated in both cell lines. Alteration in the global DNA methylation level was not observed, but certain methylation changes in gene promoters were detected. SAM-induced γ-H2AX elevation could be associated with activated DNA repair pathway showing upregulated gene expression (e.g., HUS1). Remarkable genomic stability elevation, namely, decreased micronucleus number and comet tail length was observed only in SW480 after treatment. SAM has the potential to induce senescence, DNA repair, genome stability and to reduce CRC progression. However, the different therapeutic responses of HT-29 and SW480 to SAM emphasize the importance of the molecular characterization of CRC cases prior to methyl donor supplementation.
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Affiliation(s)
- Sára Zsigrai
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- Correspondence:
| | - Alexandra Kalmár
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
| | - Zsófia B. Nagy
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
| | - Barbara K. Barták
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
| | - Gábor Valcz
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
| | - Krisztina A. Szigeti
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
| | - Orsolya Galamb
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
| | - Titanilla Dankó
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary; (T.D.); (A.S.); (G.B.); (V.S.)
| | - Anna Sebestyén
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary; (T.D.); (A.S.); (G.B.); (V.S.)
| | - Gábor Barna
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary; (T.D.); (A.S.); (G.B.); (V.S.)
| | - Vanessza Szabó
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary; (T.D.); (A.S.); (G.B.); (V.S.)
| | - Orsolya Pipek
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (O.P.); (A.M.-H.); (I.C.)
| | - Anna Medgyes-Horváth
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (O.P.); (A.M.-H.); (I.C.)
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (O.P.); (A.M.-H.); (I.C.)
| | - Zsolt Tulassay
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
- Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
| | - Péter Igaz
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
| | - István Takács
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
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Aberuyi N, Rahgozar S, Ghodousi ES, Ghaedi K. Drug Resistance Biomarkers and Their Clinical Applications in Childhood Acute Lymphoblastic Leukemia. Front Oncol 2020; 9:1496. [PMID: 32010613 PMCID: PMC6978753 DOI: 10.3389/fonc.2019.01496] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022] Open
Abstract
Biomarkers are biological molecules found in body fluids or tissues, which can be considered as indications of a normal or abnormal process, or of a condition or disease. There are various types of biomarkers based on their application and molecular alterations. Treatment-sensitivity or drug resistance biomarkers include prognostic and predictive molecules with utmost importance in selecting appropriate treatment protocols and improving survival rates. Acute lymphoblastic leukemia (ALL) is the most prevalent hematological malignancy diagnosed in children with nearly 80% cure rate. Despite the favorable survival rates of childhood ALL (chALL), resistance to chemotherapeutic agents and, as a consequence, a dismal prognosis develops in a significant number of patients. Therefore, there are urgent needs to have robust, sensitive, and disease-specific molecular prognostic and predictive biomarkers, which could allow better risk classification and then better clinical results. In this article, we review the currently known drug resistance biomarkers, including somatic or germ line nucleic acids, epigenetic alterations, protein expressions and metabolic variations. Moreover, biomarkers with potential clinical applications are discussed.
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Affiliation(s)
- Narges Aberuyi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Soheila Rahgozar
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Elaheh Sadat Ghodousi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Kamran Ghaedi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
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7
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Alsaleh H, Haddrill PR. Identifying blood-specific age-related DNA methylation markers on the Illumina MethylationEPIC® BeadChip. Forensic Sci Int 2019; 303:109944. [PMID: 31546163 DOI: 10.1016/j.forsciint.2019.109944] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/14/2019] [Accepted: 09/01/2019] [Indexed: 01/02/2023]
Abstract
The past decade has seen rapid development in DNA methylation (DNAm) microarrays, including the Illumina HumanMethylation27 and HumanMethylation450 (450K) chips, which have played an essential role in identifying and evaluating age-related (AR) DNAm markers in different tissues. Recently, a new array, the Illumina MethylationEPIC (EPIC) was introduced, with nearly double the number of probes as the 450K (∼850,000 probes). In this study, we test these newly added probes for age association using a large cohort of 754 DNAm profiles from blood samples assayed on the EPIC BeadChip, for individuals aged 0-88 years old. 52 AR CpG sites (Spearman's abs(rho) >0.6 and P-value <10-83) were identified, 21 of which were novel sites and mapped to 18 genes, nine of which (LHFPL4, SLC12A8, EGFEM1P, GPR158, TAL1, KIAA1755, LOC730668, DUSP16, and FAM65C) have never previously been reported to be associated with age. The data were subsequently split into a 527-sample training set and a 227-sample testing set to build and validate two age prediction models using elastic net regression and multivariate regression. Elastic net regression selected 425 CpG markers with a mean absolute deviation (MAD) of 2.6 years based on the testing set. To build a multivariate linear regression model, AR CpG sites with R2 > 0.5 at FDR < 0.05 were input into stepwise regression to select the best subset for age prediction. The resulting six CpG markers were linearly modelled with age and explained 81% of age-correlated variation in DNAm levels. Age estimation accuracy using bootstrap analysis was 4.5 years, with 95% confidence intervals of 4.56 to 4.57 years based on the testing set. These results suggest that EPIC BeadChip probes for age estimation fall within the range of probes found on the previous Illumina HumanMethylation platforms in terms of their age-prediction ability.
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Affiliation(s)
- Hussain Alsaleh
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, Scotland, UK; General Department for Forensic Evidence, State of Kuwait Ministry of Interior, Kuwait.
| | - Penelope R Haddrill
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, Scotland, UK
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8
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Kachroo P, Szymczak S, Heinsen FA, Forster M, Bethune J, Hemmrich-Stanisak G, Baker L, Schrappe M, Stanulla M, Franke A. NGS-based methylation profiling differentiates TCF3-HLF and TCF3-PBX1 positive B-cell acute lymphoblastic leukemia. Epigenomics 2018; 10:133-147. [DOI: 10.2217/epi-2017-0080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To determine whether methylation differences between mostly fatal TCF3-HLF and curable TCF3-PBX1 pediatric acute lymphoblastic leukemia subtypes can be associated with differential gene expression and remission. Materials & methods: Five (extremely rare) TCF3-HLF versus five (very similar) TCF3-PBX1 patients were sampled before and after remission and analyzed using reduced representation bisulfite sequencing and RNA-sequencing. Results: We identified 7000 differentially methylated CpG sites between subtypes, of which 78% had lower methylation levels in TCF3-HLF. Gene expression was negatively correlated with CpG sites in 23 genes. KBTBD11 clearly differed in methylation and expression between subtypes and before and after remission in TCF3-HLF samples. Conclusion: KBTBD11 hypomethylation may be a promising potential target for further experimental validation especially for the TCF3-HLF subtype.
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Affiliation(s)
- Priyadarshini Kachroo
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
- Channing Laboratory, Department of Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Silke Szymczak
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
- Institute of Medical Informatics & Statistics, Christian Albrechts University of Kiel, Kiel 24105, Germany
| | - Femke-Anouska Heinsen
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
| | - Jörn Bethune
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
| | - Georg Hemmrich-Stanisak
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
| | - Lewis Baker
- Department of Applied Mathematics, University of Colorado, Boulder, CO 80309, USA
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Martin Stanulla
- Pediatric Hematology & Oncology, Hannover Medical School, Hannover 30625, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel 24105, Germany
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9
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Bachu M, Dey A, Ozato K. Chromatin Landscape of the IRF Genes and Role of the Epigenetic Reader BRD4. J Interferon Cytokine Res 2018; 36:470-5. [PMID: 27379869 DOI: 10.1089/jir.2015.0179] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Histone post-translational modification patterns represent epigenetic states of genomic genes and denote the state of their transcription, past history, and future potential in gene expression. Genome-wide chromatin modification patterns reported from various laboratories are assembled in the ENCODE database, providing a fertile ground for understanding epigenetic regulation of any genes of interest across many cell types. The IRF family genes critically control innate immunity as they direct expression and activities of interferons. While these genes have similar structural and functional traits, their chromatin landscapes and epigenetic features have not been systematically evaluated. Here, by mining ENCODE database using an imputational approach, we summarize chromatin modification patterns for 6 of 9 IRF genes and show characteristic features that connote their epigenetic states. BRD4 is a BET bromodomain protein that "reads and translates" epigenetic marks into transcription. We review recent findings that BRD4 controls constitutive and signal-dependent transcription of many genes, including IRF genes. BRD4 dynamically binds to various genomic genes with a spatial and temporal specificity. Of particular importance, BRD4 is shown to critically regulate IRF-dependent anti-pathogen protection, inflammatory responses triggered by NF-κB, and the growth and spread of many cancers. The advent of small molecule inhibitors that disrupt binding of BET bromdomain to acetylated histone marks has opened new therapeutic possibilities for cancer and inflammatory diseases.
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Affiliation(s)
- Mahesh Bachu
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland
| | - Anup Dey
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland
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Rani L, Mathur N, Gupta R, Gogia A, Kaur G, Dhanjal JK, Sundar D, Kumar L, Sharma A. Genome-wide DNA methylation profiling integrated with gene expression profiling identifies PAX9 as a novel prognostic marker in chronic lymphocytic leukemia. Clin Epigenetics 2017; 9:57. [PMID: 28572861 PMCID: PMC5450117 DOI: 10.1186/s13148-017-0356-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 05/18/2017] [Indexed: 12/22/2022] Open
Abstract
Background In chronic lymphocytic leukemia (CLL), epigenomic and genomic studies have expanded the existing knowledge about the disease biology and led to the identification of potential biomarkers relevant for implementation of personalized medicine. In this study, an attempt has been made to examine and integrate the global DNA methylation changes with gene expression profile and their impact on clinical outcome in early stage CLL patients. Results The integration of DNA methylation profile (n = 14) with the gene expression profile (n = 21) revealed 142 genes as hypermethylated-downregulated and; 62 genes as hypomethylated-upregulated in early stage CLL patients compared to CD19+ B-cells from healthy individuals. The mRNA expression levels of 17 genes identified to be differentially methylated and/or differentially expressed was further examined in early stage CLL patients (n = 93) by quantitative real time PCR (RQ-PCR). Significant differences were observed in the mRNA expression of MEIS1, PMEPA1, SOX7, SPRY1, CDK6, TBX2, and SPRY2 genes in CLL cells as compared to B-cells from healthy individuals. The analysis in the IGHV mutation based categories (Unmutated = 39, Mutated = 54) revealed significantly higher mRNA expression of CRY1 and PAX9 genes in the IGHV unmutated subgroup (p < 0.001). The relative risk of treatment initiation was significantly higher among patients with high expression of CRY1 (RR = 1.91, p = 0.005) or PAX9 (RR = 1.87, p = 0.001). High expression of CRY1 (HR: 3.53, p < 0.001) or PAX9 (HR: 3.14, p < 0.001) gene was significantly associated with shorter time to first treatment. The high expression of PAX9 gene (HR: 3.29, 95% CI 1.172–9.272, p = 0.016) was also predictive of shorter overall survival in CLL. Conclusions The DNA methylation changes associated with mRNA expression of CRY1 and PAX9 genes allow risk stratification of early stage CLL patients. This comprehensive analysis supports the concept that the epigenetic changes along with the altered expression of genes have the potential to predict clinical outcome in early stage CLL patients. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0356-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lata Rani
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Nitin Mathur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Ajay Gogia
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Gurvinder Kaur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Jaspreet Kaur Dhanjal
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory of Advanced Biomedicine (DAILAB), Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110016 India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory of Advanced Biomedicine (DAILAB), Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110016 India
| | - Lalit Kumar
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Atul Sharma
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
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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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12
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Aberrant DNA methylation of acute myeloid leukemia and colorectal cancer in a Chinese pedigree with a MLL3 germline mutation. Tumour Biol 2016; 37:12609-12618. [PMID: 27405564 DOI: 10.1007/s13277-016-5130-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/29/2016] [Indexed: 12/14/2022] Open
Abstract
Unlike genetic aberrations, epigenetic alterations do not modify the deoxyribonucleic acid (DNA) coding sequence and can be reversed pharmacologically. Identifying a particular epigenetic alteration such as abnormal DNA methylation may provide better understanding of cancers and improve current therapy. In a Chinese pedigree with colorectal carcinoma and acute myeloid leukemia, we examined the genome-wide DNA methylation level of cases and explored the role of methylation in pathogenesis and progression. DNA methylation status in the four cases, which all harbor a MLL3 germline mutation, differed from that of the normal control, and hypermethylation was more prevalent. Also, more CpG sites were hypermethylated in the acute-phase AML patient than in the AML patient in remission. Fifty-nine hyper- or hypomethylated genes were identified as common to all four cases. Genome-wide DNA methylation analysis demonstrated that differentially methylated sites among acute myeloid leukemia and colorectal carcinoma cases and the control were in both promoters (CpG island) and gene body regions (shelf/shore areas). Hypermethylation was more prevalent in cancer cases. The study supports the suggestion that the level of DNA methylation changes in AML progression.
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13
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Kim SY, Shin DY, Kim SM, Lee M, Kim EJ. Aberrant DNA methylation-induced gene inactivation is associated with the diagnosis and/or therapy of T-cell leukemias. Leuk Res 2016; 47:116-22. [PMID: 27318093 DOI: 10.1016/j.leukres.2016.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/13/2016] [Accepted: 05/26/2016] [Indexed: 12/31/2022]
Abstract
Aberrant hypermethylation of tumor suppressor genes is known to play an important role in the development of many tumors, and aberrant DNA hypermethylation was recently identified in hematologic malignancies, where it is thought to hold relevance in leukemogenesis. Here, we report that there are differences in the DNA methylation patterns seen in normal peripheral blood and two T-cell leukemia cell lines. We identify nine genes (CLEC4E, CR1, DBC1, EPO, HAL-DOA, IGF2, IL12B, ITGA1, and LMX1B) that are significantly hypermethylated in T-cell leukemias cell lines, and suggest that aberrant hypermethylation of these normally unmethylated genes may induce their transcriptional and expressional silencing. Furthermore, we observed that the expression levels of DNMT1 and DNMT3a were significantly decreased by 5-aza-2'-deoxycytidine (5-Aza-dC), which is a demethylation agent known to deplete DNA methyltransferases (DNMTs) in leukemia cancer cells and restore the expression levels of their target genes in Jurkat cells. This result suggests that the overexpression of DNMTs could contribute to the development of T-cell leukemias by inducing hypermethylation of the target genes. Together, our results show that aberrant hypermethylation is an important molecular mechanism in the progression of T-cell leukemias, and thus could prove useful as a prognostic and/or diagnostic marker. Moreover, 5-Aza-dC might be a promising candidate for the treatment of T-cell leukemia.
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Affiliation(s)
- Sun Young Kim
- Division of Radiation Effect, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea
| | - Dong-Yeop Shin
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Korea
| | - Sang-Man Kim
- Health Services Management, KH School of Management, Kyung Hee University, Seoul 02453, Korea
| | - Minyoung Lee
- Division of Radiation Effect, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea.
| | - Eun Ju Kim
- Division of Radiation Effect, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Korea; Health Services Management, KH School of Management, Kyung Hee University, Seoul 02453, Korea.
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EZH2 mutations and promoter hypermethylation in childhood acute lymphoblastic leukemia. J Cancer Res Clin Oncol 2016; 142:1641-50. [DOI: 10.1007/s00432-016-2174-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/26/2016] [Indexed: 11/29/2022]
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