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Kirkiz E, Meers O, Grebien F, Buschbeck M. Histone Variants and Their Chaperones in Hematological Malignancies. Hemasphere 2023; 7:e927. [PMID: 37449197 PMCID: PMC10337764 DOI: 10.1097/hs9.0000000000000927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Epigenetic regulation occurs on the level of compacting DNA into chromatin. The functional unit of chromatin is the nucleosome, which consists of DNA wrapped around a core of histone proteins. While canonical histone proteins are incorporated into chromatin through a replication-coupled process, structural variants of histones, commonly named histone variants, are deposited into chromatin in a replication-independent manner. Specific chaperones and chromatin remodelers mediate the locus-specific deposition of histone variants. Although histone variants comprise one of the least understood layers of epigenetic regulation, it has been proposed that they play an essential role in directly regulating gene expression in health and disease. Here, we review the emerging evidence suggesting that histone variants have a role at different stages of hematopoiesis, with a particular focus on the histone variants H2A, H3, and H1. Moreover, we discuss the current knowledge on how the dysregulation of histone variants can contribute to hematopoietic malignancies.
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Affiliation(s)
- Ecem Kirkiz
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Oliver Meers
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
- PhD Programme in Biomedicine, University of Barcelona, Spain
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Marcus Buschbeck
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
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Gao J, Gurbuxani S, Zak T, Kocherginsky M, Ji P, Wehbe F, Chen Q, Chen YH, Lu X, Jennings L, Frankfurt O, Altman J, Sukhanova M. Comparison of myeloid neoplasms with nonclassic 3q26.2/MECOM versus classic inv(3)/t(3;3) rearrangements reveals diverse clinicopathologic features, genetic profiles, and molecular mechanisms of MECOM activation. Genes Chromosomes Cancer 2022; 61:71-80. [PMID: 34668265 DOI: 10.1002/gcc.23004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 11/05/2022] Open
Abstract
MECOM rearrangements are recurrent in myeloid neoplasms and associated with poor prognosis. However, only inv(3)(q21q26.2) and t(3;3)(q21;q26.2), the classic MECOM rearrangements resulting in RPN1-MECOM rearrangement with Mecom overexpression and GATA2 haploinsufficiency, define the distinct subtype of acute myeloid leukemia (AML), and serve as presumptive evidence for myelodysplastic syndrome based on the current World Health Organization classification. Myeloid neoplasms with nonclassic 3q26.2/MECOM rearrangements have been found to be clinically aggressive, but comparative analysis of clinicopathologic and genomic features is limited. We retrospectively studied cohorts of myeloid neoplasms with classic and nonclassic MECOM rearrangements. Cases with classic rearrangements consisted predominantly of AML, often with inv(3) or t(3;3) as the sole chromosome abnormality, whereas the group of nonclassic rearrangements included a variety of myeloid neoplasms, often with complex karyotype without TP53 mutations and similarly dismal overall survival. Immunohistochemistry revealed Mecom protein overexpression in both groups, but overexpression in cases with nonclassic rearrangements was mediated through a mechanism other than GATA2 distal enhancer involvement typical for classic rearrangement. Our results demonstrated that myeloid neoplasms with nonclassic 3q26.2/MECOM rearrangements encompass a diverse group of diseases with poor clinical outcome, overexpression of Mecom protein as a result of the nonclassic mechanism of MECOM activation.
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Affiliation(s)
- Juehua Gao
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sandeep Gurbuxani
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Taylor Zak
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Masha Kocherginsky
- Department of Preventive Medicine (Health and Biomedical Informatics), Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Peng Ji
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Firas Wehbe
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Preventive Medicine (Health and Biomedical Informatics), Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Qing Chen
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Yi-Hua Chen
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xinyan Lu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lawrence Jennings
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Olga Frankfurt
- Department of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jessica Altman
- Department of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Madina Sukhanova
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Nguyen NHK, Wu H, Tan H, Peng J, Rubnitz JE, Cao X, Pounds S, Lamba JK. Global Proteomic Profiling of Pediatric AML: A Pilot Study. Cancers (Basel) 2021; 13:cancers13133161. [PMID: 34202615 PMCID: PMC8268478 DOI: 10.3390/cancers13133161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/14/2021] [Accepted: 06/19/2021] [Indexed: 12/17/2022] Open
Abstract
Acute Myeloid Leukemia (AML) is a heterogeneous disease with several recurrent cytogenetic abnormalities. Despite genomics and transcriptomics profiling efforts to understand AML's heterogeneity, studies focused on the proteomic profiles associated with pediatric AML cytogenetic features remain limited. Furthermore, the majority of biological functions within cells are operated by proteins (i.e., enzymes) and most drugs target the proteome rather than the genome or transcriptome, thus, highlighting the significance of studying proteomics. Here, we present our results from a pilot study investigating global proteomic profiles of leukemic cells obtained at diagnosis from 16 pediatric AML patients using a robust TMT-LC/LC-MS/MS platform. The proteome profiles were compared among patients with or without core binding factor (CBF) translocation indicated by a t(8;21) or inv(16) cytogenetic abnormality, minimal residual disease status at the end of the first cycle of chemotherapy (MRD1), and in vitro chemosensitivity of leukemic cells to cytarabine (Ara-C LC50). Our results established proteomic differences between CBF and non-CBF AML subtypes, providing insights to AML subtypes physiology, and identified potential druggable proteome targets such as THY1 (CD90), NEBL, CTSF, COL2A1, CAT, MGLL (MAGL), MACROH2A2, CLIP2 (isoform 1 and 2), ANPEP (CD13), MMP14, and AK5.
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Affiliation(s)
- Nam H. K. Nguyen
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA;
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (H.W.); (S.P.)
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (H.T.); (J.P.)
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (H.T.); (J.P.)
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jeffrey E. Rubnitz
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Xueyuan Cao
- College of Nursing, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (H.W.); (S.P.)
| | - Jatinder K. Lamba
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA;
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
- Correspondence: ; Tel.: +1-352-273-6425
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The diagnostic and prognostic value of H2AFY in hepatocellular carcinoma. BMC Cancer 2021; 21:418. [PMID: 33858382 PMCID: PMC8051056 DOI: 10.1186/s12885-021-08161-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 04/07/2021] [Indexed: 12/17/2022] Open
Abstract
Background The potential correlation between H2AFY (also known as MacroH2A1) and the clinical characteristics of hepatocellular carcinoma (HCC) patients was analysed through gene expression profiles and clinical data in The Cancer Genome Atlas (TCGA) database, and the diagnostic and prognostic value of H2AFY in HCC was discussed. Methods The gene expression data of HCC and the corresponding clinical characteristics of HCC patients were downloaded from the TCGA database. The differences in H2AFY in normal liver tissues and HCC were analysed. The relationship between H2AFY and clinical characteristics was analysed by Wilcoxon signed-rank test, logistic regression and Kruskal-Wallis test. The Kaplan-Meier method and the Cox regression method were used to analyse the relationship between overall survival and clinical characteristics of the patients. An ROC curve was used to predict the diagnostic value of H2AFY in HCC. Gene set enrichment analysis (GSEA) was used to analyse the pathway enrichment of H2AFY. Result Compared with normal liver tissues, H2AFY was significantly highly expressed in HCC. H2AFY was positively correlated with the age, clinical stage, G stage (grade) and T stage (tumor stage) of liver cancer patients. Higher H2AFY expression predicted a poor prognosis in HCC patients. Cox regression analysis suggested that H2AFY was an independent risk factor for the prognosis of HCC patients. The ROC curve suggested that H2AFY had certain diagnostic value in HCC. GSEA suggested that H2AFY was correlated with lipid metabolism and a variety of tumour pathways. Conclusion Our study showed that H2AFY was significantly overexpressed in HCC. H2AFY may be a potential diagnostic and prognostic marker for HCC, and high expression of H2AFY predicts a poor prognosis in patients with HCC.
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Brenner AK, Aasebø E, Hernandez-Valladares M, Selheim F, Berven F, Grønningsæter IS, Bartaula-Brevik S, Bruserud Ø. The Capacity of Long-Term in Vitro Proliferation of Acute Myeloid Leukemia Cells Supported Only by Exogenous Cytokines Is Associated with a Patient Subset with Adverse Outcome. Cancers (Basel) 2019; 11:cancers11010073. [PMID: 30634713 PMCID: PMC6356272 DOI: 10.3390/cancers11010073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/28/2018] [Accepted: 01/02/2019] [Indexed: 12/15/2022] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive malignancy, which is highly heterogeneous with regard to chemosensitivity and biological features. The AML cell population is organized in a hierarchy that is reflected in the in vitro growth characteristics, with only a minority of cells being able to proliferate for more than two weeks. In this study, we investigated the ability of AML stem cells to survive and proliferate in suspension cultures in the presence of exogenous mediators but without supporting non-leukemic cells. We saw that a high number of maintained stem cells (i.e., a large number of clonogenic cells after five weeks of culture) was associated with decreased overall survival for patients receiving intensive chemotherapy; this prognostic impact was also detected in the multivariate/adjusted analysis. Furthermore, the patients with many clonogenic cells presented more frequently with mutations in transcription-related genes, and also showed a higher abundance of proteins involved in transcription at the time of diagnosis. In conclusion, the growth characteristics of the long-term proliferating leukemic stem cells seem to have an independent prognostic impact in human AML, and these characteristics appear to be reflected by the mutational landscape and the proteome of the patients at the time of diagnosis.
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Affiliation(s)
- Annette K Brenner
- Department of Medicine, Haukeland University Hospital; 5021 Bergen, Norwa.
- Section for Hematology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.
| | - Elise Aasebø
- Section for Hematology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.
- The Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
| | - Maria Hernandez-Valladares
- Section for Hematology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.
- The Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
| | - Frode Selheim
- The Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
| | - Frode Berven
- The Proteomics Unit at the University of Bergen, Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
| | - Ida-Sofie Grønningsæter
- Department of Medicine, Haukeland University Hospital; 5021 Bergen, Norwa.
- Section for Hematology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.
| | - Sushma Bartaula-Brevik
- Section for Hematology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.
| | - Øystein Bruserud
- Department of Medicine, Haukeland University Hospital; 5021 Bergen, Norwa.
- Section for Hematology, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.
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