1
|
Perlman BS, Burget N, Zhou Y, Schwartz GW, Petrovic J, Modrusan Z, Faryabi RB. Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance. Nat Commun 2024; 15:8070. [PMID: 39277592 PMCID: PMC11401928 DOI: 10.1038/s41467-024-52375-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 09/04/2024] [Indexed: 09/17/2024] Open
Abstract
Recent advances in high-resolution mapping of spatial interactions among regulatory elements support the existence of complex topological assemblies of enhancers and promoters known as enhancer-promoter hubs or cliques. Yet, organization principles of these multi-interacting enhancer-promoter hubs and their potential role in regulating gene expression in cancer remain unclear. Here, we systematically identify enhancer-promoter hubs in breast cancer, lymphoma, and leukemia. We find that highly interacting enhancer-promoter hubs form at key oncogenes and lineage-associated transcription factors potentially promoting oncogenesis of these diverse cancer types. Genomic and optical mapping of interactions among enhancer and promoter elements further show that topological alterations in hubs coincide with transcriptional changes underlying acquired resistance to targeted therapy in T cell leukemia and B cell lymphoma. Together, our findings suggest that enhancer-promoter hubs are dynamic and heterogeneous topological assemblies with the potential to control gene expression circuits promoting oncogenesis and drug resistance.
Collapse
Affiliation(s)
- Brent S Perlman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA
| | - Noah Burget
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA
| | - Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA
| | - Gregory W Schwartz
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Jelena Petrovic
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, USA
| | - Zora Modrusan
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, USA.
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA.
| |
Collapse
|
2
|
Nwabo Kamdje AH, Dongmo Fogang HP, Mimche PN. Role of epigenetic in cancer biology, in hematologic malignancies and in anticancer therapy. FRONTIERS IN MOLECULAR MEDICINE 2024; 4:1426454. [PMID: 39308891 PMCID: PMC11412843 DOI: 10.3389/fmmed.2024.1426454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 08/08/2024] [Indexed: 09/25/2024]
Abstract
Major epigenetic changes are associated with carcinogenesis, including aberrant DNA methylations and post-translational modifications of histone. Indeed evidence accumulated in recent years indicates that inactivating DNA hypermethylation preferentially targets the subset of polycomb group (PcG) genes that are regulators of developmental processes. Conversely, activating DNA hypomethylation targets oncogenic signaling pathway genes, but outcomes of both events lead in the overexpression of oncogenic signaling pathways that contribute to the stem-like state of cancer cells. On the basis of recent evidence from population-basedclinical and experimental studies, we hypothesize that factors associated with risk for developing a hematologic malignancy (HM), such as metabolic syndrome and chronic inflammation, may trigger epigenetic mechanisms to increase the transcriptional expression of oncogenes and activate oncogenic signaling pathways. Signaling pathways associated with such risk factors include but are not limited to pro-inflammatory nuclear factor κB (NF-κB) and mitogenic, growth, and survival Janus kinase (JAK) intracellular non-receptor tyrosine kinase-triggered pathways. The latter includes signaling pathways such as transducer and activator of transcription (STAT), Ras GTPases/mitogen-activated protein kinases (MAPKs)/extracellular signal-related kinases (ERKs), phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR), and β-catenin pathways. Recent findings on epigenetic mechanisms at work in the biology of cancer and in HMs and their importance in the etiology and pathogenesis of these diseases are herein summarized and discussed. Furthermore, the role of epigenetic processes in the determination of biological identity, the consequences for interindividual variability in disease clinical profile, and the potential of epigenetic drugs in HMs are also considered.
Collapse
Affiliation(s)
- Armel Hervé Nwabo Kamdje
- Department of Physiological Sciences and Biochemistry, Faculty of Medicine and Biomedical Sciences, University of Garoua, Garoua, Cameroon
| | - Hervet Paulain Dongmo Fogang
- Department of Physiological Sciences and Biochemistry, Faculty of Medicine and Biomedical Sciences, University of Garoua, Garoua, Cameroon
| | - Patrice N. Mimche
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, IN, United States
| |
Collapse
|
3
|
Zhao H, Huang Y, Yang W, Huang C, Ou Z, He J, Yang M, Wu J, Yao H, Yang Y, Yi J, Kong L. Viola yedoensis Makino alleviates lipopolysaccharide-induced intestinal oxidative stress and inflammatory response by regulating the gut microbiota and NF-κB-NLRP3/ Nrf2-MAPK signaling pathway in broiler. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 282:116692. [PMID: 38971097 DOI: 10.1016/j.ecoenv.2024.116692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/29/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Viola yedoensis Makino (Vy) is a well-known traditional Chinese medicine widely used to treat inflammatory diseases. However, the regulatory effects of dietary Vy supplementation on lipopolysaccharide (LPS)-induced intestinal damage in broilers and the underlying molecular mechanisms remain unclear. In this study, broilers were intraperitoneally injected with 1 mg/kg LPS on days 17, 19 and 21 to induce intestinal damage. Vy supplementation at 0.5, 1.5 and 4.5 % in the diet was administered separately for 21 days to investigate the potential protective effects of Vy supplementation against LPS-induced intestinal impairment in broilers. Vy supplementation improved intestinal morphology and restored growth performance. Vy supplementation attenuated intestinal inflammation by regulating the nuclear factor kappa B (NF-κB) / NLR family pyrin domain-containing 3 (NLRP3) signaling pathway and inhibited its downstream pro-inflammatory factor levels. In addition, Vy supplementation relieved intestinal oxidative impairment by regulating the nuclear factor erythroid-2 related factor 2 (Nrf2) / mitogen-activated protein kinase (MAPK) signaling pathway and downstream antioxidant enzyme activity. Vy supplementation reduced LPS-induced mitochondrial damage and apoptosis. Furthermore, Vy supplementation alleviated LPS-induced intestinal inflammation and oxidative damage in chickens by increasing the abundance of protective bacteria (Lactobacillus and Romboutsia) and reducing the number of pathogenic bacteria (unclassified_f_Ruminococcaceae, unclassified_f_Oscillospiraceae and norank_f_norank_o_Clostridia_vadinBB60_group). Overall, Vy supplementation effectively ameliorated LPS-induced intestinal damage by regulating the NF-κB-NLRP3/Nrf2-MAPK signaling pathway and maintaining intestinal microbiota balance. Vy supplementation can be used as a dietary supplement to protect broilers against intestinal inflammation and oxidative damage.
Collapse
Affiliation(s)
- Haoqiang Zhao
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - You Huang
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Wenjiang Yang
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Chunlin Huang
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Zhaoping Ou
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Jiayu He
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Mingqi Yang
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Jiao Wu
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Huan Yao
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Yu Yang
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Jine Yi
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China.
| | - Li Kong
- Hunan Engineering Research Center of Livestock and Poultry Health Care, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China.
| |
Collapse
|
4
|
Perlman BS, Burget N, Zhou Y, Schwartz GW, Petrovic J, Modrusan Z, Faryabi RB. Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601745. [PMID: 39005446 PMCID: PMC11244972 DOI: 10.1101/2024.07.02.601745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Recent advances in high-resolution mapping of spatial interactions among regulatory elements support the existence of complex topological assemblies of enhancers and promoters known as enhancer-promoter hubs or cliques. Yet, organization principles of these multi-interacting enhancer-promoter hubs and their potential role in regulating gene expression in cancer remains unclear. Here, we systematically identified enhancer-promoter hubs in breast cancer, lymphoma, and leukemia. We found that highly interacting enhancer-promoter hubs form at key oncogenes and lineage-associated transcription factors potentially promoting oncogenesis of these diverse cancer types. Genomic and optical mapping of interactions among enhancer and promoter elements further showed that topological alterations in hubs coincide with transcriptional changes underlying acquired resistance to targeted therapy in T cell leukemia and B cell lymphoma. Together, our findings suggest that enhancer-promoter hubs are dynamic and heterogeneous topological assemblies with the potential to control gene expression circuits promoting oncogenesis and drug resistance.
Collapse
|
5
|
Huang W, Zhu Q, Shi Z, Tu Y, Li Q, Zheng W, Yuan Z, Li L, Zu X, Hao Y, Chu B, Jiang Y. Dual inhibitors of DNMT and HDAC induce viral mimicry to induce antitumour immunity in breast cancer. Cell Death Discov 2024; 10:143. [PMID: 38490978 PMCID: PMC10943227 DOI: 10.1038/s41420-024-01895-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
The existing conventional treatments for breast cancer, including immune checkpoint blockade, exhibit limited effects in some cancers, particularly triple-negative breast cancer. Epigenetic alterations, specifically DNMT and HDAC alterations, are implicated in breast cancer pathogenesis. We demonstrated that DNMTs and HDACs are overexpressed and positively correlated in breast cancer. The combination of DNMT and HDAC inhibitors has shown synergistic antitumour effects, and our previously designed dual DNMT and HDAC inhibitor (termed DNMT/HDACi) 15a potently inhibits breast cancer cell proliferation, migration, and invasion and induces apoptosis in vitro and in vivo. Mechanistically, 15a induces a viral mimicry response by promoting the expression of endogenous retroviral elements in breast cancer cells, thus increasing the intracellular level of double-stranded RNA to activate the RIG-I-MAVS pathway. This in turn promotes the production of interferons and chemokines and augments the expression of interferon-stimulated genes and PD-L1. The combination of 15a and an anti-PD-L1 antibody had an additive effect in vivo. These findings indicate that this DNMT/HDACi has immunomodulatory functions and enhances the effectiveness of immune checkpoint blockade therapy. A novel dual DNMT and HDAC inhibitor induces viral mimicry, which induces the accumulation of dsRNA to activate tumoral IFN signalling and cytokine production to enhance the immune response in breast cancer.
Collapse
Affiliation(s)
- Wenjun Huang
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Qingyun Zhu
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
- The First Affiliated Hospital, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Zhichao Shi
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Yao Tu
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Qinyuan Li
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China
| | - Wenwen Zheng
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Zigao Yuan
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China
| | - Lulu Li
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China
| | - Xuyu Zu
- The First Affiliated Hospital, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Yue Hao
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China.
| | - Bizhu Chu
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China.
| | - Yuyang Jiang
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China.
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China.
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
6
|
Abstract
Evidence implicating Eph receptor tyrosine kinases and their ephrin ligands (that together make up the 'Eph system') in cancer development and progression has been accumulating since the discovery of the first Eph receptor approximately 35 years ago. Advances in the past decade and a half have considerably increased the understanding of Eph receptor-ephrin signalling mechanisms in cancer and have uncovered intriguing new roles in cancer progression and drug resistance. This Review focuses mainly on these more recent developments. I provide an update on the different mechanisms of Eph receptor-ephrin-mediated cell-cell communication and cell autonomous signalling, as well as on the interplay of the Eph system with other signalling systems. I further discuss recent advances in elucidating how the Eph system controls tumour expansion, invasiveness and metastasis, supports cancer stem cells, and drives therapy resistance. In addition to functioning within cancer cells, the Eph system also mediates the reciprocal communication between cancer cells and cells of the tumour microenvironment. The involvement of the Eph system in tumour angiogenesis is well established, but recent findings also demonstrate roles in immune cells, cancer-associated fibroblasts and the extracellular matrix. Lastly, I discuss strategies under evaluation for therapeutic targeting of Eph receptors-ephrins in cancer and conclude with an outlook on promising future research directions.
Collapse
Affiliation(s)
- Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
| |
Collapse
|
7
|
Stergiou IE, Papadakos SP, Karyda A, Tsitsilonis OE, Dimopoulos MA, Theocharis S. EPH/Ephrin Signaling in Normal Hematopoiesis and Hematologic Malignancies: Deciphering Their Intricate Role and Unraveling Possible New Therapeutic Targets. Cancers (Basel) 2023; 15:3963. [PMID: 37568780 PMCID: PMC10417178 DOI: 10.3390/cancers15153963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Erythropoietin-producing hepatocellular carcinoma receptors (EPHs) represent the largest family of receptor tyrosine kinases (RTKs). EPH interaction with ephrins, their membrane-bound ligands, holds a pivotal role in embryonic development, while, though less active, it is also implicated in various physiological functions during adult life. In normal hematopoiesis, different patterns of EPH/ephrin expression have been correlated with hematopoietic stem cell (HSC) maintenance and lineage-committed hematopoietic progenitor cell (HPC) differentiation, as well as with the functional properties of their mature offspring. Research in the field of hematologic malignancies has unveiled a rather complex involvement of the EPH/ephrinsignaling pathway in the pathophysiology of these neoplasms. Aberrations in genetic, epigenetic, and protein levels have been identified as possible players implicated both in tumor progression and suppression, while correlations have also been highlighted regarding prognosis and response to treatment. Initial efforts to therapeutically target the EPH/ephrin axis have been undertaken in the setting of hematologic neoplasia but are mainly confined to the preclinical level. To this end, deciphering the complexity of this signaling pathway both in normal and malignant hematopoiesis is necessary.
Collapse
Affiliation(s)
- Ioanna E. Stergiou
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Stavros P. Papadakos
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.P.P.); (A.K.)
| | - Anna Karyda
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.P.P.); (A.K.)
| | - Ourania E. Tsitsilonis
- Flow Cytometry Unit, Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece;
| | - Meletios-Athanasios Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Alexandra Hospital, 11528 Athens, Greece
| | - Stamatios Theocharis
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.P.P.); (A.K.)
| |
Collapse
|
8
|
Schelker RC, Kratzer A, Müller G, Brochhausen C, Hart C, Stempfl T, Heudobler D, Moehle C, Herr W, Iberl S, Grassinger J. Stanniocalcin 1 is overexpressed in multipotent mesenchymal stromal cells from acute myeloid leukemia patients. ACTA ACUST UNITED AC 2021; 26:565-576. [PMID: 34384344 DOI: 10.1080/16078454.2021.1962048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Objectives: Multipotent mesenchymal stromal cells (MSC) play a pivotal role in the bone marrow (BM) niche. Stanniocalcin 1 (STC1) secreted by MSC has been demonstrated to promote the survival of neoplastic cells and was suggested a marker for minimal residual disease of acute myeloid leukemia (AML). Therefore, we evaluated the expression of STC1 in MSC from AML patients (MSCAML) compared to MSC from healthy donors (MSCHD).Methods: Liquid culture assays of MSCAML and MSCHD were performed to compare expansion capacity. Gene expression profiles of MSCAML vs. MSCHD were established. Secretion of STC1 was tested by ELISA in MSCAML vs. MSCHD and expression of STC1 in AML- vs. HD-BM by immunohistochemistry. In addition, co-cultures of AML cells on MSC were initiated and ultrastructural intercellular communication patterns were investigated. Finally, the effect of blocking STC1 on AML cells was evaluated.Results: MSCAML showed significant decreased expansion capacity compared to MSCHD. Gene analysis revealed marked overexpression of STC1 in MSCAML. ELISA and immunohistochemical findings confirmed this observation. Electron microscopy analysis showed reciprocal stimulation between AML cells and MSC. Blockade of STC1 did not significantly affect AML cell proliferation and apoptosis.Discussion: Characteristics of MSC differ depending on whether they originate from AML patients or from HD. STC1 was mostly overexpressed in MSCAML compared to MSCHD. In vitro blockade of STC1, however, was not associated with AML cell proliferation and apoptosis.Conclusion: Differences in expression levels of glycoproteins from MSCAML compared to MSCHD not necessarily assume that these molecules are niche-relevant in leukemic disease.
Collapse
Affiliation(s)
- Roland Christian Schelker
- Department of Internal Medicine III, Hematology & Oncology, University Hospital of Regensburg, Regensburg, Germany
| | - Andrea Kratzer
- Department of Internal Medicine III, Hematology & Oncology, University Hospital of Regensburg, Regensburg, Germany
| | - Gunnar Müller
- Department of Internal Medicine III, Hematology & Oncology, University Hospital of Regensburg, Regensburg, Germany
| | | | - Christina Hart
- Department of Internal Medicine III, Hematology & Oncology, University Hospital of Regensburg, Regensburg, Germany
| | - Thomas Stempfl
- Center of Excellence for Fluorescent Bioanalytics (KFB), University of Regensburg, Regensburg, Germany
| | - Daniel Heudobler
- Department of Internal Medicine III, Hematology & Oncology, University Hospital of Regensburg, Regensburg, Germany
| | - Christoph Moehle
- Center of Excellence for Fluorescent Bioanalytics (KFB), University of Regensburg, Regensburg, Germany
| | - Wolfgang Herr
- Department of Internal Medicine III, Hematology & Oncology, University Hospital of Regensburg, Regensburg, Germany
| | - Sabine Iberl
- Department of Internal Medicine III, Hematology & Oncology, University Hospital of Regensburg, Regensburg, Germany
| | - Jochen Grassinger
- Department of Internal Medicine III, Hematology & Oncology, University Hospital of Regensburg, Regensburg, Germany.,St. Elisabeth Hospital, Straubing, Germany
| |
Collapse
|
9
|
Sun G, Shvab A, Leclerc GJ, Li B, Beckedorff F, Shiekhattar R, Barredo JC. Protein Kinase D-Dependent Downregulation of Immediate Early Genes through Class IIA Histone Deacetylases in Acute Lymphoblastic Leukemia. Mol Cancer Res 2021; 19:1296-1307. [PMID: 33980612 DOI: 10.1158/1541-7786.mcr-20-0808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/12/2021] [Accepted: 05/04/2021] [Indexed: 11/16/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a leading cause of cancer-related death in children and adolescents, and cure rates for relapsed/refractory ALL remain dismal, highlighting the need for novel targeted therapies. To identify genome-wide metabolic-stress regulated genes, we used RNA-sequencing in ALL cells treated with AICAR, an AMPK activator. RNA-sequencing identified the immediate early genes (IEGs) as a subset of genes downregulated by AICAR. We show that AICAR-induced IEGs downregulation was blocked by an adenosine uptake inhibitor indicating AICAR was responsible for IEGs reprogramming. Using pharmacologic and genetic models we established this mechanism was AMPK-independent. Further investigations using kinase assays, PKD/PKC inhibitors and rescue experiments, demonstrated that AICAR directly inhibited PKD kinase activity and identified PKD as responsible for IEGs downregulation. Mechanistically, PKD inhibition suppressed phosphorylation and nuclear export of class IIa HDACs, which lowered histone H3 acetylation and decreased NFκB(p65) recruitment to IEGs promoters. Finally, PKD inhibition induced apoptosis via DUSP1/DUSP6 downregulation eliciting a DNA damage response. More importantly, ALL patient cells exhibited the same PKD-HDACs-IEGs-mediated mechanism. As proof of principle of the therapeutic potential of targeting PKD, we established the in vivo relevance of our findings using an NSG ALL mouse model. In conclusion, we identified a previously unreported PKD-dependent survival mechanism in response to AICAR-induced cellular stress in ALL through regulation of DUSPs and IEGs' expression. IMPLICATIONS: PKD mediates early transcriptional responses in ALL cells as an adaptive survival mechanism to overcome cellular stress.
Collapse
Affiliation(s)
- Guangyan Sun
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, Florida
| | - Anna Shvab
- Cancer Biology Program, University of Miami Miller School of Medicine, Miami, Florida
| | - Guy J Leclerc
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, Florida
| | - Bin Li
- Stemsynergy Therapeutics, Inc, Miami, Florida
| | - Felipe Beckedorff
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Ramin Shiekhattar
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Julio C Barredo
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, Florida. .,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida.,Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| |
Collapse
|
10
|
Southekal S, Mishra NK, Guda C. Pan-Cancer Analysis of Human Kinome Gene Expression and Promoter DNA Methylation Identifies Dark Kinase Biomarkers in Multiple Cancers. Cancers (Basel) 2021; 13:cancers13061189. [PMID: 33801837 PMCID: PMC8001681 DOI: 10.3390/cancers13061189] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022] Open
Abstract
Kinases are a group of intracellular signaling molecules that play critical roles in various biological processes. Even though kinases comprise one of the most well-known therapeutic targets, many have been understudied and therefore warrant further investigation. DNA methylation is one of the key epigenetic regulators that modulate gene expression. In this study, the human kinome's DNA methylation and gene expression patterns were analyzed using the level-3 TCGA data for 32 cancers. Unsupervised clustering based on kinome data revealed the grouping of cancers based on their organ level and tissue type. We further observed significant differences in overall kinase methylation levels (hyper- and hypomethylation) between the tumor and adjacent normal samples from the same tissue. Methylation expression quantitative trait loci (meQTL) analysis using kinase gene expression with the corresponding methylated probes revealed a highly significant and mostly negative association (~92%) within 1.5 kb from the transcription start site (TSS). Several understudied (dark) kinases (PKMYT1, PNCK, BRSK2, ERN2, STK31, STK32A, and MAPK4) were also identified with a significant role in patient survival. This study leverages results from multi-omics data to identify potential kinase markers of prognostic and diagnostic importance and further our understanding of kinases in cancer.
Collapse
Affiliation(s)
| | | | - Chittibabu Guda
- Correspondence: (N.K.M.); (C.G.); Tel.: +1-402-559-5954 (C.G.)
| |
Collapse
|
11
|
K. Bhanumathy K, Balagopal A, Vizeacoumar FS, Vizeacoumar FJ, Freywald A, Giambra V. Protein Tyrosine Kinases: Their Roles and Their Targeting in Leukemia. Cancers (Basel) 2021; 13:cancers13020184. [PMID: 33430292 PMCID: PMC7825731 DOI: 10.3390/cancers13020184] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Protein phosphorylation is a key regulatory mechanism that controls a wide variety of cellular responses. This process is catalysed by the members of the protein kinase superfamily that are classified into two main families based on their ability to phosphorylate either tyrosine or serine and threonine residues in their substrates. Massive research efforts have been invested in dissecting the functions of tyrosine kinases, revealing their importance in the initiation and progression of human malignancies. Based on these investigations, numerous tyrosine kinase inhibitors have been included in clinical protocols and proved to be effective in targeted therapies for various haematological malignancies. In this review, we provide insights into the role of tyrosine kinases in leukaemia and discuss their targeting for therapeutic purposes with the currently available inhibitory compounds. Abstract Protein kinases constitute a large group of enzymes catalysing protein phosphorylation and controlling multiple signalling events. The human protein kinase superfamily consists of 518 members and represents a complicated system with intricate internal and external interactions. Protein kinases are classified into two main families based on the ability to phosphorylate either tyrosine or serine and threonine residues. Among the 90 tyrosine kinase genes, 58 are receptor types classified into 20 groups and 32 are of the nonreceptor types distributed into 10 groups. Tyrosine kinases execute their biological functions by controlling a variety of cellular responses, such as cell division, metabolism, migration, cell–cell and cell matrix adhesion, cell survival and apoptosis. Over the last 30 years, a major focus of research has been directed towards cancer-associated tyrosine kinases owing to their critical contributions to the development and aggressiveness of human malignancies through the pathological effects on cell behaviour. Leukaemia represents a heterogeneous group of haematological malignancies, characterised by an uncontrolled proliferation of undifferentiated hematopoietic cells or leukaemia blasts, mostly derived from bone marrow. They are usually classified as chronic or acute, depending on the rates of their progression, as well as myeloid or lymphoblastic, according to the type of blood cells involved. Overall, these malignancies are relatively common amongst both children and adults. In malignant haematopoiesis, multiple tyrosine kinases of both receptor and nonreceptor types, including AXL receptor tyrosine kinase (AXL), Discoidin domain receptor 1 (DDR1), Vascular endothelial growth factor receptor (VEGFR), Fibroblast growth factor receptor (FGFR), Mesenchymal–epithelial transition factor (MET), proto-oncogene c-Src (SRC), Spleen tyrosine kinase (SYK) and pro-oncogenic Abelson tyrosine-protein kinase 1 (ABL1) mutants, are implicated in the pathogenesis and drug resistance of practically all types of leukaemia. The role of ABL1 kinase mutants and their therapeutic inhibitors have been extensively analysed in scientific literature, and therefore, in this review, we provide insights into the impact and mechanism of action of other tyrosine kinases involved in the development and progression of human leukaemia and discuss the currently available and emerging treatment options based on targeting these molecules.
Collapse
Affiliation(s)
- Kalpana K. Bhanumathy
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (A.B.); (F.J.V.)
- Correspondence: (K.K.B.); (V.G.); Tel.: +1-(306)-716-7456 (K.K.B.); +39-0882-416574 (V.G.)
| | - Amrutha Balagopal
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (A.B.); (F.J.V.)
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (F.S.V.); (A.F.)
| | - Franco J. Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (A.B.); (F.J.V.)
- Cancer Research Department, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (F.S.V.); (A.F.)
| | - Vincenzo Giambra
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, FG, Italy
- Correspondence: (K.K.B.); (V.G.); Tel.: +1-(306)-716-7456 (K.K.B.); +39-0882-416574 (V.G.)
| |
Collapse
|
12
|
Hamraz M, Gul N, Raza M, Khan DM, Khalil U, Zubair S, Khan Z. Robust proportional overlapping analysis for feature selection in binary classification within functional genomic experiments. PeerJ Comput Sci 2021; 7:e562. [PMID: 34141889 PMCID: PMC8176540 DOI: 10.7717/peerj-cs.562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/04/2021] [Indexed: 05/10/2023]
Abstract
In this paper, a novel feature selection method called Robust Proportional Overlapping Score (RPOS), for microarray gene expression datasets has been proposed, by utilizing the robust measure of dispersion, i.e., Median Absolute Deviation (MAD). This method robustly identifies the most discriminative genes by considering the overlapping scores of the gene expression values for binary class problems. Genes with a high degree of overlap between classes are discarded and the ones that discriminate between the classes are selected. The results of the proposed method are compared with five state-of-the-art gene selection methods based on classification error, Brier score, and sensitivity, by considering eleven gene expression datasets. Classification of observations for different sets of selected genes by the proposed method is carried out by three different classifiers, i.e., random forest, k-nearest neighbors (k-NN), and support vector machine (SVM). Box-plots and stability scores of the results are also shown in this paper. The results reveal that in most of the cases the proposed method outperforms the other methods.
Collapse
Affiliation(s)
- Muhammad Hamraz
- Department of Statistics, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Naz Gul
- Department of Statistics, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mushtaq Raza
- Department of Computer Sciences, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Dost Muhammad Khan
- Department of Statistics, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Umair Khalil
- Department of Statistics, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Seema Zubair
- Department of Mathematics, Statistics and Computer Science, University of Agriculture Peshawar, Peshawar, Pakistan
| | - Zardad Khan
- Department of Statistics, Abdul Wali Khan University Mardan, Mardan, Pakistan
| |
Collapse
|
13
|
Ricci B, Millner TO, Pomella N, Zhang X, Guglielmi L, Badodi S, Ceric D, Gemma C, Cognolato E, Zhang Y, Brandner S, Barnes MR, Marino S. Polycomb-mediated repression of EphrinA5 promotes growth and invasion of glioblastoma. Oncogene 2020; 39:2523-2538. [PMID: 31988455 PMCID: PMC7082224 DOI: 10.1038/s41388-020-1161-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 11/22/2022]
Abstract
Glioblastoma (GBM) is the most common and most aggressive intrinsic brain tumour in adults. Integrated transcriptomic and epigenomic analyses of glioblastoma initiating cells (GIC) in a mouse model uncovered a novel epigenetic regulation of EfnA5. In this model, Bmi1 enhances H3K27me3 at the EfnA5 locus and reinforces repression of selected target genes in a cellular context-dependent fashion. EfnA5 mediates Bmi1-dependent proliferation and invasion in vitro and tumour formation in an allograft model. Importantly, we show that this novel Polycomb feed-forward loop is also active in human GIC and we provide pre-clinical evidence of druggability of the EFNA5 signalling pathway in GBM xenografts overexpressing Bmi1.
Collapse
Affiliation(s)
- Barbara Ricci
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Thomas O Millner
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Nicola Pomella
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Xinyu Zhang
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Loredana Guglielmi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Sara Badodi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Dario Ceric
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Carolina Gemma
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Erica Cognolato
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Ying Zhang
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, WC1N 3BG, UK
| | - Sebastian Brandner
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, WC1N 3BG, UK
| | - Michael R Barnes
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Silvia Marino
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
| |
Collapse
|
14
|
Darling TK, Lamb TJ. Emerging Roles for Eph Receptors and Ephrin Ligands in Immunity. Front Immunol 2019; 10:1473. [PMID: 31333644 PMCID: PMC6620610 DOI: 10.3389/fimmu.2019.01473] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/13/2019] [Indexed: 12/30/2022] Open
Abstract
Eph receptors are the largest family of receptor tyrosine kinases and mediate a myriad of essential processes in humans from embryonic development to adult tissue homeostasis through interactions with membrane-bound ephrin ligands. The ubiquitous expression of Eph receptors and ephrin ligands among the cellular players of the immune system underscores the importance of these molecules in orchestrating an optimal immune response. This review provides an overview of the various roles of Eph receptors and ephrin ligands in immune cell development, activation, and migration. We also discuss the role of Eph receptors in disease pathogenesis as well as the implications of Eph receptors as future immunotherapy targets. Given the diverse and critical roles of Eph receptors and ephrin ligands throughout the immune system during both resting and activated states, this review aims to highlight the critical yet underappreciated roles of this family of signaling molecules in the immune system.
Collapse
Affiliation(s)
- Thayer K Darling
- Immunology and Molecular Pathogenesis Program, Emory University Laney Graduate School, Atlanta, GA, United States.,Department of Pathology, University of Utah, Salt Lake City, UT, United States
| | - Tracey J Lamb
- Department of Pathology, University of Utah, Salt Lake City, UT, United States
| |
Collapse
|
15
|
Misra A, Chakrabarti SS, Gambhir IS. New genetic players in late-onset Alzheimer's disease: Findings of genome-wide association studies. Indian J Med Res 2019; 148:135-144. [PMID: 30381536 PMCID: PMC6206761 DOI: 10.4103/ijmr.ijmr_473_17] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Late-onset Alzheimer's disease (LOAD) or sporadic AD is the most common form of AD. The precise pathogenetic changes that trigger the development of AD remain largely unknown. Large-scale genome-wide association studies (GWASs) have identified single-nucleotide polymorphisms in multiple genes which are associated with AD; most notably, these are ABCA7, bridging integrator 1(B1N1), triggering receptor expressed on myeloid cells 2 (TREM2), CD33, clusterin (CLU), complement receptor 1 (CRI), ephrin type-A receptor 1 (EPHA1), membrane-spanning 4-domains, subfamily A (MS4A) and phosphatidylinositol binding clathrin assembly protein (PICALM) genes. The proteins coded by the candidate genes participate in a variety of cellular processes such as oxidative balance, protein metabolism, cholesterol metabolism and synaptic function. This review summarizes the major gene loci affecting LOAD identified by large GWASs. Tentative mechanisms have also been elaborated in various studies by which the proteins coded by these genes may exert a role in AD pathogenesis have also been elaborated. The review suggests that these may together affect LOAD pathogenesis in a complementary fashion.
Collapse
Affiliation(s)
- Anamika Misra
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | | | - Indrajeet Singh Gambhir
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| |
Collapse
|
16
|
Fecková B, Kimáková P, Ilkovičová L, Szentpéteriová E, Macejová M, Košuth J, Zulli A, Debeljak N, Hudler P, Jašek K, Kašubová I, Kubatka P, Solár P. Methylation of the first exon in the erythropoietin receptor gene does not correlate with its mRNA and protein level in cancer cells. BMC Genet 2019; 20:1. [PMID: 30606107 PMCID: PMC6318971 DOI: 10.1186/s12863-018-0706-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/13/2018] [Indexed: 01/13/2023] Open
Abstract
Background Erythropoietin receptor (EPOR) is a functional membrane-bound cytokine receptor. Erythropoietin (EPO) represents an important hematopoietic factor for production, maturation and differentiation of erythroid progenitors. In non-hematopoietic tissue, EPO/EPOR signalization could also play cytoprotective and anti-apoptotic role. Several studies identified pro-stimulating EPO/EPOR effects in tumor cells; however, numerous studies opposed this fact due to the usage of unspecific EPOR antibodies and thus potential absence or very low levels of EPOR in tumor cells. It seems that this problem is more complex and therefore we have decided to focus on EPOR expression at several levels such as the role of methylation in the regulation of EPOR expression, identification of possible EPOR transcripts and the presence of EPOR protein in selected tumor cells. Methods Methylation status was analysed by bisulfite conversion reaction, PCR and sequencing. The expression of EPOR was monitored by quantitative RT-PCR and western blot analysis. Results In this study we investigated the methylation status of exon 1 of EPOR gene in selected human cancer cell lines. Our results indicated that CpGs methylation in exon 1 do not play a significant role in the regulation of EPOR transcription. However, methylation status of EPOR exon 1 was cell type dependent. We also observed the existence of two EPOR splice variants in human ovarian adenocarcinoma cell line - A2780 and confirmed the expression of EPOR protein in these cells using specific A82 anti-EPOR antibody. Conclusion We outlined the methylation status of all selected cancer cell lines in exon 1 of EPOR gene and these results could benefit future investigations. Moreover, A82 antibody confirmed our previous results demonstrating the presence of functional EPOR in human ovarian adenocarcinoma A2780 cells.
Collapse
Affiliation(s)
- Barbora Fecková
- Department of Cell Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, SK-04154, Košice, Slovak Republic
| | - Patrícia Kimáková
- Department of Cell Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, SK-04154, Košice, Slovak Republic
| | - Lenka Ilkovičová
- Department of Cell Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, SK-04154, Košice, Slovak Republic
| | - Erika Szentpéteriová
- Department of Cell Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, SK-04154, Košice, Slovak Republic
| | - Mária Macejová
- Department of Cell Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, SK-04154, Košice, Slovak Republic
| | - Ján Košuth
- Department of Cell Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, SK-04154, Košice, Slovak Republic
| | - Anthony Zulli
- Centre for Chronic Disease, College of Health & Biomedicine, Victoria University, Melbourne, Victoria, Australia
| | - Nataša Debeljak
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, SI1000, Ljubljana, Slovenia
| | - Petra Hudler
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, SI1000, Ljubljana, Slovenia
| | - Karin Jašek
- Biomedical Centre Martin, Division of Oncology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, SK03601, Martin, Slovak Republic
| | - Ivana Kašubová
- Biomedical Centre Martin, Division of Oncology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, SK03601, Martin, Slovak Republic
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, SK03601, Martin, Slovak Republic.,Department of Experimental Carcinogenesis, Biomedical Centre Martin, Division of Oncology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, SK03601, Martin, Slovak Republic
| | - Peter Solár
- Department of Cell Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, SK-04154, Košice, Slovak Republic. .,Institute of Medical Biology, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, SK04011, Košice, Slovak Republic.
| |
Collapse
|
17
|
Ibáñez M, Carbonell-Caballero J, Such E, García-Alonso L, Liquori A, López-Pavía M, Llop M, Alonso C, Barragán E, Gómez-Seguí I, Neef A, Hervás D, Montesinos P, Sanz G, Sanz MA, Dopazo J, Cervera J. The modular network structure of the mutational landscape of Acute Myeloid Leukemia. PLoS One 2018; 13:e0202926. [PMID: 30303964 PMCID: PMC6179200 DOI: 10.1371/journal.pone.0202926] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is associated with the sequential accumulation of acquired genetic alterations. Although at diagnosis cytogenetic alterations are frequent in AML, roughly 50% of patients present an apparently normal karyotype (NK), leading to a highly heterogeneous prognosis. Due to this significant heterogeneity, it has been suggested that different molecular mechanisms may trigger the disease with diverse prognostic implications. We performed whole-exome sequencing (WES) of tumor-normal matched samples of de novo AML-NK patients lacking mutations in NPM1, CEBPA or FLT3-ITD to identify new gene mutations with potential prognostic and therapeutic relevance to patients with AML. Novel candidate-genes, together with others previously described, were targeted resequenced in an independent cohort of 100 de novo AML patients classified in the cytogenetic intermediate-risk (IR) category. A mean of 4.89 mutations per sample were detected in 73 genes, 35 of which were mutated in more than one patient. After a network enrichment analysis, we defined a single in silico model and established a set of seed-genes that may trigger leukemogenesis in patients with normal karyotype. The high heterogeneity of gene mutations observed in AML patients suggested that a specific alteration could not be as essential as the interaction of deregulated pathways.
Collapse
Affiliation(s)
- Mariam Ibáñez
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, Valencia, Spain
| | - José Carbonell-Caballero
- ProCURE, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Spain
| | - Esperanza Such
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
| | - Luz García-Alonso
- European Molecular Biology Laboratory—European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Alessandro Liquori
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
| | - María López-Pavía
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Marta Llop
- Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
- Department of Medical Pathology, Hospital Universitario La Fe, Valencia, Spain
| | - Carmen Alonso
- Hematology Service, Hospital Arnau de Villanoba, Valencia, Spain
| | - Eva Barragán
- Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
- Department of Medical Pathology, Hospital Universitario La Fe, Valencia, Spain
| | - Inés Gómez-Seguí
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
| | - Alexander Neef
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | | | - Pau Montesinos
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
| | - Guillermo Sanz
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
| | - Miguel Angel Sanz
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
| | - Joaquín Dopazo
- Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, Valencia, Spain
- Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla, Spain
- * E-mail: (JC); (JD)
| | - José Cervera
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
- Genetics Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- * E-mail: (JC); (JD)
| |
Collapse
|
18
|
Genomic Profile and Pathologic Features of Diffuse Large B-Cell Lymphoma Subtype of Methotrexate-associated Lymphoproliferative Disorder in Rheumatoid Arthritis Patients. Am J Surg Pathol 2018; 42:936-950. [DOI: 10.1097/pas.0000000000001071] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
19
|
|
20
|
Liu X, Wang Y, Sun L, Min J, Liu J, Chen D, Zhang H, Zhang H, Zhang H, Zhou Y, Liu L. Long noncoding RNA BC005927 upregulates EPHB4 and promotes gastric cancer metastasis under hypoxia. Cancer Sci 2018; 109:988-1000. [PMID: 29383777 PMCID: PMC5891181 DOI: 10.1111/cas.13519] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/10/2018] [Accepted: 01/22/2018] [Indexed: 01/03/2023] Open
Abstract
Hypoxia plays a critical role in the metastasis of gastric cancer (GC), yet the underlying mechanism remains largely unclear. It is also not known whether long, noncoding RNAs (lncRNAs) are involved in the contribution of hypoxia to GC metastasis. In the present study, we found that lncRNA BC005927 can be induced by hypoxia in GC cells and mediates hypoxia-induced GC cell metastasis. Furthermore, BC005927 is frequently upregulated in GC samples and increased BC005927 expression was correlated with a higher tumor-node-metastasis stage. GC patients with higher BC005927 expression had poorer prognoses than those with lower expression. Additional experiments showed that BC005927 expression is induced by hypoxia inducible factor-1 alpha (HIF-1α); ChIP assay and luciferase reporter assays confirmed that this lncRNA is a direct transcriptional target of HIF-1α. Next, we found that EPHB4, a metastasis-related gene, is regulated by BC005927 and that the expression of EPHB4 was positively correlated with that of BC005927 in the clinical GC samples assessed. Intriguingly, EPHB4 expression was also increased under hypoxia, and its upregulation by BC005927 resulted in hypoxia-induced GC cell metastasis. These results advance the current understanding of the role of BC005927 in the regulation of hypoxia signaling and offer new avenues for the development of therapeutic interventions against cancer progression.
Collapse
Affiliation(s)
- Xiangqiang Liu
- Department of Oncology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.,Department of Gastroenterology, Guangzhou General Hospital of the Guangzhou Military Command of the PLA, Guangzhou, China
| | - Yafang Wang
- Department of Oncology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Li Sun
- State Key Laboratory of Cancer Biology & Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Jie Min
- Department of Oncology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Jiaming Liu
- State Key Laboratory of Cancer Biology & Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Di Chen
- State Key Laboratory of Cancer Biology & Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Hongbo Zhang
- State Key Laboratory of Cancer Biology & Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Hongwei Zhang
- State Key Laboratory of Cancer Biology & Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Helong Zhang
- Department of Oncology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yongan Zhou
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Lili Liu
- Department of Oncology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| |
Collapse
|
21
|
The putative tumor suppressor gene EphA7 is a novel BMI-1 target. Oncotarget 2018; 7:58203-58217. [PMID: 27533460 PMCID: PMC5295425 DOI: 10.18632/oncotarget.11279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/08/2016] [Indexed: 11/25/2022] Open
Abstract
Bmi1 was originally identified as a gene that contributes to the development of mouse lymphoma by inhibiting MYC-induced apoptosis through repression of Ink4a and Arf. It codes for the Polycomb group protein BMI-1 and acts primarily as a transcriptional repressor via chromatin modifications. Although it binds to a large number of genomic regions, the direct BMI-1 target genes described so far do not explain the full spectrum of BMI-1-mediated effects. Here we identify the putative tumor suppressor gene EphA7 as a novel direct BMI-1 target in neural cells and lymphocytes. EphA7 silencing has been reported in several different human tumor types including lymphomas, and our data suggest BMI1 overexpression as a novel mechanism leading to EphA7 inactivation via H3K27 trimethylation and DNA methylation.
Collapse
|
22
|
Liu X, Xu Y, Jin Q, Wang W, Zhang S, Wang X, Zhang Y, Xu X, Huang J. EphA8 is a prognostic marker for epithelial ovarian cancer. Oncotarget 2018; 7:20801-9. [PMID: 26989075 PMCID: PMC4991493 DOI: 10.18632/oncotarget.8018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/15/2016] [Indexed: 01/11/2023] Open
Abstract
EphA8 is one of the Eph receptors in the Eph/ephrin receptor tyrosine kinase (RTK) subfamily. During tumorigenesis, EphA8 is involved in angiogenesis, cell adhesion and migration. In this study, we determined the mRNA and protein expression levels of EphA8 in cancerous and normal ovarian tissue samples by quantitative reverse transcription PCR (qRT-PCR) (N = 60) and tissue microarray immunohistochemistry analysis (TMA-IHC) (N = 223) respectively. EphA8 protein levels in cancer tissues were correlated with epithelial ovarian cancer (EOC) patients’ clinical characteristics and overall survival. Both EphA8 mRNA and protein levels were significantly higher in EOC tissues than in normal or benign ovarian tissues (all P < 0.05). High EphA8 protein level was associated older age at diagnosis, higher FIGO stage, positive lymph nodes, presence of metastasis, positive ascitic fluid, and higher serum CA-125 level. High EphA8 protein level is an independent prognostic marker in EOC. We conclude that EphA8 acts as an oncogene in EOC development and progression. Detection of EphA8 expression could be a useful prognosis marker and targeting EphA8 represents a novel strategy for EOC treatment.
Collapse
Affiliation(s)
- Xiaoqin Liu
- Department of Nursing, Nantong University, Nantong 226001, Jiangsu, China
| | - Yunzhao Xu
- Department of Obstetrics and Gynecology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| | - Qin Jin
- Department of Pathology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| | - Wei Wang
- Department of Pathology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| | - Shu Zhang
- Department of Pathology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| | - Xudong Wang
- Department of Laboratory Medicine, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| | - Yuquan Zhang
- Department of Obstetrics and Gynecology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| | - Xujuan Xu
- Department of Nursing, Nantong University, Nantong 226001, Jiangsu, China
| | - Jianfei Huang
- Department of Pathology, Nantong University Affiliated Hospital, Nantong 226001, Jiangsu, China
| |
Collapse
|
23
|
Li Y, Wang H, Chen X, Mai H, Li C, Wen F. Aberrant EPHB4 gene methylation and childhood acute lymphoblastic leukemia. Oncol Lett 2017; 14:4433-4440. [PMID: 29085439 PMCID: PMC5649587 DOI: 10.3892/ol.2017.6755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/06/2016] [Indexed: 11/22/2022] Open
Abstract
The present study aimed to investigate the association between aberrant DNA methylation of the promoter region of the ephrin type-B receptor 4 (EPHB4) gene and the development of childhood acute lymphoblastic leukemia (ALL). Bisulfite sequencing polymerase chain reaction (BSP) was performed to determine the methylation density of cytosine-guanine pair islands in the promoter region of EPHB4, in bone marrow samples from 40 children with ALL. The mRNA and protein expression levels of EPHB4 were detected using reverse transcription-quantitative polymerase chain reaction and western blot analysis. A total of 10 children with idiopathic thrombocytopenic purpura (ITP) were recruited as controls. The results revealed that the average methylation density of the bone marrow samples from the patients with ALL was significantly higher, compared with the patients with ITP (P=0.046). The relative mRNA expression levels of EPHB4 in the patients with ITP (25.08±4.03) and the patients with ALL without methylation (12.33±2.16) were significantly higher, compared with that observed in the patients with ALL with methylation (6.48±2.73; P<0.01). Pearson analysis revealed a significant negative linear correlation between EPHB4 gene methylation and its expression levels (r=−0.957; P<0.01). Western blot analysis indicated that EPHB4 protein expression levels were low in the methylated ALL samples. An evaluation of the two-year disease-free survival (DFS) of the patients with ALL was performed, which revealed that the patients with unmethylated ALL exhibited a significantly higher two-year DFS rate, as compared with patients with methylated ALL (P=0.036). These results suggest that the methylation of the EPHB4 gene is prevalent in childhood ALL and may result in expressional inactivation, which consequently promotes ALL pathogenesis and is associated with an unfavorable prognosis. Therefore, the EPHB4 gene may function as a potential tumor suppressor in childhood ALL.
Collapse
|
24
|
Higuchi T, Hashida Y, Taniguchi A, Kamioka M, Daibata M. Differential gene expression profiling linked to tumor progression of splenic marginal zone lymphoma. Sci Rep 2017; 7:11026. [PMID: 28887496 PMCID: PMC5591298 DOI: 10.1038/s41598-017-11389-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/23/2017] [Indexed: 11/22/2022] Open
Abstract
The genetic events that lead to aggressive transformation of cases of splenic marginal zone lymphoma (SMZL) after the chronic clinical stage have not been well understood. We aimed to find candidate genes associated with aggressive features of SMZL. We have successfully established two SMZL cell lines, designated SL-15 and SL-22, derived from the same patient's tumor clone in chronic and aggressive phases, respectively. Microarray analysis identified cell cycle-associated genes-specifically PLK1-as the most significantly upregulated in primary aggressive SMZL cells compared with cells from chronic phase. EPHA4 and MS4A1 (CD20) were found to be downregulated dramatically. These gene expression patterns were reproduced in both cell lines. Genetic knockdown of PLK1 resulted in inhibition of cell proliferation and induction of apoptosis in SL-22 cells, which expressed higher levels of PLK1 than SL-15 cells. SL-22 cells needed higher concentrations of chemical PLK1 inhibitors to achieve greater effects. In addition, we found homozygous deletion of the MS4A1 gene as a newly identified molecular mechanism of CD20-negative conversion. Our findings are expected to stimulate further studies on whether PLK1 could be a potential therapeutic target for this tumor. Furthermore, cases with CD20-negatively converted lymphomas should be screened for the genomic loss of MS4A1.
Collapse
Affiliation(s)
- Tomonori Higuchi
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Nankoku, Kochi, 783-8505, Japan
| | - Yumiko Hashida
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Nankoku, Kochi, 783-8505, Japan
| | - Ayuko Taniguchi
- Department of Hematology and Respiratory Medicine, Kochi Medical School, Kochi University, Nankoku, Kochi, 783-8505, Japan
| | - Mikio Kamioka
- Department of Laboratory Medicine, Kochi Medical School, Kochi University, Nankoku, Kochi, 783-8505, Japan
| | - Masanori Daibata
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Nankoku, Kochi, 783-8505, Japan.
| |
Collapse
|
25
|
Targeted therapies in hematological malignancies using therapeutic monoclonal antibodies against Eph family receptors. Exp Hematol 2017; 54:31-39. [PMID: 28751189 DOI: 10.1016/j.exphem.2017.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 12/16/2022]
Abstract
The use of monoclonal antibodies (mAbs) and molecules derived from them has achieved considerable attention and success in recent years, establishing this mode of therapy as an important therapeutic strategy in many cancers, in particular hematological tumors. mAbs recognize cell surface antigens expressed on target cells and mediate their function through various mechanisms such as antibody-dependent cellular cytotoxicity, complement-dependent cytotoxicity, or immune system modulation. The efficacy of mAb therapy can be improved when they are conjugated to a highly potent payloads, including cytotoxic drugs and radiolabeled isotopes. The Eph family of proteins has received considerable attention in recent years as therapeutic targets for treatment of both solid and hematological cancers. High expression of Eph receptors on cancer cells compared with low expression levels in normal adult tissues makes them an attractive candidate for cancer immunotherapy. In this review, we detail the modes of action of antibody-based therapies with a focus on the Eph family of proteins as potential targets for therapy in hematological malignancies.
Collapse
|
26
|
EphA3 targeting reduces in vitro adhesion and invasion and in vivo growth and angiogenesis of multiple myeloma cells. Cell Oncol (Dordr) 2017; 40:483-496. [PMID: 28721629 DOI: 10.1007/s13402-017-0338-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2017] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Multiple myeloma (MM) is a hematologic malignancy characterized by a clonal expansion of plasma cells (PCs) in the bone marrow (BM). Since MM has so far remained incurable, further insights into its pathogenesis and the concomitant identification of new therapeutic targets are urgently needed. The tyrosine kinase receptor EphA3 is known to be involved in various cellular processes including cell viability, cell movement and cell-cell interactions. Recently, EphA3 has emerged as a potential therapeutic target in several hematologic and solid tumors. Here, we aimed to uncover the role of EphA3 in MM. METHODS EphA3 mRNA and protein expression in primary MM bone marrow plasma cells (BMPCs), in MM-derived cell lines and in healthy controls (HCs) was assessed using qRT-PCR, Western blotting and flow cytometry. The effects of siRNA-mediated EphA3 silencing and anti EphA3 antibody (EphA3mAb) treatment on MM PC trafficking and viability were evaluated using in vitro assays. The effects of EphA3mAb treatment were also assessed in two MM-derived mouse xenograft models. RESULTS We found that EphA3 was overexpressed in primary MM BMPCs and MM-derived cell lines compared to HCs. We also found that siRNA-mediated EphA3 silencing and EphA3mAb treatment significantly inhibited the ability of MM PCs to adhere to fibronectin and stromal cells and to invade in vitro, without affecting cell proliferation and viability. Gene expression profiling showed that EphA3 silencing resulted in expression modulation of several molecules that regulate adhesion, migration and invasion processes. Importantly, we found that EphA3mAb treatment significantly inhibited in vivo tumor growth and angiogenesis in two MM-derived mouse xenograft models. CONCLUSIONS Our findings suggest that EphA3 plays an important role in the pathogenesis of MM and provide support for the notion that its targeting may represent a novel therapeutic opportunity for MM.
Collapse
|
27
|
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
|
28
|
|
29
|
Heidari N, Abroun S, Bertacchini J, Vosoughi T, Rahim F, Saki N. Significance of Inactivated Genes in Leukemia: Pathogenesis and Prognosis. CELL JOURNAL 2017; 19:9-26. [PMID: 28580304 PMCID: PMC5448318 DOI: 10.22074/cellj.2017.4908] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/14/2017] [Indexed: 11/04/2022]
Abstract
Epigenetic and genetic alterations are two mechanisms participating in leukemia, which can inactivate genes involved in leukemia pathogenesis or progression. The purpose of this review was to introduce various inactivated genes and evaluate their possible role in leukemia pathogenesis and prognosis. By searching the mesh words "Gene, Silencing AND Leukemia" in PubMed website, relevant English articles dealt with human subjects as of 2000 were included in this study. Gene inactivation in leukemia is largely mediated by promoter's hypermethylation of gene involving in cellular functions such as cell cycle, apoptosis, and gene transcription. Inactivated genes, such as ASPP1, TP53, IKZF1 and P15, may correlate with poor prognosis in acute lymphoid leukemia (ALL), chronic lymphoid leukemia (CLL), chronic myelogenous leukemia (CML) and acute myeloid leukemia (AML), respectively. Gene inactivation may play a considerable role in leukemia pathogenesis and prognosis, which can be considered as complementary diagnostic tests to differentiate different leukemia types, determine leukemia prognosis, and also detect response to therapy. In general, this review showed some genes inactivated only in leukemia (with differences between B-ALL, T-ALL, CLL, AML and CML). These differences could be of interest as an additional tool to better categorize leukemia types. Furthermore; based on inactivated genes, a diverse classification of Leukemias could represent a powerful method to address a targeted therapy of the patients, in order to minimize side effects of conventional therapies and to enhance new drug strategies.
Collapse
Affiliation(s)
- Nazanin Heidari
- Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeid Abroun
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Jessika Bertacchini
- Signal Transduction Unit, Department of Surgery, Medicine, Dentistry and Morphology, University of Modena and Reggio Emilia, Modena, Italy
| | - Tina Vosoughi
- Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fakher Rahim
- Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| |
Collapse
|
30
|
Wei W, Wang H, Ji S. Paradoxes of the EphB1 receptor in malignant brain tumors. Cancer Cell Int 2017; 17:21. [PMID: 28194092 PMCID: PMC5299699 DOI: 10.1186/s12935-017-0384-z] [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: 09/23/2016] [Accepted: 01/20/2017] [Indexed: 02/07/2023] Open
Abstract
Eph receptors are a subfamily of receptor tyrosine kinases. Eph receptor-mediated forward and ephrin ligand-mediated reverse signalings are termed bidirectional signaling. Increasing evidence shows that Eph/ephrin signaling regulates cell migration, adhesion, morphological changes, differentiation, proliferation and survival through cell–cell communication. Some recent studies have started to implicate Eph/ephrin signaling in tumorigenesis, metastasis, and angiogenesis. Previous studies have shown that EphB1 receptor and its ephrin ligands are expressed in the central nervous system. EphB1/ephrin signaling plays an important role in the regulation of synapse formation and maturation, migration of neural progenitors, establishment of tissue patterns, and the development of immune organs. Besides, various recent studies have detected the abnormal expression of EphB1 receptor in different brain tumors. However, the underlying molecular mechanisms of EphB1/ephrins signaling in the development of these tumors are not fully understood. This review focuses on EphB1 that has both tumor-suppressing and -promoting roles in some brain tumors. Understanding the intracellular mechanisms of EphB1 in tumorigenesis and metastasis of brain tumors might provide a foundation for the development of EphB1-targeted therapies.
Collapse
Affiliation(s)
- Wenqiang Wei
- Laboratory of Cell Signal Transduction, Medical School, Henan University, Kaifeng, 475004 China.,Department of Microbiology, Medical School, Henan University, Kaifeng, 475004 China
| | - Hongju Wang
- Department of Anatomy, Medical School, Henan University, Kaifeng, 475004 China
| | - Shaoping Ji
- Laboratory of Cell Signal Transduction, Medical School, Henan University, Kaifeng, 475004 China.,Department of Oncology, The First Affiliated Hospital, Henan University, Kaifeng, 475001 China
| |
Collapse
|
31
|
Ponsuksili S, Reyer H, Trakooljul N, Murani E, Wimmers K. Single- and Bayesian Multi-Marker Genome-Wide Association for Haematological Parameters in Pigs. PLoS One 2016; 11:e0159212. [PMID: 27434032 PMCID: PMC4951017 DOI: 10.1371/journal.pone.0159212] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/28/2016] [Indexed: 12/15/2022] Open
Abstract
Haematological traits are important traits that show associations with immune and metabolic status, as well as diseases in humans and animals. Mapping genome regions that affect the blood cell traits can contribute to the identification of genomic features useable as biomarkers for immune, disease and metabolic status. A genome-wide association study (GWAS) was conducted using PorcineSNP60 BeadChips. Single-marker and Bayesian multi-marker approaches were integrated to identify genomic regions and corresponding genes overlapping for both methods. GWAS was performed for haematological traits of 591 German Landrace pig. Heritability estimates for haematological traits were medium to high. In total 252 single SNPs associated with 12 haematological traits were identified (NegLog10 of p-value > 5). The Bayesian multi-marker approach revealed 102 QTL regions across the genome, indicated by 1-Mb windows with contribution to additive genetic variance above 0.5%. The integration of both methods resulted in 24 overlapping QTL regions. This study identified overlapping QTL regions from single- and multi-marker approaches for haematological traits. Identifying candidate genes that affect blood cell traits provides the first step towards the understanding of the molecular basis of haematological phenotypes.
Collapse
Affiliation(s)
- Siriluck Ponsuksili
- Research Unit ‘Functional Genome Analyses’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Henry Reyer
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Nares Trakooljul
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Eduard Murani
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
- * E-mail:
| |
Collapse
|
32
|
Regulation of EBV LMP1-triggered EphA4 downregulation in EBV-associated B lymphoma and its impact on patients' survival. Blood 2016; 128:1578-89. [PMID: 27338098 DOI: 10.1182/blood-2016-02-702530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/15/2016] [Indexed: 12/21/2022] Open
Abstract
Epstein-Barr virus (EBV), an oncogenic human virus, is associated with several lymphoproliferative disorders, including Burkitt lymphoma, Hodgkin disease, diffuse large B-cell lymphoma (DLBCL), and posttransplant lymphoproliferative disorder (PTLD). In vitro, EBV transforms primary B cells into lymphoblastoid cell lines (LCLs). Recently, several studies have shown that receptor tyrosine kinases (RTKs) play important roles in EBV-associated neoplasia. However, details of the involvement of RTKs in EBV-regulated B-cell neoplasia and malignancies remain largely unclear. Here, we found that erythropoietin-producing hepatocellular receptor A4 (EphA4), which belongs to the largest RTK Eph family, was downregulated in primary B cells post-EBV infection at the transcriptional and translational levels. Overexpression and knockdown experiments confirmed that EBV-encoded latent membrane protein 1 (LMP1) was responsible for this EphA4 suppression. Mechanistically, LMP1 triggered the extracellular signal-regulated kinase (ERK) pathway and promoted Sp1 to suppress EphA4 promoter activity. Functionally, overexpression of EphA4 prevented LCLs from proliferation. Pathologically, the expression of EphA4 was detected in EBV(-) tonsils but not in EBV(+) PTLD. In addition, an inverse correlation of EphA4 expression and EBV presence was verified by immunochemical staining of EBV(+) and EBV(-) DLBCL, suggesting EBV infection was associated with reduced EphA4 expression. Analysis of a public data set showed that lower EphA4 expression was correlated with a poor survival rate of DLBCL patients. Our findings provide a novel mechanism by which EphA4 can be regulated by an oncogenic LMP1 protein and explore its possible function in B cells. The results provide new insights into the role of EphA4 in EBV(+) PTLD and DLBCL.
Collapse
|
33
|
San Jose-Eneriz E, Agirre X, Rodríguez-Otero P, Prosper F. Epigenetic regulation of cell signaling pathways in acute lymphoblastic leukemia. Epigenomics 2016; 5:525-38. [PMID: 24059799 DOI: 10.2217/epi.13.56] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a heterogeneous cancer that is characterized by rapid and uncontrolled proliferation of immature B- or T-lymphoid precursors. Although ALL has been regarded as a genetic disease for many years, the crucial importance of epigenetic alterations in leukemogenesis has become increasingly evident. Epigenetic mechanisms, which include DNA methylation and histone modifications, are critical for gene regulation during many key biological processes. Here, we review the cell signaling pathways that are regulated by DNA methylation or histone modifications in ALL. Recent studies have highlighted the fundamental role of these modifications in ALL development, and suggested that future investigation into the specific genes and pathways that are altered by epigenetic mechanisms can contribute to the development of novel drug-based therapies for ALL.
Collapse
Affiliation(s)
- Edurne San Jose-Eneriz
- Oncology Division, Foundation for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | | | | |
Collapse
|
34
|
Kuang SQ, Medina-Martinez O, Guo DC, Gong L, Regalado ES, Reynolds CL, Boileau C, Jondeau G, Prakash SK, Kwartler CS, Zhu LY, Peters AM, Duan XY, Bamshad MJ, Shendure J, Nickerson DA, Santos-Cortez RL, Dong X, Leal SM, Majesky MW, Swindell EC, Jamrich M, Milewicz DM. FOXE3 mutations predispose to thoracic aortic aneurysms and dissections. J Clin Invest 2016; 126:948-61. [PMID: 26854927 PMCID: PMC4767350 DOI: 10.1172/jci83778] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 12/10/2015] [Indexed: 12/11/2022] Open
Abstract
The ascending thoracic aorta is designed to withstand biomechanical forces from pulsatile blood. Thoracic aortic aneurysms and acute aortic dissections (TAADs) occur as a result of genetically triggered defects in aortic structure and a dysfunctional response to these forces. Here, we describe mutations in the forkhead transcription factor FOXE3 that predispose mutation-bearing individuals to TAAD. We performed exome sequencing of a large family with multiple members with TAADs and identified a rare variant in FOXE3 with an altered amino acid in the DNA-binding domain (p.Asp153His) that segregated with disease in this family. Additional pathogenic FOXE3 variants were identified in unrelated TAAD families. In mice, Foxe3 deficiency reduced smooth muscle cell (SMC) density and impaired SMC differentiation in the ascending aorta. Foxe3 expression was induced in aortic SMCs after transverse aortic constriction, and Foxe3 deficiency increased SMC apoptosis and ascending aortic rupture with increased aortic pressure. These phenotypes were rescued by inhibiting p53 activity, either by administration of a p53 inhibitor (pifithrin-α), or by crossing Foxe3-/- mice with p53-/- mice. Our data demonstrate that FOXE3 mutations lead to a reduced number of aortic SMCs during development and increased SMC apoptosis in the ascending aorta in response to increased biomechanical forces, thus defining an additional molecular pathway that leads to familial thoracic aortic disease.
Collapse
MESH Headings
- Adult
- Aortic Dissection/genetics
- Aortic Dissection/metabolism
- Aortic Dissection/pathology
- Animals
- Aorta/metabolism
- Aorta/pathology
- Aortic Aneurysm, Thoracic/genetics
- Aortic Aneurysm, Thoracic/metabolism
- Aortic Aneurysm, Thoracic/pathology
- Apoptosis
- Cells, Cultured
- Cyclin-Dependent Kinase Inhibitor p21/metabolism
- Female
- Forkhead Transcription Factors/genetics
- Gene Expression
- Genetic Association Studies
- Genetic Predisposition to Disease
- Humans
- Male
- Mice, Inbred C57BL
- Mice, Knockout
- Middle Aged
- Muscle, Smooth, Vascular/pathology
- Mutation, Missense
- Myocytes, Smooth Muscle/physiology
- Pedigree
- Tumor Suppressor Protein p53/genetics
- Vascular Remodeling
- Zebrafish
Collapse
Affiliation(s)
- Shao-Qing Kuang
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | - Dong-chuan Guo
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Limin Gong
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ellen S. Regalado
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Corey L. Reynolds
- Mouse Phenotyping Core, Baylor College of Medicine, Houston, Texas, USA
| | - Catherine Boileau
- AP-HP, Hôpital Bichat, Centre National de Référence pour le syndrome de Marfan et apparentés, Paris, France; Université Paris 7, Paris, France; INSERM, U1148, Paris, France
| | - Guillaume Jondeau
- AP-HP, Hôpital Bichat, Centre National de Référence pour le Syndrome de Marfan et apparentés, Paris, France; Université Paris 7, Paris, France; AP-HP, Hôpital Bichat, Service de Cardiologie, Paris, France
| | - Siddharth K. Prakash
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Callie S. Kwartler
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Lawrence Yang Zhu
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Andrew M. Peters
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Xue-Yan Duan
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | - Michael J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Debbie A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Regie L. Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Xiurong Dong
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Departments of Pediatrics and Pathology, University of Washington, Seattle, Washington, USA
| | - Suzanne M. Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Mark W. Majesky
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Departments of Pediatrics and Pathology, University of Washington, Seattle, Washington, USA
| | - Eric C. Swindell
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | - Dianna M. Milewicz
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| |
Collapse
|
35
|
Feng Y, Tian J, Krylova I, Xu T, Xie HQ, Guo TL, Zhao B. Chronic TCDD exposure results in the dysregulation of gene expression in splenic B-lymphocytes and in the impairments in T-cell and B-cell differentiation in mouse model. J Environ Sci (China) 2016; 39:218-227. [PMID: 26899660 DOI: 10.1016/j.jes.2015.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/01/2015] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) exposure in humans is associated with marked immune suppressions and increased incidence of lymphoblastic diseases. To elucidate mechanisms of impairments in humoral immune responses, we used a murine model. Following a 20-week administration of low doses of TCDD, we observed severely reduced antibody titers, dramatically decreased number of splenic Th1 and Th2 cells and an increase in CD19(+) B cells. Transcriptional profiling of CD19(+) B cells showed that markers of pre-B cells were significantly elevated, indicating delayed B cell maturation. These changes in B cells were accompanied by decreases of T helper cell numbers and reduced IgM and IgG titers. A transcriptome analysis of splenic B cells followed by Ingenuity Pathway Analysis (IPA) revealed a set of differentially expressed genes known to play roles in tumorigenesis, cell-proliferation and cell-migration. The most up-regulated transcript gene was Eph receptor A2 (EphA2), a known oncogene, and the most down-regulated transcript was ZBTB16 that codes for a negative transcriptional regulator important in epigenetic chromatin remodeling. IPA identified cAMP-responsive element modulator (CREM) and cAMP-responsive element binding protein 1 (CREB1) as top upstream regulators. Consistently, a MAPPER promoter database analysis showed that all top dysregulated genes had CREM and/or CREB1 binding sites in their promoter regions. In summary, our data showed that chronic TCDD exposure in mice caused suppressed humoral immunity accompanied with profound dysregulation of gene expression in splenic B-lymphocytes, likely through cAMP-dependent pathways. This dysregulation resulted in impairments in T-cell and B-cell differentiation and activation of the tumorigenic transcription program.
Collapse
Affiliation(s)
- Yu Feng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Jijing Tian
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | | | - Tuan Xu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Heidi Qunhui Xie
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Tai L Guo
- Department of Veterinary Biosciences and Diagnostic Imaging, College of Veterinary Medicine, University of Georgia, Athens, GA 30602-7382, USA
| | - Bin Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| |
Collapse
|
36
|
Chen L, Yang J, Huang T, Kong X, Lu L, Cai YD. Mining for novel tumor suppressor genes using a shortest path approach. J Biomol Struct Dyn 2015. [PMID: 26209080 DOI: 10.1080/07391102.2015.1042915] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cancer, being among the most serious diseases, causes many deaths every year. Many investigators have devoted themselves to designing effective treatments for this disease. Cancer always involves abnormal cell growth with the potential to invade or spread to other parts of the body. In contrast, tumor suppressor genes (TSGs) act as guardians to prevent a disordered cell cycle and genomic instability in normal cells. Studies on TSGs can assist in the design of effective treatments against cancer. In this study, we propose a computational method to discover potential TSGs. Based on the known TSGs, a number of candidate genes were selected by applying the shortest path approach in a weighted graph that was constructed using protein-protein interaction network. The analysis of selected genes shows that some of them are new TSGs recently reported in the literature, while others may be novel TSGs.
Collapse
Affiliation(s)
- Lei Chen
- a College of Life Science , Shanghai University , Shanghai 200444 , P.R. China.,b College of Information Engineering , Shanghai Maritime University , Shanghai 201306 , P.R. China
| | - Jing Yang
- c The Key Laboratory of Stem Cell Biology , Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) , Shanghai 200025 , P.R. China
| | - Tao Huang
- c The Key Laboratory of Stem Cell Biology , Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) , Shanghai 200025 , P.R. China
| | - Xiangyin Kong
- c The Key Laboratory of Stem Cell Biology , Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) , Shanghai 200025 , P.R. China
| | - Lin Lu
- d Department of Radiology , Columbia University Medical Center , New York , NY 10032 , USA
| | - Yu-Dong Cai
- a College of Life Science , Shanghai University , Shanghai 200444 , P.R. China
| |
Collapse
|
37
|
Villanueva A, Portela A, Sayols S, Battiston C, Hoshida Y, Méndez-González J, Imbeaud S, Letouzé E, Hernandez-Gea V, Cornella H, Pinyol R, Solé M, Fuster J, Zucman-Rossi J, Mazzaferro V, Esteller M, Llovet JM. DNA methylation-based prognosis and epidrivers in hepatocellular carcinoma. Hepatology 2015; 61:1945-56. [PMID: 25645722 DOI: 10.1002/hep.27732] [Citation(s) in RCA: 290] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 01/25/2015] [Indexed: 12/07/2022]
Abstract
UNLABELLED Epigenetic deregulation has emerged as a driver in human malignancies. There is no clear understanding of the epigenetic alterations in hepatocellular carcinoma (HCC) and of the potential role of DNA methylation markers as prognostic biomarkers. Analysis of tumor tissue from 304 patients with HCC treated with surgical resection allowed us to generate a methylation-based prognostic signature using a training-validation scheme. Methylome profiling was done with the Illumina HumanMethylation450 array (Illumina, Inc., San Diego, CA), which covers 96% of known cytosine-phosphate-guanine (CpG) islands and 485,000 CpG, and transcriptome profiling was performed with Affymetrix Human Genome U219 Plate (Affymetrix, Inc., Santa Clara, CA) and miRNA Chip 2.0. Random survival forests enabled us to generate a methylation signature based on 36 methylation probes. We computed a risk score of mortality for each individual that accurately discriminated patient survival both in the training (221 patients; 47% hepatitis C-related HCC) and validation sets (n = 83; 47% alcohol-related HCC). This signature correlated with known predictors of poor outcome and retained independent prognostic capacity of survival along with multinodularity and platelet count. The subset of patients identified by this signature was enriched in the molecular subclass of proliferation with progenitor cell features. The study confirmed a high prevalence of genes known to be deregulated by aberrant methylation in HCC (e.g., Ras association [RalGDS/AF-6] domain family member 1, insulin-like growth factor 2, and adenomatous polyposis coli) and other solid tumors (e.g., NOTCH3) and describes potential candidate epidrivers (e.g., septin 9 and ephrin B2). CONCLUSIONS A validated signature of 36 DNA methylation markers accurately predicts poor survival in patients with HCC. Patients with this methylation profile harbor messenger RNA-based signatures indicating tumors with progenitor cell features.
Collapse
Affiliation(s)
- Augusto Villanueva
- Liver Cancer Research Program, Division of Liver Diseases, Tisch Cancer Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Barcelona-Clínic Liver Cancer Group (Liver Cancer Translational Research Laboratory, Liver Unit, Pathology Department, Surgery Department), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Hospital Clínic de Barcelona, Universitat de Barcelona (UB), Barcelona, Spain
| | - Anna Portela
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Sergi Sayols
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Institute of Molecular Biology, Mainz, Germany
| | - Carlo Battiston
- Gastrointestinal Surgery and Liver Transplantation Unit, National Cancer Institute, Milan, Italy
| | - Yujin Hoshida
- Liver Cancer Research Program, Division of Liver Diseases, Tisch Cancer Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jesús Méndez-González
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Sandrine Imbeaud
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, IUH, Paris, France.,Université Paris Descartes; Université Paris Diderot, Université Paris 13, Labex Immuno-oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Eric Letouzé
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Virginia Hernandez-Gea
- Barcelona-Clínic Liver Cancer Group (Liver Cancer Translational Research Laboratory, Liver Unit, Pathology Department, Surgery Department), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Hospital Clínic de Barcelona, Universitat de Barcelona (UB), Barcelona, Spain
| | - Helena Cornella
- Barcelona-Clínic Liver Cancer Group (Liver Cancer Translational Research Laboratory, Liver Unit, Pathology Department, Surgery Department), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Hospital Clínic de Barcelona, Universitat de Barcelona (UB), Barcelona, Spain
| | - Roser Pinyol
- Barcelona-Clínic Liver Cancer Group (Liver Cancer Translational Research Laboratory, Liver Unit, Pathology Department, Surgery Department), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Hospital Clínic de Barcelona, Universitat de Barcelona (UB), Barcelona, Spain
| | - Manel Solé
- Barcelona-Clínic Liver Cancer Group (Liver Cancer Translational Research Laboratory, Liver Unit, Pathology Department, Surgery Department), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Hospital Clínic de Barcelona, Universitat de Barcelona (UB), Barcelona, Spain
| | - Josep Fuster
- Barcelona-Clínic Liver Cancer Group (Liver Cancer Translational Research Laboratory, Liver Unit, Pathology Department, Surgery Department), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Hospital Clínic de Barcelona, Universitat de Barcelona (UB), Barcelona, Spain
| | - Jessica Zucman-Rossi
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, IUH, Paris, France.,Université Paris Descartes; Université Paris Diderot, Université Paris 13, Labex Immuno-oncology, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Vincenzo Mazzaferro
- Gastrointestinal Surgery and Liver Transplantation Unit, National Cancer Institute, Milan, Italy
| | - Manel Esteller
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Josep M Llovet
- Liver Cancer Research Program, Division of Liver Diseases, Tisch Cancer Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,Barcelona-Clínic Liver Cancer Group (Liver Cancer Translational Research Laboratory, Liver Unit, Pathology Department, Surgery Department), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Hospital Clínic de Barcelona, Universitat de Barcelona (UB), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | | |
Collapse
|
38
|
Kampen KR, Scherpen FJG, Garcia-Manero G, Yang H, Kaspers GJL, Cloos J, Zwaan CM, van den Heuvel-Eibrink MM, Kornblau SM, De Bont ESJM. EphB1 Suppression in Acute Myelogenous Leukemia: Regulating the DNA Damage Control System. Mol Cancer Res 2015; 13:982-92. [PMID: 25944917 DOI: 10.1158/1541-7786.mcr-14-0660-t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/24/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED Loss of ephrin receptor (EphB1) expression may associate with aggressive cancer phenotypes; however, the mechanism of action remains unclear. To gain detailed insight into EphB1 function in acute myelogenous leukemia (AML), comprehensive analysis of EphB1 transcriptional regulation was conducted. In AML cells, EphB1 transcript was inversely correlated with EphB1 promoter methylation. The presence of EphB1 allowed EfnB1 ligand-mediated p53 DNA binding, leading to restoration of the DNA damage response (DDR) cascade by the activation of ATR, Chk1, p53, p21, p38, CDK1(tyr15), and Bax, and downregulation of HSP27 and Bcl2. Comparatively, reintroduction of EphB1 expression in EphB1-methylated AML cells enhanced the same cascade of ATR, Chk1, p21, and CDK1(tyr15), which consequently enforced programmed cell death. Interestingly, in pediatric AML samples, EphB1 peptide phosphorylation and mRNA expression were actively suppressed as compared with normal bone marrow, and a significant percentage of the primary AML specimens had EphB1 promoter hypermethylation. Finally, EphB1 repression associated with a poor overall survival in pediatric AML. Combined, the contribution of EphB1 to the DDR system reveals a tumor-suppressor function for EphB1 in pediatric AML. IMPLICATIONS The tumor-suppressor function of EphB1 is clinically relevant across many malignancies, suggesting that EphB1 is an important regulator of common cancer cell transforming pathways.
Collapse
Affiliation(s)
- K R Kampen
- Department of Pediatric Oncology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - F J G Scherpen
- Department of Pediatric Oncology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - G Garcia-Manero
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - H Yang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - G J L Kaspers
- Department of Pediatric Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - J Cloos
- Department of Pediatric Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - C M Zwaan
- Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | | | - S M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - E S J M De Bont
- Department of Pediatric Oncology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
| |
Collapse
|
39
|
Wang HC, Chang FR, Huang TJ, Kuo CY, Tsai YC, Wu CC. (-)-Liriopein B Suppresses Breast Cancer Progression via Inhibition of Multiple Kinases. Chem Res Toxicol 2015; 28:897-906. [PMID: 25856345 DOI: 10.1021/tx500518j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Numerous breast cancer patients who achieve an initial response to HER-targeted therapy rapidly develop resistance within one year, leading to treatment failure. Observations from clinical samples indicate that such resistance correlates with an increase in Src, EGFR, and PI3K/Akt activities and a decrease in PTEN activity. Furthermore, Akt survival signaling activation is also found in tumors treated by toxic chemotherapeutic agents. Because cotreatment with a PI3K inhibitor is a promising strategy to delay acquired resistance by preventing secondary gene activation, we therefore investigated the effects of a newly identified compound, (-)-Liriopein B (LB), on PI3K/Akt signaling activity in breast cancer cells. Our results showed that nontoxic doses of LB are able to inhibit AKT activation in both luminal-like MCF-7 and basal-like MDA-MB-231 breast cancer cells. Low doses of LB also inhibited cell migration, invasion, and cancer-stem cell sphere formation. Suppression of EGF-induced EGFR and ERK1/2 activation by LB might contribute in part to retardation of cancer progression. Furthermore, LB increases sensitivity of MDA-MB-231 cells to gefitinib in vitro, suggesting that EGFR may not be the only target of LB. Finally, a small scale in vitro kinase assay screen demonstrated that LB has a potent inhibitory effect on multiple kinases, including PI3K, Src, EGFR, Tie2, lck, lyn, RTK5, FGFR1, Abl, and Flt. In conclusion, this study demonstrates for the first time that the compound LB improves tumor therapeutic efficacy and suggests LB as a promising candidate for studying new leads in the development of kinase inhibitors.
Collapse
Affiliation(s)
- Hui-Chun Wang
- †Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.,‡PhD Program in Translational Medicine, College of Medicine and PhD Program in Toxicology, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.,§Translational Research Center and Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan.,∥Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Fang-Rong Chang
- †Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.,∥Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Tzu-Jung Huang
- †Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Ching-Ying Kuo
- †Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yu-Chi Tsai
- †Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chin-Chung Wu
- †Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.,‡PhD Program in Translational Medicine, College of Medicine and PhD Program in Toxicology, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.,∥Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| |
Collapse
|
40
|
Li S, Zhu Y, Ma C, Qiu Z, Zhang X, Kang Z, Wu Z, Wang H, Xu X, Zhang H, Ren G, Tang J, Li X, Guan M. Downregulation of EphA5 by promoter methylation in human prostate cancer. BMC Cancer 2015; 15:18. [PMID: 25609195 PMCID: PMC4307617 DOI: 10.1186/s12885-015-1025-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 01/14/2015] [Indexed: 11/30/2022] Open
Abstract
Background EphA5 is a member of the Eph/ephrin family and plays a critical role in the regulation of carcinogenesis. A significant reduction of EphA5 transcripts in high-grade prostate cancer tissue was shown using a transcriptomic analysis, compared to the low-grade prostate cancer tissue. As less is known about the mechanism of EphA5 downregulation and the function of EphA5, here we investigated the expression and an epigenetic change of EphA5 in prostate cancer and determined if these findings were correlated with clinicopathologic characteristics of prostate cancer. Methods Seven prostate cell lines (RWPE-1, LNCap, LNCap-LN3, CWR22rv-1, PC-3, PC-3M-LN4, and DU145), thirty-nine BPH, twenty-two primary prostate carcinomas, twenty-three paired noncancerous and cancerous prostate tissues were examined via qRT-PCR, methylation-specific PCR, bisulfite sequencing, immunohistochemistry and western blotting. The role of EphA5 in prostate cancer cell migration and invasion was examined by wound healing and transwell assay. Results Downregulation or loss of EphA5 mRNA or protein expression was detected in 28 of 45 (62.2%) prostate carcinomas, 2 of 39 (5.1%) hyperplasias, and all 6 prostate cancer cell lines. Methylation of the EphA5 promoter region was present in 32 of 45 (71.1%) carcinoma samples, 3 of 39 (7.7%) hyperplasias, and the 6 prostate cancer cell lines. Among 23 paired prostate carcinoma tissues, 16 tumor samples exhibited the hypermethylation of EphA5, and 15 of these 16 specimens (93.8%) shown the downregulation of EphA5 expression than that of their respectively matched noncancerous samples. Immunostaining analysis demonstrated that the EphA5 protein was absent or down-regulated in 10 of 13 (76.9%) available carcinoma samples, and 8 of these 10 samples (80.0%) exhibited hypermethylation. The frequency of EphA5 methylation was higher in cancer patients with an elevated Gleason score or T3-T4 staging. Following the treatment of 6 prostate cancer cell lines with 5-aza-2′-deoxycytidine, the levels of EphA5 mRNA were significantly increased. Prostate cancer cells invasion and migration were significantly suppressed by ectopic expression of EphA5 in vitro. Conclusion Our study provides evidence that EphA5 is a potential target for epigenetic silencing in primary prostate cancer and is a potentially valuable prognosis predictor and thereapeutic marker for prostate cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1025-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shibao Li
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical School, Fudan University, 12 Central Urumqi Road, Shanghai, 200040, China.
| | - Yingfeng Zhu
- Department of Pathology, Huashan Hospital North, Fudan University, Shanghai, China.
| | - Chunguang Ma
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Zhenhua Qiu
- Department of Laboratory Medicine, The people's hospital of GaoZhou, GaoZhou, China.
| | - Xinju Zhang
- Central Laboratory, Huashan Hospital, Shanghai Medical School, Fudan University, Shanghai, China.
| | - Zhihua Kang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical School, Fudan University, 12 Central Urumqi Road, Shanghai, 200040, China. .,Central Laboratory, Huashan Hospital, Shanghai Medical School, Fudan University, Shanghai, China.
| | - Zhiyuan Wu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical School, Fudan University, 12 Central Urumqi Road, Shanghai, 200040, China. .,Central Laboratory, Huashan Hospital, Shanghai Medical School, Fudan University, Shanghai, China.
| | - Hua Wang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical School, Fudan University, 12 Central Urumqi Road, Shanghai, 200040, China. .,Central Laboratory, Huashan Hospital, Shanghai Medical School, Fudan University, Shanghai, China.
| | - Xiao Xu
- Central Laboratory, Huashan Hospital, Shanghai Medical School, Fudan University, Shanghai, China.
| | - Hu Zhang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.
| | - Guoqiang Ren
- Department of Pathology, Huashan Hospital North, Fudan University, Shanghai, China.
| | - Jianmin Tang
- Department of Pathology, Huashan Hospital North, Fudan University, Shanghai, China.
| | - Xiangyu Li
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical School, Fudan University, 12 Central Urumqi Road, Shanghai, 200040, China.
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical School, Fudan University, 12 Central Urumqi Road, Shanghai, 200040, China. .,Central Laboratory, Huashan Hospital, Shanghai Medical School, Fudan University, Shanghai, China.
| |
Collapse
|
41
|
MacDonald IA, Hathaway NA. Epigenetic roots of immunologic disease and new methods for examining chromatin regulatory pathways. Immunol Cell Biol 2014; 93:261-70. [PMID: 25533290 DOI: 10.1038/icb.2014.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 10/31/2014] [Indexed: 12/19/2022]
Abstract
The ability to accurately quantitate and experimentally examine epigenetic modifications across the human genome has exploded in the past decade. This has given rise to a wealth of new information concerning the contributions of epigenetic regulatory networks to the pathogenesis of human disease. In particular, immunological disorders have strong developmental roots in chromatin regulatory pathways. In this review, we focus on the epigenetic signatures and new discoveries revealing the epigenetic compositions of specific immunological cancers and autoimmune diseases. We also comment on the conserved epigenetic roots among diverse immunological disorders and suggest inhibition strategies that may be relevant for future treatment. Finally, we highlight emerging experimental tools with the capability to examine the mechanisms of chromatin regulatory enzymes with a high level of temporal control. The knowledge of genetic and epigenetic defects in immunological disease combined with new experimental approaches will elucidate the contribution of individual enzymes in complex epigenetic regulatory networks. This could lead to new diagnostic and therapeutic approaches for some very diverse and difficult to treat human diseases.
Collapse
Affiliation(s)
- Ian A MacDonald
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Nathaniel A Hathaway
- 1] Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
42
|
Xiao Z, Carrasco R, Kinneer K, Sabol D, Jallal B, Coats S, Tice DA. EphB4 promotes or suppresses Ras/MEK/ERK pathway in a context-dependent manner. Cancer Biol Ther 2014; 13:630-7. [DOI: 10.4161/cbt.20080] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
43
|
Gucciardo E, Sugiyama N, Lehti K. Eph- and ephrin-dependent mechanisms in tumor and stem cell dynamics. Cell Mol Life Sci 2014; 71:3685-710. [PMID: 24794629 PMCID: PMC11113620 DOI: 10.1007/s00018-014-1633-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/31/2014] [Accepted: 04/17/2014] [Indexed: 01/17/2023]
Abstract
The erythropoietin-producing hepatocellular (Eph) receptors comprise the largest family of receptor tyrosine kinases (RTKs). Initially regarded as axon-guidance and tissue-patterning molecules, Eph receptors have now been attributed with various functions during development, tissue homeostasis, and disease pathogenesis. Their ligands, ephrins, are synthesized as membrane-associated molecules. At least two properties make this signaling system unique: (1) the signal can be simultaneously transduced in the receptor- and the ligand-expressing cell, (2) the signaling outcome through the same molecules can be opposite depending on cellular context. Moreover, shedding of Eph and ephrin ectodomains as well as ligand-dependent and -independent receptor crosstalk with other RTKs, proteases, and adhesion molecules broadens the repertoire of Eph/ephrin functions. These integrated pathways provide plasticity to cell-microenvironment communication in varying tissue contexts. The complex molecular networks and dynamic cellular outcomes connected to the Eph/ephrin signaling in tumor-host communication and stem cell niche are the main focus of this review.
Collapse
Affiliation(s)
- Erika Gucciardo
- Research Programs Unit, Genome-Scale Biology, Biomedicum Helsinki, University of Helsinki, P.O.B. 63, 00014 Helsinki, Finland
| | - Nami Sugiyama
- Research Programs Unit, Genome-Scale Biology, Biomedicum Helsinki, University of Helsinki, P.O.B. 63, 00014 Helsinki, Finland
- Department of Biosystems Science and Bioengineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Kaisa Lehti
- Research Programs Unit, Genome-Scale Biology, Biomedicum Helsinki, University of Helsinki, P.O.B. 63, 00014 Helsinki, Finland
| |
Collapse
|
44
|
Gautrey HE, van Otterdijk SD, Cordell HJ, Mathers JC, Strathdee G. DNA methylation abnormalities at gene promoters are extensive and variable in the elderly and phenocopy cancer cells. FASEB J 2014; 28:3261-72. [PMID: 24858281 DOI: 10.1096/fj.13-246173] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Abnormal patterns of DNA methylation are one of the hallmarks of cancer cells. The process of aging has also been associated with similar, albeit less dramatic, changes in methylation patterns, leading to the hypothesis that age-related changes in DNA methylation may partially underlie the increased risk of cancer in the elderly. Here we studied 377 participants aged 85 yr from the Newcastle 85+ Study to investigate the extent of, and interindividual variation in, age-related changes in DNA methylation at specific CpG islands. Using highly quantitative pyrosequencing analysis, we found extensive and highly variable methylation of promoter-associated CpG islands with levels ranging from 4% to 35%, even at known tumor suppressor genes such as TWIST2. Furthermore, the interindividual differences in methylation seen across this elderly population phenocopies multiple features of the altered methylation patterns seen in cancer cells. Both aging- and cancer-related methylation can occur at similar sets of genes, both result in the formation of densely methylated, and likely transcriptionally repressed, alleles, and both exhibit coordinate methylation across multiple loci. In addition, high methylation levels were associated with subsequent diagnosis of leukemia or lymphoma during a 3-yr follow-up period (P=0.00008). These data suggest that the accumulation of age-related changes in promoter-associated CpG islands may contribute to the increased cancer risk seen during aging.-Gautrey, H. E., van Otterdijk, S. D., Cordell, H. J., Newcastle 85+ study core team, Mathers, J. C., Strathdee, G. DNA methylation abnormalities at gene promoters are extensive and variable in the elderly and phenocopy cancer cells.
Collapse
Affiliation(s)
| | | | | | | | - John C Mathers
- Human Nutrition Research Centre, Institute for Ageing and Health, Campus for Ageing and Vitality, Newcastle University, Newcastle Upon Tyne, UK; and
| | | |
Collapse
|
45
|
Expression of Eph A4, Eph B2 and Eph B4 receptors in AML. Pathol Oncol Res 2014; 20:901-7. [PMID: 24764074 DOI: 10.1007/s12253-014-9767-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 03/20/2014] [Indexed: 12/22/2022]
Abstract
Eph receptors represent the largest subfamily of receptor tyrosine kinases (RTKs). The up- regulation of Eph receptors has been documented in various solid tumors, where it often correlates with poor prognosis. Their significance in hematologic malignancies is still unclear. This study aimed to investigate the expression of Eph A4, Eph B2, and Eph B4 mRNA in non - M3 AML patients and determine their prognostic significance. Bone marrow samples from 101 newly diagnosed non - M3 AML patients and 26 healthy controls for comparison were quantified by real time reverse transcriptase polymerase chain reaction (RT-PCR), and the comparative cycle threshold (Ct) method was used to determine their relative expression levels to GUS control gene. The results showed that expression of all selected Eph receptors was significantly lower in AML patients comparing to controls. It also differed according to FAB subtypes. The decreased expression levels of Eph A4 were associated with higher leukocytes (p = 0.022) and blast cell counts (p = 0.001), and unfavorable FLT3-ITD mutation. Our study revealed significant correlation between lower EphB2 expression levels, and higher complete remission rate (p = 0.009724) and longer overall survival. Additionally, we found that patients with shorter RFS had decreased EphB4 expression (p = 0.00). In conclusion, the results suggest the prognostic impact of decreased expression levels of some Eph receptors in AML patients.
Collapse
|
46
|
Stevenson WS, Best OG, Przybylla A, Chen Q, Singh N, Koleth M, Pierce S, Kennedy T, Tong W, Kuang SQ, Garcia-Manero G. DNA methylation of membrane-bound tyrosine phosphatase genes in acute lymphoblastic leukaemia. Leukemia 2014; 28:787-93. [PMID: 24045499 DOI: 10.1038/leu.2013.270] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 08/20/2013] [Accepted: 09/03/2013] [Indexed: 02/03/2023]
Abstract
Aberrant DNA promoter methylation with associated gene silencing is a common epigenetic abnormality in acute lymphoblastic leukaemia (ALL) and is associated with poor survival. We have identified a family of transmembrane tyrosine phosphatase proteins as targets of hypermethylation in ALL and high-grade B cell lymphoma and demonstrated that this abnormal methylation correlates with transcript expression. PTPRG was methylated in 63% of ALL samples, PTPRK in 47%, PTPRM in 64% and PTPRO in 54% of cases, with most ALL samples containing methylation at multiple phosphatase loci. PTPRK promoter methylation was associated with a decreased overall survival in the cohort. Restoration of PTPRK transcript levels in leukaemia cells, where phosphatase transcript was silenced, reduced cell proliferation, inhibited colony formation and increased sensitivity to cytotoxic chemotherapy. These biological changes were associated with a reduction in levels of phosphorylated Erk1/2, Akt, STAT3 and STAT5 suggesting functional phosphatase activity after transcript re-expression. Methylation of the phosphatase promoters was reversible with decitabine and a histone deacetylase inhibitor, suggesting that PTPRK-mediated cell signalling pathways may be targeted with epigenetic therapies in lymphoid malignancy.
Collapse
Affiliation(s)
- W S Stevenson
- 1] Department of Haematology, Royal North Shore Hospital, Pathology North, Sydney, Australia [2] Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Sydney, Australia
| | - O G Best
- Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Sydney, Australia
| | - A Przybylla
- Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Sydney, Australia
| | - Q Chen
- 1] Department of Haematology, Royal North Shore Hospital, Pathology North, Sydney, Australia [2] Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Sydney, Australia
| | - N Singh
- Department of Haematology, Royal North Shore Hospital, Pathology North, Sydney, Australia
| | - M Koleth
- Department of Haematology, Royal North Shore Hospital, Pathology North, Sydney, Australia
| | - S Pierce
- Department of Leukemia, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - T Kennedy
- Department of Haematology, Royal North Shore Hospital, Pathology North, Sydney, Australia
| | - W Tong
- Department of Leukemia, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - S-Q Kuang
- Department of Leukemia, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - G Garcia-Manero
- Department of Leukemia, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
47
|
Wang CX, Wang X, Liu HB, Zhou ZH. Aberrant DNA methylation and epigenetic inactivation of hMSH2 decrease overall survival of acute lymphoblastic leukemia patients via modulating cell cycle and apoptosis. Asian Pac J Cancer Prev 2014; 15:355-62. [PMID: 24528056 DOI: 10.7314/apjcp.2014.15.1.355] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Altered regulation of many transcription factors has been shown to play important roles in the development of leukemia. hMSH2 can modulate the activity of some important transcription factors and is known to be a regulator of hematopoietic differentiation. Herein, we investigated epigenetic regulation of hMSH2 and its influence on cell growth and overall survival of acute lymphoblastic leukemia (ALL) patients. METHODS hMSH2 promoter methylation status was assessed by COBRA and pyrosequencing in 60 ALL patients and 30 healthy volunteers. mRNA and protein expression levels of hMSH2, PCNA, CyclinD1, Bcl-2 and Bax were determined by real time PCR and Western blotting, respectively. The influence of hMSH2 on cell proliferation and survival was assessed in transient and stable expression systems. RESULTS mRNA and protein expression of hMSH2 and Bcl-2 was decreased, and that of PCNA, CyclinD1 and Bax was increased in ALL patients as compared to healthy volunteers (P<0.05). hMSH2 was inactivated in ALL patients through promoter hypermethylation. Furthermore, hMSH2 hypermethylation was found in relapsed ALL patients (85.7% of all cases). The median survival of patients with hMSH2 methylation was shorter than that of patients without hMSH2 methylation (log-rank test, P=0.0035). Over-expression of hMSH2 in cell lines resulted in a significant reduction in growth and induction of apoptosis. CONCLUSIONS This study suggests that aberrant DNA methylation and epigenetic inactivation of hMSH2 play an important role in the development of ALL through altering cell growth and survival.
Collapse
Affiliation(s)
- Cai-Xia Wang
- Department of Internal Medicine, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China E-mail :
| | | | | | | |
Collapse
|
48
|
|
49
|
Wang H, Wen J, Wang H, Guo Q, Shi S, Shi Q, Zhou X, Liu Q, Lu G, Wang J. Loss of expression of EphB1 protein in serous carcinoma of ovary associated with metastasis and poor survival. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2013; 7:313-321. [PMID: 24427352 PMCID: PMC3885486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/22/2013] [Indexed: 06/03/2023]
Abstract
Aberrant expression of receptors tyrosine kinase of Eph gene in human cancers is extensively documented. We previously found that EphB1 subtype is down-regulated in gastric cancer and colorectal cancer. Fore the more, decreased expression of EphB1 is related to invasion and metastasis in cancers. There is no published data regarding the role of EphB1 in ovarian cancer, which is the focus of the present study. The expression of EphB1 protein was determined in tissues from 74 patients with serous ovarian carcinoma and 12 normal ovarian epithelial tissues. The expression level of EphB1 protein in serous ovarian carcinoma was analyzed with respect to clinicopathological parameters and survival. EphB1 protein was positively stained in 12 normal ovarian epithelial samples, and negatively stained in 32 out of 74 (43.2%) serous ovarian cancers. Loss of expression of EphB1 protein was associated with higher tumor grade (P=0.006), metastasis (P=0.049) and high proliferative index Ki67 expression (P=0.022), but not with FIGO stage (P=0.0937), age at diagnosis (P=0.624), and diameter of carcinoma (P=0.108). In addition, loss of EphB1 protein in serous ovarian carcinoma was associated with a significantly worse overall survival (P=0.015). Our data indicate that loss of EphB1 protein is associated with metastasis and poorer survival in patients with serous ovarian cancer. EphB1 may be used as a prognostic marker and a therapeutic target in serous ovarian carcinoma.
Collapse
Affiliation(s)
- Haiyan Wang
- Department of Pathology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing 210002, China
| | - Juanjuan Wen
- Department of Pathology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing 210002, China
| | - Hai Wang
- Department of Pathology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing 210002, China
| | - Qinq Guo
- Department of Pathology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing 210002, China
| | - Shanshan Shi
- Department of Pathology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing 210002, China
| | - Qunli Shi
- Department of Pathology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing 210002, China
| | - Xiaojun Zhou
- Department of Pathology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing 210002, China
| | - Qi Liu
- Department of Obstetrics and Gynecology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing 210002, China
| | - Guangming Lu
- Department of Radiology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing 210002, China
| | - Jiandong Wang
- Department of Pathology, Jinling Hospital, Nanjing Clinical School of Southern Medical UniversityNanjing 210002, China
| |
Collapse
|
50
|
PRC2 overexpression and PRC2-target gene repression relating to poorer prognosis in small cell lung cancer. Sci Rep 2013; 3:1911. [PMID: 23714854 PMCID: PMC3665955 DOI: 10.1038/srep01911] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/14/2013] [Indexed: 01/09/2023] Open
Abstract
Small cell lung cancer (SCLC) is a subtype of lung cancer with poor prognosis. Expression array analysis of 23 SCLC cases and 42 normal tissues revealed that EZH2 and other PRC2 members were highly expressed in SCLC. ChIP-seq for H3K27me3 suggested that genes with H3K27me3(+) in SCLC were extended not only to PRC2-target genes in ES cells but also to other target genes such as cellular adhesion-related genes. These H3K27me3(+) genes in SCLC were repressed significantly, and introduction of the most repressed gene JUB into SCLC cell line lead to growth inhibition. Shorter overall survival of clinical SCLC cases correlated to repression of JUB alone, or a set of four genes including H3K27me3(+) genes. Treatment with EZH2 inhibitors, DZNep and GSK126, resulted in growth repression of SCLC cell lines. High PRC2 expression was suggested to contribute to gene repression in SCLC, and may play a role in genesis of SCLC.
Collapse
|