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Qu B, Han X, Zhao L, Zhang F, Gao Q. Relationship of HIF‑1α expression with apoptosis and cell cycle in bone marrow mesenchymal stem cells from patients with myelodysplastic syndrome. Mol Med Rep 2022; 26:239. [PMID: 35642674 PMCID: PMC9185697 DOI: 10.3892/mmr.2022.12755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
Myelodysplastic syndrome (MDS) is a group of abnormal clonal disorders with ineffective hematopoiesis, which are incurable with conventional therapy. Of note, MDS features an abnormal bone marrow microenvironment, which is related to its incidence. The hypoxia-inducible factor-1α (HIF-1α) transcriptional signature is generally activated in bone marrow stem/progenitor cells of patients with MDS. To analyze the expression of HIF-1α in bone marrow mesenchymal stem cells (BM-MSCs) and the apoptosis and cell cycle features associated with the disease, BM-MSCs were obtained from 40 patients with a definitive diagnosis of MDS and 20 subjects with hemocytopenia but a negative diagnosis of MDS as a control group. Reverse transcription-quantitative PCR and western blot analyses were used to measure HIF-1α expression in cells from the two groups and apoptosis and cell cycle were also analyzed and compared between the groups using flow cytometry assays. BM-MSCs from both the control group and the MDS group exhibited a fibroblast-like morphology, had similar growth cycles and were difficult to passage stably. It was observed that BM-MSCs from the MDS group had significantly higher HIF-1α expression levels than the control group (P<0.05). Furthermore, the BM-MSCs from the MDS group had a higher proportion of cells in early apoptosis (5.22±1.34 vs. 2.04±0.08%; P<0.0001) and late apoptosis (3.38±0.43 vs. 1.23±0.11%; P<0.01) and exhibited cell cycle arrest. This may be a noteworthy aspect of the pathogenesis of MDS and may be related to high HIF-1α expression under a hypoxic state in the bone marrow microenvironment. Furthermore, the expression of HIF-1α in bone marrow tissue sections from patients with MDS in the International Prognostic Scoring System (IPSS) lower-risk group was higher than that from patients with MDS in the IPSS high-risk group. These results revealed the role of HIF-1α as a central pathobiology mediator of MDS and an effective therapeutic target for a broad spectrum of patients with MDS, particularly for patients in the lower-risk group.
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Affiliation(s)
- Beibei Qu
- Department of Hematology, Jiading District Central Hospital, Affiliated Shanghai University of Medicine and Health Sciences, Shanghai 201800, P.R. China
| | - Xiuhua Han
- Department of Hematology, Jiading District Central Hospital, Affiliated Shanghai University of Medicine and Health Sciences, Shanghai 201800, P.R. China
| | - Lan Zhao
- Department of Hematology, Jiading District Central Hospital, Affiliated Shanghai University of Medicine and Health Sciences, Shanghai 201800, P.R. China
| | - Feifei Zhang
- Department of Hematology, Jiading District Central Hospital, Affiliated Shanghai University of Medicine and Health Sciences, Shanghai 201800, P.R. China
| | - Qingmei Gao
- Department of Hematology, Jiading District Central Hospital, Affiliated Shanghai University of Medicine and Health Sciences, Shanghai 201800, P.R. China
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Fultang L, Gneo L, De Santo C, Mussai FJ. Targeting Amino Acid Metabolic Vulnerabilities in Myeloid Malignancies. Front Oncol 2021; 11:674720. [PMID: 34094976 PMCID: PMC8174708 DOI: 10.3389/fonc.2021.674720] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/26/2021] [Indexed: 01/02/2023] Open
Abstract
Tumor cells require a higher supply of nutrients for growth and proliferation than normal cells. It is well established that metabolic reprograming in cancers for increased nutrient supply exposes a host of targetable vulnerabilities. In this article we review the documented changes in expression patterns of amino acid metabolic enzymes and transporters in myeloid malignancies and the growing list of small molecules and therapeutic strategies used to disrupt amino acid metabolic circuits within the cell. Pharmacological inhibition of amino acid metabolism is effective in inducing cell death in leukemic stem cells and primary blasts, as well as in reducing tumor burden in in vivo murine models of human disease. Thus targeting amino acid metabolism provides a host of potential translational opportunities for exploitation to improve the outcomes for patients with myeloid malignancies.
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Affiliation(s)
- Livingstone Fultang
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Luciana Gneo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Carmela De Santo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Francis J Mussai
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
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3
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Bauer M, Vaxevanis C, Heimer N, Al-Ali HK, Jaekel N, Bachmann M, Wickenhauser C, Seliger B. Expression, Regulation and Function of microRNA as Important Players in the Transition of MDS to Secondary AML and Their Cross Talk to RNA-Binding Proteins. Int J Mol Sci 2020; 21:ijms21197140. [PMID: 32992663 PMCID: PMC7582632 DOI: 10.3390/ijms21197140] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/14/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Myelodysplastic syndromes (MDS), heterogeneous diseases of hematopoietic stem cells, exhibit a significant risk of progression to secondary acute myeloid leukemia (sAML) that are typically accompanied by MDS-related changes and therefore significantly differ to de novo acute myeloid leukemia (AML). Within these disorders, the spectrum of cytogenetic alterations and oncogenic mutations, the extent of a predisposing defective osteohematopoietic niche, and the irregularity of the tumor microenvironment is highly diverse. However, the exact underlying pathophysiological mechanisms resulting in hematopoietic failure in patients with MDS and sAML remain elusive. There is recent evidence that the post-transcriptional control of gene expression mediated by microRNAs (miRNAs), long noncoding RNAs, and/or RNA-binding proteins (RBPs) are key components in the pathogenic events of both diseases. In addition, an interplay between RBPs and miRNAs has been postulated in MDS and sAML. Although a plethora of miRNAs is aberrantly expressed in MDS and sAML, their expression pattern significantly depends on the cell type and on the molecular make-up of the sample, including chromosomal alterations and single nucleotide polymorphisms, which also reflects their role in disease progression and prediction. Decreased expression levels of miRNAs or RBPs preventing the maturation or inhibiting translation of genes involved in pathogenesis of both diseases were found. Therefore, this review will summarize the current knowledge regarding the heterogeneity of expression, function, and clinical relevance of miRNAs, its link to molecular abnormalities in MDS and sAML with specific focus on the interplay with RBPs, and the current treatment options. This information might improve the use of miRNAs and/or RBPs as prognostic markers and therapeutic targets for both malignancies.
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Affiliation(s)
- Marcus Bauer
- Institute of Pathology, Martin Luther University Halle-Wittenberg, 06112 Halle, Germany; (M.B.); (C.W.)
| | - Christoforos Vaxevanis
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle 06112, Germany; (C.V.); (N.H.)
| | - Nadine Heimer
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle 06112, Germany; (C.V.); (N.H.)
| | - Haifa Kathrin Al-Ali
- Department of Hematology/Oncology, University Hospital Halle, 06112 Halle, Germany; (H.K.A.-A.); (N.J.)
| | - Nadja Jaekel
- Department of Hematology/Oncology, University Hospital Halle, 06112 Halle, Germany; (H.K.A.-A.); (N.J.)
| | - Michael Bachmann
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Radiopharmaceutical Cancer Research, 01328 Dresden, Germany;
| | - Claudia Wickenhauser
- Institute of Pathology, Martin Luther University Halle-Wittenberg, 06112 Halle, Germany; (M.B.); (C.W.)
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle 06112, Germany; (C.V.); (N.H.)
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany
- Correspondence: ; Tel.: +49-345-557-4054
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4
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Huang J, Liu Z, Sun Y, Zhong Q, Xu L, Ou R, Li C, Chen R, Yao M, Zhang Q, Liu S. Use of methylation profiling to identify significant differentially methylated genes in bone marrow mesenchymal stromal cells from acute myeloid leukemia. Int J Mol Med 2018; 41:679-686. [PMID: 29207054 PMCID: PMC5752236 DOI: 10.3892/ijmm.2017.3271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/19/2017] [Indexed: 01/01/2023] Open
Abstract
The present study aimed to characterize the epigenetic architecture by studying the DNA methylation signature in bone marrow mesenchymal stem cells (BM‑MSCs) from patients with acute myeloid leukemia (AML). Microarray dataset GSE79695 was downloaded from the Gene Expression Omnibus database. Differentially methylated sites and differentially methylated CpG islands were identified in BM‑MSC samples from patients with AML compared with controls. MicroRNAs (miRs) encoding genes covering differentially methylated sites were found and the regulation network was constructed. Pathway enrichment analysis of hypermethylated genes and hypomethylated genes was performed, followed by protein‑protein interaction (PPI) network construction. Moreover, the identified differentially methylated genes were compared with the leukemia‑related marker/therapeutic genes from the literature. Overall, 228 hypermethylated CpG site probes covering 183 gene symbols and 523 hypomethylated CpG sites probes covering 362 gene symbols were identified in the BM‑MSCs from AML patients. Furthermore, 4 genes with CpG island hypermethylation were identified, including peptidase M20 domain containing 1 (PM20D1). The hsa‑miR‑596‑encoding gene MIR596 was found to be hypermethylated and the regulation network based on hsa‑miR‑596 and its targets (such as cytochrome P450 family 1 subfamily B member 1) was constructed. Hypermethylated and hypomethylated genes were enriched in different Kyoto Encyclopedia of Genes and Genomes pathways, including 'hsa05221: Acute myeloid leukemia' and 'hsa05220: Chronic myeloid leukemia', which the hypomethylated gene mitogen‑activated protein kinase 3 (MAPK3) was involved in. In addition, MAPK3, lysine demethylase 2B and RAP1A, member of RAS oncogene family were hubs in the PPI network of methylated genes. In conclusion, PM20D1 with hypermethylation of CpG islands may be associated with the energy expenditure of patients with AML. Furthermore, the aberrantly hypermethylated miR‑159‑encoding gene MIR159 may be a potential biomarker of AML.
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Affiliation(s)
- Jing Huang
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317
- Department of Hematology, The First Hospital of Kashgar, Kashgar, Xinjiang 844000, P.R. China
| | - Zhi Liu
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317
| | - Yufan Sun
- Department of Hematology, The First Hospital of Kashgar, Kashgar, Xinjiang 844000, P.R. China
| | - Qi Zhong
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317
| | - Li Xu
- Department of Hematology, The First Hospital of Kashgar, Kashgar, Xinjiang 844000, P.R. China
| | - Ruimin Ou
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317
| | - Cheng Li
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317
| | - Rui Chen
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317
| | - Mengdong Yao
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317
| | - Qing Zhang
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317
| | - Shuang Liu
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317
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Ozdogan H, Gur Dedeoglu B, Oztemur Islakoglu Y, Aydos A, Kose S, Atalay A, Yegin ZA, Avcu F, Uckan Cetinkaya D, Ilhan O. DICER1 gene and miRNA dysregulation in mesenchymal stem cells of patients with myelodysplastic syndrome and acute myeloblastic leukemia. Leuk Res 2017; 63:62-71. [PMID: 29102598 DOI: 10.1016/j.leukres.2017.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/20/2017] [Accepted: 10/18/2017] [Indexed: 01/08/2023]
Abstract
Multipotent mesenchymal stem cells (MSC) are key components of the bone marrow (BM) microenvironment. The contribution of this microenvironment to the pathophysiology of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) is not well defined. A recent study in mice demonstrated that DICER1 gene deletion in osteoprogenitor cells from the BM microenvironment suppressed osteogenic differentiation and induced MDS and AML-like haematological findings. The present study evaluated the expression profiles of microRNAs (miRNAs) and DICER1 gene in BM-derived MSC of patients with AML (n=12), MDS (n=10) and healthy controls (HC) (n=8).miRNA expression profiles were analyzed by microarray and confirmations were performed using quantitative real-time PCR (qRT-PCR). Patient MSC displayed impaired proliferative and differentiation potential compared to HC. DICER1 gene expression was lower in MSC from MDS and AML patients than HC and some differentially expressed miRNAs indicated the potential involvement of DICER1 in the pathogenesis of MDS and AML. qRT-PCR confirmation revealed down-regulated miRNAs (hsa-miR-30d-5p, hsa-miR-222-3p and hsa-miR-30a-3p in MDS; hsa-miR-1275, hsa-miR-4725-5p and hsa-miR-143-3p in AML) and over-expressed miRNAs (hsa-miR-4462 in MDS; hsa-miR-134-5p and hsa-miR-874-3p in AML) in MDS and AML. Thus, our findings validate the results of the aforementioned animal study and demonstrate downregulation of DICER1 gene and abnormal miRNA profile in MDS and AML, which may have implications for understanding MDS and AML pathogenesis and contribute to developing targeted treatment strategies.
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Affiliation(s)
- Hakan Ozdogan
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | | | | | - Alp Aydos
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Sevil Kose
- Center for Stem Cell Research and Development (PEDI-STEM), Hacettepe University, Ankara, Turkey
| | - Arzu Atalay
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Zeynep Arzu Yegin
- Department of Hematology, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Ferit Avcu
- Department of Hematology, Memorial Hospital, Ankara, Turkey
| | - Duygu Uckan Cetinkaya
- Center for Stem Cell Research and Development (PEDI-STEM), Hacettepe University, Ankara, Turkey
| | - Osman Ilhan
- Department of Hematology, Faculty of Medicine, Ankara University, Ankara, Turkey
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6
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Bhagat TD, Chen S, Bartenstein M, Barlowe AT, Von Ahrens D, Choudhary GS, Tivnan P, Amin E, Marcondes AM, Sanders MA, Hoogenboezem RM, Kambhampati S, Ramachandra N, Mantzaris I, Sukrithan V, Laurence R, Lopez R, Bhagat P, Giricz O, Sohal D, Wickrema A, Yeung C, Gritsman K, Aplan P, Hochedlinger K, Yu Y, Pradhan K, Zhang J, Greally JM, Mukherjee S, Pellagatti A, Boultwood J, Will B, Steidl U, Raaijmakers MHGP, Deeg HJ, Kharas MG, Verma A. Epigenetically Aberrant Stroma in MDS Propagates Disease via Wnt/β-Catenin Activation. Cancer Res 2017; 77:4846-4857. [PMID: 28684528 DOI: 10.1158/0008-5472.can-17-0282] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/06/2017] [Accepted: 06/30/2017] [Indexed: 11/16/2022]
Abstract
The bone marrow microenvironment influences malignant hematopoiesis, but how it promotes leukemogenesis has not been elucidated. In addition, the role of the bone marrow stroma in regulating clinical responses to DNA methyltransferase inhibitors (DNMTi) is also poorly understood. In this study, we conducted a DNA methylome analysis of bone marrow-derived stromal cells from myelodysplastic syndrome (MDS) patients and observed widespread aberrant cytosine hypermethylation occurring preferentially outside CpG islands. Stroma derived from 5-azacytidine-treated patients lacked aberrant methylation and DNMTi treatment of primary MDS stroma enhanced its ability to support erythroid differentiation. An integrative expression analysis revealed that the WNT pathway antagonist FRZB was aberrantly hypermethylated and underexpressed in MDS stroma. This result was confirmed in an independent set of sorted, primary MDS-derived mesenchymal cells. We documented a WNT/β-catenin activation signature in CD34+ cells from advanced cases of MDS, where it associated with adverse prognosis. Constitutive activation of β-catenin in hematopoietic cells yielded lethal myeloid disease in a NUP98-HOXD13 mouse model of MDS, confirming its role in disease progression. Our results define novel epigenetic changes in the bone marrow microenvironment, which lead to β-catenin activation and disease progression of MDS. Cancer Res; 77(18); 4846-57. ©2017 AACR.
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Affiliation(s)
- Tushar D Bhagat
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Si Chen
- Erasmus Medical Center Cancer Institute, Department of Hematology and Erasmus Stem Cell Institute, Rotterdam, the Netherlands
| | | | | | - Dagny Von Ahrens
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Gaurav S Choudhary
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Patrick Tivnan
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elianna Amin
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - A Mario Marcondes
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Division of Oncology, University of Washington, Seattle, Washington
| | - Mathijs A Sanders
- Erasmus Medical Center Cancer Institute, Department of Hematology and Erasmus Stem Cell Institute, Rotterdam, the Netherlands
| | - Remco M Hoogenboezem
- Erasmus Medical Center Cancer Institute, Department of Hematology and Erasmus Stem Cell Institute, Rotterdam, the Netherlands
| | | | - Nandini Ramachandra
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Iaonnis Mantzaris
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Vineeth Sukrithan
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Remi Laurence
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Robert Lopez
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Prafullla Bhagat
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Orsi Giricz
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Davendra Sohal
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | | | - Cecilia Yeung
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kira Gritsman
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Peter Aplan
- National Institutes of Health, Bethesda, Maryland
| | | | - Yiting Yu
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Kith Pradhan
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Jinghang Zhang
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - John M Greally
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | | | - Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, NDCLS, NIHR Biomedical Research Centre, Oxford University Hospitals, Oxford, United Kingdom
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, NDCLS, NIHR Biomedical Research Centre, Oxford University Hospitals, Oxford, United Kingdom
| | - Britta Will
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Ulrich Steidl
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Marc H G P Raaijmakers
- Erasmus Medical Center Cancer Institute, Department of Hematology and Erasmus Stem Cell Institute, Rotterdam, the Netherlands.
| | - H Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. .,Division of Oncology, University of Washington, Seattle, Washington
| | | | - Amit Verma
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York.
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7
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Abstract
Research in the last few years has revealed a sophisticated interaction network between multiple bone marrow cells that regulate different hematopoietic stem cell (HSC) properties such as proliferation, differentiation, localization, and self-renewal during homeostasis. These mechanisms are essential to keep the physiological HSC numbers in check and interfere with malignant progression. In addition to the identification of multiple mutations and chromosomal aberrations driving the progression of myeloid malignancies, alterations in the niche compartment recently gained attention for contributing to disease progression. Leukemic cells can remodel the niche into a permissive environment favoring leukemic stem cell expansion over normal HSC maintenance, and evidence is accumulating that certain niche alterations can even induce leukemic transformation. Relapse after chemotherapy is still a major challenge during treatment of myeloid malignancies, and cure is only rarely achieved. Recent progress in understanding the niche-imposed chemoresistance mechanisms will likely contribute to the improvement of current therapeutic strategies. This article discusses the role of different niche cells and their stage- and disease-specific roles during progression of myeloid malignancies and in response to chemotherapy.
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8
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Huang JC, Basu SK, Zhao X, Chien S, Fang M, Oehler VG, Appelbaum FR, Becker PS. Mesenchymal stromal cells derived from acute myeloid leukemia bone marrow exhibit aberrant cytogenetics and cytokine elaboration. Blood Cancer J 2015; 5:e302. [PMID: 25860293 PMCID: PMC4450324 DOI: 10.1038/bcj.2015.17] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 02/08/2023] Open
Abstract
Bone marrow-derived mesenchymal stromal cells (BM-MSCs) play a fundamental role in the BM microenvironment (BME) and abnormalities of these cells may contribute to acute myeloid leukemia (AML) pathogenesis. The aim of the study was to characterize the cytokine and gene expression profile, immunophenotype and cytogenetics of BM-MSCs from AML patients compared to normal BM-MSCs from healthy donors. AML BM-MSCs showed decreased monocyte chemoattractant protein-1 levels compared to normal BM-MSCs. AML BM-MSCs expressed similar β1 integrin, CD44, CD73, CD90 and E-cadherin compared to normal BM-MSCs. Cytogenetic analysis revealed chromosomal aberrations in AML BM-MSCs, some overlapping with and others distinct from their corresponding AML blasts. No significant difference in gene expression was detected between AML BM-MSCs compared to normal BM-MSCs; however, comparing the differences between AML and MSCs from AML patients with the differences between normal hematopoietic cells and normal MSCs by Ingenuity pathway analysis showed key distinctions of the AML setting: (1) upstream gene regulation by transforming growth factor beta 1, tumor necrosis factor, tissue transglutaminase 2, CCAAT/enhancer binding protein alpha and SWItch/Sucrose NonFermentable related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4; (2) integrin and interleukin 8 signaling as overrepresented canonical pathways; and (3) upregulation of transcription factors FBJ murine osteosarcoma viral oncogene homolog and v-myb avian myeloblastosis viral oncogene homolog. Thus, phenotypic abnormalities of AML BM-MSCs highlight a dysfunctional BME that may impact AML survival and proliferation.
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Affiliation(s)
- J C Huang
- 1] Division of Hematology, Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA [2] Division of Gerontology & Geriatric Medicine, University of Washington, Seattle, WA, USA
| | - S K Basu
- Section of Hematology & Oncology, West Virginia University School of Medicine, Morgantown, WV, USA
| | - X Zhao
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - S Chien
- Division of Hematology, Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
| | - M Fang
- 1] Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA [2] Department of Pathology and Laboratory Medicine, University of Washington, Seattle Cancer Care Alliance, Seattle, WA, USA
| | - V G Oehler
- 1] Division of Hematology, Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA [2] Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - F R Appelbaum
- 1] Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA [2] Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - P S Becker
- 1] Division of Hematology, Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA [2] Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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9
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Increased expression of interferon signaling genes in the bone marrow microenvironment of myelodysplastic syndromes. PLoS One 2015; 10:e0120602. [PMID: 25803272 PMCID: PMC4372597 DOI: 10.1371/journal.pone.0120602] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 01/24/2015] [Indexed: 11/19/2022] Open
Abstract
Introduction The bone marrow (BM) microenvironment plays an important role in the pathogenesis of myelodysplastic syndromes (MDS) through a reciprocal interaction with resident BM hematopoietic cells. We investigated the differences between BM mesenchymal stromal cells (MSCs) in MDS and normal individuals and identified genes involved in such differences. Materials and Methods BM-derived MSCs from 7 MDS patients (3 RCMD, 3 RAEB-1, and 1 RAEB-2) and 7 controls were cultured. Global gene expression was analyzed using a microarray. Result We found 314 differentially expressed genes (DEGs) in RCMD vs. control, 68 in RAEB vs. control, and 51 in RAEB vs. RCMD. All comparisons were clearly separated from one another by hierarchical clustering. The overall similarity between differential expression signatures from the RCMD vs. control comparison and the RAEB vs. control comparison was highly significant (p = 0), which indicates a common transcriptomic response in these two MDS subtypes. RCMD and RAEB simultaneously showed an up-regulation of interferon alpha/beta signaling and the ISG15 antiviral mechanism, and a significant fraction of the RAEB vs. control DEGs were also putative targets of transcription factors IRF and ICSBP. Pathways that involved RNA polymerases I and III and mitochondrial transcription were down-regulated in RAEB compared to RCMD. Conclusion Gene expression in the MDS BM microenvironment was different from that in normal BM and exhibited altered expression according to disease progression. The present study provides genetic evidence that inflammation and immune dysregulation responses that involve the interferon signaling pathway in the BM microenvironment are associated with MDS pathogenesis, which suggests BM MSCs as a possible therapeutic target in MDS.
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10
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Calkoen FGJ, Vervat C, van Pel M, de Haas V, Vijfhuizen LS, Eising E, Kroes WGM, 't Hoen PAC, van den Heuvel-Eibrink MM, Egeler RM, van Tol MJD, Ball LM. Despite differential gene expression profiles pediatric MDS derived mesenchymal stromal cells display functionality in vitro. Stem Cell Res 2015; 14:198-210. [PMID: 25679997 DOI: 10.1016/j.scr.2015.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 12/03/2014] [Accepted: 01/19/2015] [Indexed: 12/21/2022] Open
Abstract
Pediatric myelodysplastic syndrome (MDS) is a heterogeneous disease covering a spectrum ranging from aplasia (RCC) to myeloproliferation (RAEB(t)). In adult-type MDS there is increasing evidence for abnormal function of the bone-marrow microenvironment. Here, we extensively studied the mesenchymal stromal cells (MSCs) derived from children with MDS. MSCs were expanded from the bone-marrow of 17 MDS patients (RCC: n=10 and advanced MDS: n=7) and pediatric controls (n=10). No differences were observed with respect to phenotype, differentiation capacity, immunomodulatory capacity or hematopoietic support. mRNA expression analysis by Deep-SAGE revealed increased IL-6 expression in RCC- and RAEB(t)-MDS. RCC-MDS MSC expressed increased levels of DKK3, a protein associated with decreased apoptosis. RAEB(t)-MDS revealed increased CRLF1 and decreased DAPK1 expressions. This pattern has been associated with transformation in hematopoietic malignancies. Genes reported to be differentially expressed in adult MDS-MSC did not differ between MSC of pediatric MDS and controls. An altered mRNA expression profile, associated with cell survival and malignant transformation, of MSC derived from children with MDS strengthens the hypothesis that the micro-environment is of importance in this disease. Our data support the understanding that pediatric and adult MDS are two different diseases. Further evaluation of the pathways involved might reveal additional therapy targets.
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Affiliation(s)
- F G J Calkoen
- Department of Pediatrics, Section Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, Leiden, The Netherlands.
| | - C Vervat
- Department of Pediatrics, Section Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, Leiden, The Netherlands
| | - M van Pel
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - V de Haas
- Dutch Childhood Oncology Group (DCOG), The Hague, The Netherlands
| | - L S Vijfhuizen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - E Eising
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - W G M Kroes
- Laboratory for Diagnostic Genome Analysis, Leiden University Medical Center, Leiden, The Netherlands
| | - P A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - M M van den Heuvel-Eibrink
- Dutch Childhood Oncology Group (DCOG), The Hague, The Netherlands; Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - R M Egeler
- Department of Pediatrics, Section Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, Leiden, The Netherlands; Department of Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - M J D van Tol
- Department of Pediatrics, Section Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, Leiden, The Netherlands
| | - L M Ball
- Department of Pediatrics, Section Immunology, Hematology/Oncology and Hematopoietic Stem Cell Transplantation, Leiden University Medical Center, Leiden, The Netherlands
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11
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Pelleri MC, Piovesan A, Caracausi M, Berardi AC, Vitale L, Strippoli P. Integrated differential transcriptome maps of Acute Megakaryoblastic Leukemia (AMKL) in children with or without Down Syndrome (DS). BMC Med Genomics 2014; 7:63. [PMID: 25476127 PMCID: PMC4304173 DOI: 10.1186/s12920-014-0063-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 11/12/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The incidence of Acute Megakaryoblastic Leukemia (AMKL) is 500-fold higher in children with Down Syndrome (DS) compared with non-DS children, but the relevance of trisomy 21 as a specific background of AMKL in DS is still an open issue. Several Authors have determined gene expression profiles by microarray analysis in DS and/or non-DS AMKL. Due to the rarity of AMKL, these studies were typically limited to a small group of samples. METHODS We generated integrated quantitative transcriptome maps by systematic meta-analysis from any available gene expression profile dataset related to AMKL in pediatric age. This task has been accomplished using a tool recently described by us for the generation and the analysis of quantitative transcriptome maps, TRAM (Transcriptome Mapper), which allows effective integration of data obtained from different experimenters, experimental platforms and data sources. This allowed us to explore gene expression changes involved in transition from normal megakaryocytes (MK, n=19) to DS (n=43) or non-DS (n=45) AMKL blasts, including the analysis of Transient Myeloproliferative Disorder (TMD, n=20), a pre-leukemia condition. RESULTS We propose a biological model of the transcriptome depicting progressive changes from MK to TMD and then to DS AMKL. The data indicate the repression of genes involved in MK differentiation, in particular the cluster on chromosome 4 including PF4 (platelet factor 4) and PPBP (pro-platelet basic protein); the gene for the mitogen-activated protein kinase MAP3K10 and the thrombopoietin receptor gene MPL. Moreover, comparing both DS and non-DS AMKL with MK, we identified three potential clinical markers of progression to AMKL: TMEM241 (transmembrane protein 241) was the most over-expressed single gene, while APOC2 (apolipoprotein C-II) and ZNF587B (zinc finger protein 587B) appear to be the most discriminant markers of progression, specifically to DS AMKL. Finally, the chromosome 21 (chr21) genes resulted to be the most over-expressed in DS and non-DS AMKL, as well as in TMD, pointing out a key role of chr21 genes in differentiating AMKL from MK. CONCLUSIONS Our study presents an integrated original model of the DS AMLK transcriptome, providing the identification of genes relevant for its pathophysiology which can potentially be new clinical markers.
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Affiliation(s)
- Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Anna Concetta Berardi
- Research Laboratory Stem Cells, U.O.C. Immunohematology-Transfusion Medicine and Laboratory of Hematology, Santo Spirito's Hospital, Via del Circuito, 65100, Pescara, Italy.
| | - Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy.
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126, Bologna, BO, Italy. .,Interdepartmental Center for Cancer Research Giorgio Prodi (CIRC), S. Orsola-Malpighi Hospital, University of Bologna, Via Massarenti 9, 40138, Bologna, BO, Italy.
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12
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Wang J, Xiao Z. Mesenchymal stem cells in pathogenesis of myelodysplastic syndromes. Stem Cell Investig 2014; 1:16. [PMID: 27358862 DOI: 10.3978/j.issn.2306-9759.2014.08.02] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/18/2014] [Indexed: 01/13/2023]
Abstract
Myelodysplastic syndromes (MDS) are clonal malignant stem cell disorders characterized by inefficient hematopoiesis. The role of the marrow microenvironment in the pathogenesis of the disease has been controversial. Emerging evidence indicated that mesenchymal stem cells (MSC) derived from MDS patients were cytogenetically abnormal, and they showed a deficient hematopoietic-supportive capacity and increased production of cytokine such as tumor necrosis factor α (TNF-α), interleukin 6 (IL-6), interferon γ (IFN-γ). From the point of some evidence, the abnormal microenvironment seems to participate in the progression of the disease by contributing to the selective expansion of the malignant clone. In this review, we will discuss the most recent progress related to identification of normal MSC and the importance of the stem cell niche in development and maintenance of MDS.
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Affiliation(s)
- Jingya Wang
- 1 MDS and MPN Centre, 2 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Zhijian Xiao
- 1 MDS and MPN Centre, 2 State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
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13
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Liao R, Xu Y, Chen M, Chen X, Zhan X, Sun J. Molecular mechanism of microRNA involvement in genesis of myelodysplastic syndrome and its transformation to acute myeloid leukemia. Hematology 2013; 18:191-7. [PMID: 23321417 DOI: 10.1179/1607845412y.0000000053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Rongxia Liao
- Medical English DepartmentCollege of Basic Medicine, Third Military Medical University, Chongqing, PR China
| | - Yanmei Xu
- Cancer Institute of People's Liberation Army, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
| | - Min Chen
- Medical English DepartmentCollege of Basic Medicine, Third Military Medical University, Chongqing, PR China
| | - Xiewan Chen
- Medical English DepartmentCollege of Basic Medicine, Third Military Medical University, Chongqing, PR China
| | - Xiaoqing Zhan
- Medical English DepartmentCollege of Basic Medicine, Third Military Medical University, Chongqing, PR China
| | - Jianguo Sun
- Cancer Institute of People's Liberation Army, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
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14
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de Oliveira FM, Lucena-Araujo AR, Favarin MDC, Bonini Palma PV, Rego EM, Falcão RP, Covas DT, Fontes AM. Differential expression of AURKA and AURKB genes in bone marrow stromal mesenchymal cells of myelodysplastic syndrome: correlation with G-banding analysis and FISH. Exp Hematol 2013; 41:198-208. [DOI: 10.1016/j.exphem.2012.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 08/17/2012] [Accepted: 10/01/2012] [Indexed: 12/23/2022]
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15
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André V, Longoni D, Bresolin S, Cappuzzello C, Dander E, Galbiati M, Bugarin C, Di Meglio A, Nicolis E, Maserati E, Serafini M, Warren AJ, Te Kronnie G, Cazzaniga G, Sainati L, Cipolli M, Biondi A, D'Amico G. Mesenchymal stem cells from Shwachman-Diamond syndrome patients display normal functions and do not contribute to hematological defects. Blood Cancer J 2012; 2:e94. [PMID: 23064742 PMCID: PMC3483621 DOI: 10.1038/bcj.2012.40] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Shwachman–Diamond syndrome (SDS) is a rare inherited disorder characterized by bone marrow (BM) dysfunction and exocrine pancreatic insufficiency. SDS patients have an increased risk for myelodisplastic syndrome and acute myeloid leukemia. Mesenchymal stem cells (MSCs) are the key component of the hematopoietic microenvironment and are relevant in inducing genetic mutations leading to leukemia. However, their role in SDS is still unexplored. We demonstrated that morphology, growth kinetics and expression of surface markers of MSCs from SDS patients (SDS-MSCs) were similar to normal MSCs. Moreover, SDS-MSCs were able to differentiate into mesengenic lineages and to inhibit the proliferation of mitogen-activated lymphocytes. We demonstrated in an in vitro coculture system that SDS-MSCs, significantly inhibited neutrophil apoptosis probably through interleukin-6 production. In a long-term coculture with CD34+-sorted cells, SDS-MSCs were able to sustain CD34+ cells survival and to preserve their stemness. Finally, SDS-MSCs had normal karyotype and did not show any chromosomal abnormality observed in the hematological components of the BM of SDS patients. Despite their pivotal role in the hematopoietic stem cell niche, our data suggest that MSC themselves do not seem to be responsible for the hematological defects typical of SDS patients.
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Affiliation(s)
- V André
- Centro Ricerca 'M Tettamanti', Clinica Pediatrica Università degli Studi di Milano-Bicocca, Ospedale San Gerardo, Monza, Italy
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16
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Bresolin S, Trentin L, Zecca M, Giordan M, Sainati L, Locatelli F, Basso G, te Kronnie G. Gene expression signatures of pediatric myelodysplastic syndromes are associated with risk of evolution into acute myeloid leukemia. Leukemia 2012; 26:1717-9. [DOI: 10.1038/leu.2012.35] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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17
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Mesenchymal stromal cells of myelodysplastic syndrome and acute myeloid leukemia patients have distinct genetic abnormalities compared with leukemic blasts. Blood 2011; 118:5583-92. [PMID: 21948175 DOI: 10.1182/blood-2011-03-343467] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) are an essential cell type of the hematopoietic microenvironment. Concerns have been raised about the possibility that MSCs undergo malignant transformation. Several studies, including one from our own group, have shown the presence of cytogenetic abnormalities in MSCs from leukemia patients. The aim of the present study was to compare genetic aberrations in hematopoietic cells (HCs) and MSCs of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) patients. Cytogenetic aberrations were detected in HCs from 25 of 51 AML patients (49%) and 16 of 43 MDS patients (37%). Mutations of the FLT3 and NPM1 genes were detected in leukemic blasts in 12 (23%) and 8 (16%) AML patients, respectively. Chromosomal aberrations in MSCs were detected in 15 of 94 MDS/AML patients (16%). No chromosomal abnormalities were identified in MSCs of 36 healthy subjects. We demonstrate herein that MSCs have distinct genetic abnormalities compared with leukemic blasts. We also analyzed the main characteristics of patients with MSCs carrying chromosomal aberrations. In view of these data, the genetic alterations in MSCs may constitute a particular mechanism of leukemogenesis.
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18
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Affiliation(s)
- Henrik Hasle
- Department of Paediatrics, Aarhus University Hospital Skejby, Aarhus, Denmark.
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19
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Theilgaard-Mönch K, Boultwood J, Ferrari S, Giannopoulos K, Hernandez-Rivas JM, Kohlmann A, Morgan M, Porse B, Tagliafico E, Zwaan CM, Wainscoat J, Van den Heuvel-Eibrink MM, Mills K, Bullinger L. Gene expression profiling in MDS and AML: potential and future avenues. Leukemia 2011; 25:909-20. [PMID: 21445077 DOI: 10.1038/leu.2011.48] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Today, the classification systems for myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) already incorporate cytogenetic and molecular genetic aberrations in an attempt to better reflect disease biology. However, in many MDS/AML patients no genetic aberrations have been identified yet, and even within some cytogenetically well-defined subclasses there is considerable clinical heterogeneity. Recent advances in genomics technologies such as gene expression profiling (GEP) provide powerful tools to further characterize myeloid malignancies at the molecular level, with the goal to refine the MDS/AML classification system, incorporating as yet unknown molecular genetic and epigenetic pathomechanisms, which are likely reflected by aberrant gene expression patterns. In this study, we provide a comprehensive review on how GEP has contributed to a refined molecular taxonomy of MDS and AML with regard to diagnosis, prediction of clinical outcome, discovery of novel subclasses and identification of novel therapeutic targets and novel drugs. As many challenges remain ahead, we discuss the pitfalls of this technology and its potential including future integrative studies with other genomics technologies, which will continue to improve our understanding of malignant transformation in myeloid malignancies and thereby contribute to individualized risk-adapted treatment strategies for MDS and AML patients.
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Affiliation(s)
- K Theilgaard-Mönch
- Biotech Research and Innovation Centre & Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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20
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Chang HH, McGeachie M, Alterovitz G, Ramoni MF. Mapping transcription mechanisms from multimodal genomic data. BMC Bioinformatics 2010; 11 Suppl 9:S2. [PMID: 21044360 PMCID: PMC2967743 DOI: 10.1186/1471-2105-11-s9-s2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene expression data, raising a new computational challenge due to the tremendous size of data. RESULTS We develop a method to identify eQTLs. The method represents eQTLs as information flux between genetic variants and transcripts. We use information theory to simultaneously interrogate SNP and gene expression data, resulting in a Transcriptional Information Map (TIM) which captures the network of transcriptional information that links genetic variations, gene expression and regulatory mechanisms. These maps are able to identify both cis- and trans- regulating eQTLs. The application on a dataset of leukemia patients identifies eQTLs in the regions of the GART, PCP4, DSCAM, and RIPK4 genes that regulate ADAMTS1, a known leukemia correlate. CONCLUSIONS The information theory approach presented in this paper is able to infer the dependence networks between SNPs and transcripts, which in turn can identify cis- and trans-eQTLs. The application of our method to the leukemia study explains how genetic variants and gene expression are linked to leukemia.
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Affiliation(s)
- Hsun-Hsien Chang
- Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA.
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21
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Santos RPC, Benvenuti TT, Honda ST, Del Valle PR, Katayama MLH, Brentani HP, Carraro DM, Rozenchan PB, Brentani MM, de Lyra EC, Torres CH, Salzgeber MB, Kaiano JHL, Góes JCS, Folgueira MAAK. Influence of the interaction between nodal fibroblast and breast cancer cells on gene expression. Tumour Biol 2010; 32:145-57. [PMID: 20820980 PMCID: PMC3003151 DOI: 10.1007/s13277-010-0108-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 08/18/2010] [Indexed: 11/10/2022] Open
Abstract
Our aim was to evaluate the interaction between breast cancer cells and nodal fibroblasts, by means of their gene expression profile. Fibroblast primary cultures were established from negative and positive lymph nodes from breast cancer patients and a similar gene expression pattern was identified, following cell culture. Fibroblasts and breast cancer cells (MDA-MB231, MDA-MB435, and MCF7) were cultured alone or co-cultured separated by a porous membrane (which allows passage of soluble factors) for comparison. Each breast cancer lineage exerted a particular effect on fibroblasts viability and transcriptional profile. However, fibroblasts from positive and negative nodes had a parallel transcriptional behavior when co-cultured with a specific breast cancer cell line. The effects of nodal fibroblasts on breast cancer cells were also investigated. MDA MB-231 cells viability and migration were enhanced by the presence of fibroblasts and accordingly, MDA-MB435 and MCF7 cells viability followed a similar pattern. MDA-MB231 gene expression profile, as evaluated by cDNA microarray, was influenced by the fibroblasts presence, and HNMT, COMT, FN3K, and SOD2 were confirmed downregulated in MDA-MB231 co-cultured cells with fibroblasts from both negative and positive nodes, in a new series of RT-PCR assays. In summary, transcriptional changes induced in breast cancer cells by fibroblasts from positive as well as negative nodes are very much alike in a specific lineage. However, fibroblasts effects are distinct in each one of the breast cancer lineages, suggesting that the inter-relationships between stromal and malignant cells are dependent on the intrinsic subtype of the tumor.
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Affiliation(s)
- Rosângela Portilho Costa Santos
- Departamento de Radiologia e Oncologia, LIM24, Faculdade de Medicina, Universidade de São Paulo, Avenida Dr. Arnaldo, 455, 4º andar, sala 4124, CEP: 01246-903 São Paulo, SP, Brazil
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22
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Shipounova IN, Petrova TV, Svinareva DA, Momotuk KS, Mikhailova EA, Drize NI. Alterations in hematopoietic microenvironment in patients with aplastic anemia. Clin Transl Sci 2010; 2:67-74. [PMID: 20443870 DOI: 10.1111/j.1752-8062.2008.00074.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mechanisms of hematopoietic failure in patients with aplastic anemia (AA) are obscure. We investigate alterations in the hematopoietic microenvironment in AA patients. We present the results of studying mesenchymal stromal cells (MSC), fibroblastic colony-forming units (CFU-F), and adherent cell layers (ACL) of long-term bone marrow cultures (LTBMC) from bone marrow (BM) samples of AA patients. MSC of AA patients proliferated longer than those of donors. In half of the patients' MSC cultures, adipogenesis was impaired. Osteogenic differentiation was not achieved in 36% of AA MSC. CFU-F formed enlarged colonies, and their concentration in the BM of AA patients was significantly increased. Our data suggest that the physiological activation of the stromal microenvironment is characteristic of AA. We detected a decrease in the expression of the angiopoetin-1 (ANG-1) and vascular cell adhesion molecule-1 (VCAM-1) genes, together with an increase in the expression of vascular endothelial growth factor (VEGF) in ACL of AA patients. This indicates abnormal regulatory patterns in both osteoblastic and vascular contexts. Addition of AA patients' serum to donors' LTBMC for 3 weeks induced similar gene expression alterations. The addition of parathyroid hormone (PTH) resulted in the expression levels of analyzed genes returning to normal, in both AA LTBMC and donor cultures treated with AA serum. The physiologic status of the BM stromal microenvironment (MSC, CFU-F, and ACL of LTBMC) of AA patients was altered.
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Affiliation(s)
- Irina N Shipounova
- Laboratory for Physiology of Haemopoiesis, National Haematology Research Centre, Russian Academy of Medical Science, Moscow, Russia.
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The role of p38 mitogen-activated protein kinase in serum-induced leukemia inhibitory factor secretion by bone marrow stromal cells from pediatric myelodysplastic syndromes. Leuk Res 2010; 34:507-12. [DOI: 10.1016/j.leukres.2009.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 09/24/2009] [Accepted: 10/14/2009] [Indexed: 11/19/2022]
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24
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Shipounova IN, Petrova TV, Svinareva DA, Momotuk KS, Mikhailova EA, Drize NI. Alterations in Hematopoietic Microenvironment in Patients with Aplastic Anemia. Clin Transl Sci 2009. [DOI: 10.1111/j.1752-8062.2009.00074.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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25
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Flores-Figueroa E, Montesinos JJ, Flores-Guzmán P, Gutiérrez-Espíndola G, Arana-Trejo RM, Castillo-Medina S, Pérez-Cabrera A, Hernández-Estévez E, Arriaga L, Mayani H. Functional analysis of myelodysplastic syndromes-derived mesenchymal stem cells. Leuk Res 2008; 32:1407-16. [DOI: 10.1016/j.leukres.2008.02.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 02/06/2008] [Accepted: 02/07/2008] [Indexed: 12/20/2022]
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Apoptosis and antiapoptotic mechanisms in the progression of myelodysplastic syndrome. Exp Hematol 2008; 35:1739-46. [PMID: 17976524 DOI: 10.1016/j.exphem.2007.09.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 09/12/2007] [Accepted: 09/17/2007] [Indexed: 11/20/2022]
Abstract
Myelodysplastic syndrome (MDS), previously known as preleukemia, comprises a spectrum of heterogeneous, clonal disorders of hematopoiesis. A patient's life expectancy can range from a few months to more than a decade. Recent studies provide some insight into the pathophysiology of MDS. One mechanism contributing to the constellation of hypercellular marrow and peripheral blood cytopenia is a significant increase in programmed cell death (apoptosis) in hematopoietic cells. Tumor necrosis factor (TNF)-alpha, Fas ligand, TNF-related apoptosis-inducing ligand, and other proapoptotic cytokines are upregulated in early-stage/low-risk MDS, and neutralization of these signals can improve hematopoiesis. TNF-related apoptosis inducing ligand induces apoptosis preferentially in clonal cells, which can contribute to containment of the clone. In a proportion of patients, MDS will eventually evolve to acute leukemia. This progression has been correlated with upregulation of nuclear factor kappaB; altered expression of adaptor molecules, such as Flice inhibitory protein; and enhanced activity of antiapoptotic members of the Bcl-2 and inhibitors of apoptosis protein families. Also, the ratio of TNF receptors 1 and 2 changes in favor of receptor 2. The role of the microenvironment in the pathophysiology and progression of MDS has remained controversial, although there is evidence that stroma and matrix components, and their interactions with clonal cells, play an important role. Microarray gene-expression studies are consistent with dysregulation of apoptosis, but not all data are in agreement.
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Mayani H. Abnormal stromal cells in Myelodysplastic Syndromes: Genomics presents further evidence. Leuk Res 2007; 31:577-8. [PMID: 17113149 DOI: 10.1016/j.leukres.2006.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 10/11/2006] [Accepted: 10/16/2006] [Indexed: 10/23/2022]
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