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Neelamraju Y, Gjini E, Chhangawala S, Fan H, He S, Jing CB, Nguyen AT, Prajapati S, Sheridan C, Houvras Y, Melnick A, Look AT, Garrett-Bakelman FE. Depletion of tet2 results in age-dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome. FRONTIERS IN HEMATOLOGY 2023; 2:1235170. [PMID: 37937078 PMCID: PMC10629367 DOI: 10.3389/frhem.2023.1235170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Introduction Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis, cytopenias, and dysplasia. The gene encoding ten-eleven translocation 2 (tet2), a dioxygenase enzyme that catalyzes the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine, is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously, we reported a stable zebrafish line with a loss-of-function mutation in the tet2 gene. The tet2m/m-mutant zebrafish developed a pre-MDS state with kidney marrow dysplasia, but normal circulating blood counts by 11 months of age and accompanying anemia, signifying the onset of MDS, by 24 months of age. Methods In the current study, we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 and 15 months of age and conducted enhanced reduced representation of bisulfite sequencing (ERRBS) and bulk RNA-seq to measure changes in DNA methylation and gene expression of hematopoietic stem and progenitor cells (HSPCs). Results and discussion A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 months of age when compared with the wild type. Furthermore, hypermethylated genes were significantly enriched for targets of SUZ12 and the metal-response-element-binding transcription factor 2 (MTF2)-involved in the polycomb repressive complex 2 (PRC2). However, between 4 and 15 months of age, we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analyses identified upregulation of genes associated with mTORC1 signaling and interferon gamma and alpha responses in tet2m/m HSPCs at 4 months of age when compared with the wild type. Downregulated genes in HSPCs of tet2-mutant fish at 4 months of age were enriched for cell cycle regulation, heme metabolism, and interleukin 2 (IL2)/signal transducer and activator of transcription 5 (STAT5) signaling, possibly related to increased self-renewal and clonal advantage in HSPCs with tet2 loss of function. Finally, there was an overall inverse correlation between overall increased promoter methylation and gene expression.
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Affiliation(s)
- Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Evisa Gjini
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | | | - Hao Fan
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | | | - Ashley T. Nguyen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Subhash Prajapati
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Caroline Sheridan
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | | | - Ari Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Francine E. Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
- Department of Medicine, University of Virginia, Charlottesville, VA, United States
- University of Virginia Cancer Center, Charlottesville, VA, United States
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Kumar K, Sinha SK, Maity U, Kirti PB, Kumar KRR. Insights into established and emerging roles of SR protein family in plants and animals. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1763. [PMID: 36131558 DOI: 10.1002/wrna.1763] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 05/13/2023]
Abstract
Splicing of pre-mRNA is an essential part of eukaryotic gene expression. Serine-/arginine-rich (SR) proteins are highly conserved RNA-binding proteins present in all metazoans and plants. SR proteins are involved in constitutive and alternative splicing, thereby regulating the transcriptome and proteome diversity in the organism. In addition to their role in splicing, SR proteins are also involved in mRNA export, nonsense-mediated mRNA decay, mRNA stability, and translation. Due to their pivotal roles in mRNA metabolism, SR proteins play essential roles in normal growth and development. Hence, any misregulation of this set of proteins causes developmental defects in both plants and animals. SR proteins from the animal kingdom are extensively studied for their canonical and noncanonical functions. Compared with the animal kingdom, plant genomes harbor more SR protein-encoding genes and greater diversity of SR proteins, which are probably evolved for plant-specific functions. Evidence from both plants and animals confirms the essential role of SR proteins as regulators of gene expression influencing cellular processes, developmental stages, and disease conditions. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Kundan Kumar
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Shubham Kumar Sinha
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Upasana Maity
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
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Cheng L, Sun B, Xiong Y, Hu L, Gao L, Li J, Xie H, Chen X, Zhang W, Zhou HH. WGCNA-Based DNA Methylation Profiling Analysis on Allopurinol-Induced Severe Cutaneous Adverse Reactions: A DNA Methylation Signature for Predisposing Drug Hypersensitivity. J Pers Med 2022; 12:jpm12040525. [PMID: 35455641 PMCID: PMC9027774 DOI: 10.3390/jpm12040525] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 02/06/2023] Open
Abstract
Background: The role of aberrant DNA methylation in allopurinol-induced severe cutaneous adverse reactions (SCARs) is incompletely understood. To fill the gap, we analyze the DNA methylation profiling in allopurinol-induced Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) patients and identify the DNA methylation signature for predisposing allopurinol hypersensitivity. Methods: Genome-scale methylation analysis was conducted using the Illumina® HumanMethylation450 BeadChip. Weighted Gene Co-Expression Network Analysis (WGCNA) was utilized to analyze the data. Results: A total of 21,497 annotated promoter regions were analyzed. Ten modules were identified between allopurinol hypersensitivity and tolerance, with turquoise and yellow modules being the most significant correlation. ATG13, EPM2AIP1, and SRSF11 were the top three hub genes in the turquoise module. MIR412, MIR369, and MIR409 were the top three hub genes in the yellow module. Gene Ontology (GO) analysis revealed that the turquoise module was related to the metabolic process in intracellular organelles and the binding of various compounds, proteins, or nucleotides. The yellow module, however, was related to stimulus sensory perception in cytoskeletal elements and the activity of the receptor or transducer. Conclusion: DNA methylation plays a vital role in allopurinol-induced severe cutaneous adverse reactions (SCARs). DNA methylation profiling of SJS/TEN is significantly related to autophagy and microRNAs (miRNAs).
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Affiliation(s)
- Lin Cheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- Correspondence: (L.C.); (H.-H.Z.)
| | - Bao Sun
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China; (B.S.); (Y.X.); (L.H.); (X.C.); (W.Z.)
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
| | - Yan Xiong
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China; (B.S.); (Y.X.); (L.H.); (X.C.); (W.Z.)
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
| | - Lei Hu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China; (B.S.); (Y.X.); (L.H.); (X.C.); (W.Z.)
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
| | - Lichen Gao
- Department of Pharmacy, Department of Oncology, Cancer Institute, Changsha Central Hospital, Changsha 410004, China;
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China; (J.L.); (H.X.)
| | - Hongfu Xie
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China; (J.L.); (H.X.)
| | - Xiaoping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China; (B.S.); (Y.X.); (L.H.); (X.C.); (W.Z.)
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China; (B.S.); (Y.X.); (L.H.); (X.C.); (W.Z.)
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China; (B.S.); (Y.X.); (L.H.); (X.C.); (W.Z.)
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
- Correspondence: (L.C.); (H.-H.Z.)
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Merkerova MD, Krejcik Z. Transposable elements and Piwi‑interacting RNAs in hemato‑oncology with a focus on myelodysplastic syndrome (Review). Int J Oncol 2021; 59:105. [PMID: 34779490 DOI: 10.3892/ijo.2021.5285] [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: 06/21/2021] [Accepted: 10/12/2021] [Indexed: 11/06/2022] Open
Abstract
Our current understanding of hematopoietic stem cell differentiation and the abnormalities that lead to leukemogenesis originates from the accumulation of knowledge regarding protein‑coding genes. However, the possible impact of transposable element (TE) mobilization and the expression of P‑element‑induced WImpy testis‑interacting RNAs (piRNAs) on leukemogenesis has been beyond the scope of scientific interest to date. The expression profiles of these molecules and their importance for human health have only been characterized recently due to the rapid progress of high‑throughput sequencing technology development. In the present review, current knowledge on the expression profile and function of TEs and piRNAs was summarized, with specific focus on their reported involvement in leukemogenesis and pathogenesis of myelodysplastic syndrome.
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Affiliation(s)
| | - Zdenek Krejcik
- Institute of Hematology and Blood Transfusion, 128 20 Prague, Czech Republic
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5
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Mutation accumulation in cancer genes relates to nonoptimal outcome in chronic myeloid leukemia. Blood Adv 2021; 4:546-559. [PMID: 32045476 DOI: 10.1182/bloodadvances.2019000943] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/18/2019] [Indexed: 12/24/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm accounting for ∼15% of all leukemia. Progress of the disease from an indolent chronic phase to the more aggressive accelerated phase or blast phase (BP) occurs in a minority of cases and is associated with an accumulation of somatic mutations. We performed genetic profiling of 85 samples and transcriptome profiling of 12 samples from 59 CML patients. We identified recurrent somatic mutations in ABL1 (37%), ASXL1 (26%), RUNX1 (16%), and BCOR (16%) in the BP and observed that mutation signatures in the BP resembled those of acute myeloid leukemia (AML). We found that mutation load differed between the indolent and aggressive phases and that nonoptimal responders had more nonsilent mutations than did optimal responders at the time of diagnosis, as well as in follow-up. Using RNA sequencing, we identified other than BCR-ABL1 cancer-associated hybrid genes in 6 of the 7 BP samples. Uncovered expression alterations were in turn associated with mechanisms and pathways that could be targeted in CML management and by which somatic alterations may emerge in CML. Last, we showed the value of genetic data in CML management in a personalized medicine setting.
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Liu K, Beck D, Thoms JAI, Liu L, Zhao W, Pimanda JE, Zhou X. Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. Bioinformatics 2018; 33:2622-2630. [PMID: 28472271 DOI: 10.1093/bioinformatics/btx280] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 04/22/2017] [Indexed: 02/01/2023] Open
Abstract
Motivation Long non-coding RNAs (lncRNAs) have been implicated in the regulation of diverse biological functions. The number of newly identified lncRNAs has increased dramatically in recent years but their expression and function have not yet been described from most diseases. To elucidate lncRNA function in human disease, we have developed a novel network based method (NLCFA) integrating correlations between lncRNA, protein coding genes and noncoding miRNAs. We have also integrated target gene associations and protein-protein interactions and designed our model to provide information on the combined influence of mRNAs, lncRNAs and miRNAs on cellular signal transduction networks. Results We have generated lncRNA expression profiles from the CD34+ haematopoietic stem and progenitor cells (HSPCs) from patients with Myelodysplastic syndromes (MDS) and healthy donors. We report, for the first time, aberrantly expressed lncRNAs in MDS and further prioritize biologically relevant lncRNAs using the NLCFA. Taken together, our data suggests that aberrant levels of specific lncRNAs are intimately involved in network modules that control multiple cancer-associated signalling pathways and cellular processes. Importantly, our method can be applied to prioritize aberrantly expressed lncRNAs for functional validation in other diseases and biological contexts. Availability and implementation The method is implemented in R language and Matlab. Contact xizhou@wakehealth.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Keqin Liu
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Dominik Beck
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, 2052, Australia.,Centre for Health Technologies and School of Software, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Julie A I Thoms
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, 2052, Australia
| | - Liang Liu
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Weiling Zhao
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - John E Pimanda
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, 2052, Australia.,Centre for Health Technologies and School of Software, University of Technology Sydney, Sydney, NSW, 2007, Australia.,Department of Haematology, Prince of Wales Hospital, Randwick, NSW, 2031, Australia
| | - Xiaobo Zhou
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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Colombo AR, Zubair A, Thiagarajan D, Nuzhdin S, Triche TJ, Ramsingh G. Suppression of Transposable Elements in Leukemic Stem Cells. Sci Rep 2017; 7:7029. [PMID: 28765607 PMCID: PMC5539300 DOI: 10.1038/s41598-017-07356-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/23/2017] [Indexed: 01/15/2023] Open
Abstract
Genomic transposable elements (TEs) comprise nearly half of the human genome. The expression of TEs is considered potentially hazardous, as it can lead to insertional mutagenesis and genomic instability. However, recent studies have revealed that TEs are involved in immune-mediated cell clearance. Hypomethylating agents can increase the expression of TEs in cancer cells, inducing ‘viral mimicry’, causing interferon signalling and cancer cell killing. To investigate the role of TEs in the pathogenesis of acute myeloid leukaemia (AML), we studied TE expression in several cell fractions of AML while tracking its development (pre-leukemic haematopoietic stem cells, leukemic stem cells [LSCs], and leukemic blasts). LSCs, which are resistant to chemotherapy and serve as reservoirs for relapse, showed significant suppression of TEs and interferon pathways. Similarly, high-risk cases of myelodysplastic syndrome (MDS) showed far greater suppression of TEs than low-risk cases. We propose TE suppression as a mechanism for immune escape in AML and MDS. Repression of TEs co-occurred with the upregulation of several genes known to modulate TE expression, such as RNA helicases and autophagy genes. Thus, we have identified potential pathways that can be targeted to activate cancer immunogenicity via TEs in AML and MDS.
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Affiliation(s)
- Anthony R Colombo
- Keck School of Medicine of University of Southern California, Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, Los Angeles, California, 90033, USA
| | - Asif Zubair
- University of Southern California, Department of Molecular and Computational Biology, Los Angeles, CA, 90089-2910, USA
| | - Devi Thiagarajan
- Keck School of Medicine of University of Southern California, Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, Los Angeles, California, 90033, USA.,Langone Medical Center of New York University School of Medicine, Endocrinology Division for the Study of Diabetes, 550 1st Avenue, New York, NY, 10016, USA
| | - Sergey Nuzhdin
- University of Southern California, Department of Molecular and Computational Biology, Los Angeles, CA, 90089-2910, USA
| | - Timothy J Triche
- Keck School of Medicine of University of Southern California, Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, Los Angeles, California, 90033, USA.
| | - Giridharan Ramsingh
- Keck School of Medicine of University of Southern California, Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, Los Angeles, California, 90033, USA.
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de Necochea-Campion R, Shouse GP, Zhou Q, Mirshahidi S, Chen CS. Aberrant splicing and drug resistance in AML. J Hematol Oncol 2016; 9:85. [PMID: 27613060 PMCID: PMC5018179 DOI: 10.1186/s13045-016-0315-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/02/2016] [Indexed: 02/08/2023] Open
Abstract
The advent of next-generation sequencing technologies has unveiled a new window into the heterogeneity of acute myeloid leukemia (AML). In particular, recurrent mutations in spliceosome machinery and genome-wide aberrant splicing events have been recognized as a prominent component of this disease. This review will focus on how these factors influence drug resistance through altered splicing of tumor suppressor and oncogenes and dysregulation of the apoptotic signaling network. A better understanding of these factors in disease progression is necessary to design appropriate therapeutic strategies recognizing specific alternatively spliced or mutated oncogenic targets.
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Affiliation(s)
- Rosalia de Necochea-Campion
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Geoffrey P Shouse
- Division of Hematology/Oncology, Loma Linda University School of Medicine, 11175 Campus Street, Chan Shun Pavilion 11015, Loma Linda, CA, 92354, USA
| | - Qi Zhou
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Saied Mirshahidi
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Chien-Shing Chen
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA. .,Division of Hematology/Oncology, Loma Linda University School of Medicine, 11175 Campus Street, Chan Shun Pavilion 11015, Loma Linda, CA, 92354, USA.
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9
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Tian J, Li Z, Han Y, Jiang T, Song X, Jiang G. The progress of early growth response factor 1 and leukemia. Intractable Rare Dis Res 2016; 5:76-82. [PMID: 27195189 PMCID: PMC4869586 DOI: 10.5582/irdr.2015.01049] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Early growth response gene-1 (EGR1) widely exists in the cell nucleus of such as, zebrafish, mice, chimpanzees and humans, an it also can be observed in the cytoplasm of some tumors. EGR1 was named just after its brief and rapid expression of different stimuli. Accumulating studies have extensively demonstrated that the widespread dysregulation of EGR1 is involved in hematological malignancies such as human acute myeloid leukemia (AML), chronic myelogenous leukemia, chronic lymphocytic leukemia, multiple myeloma, and B cell lymphoma. With the deep research on EGR1, its expression, function and regulatory mechanism has been gradually elucidated, and provides more possibilities for treatment strategies of patients with leukemia. Herein, we summarize the roles of EGR1 in its biological function and relationship with leukemia.
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Affiliation(s)
- Jing Tian
- Key Laboratory for Modern Medicine and Technology of Shandong Province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
- School of Medicine and Life Sciences, Ji'nan University, Ji'nan, Shandong, China
| | - Ziwei Li
- Key Laboratory for Modern Medicine and Technology of Shandong Province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
- School of Medicine and Life Sciences, Ji'nan University, Ji'nan, Shandong, China
| | - Yang Han
- Key Laboratory for Modern Medicine and Technology of Shandong Province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
- School of Medicine and Life Sciences, Ji'nan University, Ji'nan, Shandong, China
| | - Tao Jiang
- Graduate School of Xuzhou Medical College, Xuzhou, Jiangsu, China
| | - Xiaoming Song
- Graduate School of Bengbu Medical College, Bengbu, Anhui, China
| | - Guosheng Jiang
- Key Laboratory for Modern Medicine and Technology of Shandong Province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
- School of Medicine and Life Sciences, Ji'nan University, Ji'nan, Shandong, China
- Address correspondence to: Dr. Guosheng Jiang, Key Laboratory for rare & uncommon diseases of Shandong Province, Institute of Basic Medicine, Shandong Academy of Medical Sciences, NO.18877 of Jingshi Road, Ji'nan, Shandong, China. E-mail:
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Guerenne L, Beurlet S, Said M, Gorombei P, Le Pogam C, Guidez F, de la Grange P, Omidvar N, Vanneaux V, Mills K, Mufti GJ, Sarda-Mantel L, Noguera ME, Pla M, Fenaux P, Padua RA, Chomienne C, Krief P. GEP analysis validates high risk MDS and acute myeloid leukemia post MDS mice models and highlights novel dysregulated pathways. J Hematol Oncol 2016; 9:5. [PMID: 26817437 PMCID: PMC4728810 DOI: 10.1186/s13045-016-0235-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 01/19/2016] [Indexed: 12/13/2022] Open
Abstract
Background In spite of the recent discovery of genetic mutations in most myelodysplasic (MDS) patients, the pathophysiology of these disorders still remains poorly understood, and only few in vivo models are available to help unravel the disease. Methods We performed global specific gene expression profiling and functional pathway analysis in purified Sca1+ cells of two MDS transgenic mouse models that mimic human high-risk MDS (HR-MDS) and acute myeloid leukemia (AML) post MDS, with NRASD12 and BCL2 transgenes under the control of different promoters MRP8NRASD12/tethBCL-2 or MRP8[NRASD12/hBCL-2], respectively. Results Analysis of dysregulated genes that were unique to the diseased HR-MDS and AML post MDS mice and not their founder mice pointed first to pathways that had previously been reported in MDS patients, including DNA replication/damage/repair, cell cycle, apoptosis, immune responses, and canonical Wnt pathways, further validating these models at the gene expression level. Interestingly, pathways not previously reported in MDS were discovered. These included dysregulated genes of noncanonical Wnt pathways and energy and lipid metabolisms. These dysregulated genes were not only confirmed in a different independent set of BM and spleen Sca1+ cells from the MDS mice but also in MDS CD34+ BM patient samples. Conclusions These two MDS models may thus provide useful preclinical models to target pathways previously identified in MDS patients and to unravel novel pathways highlighted by this study. Electronic supplementary material The online version of this article (doi:10.1186/s13045-016-0235-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura Guerenne
- Université Paris-Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Unité Mixte de Recherche (UMR-S) 1131, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM) Unité (U) 1131, Paris, France.
| | - Stéphanie Beurlet
- Université Paris-Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Unité Mixte de Recherche (UMR-S) 1131, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM) Unité (U) 1131, Paris, France.
| | - Mohamed Said
- Department of Haematological Medicine, King's College London and Kings College Hospital, London, UK.
| | - Petra Gorombei
- Université Paris-Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Unité Mixte de Recherche (UMR-S) 1131, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM) Unité (U) 1131, Paris, France.
| | - Carole Le Pogam
- Université Paris-Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Unité Mixte de Recherche (UMR-S) 1131, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM) Unité (U) 1131, Paris, France.
| | - Fabien Guidez
- Université Paris-Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Unité Mixte de Recherche (UMR-S) 1131, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM) Unité (U) 1131, Paris, France.
| | - Pierre de la Grange
- GenoSplice technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, Paris, France.
| | - Nader Omidvar
- Haematology Department, Cardiff University School of Medicine, Cardiff, UK.
| | - Valérie Vanneaux
- Assistance Publique-Hôpitaux de Paris (AP-HP), Unité de Thérapie Cellulaire, Hôpital Saint Louis, Paris, France.
| | - Ken Mills
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK.
| | - Ghulam J Mufti
- Department of Haematological Medicine, King's College London and Kings College Hospital, London, UK.
| | - Laure Sarda-Mantel
- Université Paris-Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie Hôpital Saint Louis, Paris, France. .,Assistance Publique-Hôpitaux de Paris (AP-HP), Service de Médecine Nucléaire, Hôpital Lariboisière, Paris, France.
| | - Maria Elena Noguera
- Assistance Publique-Hôpitaux de Paris (AP-HP), Laboratoire d'Hématologie, Hôpital Saint Louis, Paris, France.
| | - Marika Pla
- Université Paris-Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Unité Mixte de Recherche (UMR-S) 1131, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM) Unité (U) 1131, Paris, France. .,Université Paris-Diderot, Sorbonne Paris Cité, Département d'Expérimentation Animale, Institut Universitaire d'Hématologie, Paris, France.
| | - Pierre Fenaux
- Université Paris-Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Unité Mixte de Recherche (UMR-S) 1131, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM) Unité (U) 1131, Paris, France. .,Assistance Publique-Hôpitaux de Paris (AP-HP), Laboratoire d'Hématologie, Hôpital Saint Louis, Paris, France.
| | - Rose Ann Padua
- Université Paris-Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Unité Mixte de Recherche (UMR-S) 1131, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM) Unité (U) 1131, Paris, France. .,Assistance Publique-Hôpitaux de Paris (AP-HP), Laboratoire d'Hématologie, Hôpital Saint Louis, Paris, France.
| | - Christine Chomienne
- Université Paris-Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Unité Mixte de Recherche (UMR-S) 1131, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM) Unité (U) 1131, Paris, France. .,Assistance Publique-Hôpitaux de Paris (AP-HP), Laboratoire d'Hématologie, Hôpital Saint Louis, Paris, France.
| | - Patricia Krief
- Université Paris-Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Unité Mixte de Recherche (UMR-S) 1131, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM) Unité (U) 1131, Paris, France.
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