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Martín Castillo I, Villamón E, Calabuig M, Pastor I, Ferrer-Lores B, Amat P, Mas E, Castillo I, Blanco S, Solano C, Hernández-Boluda JC, Tormo M. Incidence and clinical correlates of NFE2 mutations in myeloid neoplasms. Br J Haematol 2024. [PMID: 38840560 DOI: 10.1111/bjh.19579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024]
Affiliation(s)
- Iván Martín Castillo
- Hematology Department, Instituto de Investigación Sanitaria INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Eva Villamón
- Hematology Department, Instituto de Investigación Sanitaria INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Marisa Calabuig
- Hematology Department, Instituto de Investigación Sanitaria INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Irene Pastor
- Hematology Department, Instituto de Investigación Sanitaria INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Blanca Ferrer-Lores
- Hematology Department, Instituto de Investigación Sanitaria INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Paula Amat
- Hematology Department, Instituto de Investigación Sanitaria INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
- Department of Medicine, University of Valencia, Valencia, Spain
| | - Eva Mas
- Hematology Department, Hospital Universitario de La Plana de Vila-Real, Villarreal, Spain
| | - Inma Castillo
- Hematology Department, Hospital Universitario de La Plana de Vila-Real, Villarreal, Spain
| | - Sara Blanco
- Hematology Department, Hospital Comarcal Francesc De Borja de Gandía, Valencia, Spain
| | - Carlos Solano
- Hematology Department, Instituto de Investigación Sanitaria INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
- Department of Medicine, University of Valencia, Valencia, Spain
| | - Juan Carlos Hernández-Boluda
- Hematology Department, Instituto de Investigación Sanitaria INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
- Department of Medicine, University of Valencia, Valencia, Spain
| | - Mar Tormo
- Hematology Department, Instituto de Investigación Sanitaria INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
- Department of Medicine, University of Valencia, Valencia, Spain
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Wang X, Bajpai AK, Gu Q, Ashbrook DG, Starlard-Davenport A, Lu L. Weighted gene co-expression network analysis identifies key hub genes and pathways in acute myeloid leukemia. Front Genet 2023; 14:1009462. [PMID: 36923792 PMCID: PMC10008864 DOI: 10.3389/fgene.2023.1009462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Introduction: Acute myeloid leukemia (AML) is the most common type of leukemia in adults. However, there is a gap in understanding the molecular basis of the disease, partly because key genes associated with AML have not been extensively explored. In the current study, we aimed to identify genes that have strong association with AML based on a cross-species integrative approach. Methods: We used Weighted Gene Co-Expression Network Analysis (WGCNA) to identify co-expressed gene modules significantly correlated with human AML, and further selected the genes exhibiting a significant difference in expression between AML and healthy mouse. Protein-protein interactions, transcription factors, gene function, genetic regulation, and coding sequence variants were integrated to identify key hub genes in AML. Results: The cross-species approach identified a total of 412 genes associated with both human and mouse AML. Enrichment analysis confirmed an association of these genes with hematopoietic and immune-related functions, phenotypes, processes, and pathways. Further, the integrated analysis approach identified a set of important module genes including Nfe2, Trim27, Mef2c, Ets1, Tal1, Foxo1, and Gata1 in AML. Six of these genes (except ETS1) showed significant differential expression between human AML and healthy samples in an independent microarray dataset. All of these genes are known to be involved in immune/hematopoietic functions, and in transcriptional regulation. In addition, Nfe2, Trim27, Mef2c, and Ets1 harbor coding sequence variants, whereas Nfe2 and Trim27 are cis-regulated, making them attractive candidates for validation. Furthermore, subtype-specific analysis of the hub genes in human AML indicated high expression of NFE2 across all the subtypes (M0 through M7) and enriched expression of ETS1, LEF1, GATA1, and TAL1 in M6 and M7 subtypes. A significant correlation between methylation status and expression level was observed for most of these genes in AML patients. Conclusion: Findings from the current study highlight the importance of our cross-species approach in the identification of multiple key candidate genes in AML, which can be further studied to explore their detailed role in leukemia/AML.
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Affiliation(s)
- Xinfeng Wang
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Akhilesh K Bajpai
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Qingqing Gu
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - David G Ashbrook
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Athena Starlard-Davenport
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Lu Lu
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
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Martin EW, Krietsch J, Reggiardo RE, Sousae R, Kim DH, Forsberg EC. Chromatin accessibility maps provide evidence of multilineage gene priming in hematopoietic stem cells. Epigenetics Chromatin 2021; 14:2. [PMID: 33407811 PMCID: PMC7789351 DOI: 10.1186/s13072-020-00377-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/04/2020] [Indexed: 02/07/2023] Open
Abstract
Hematopoietic stem cells (HSCs) have the capacity to differentiate into vastly different types of mature blood cells. The epigenetic mechanisms regulating the multilineage ability, or multipotency, of HSCs are not well understood. To test the hypothesis that cis-regulatory elements that control fate decisions for all lineages are primed in HSCs, we used ATAC-seq to compare chromatin accessibility of HSCs with five unipotent cell types. We observed the highest similarity in accessibility profiles between megakaryocyte progenitors and HSCs, whereas B cells had the greatest number of regions with de novo gain in accessibility during differentiation. Despite these differences, we identified cis-regulatory elements from all lineages that displayed epigenetic priming in HSCs. These findings provide new insights into the regulation of stem cell multipotency, as well as a resource to identify functional drivers of lineage fate.
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Affiliation(s)
- Eric W Martin
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Jana Krietsch
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Roman E Reggiardo
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Rebekah Sousae
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Daniel H Kim
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - E Camilla Forsberg
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
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Cai W, Zhou W, Han Z, Lei J, Zhuang J, Zhu P, Wu X, Yuan W. Master regulator genes and their impact on major diseases. PeerJ 2020; 8:e9952. [PMID: 33083114 PMCID: PMC7546222 DOI: 10.7717/peerj.9952] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/25/2020] [Indexed: 01/10/2023] Open
Abstract
Master regulator genes (MRGs) have become a hot topic in recent decades. They not only affect the development of tissue and organ systems but also play a role in other signal pathways by regulating additional MRGs. Because a MRG can regulate the concurrent expression of several genes, its mutation often leads to major diseases. Moreover, the occurrence of many tumors and cardiovascular and nervous system diseases are closely related to MRG changes. With the development in omics technology, an increasing amount of investigations will be directed toward MRGs because their regulation involves all aspects of an organism’s development. This review focuses on the definition and classification of MRGs as well as their influence on disease regulation.
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Affiliation(s)
- Wanwan Cai
- The Center for Heart Development, State Key Laboratory of Development Biology of Freshwater Fish, Key Laboratory of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Wanbang Zhou
- College of Physical Education, Hunan Normal University, Changsha, Hunan, China
| | - Zhe Han
- University of Maryland School of Medicine, Center for Precision Disease Modeling, Baltimore, MD, USA
| | - Junrong Lei
- College of Physical Education, Hunan Normal University, Changsha, Hunan, China
| | - Jian Zhuang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Department of Cardiac Surgery, Guangzhou, Guangdong, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Department of Cardiac Surgery, Guangzhou, Guangdong, China
| | - Xiushan Wu
- The Center for Heart Development, State Key Laboratory of Development Biology of Freshwater Fish, Key Laboratory of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Wuzhou Yuan
- The Center for Heart Development, State Key Laboratory of Development Biology of Freshwater Fish, Key Laboratory of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
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