1
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Zhang T, Zou L. Enhancers in T Cell development and malignant lesions. Cell Death Discov 2024; 10:406. [PMID: 39284807 PMCID: PMC11405840 DOI: 10.1038/s41420-024-02160-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 09/19/2024] Open
Abstract
Enhancers constitute a vital category of cis-regulatory elements with a Mediator complex within DNA sequences, orchestrating gene expression by activating promoters. In the development of T cells, some enhancers regulate the critical genes, which might also regulate T cell malignant lesions. This review is to comprehensively elucidate the contributions of enhancers in both normal T cell development and its malignant pathogenesis, proposing the idea that the precise subunits of the Mediator complex are the potential drug target for disrupting the specific gene enhancer for T cell malignant diseases.
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Affiliation(s)
- Tong Zhang
- Clinical Medicine Research Department, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, China.
- Postgraduate School in Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Lin Zou
- Clinical Medicine Research Department, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, China.
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, China.
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2
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Kim H, Tan TK, Lee DZY, Huang XZ, Ong JZL, Kelliher MA, Yeoh AEJ, Sanda T, Tan SH. Oncogenic dependency on SWI/SNF chromatin remodeling factors in T-cell acute lymphoblastic leukemia. Leukemia 2024; 38:1906-1917. [PMID: 38969731 DOI: 10.1038/s41375-024-02331-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a hematological malignancy arising from immature thymocytes. Unlike well-known oncogenic transcription factors, such as NOTCH1 and MYC, the involvement of chromatin remodeling factors in T-ALL pathogenesis is poorly understood. Here, we provide compelling evidence on how SWI/SNF chromatin remodeling complex contributes to human T-ALL pathogenesis. Integrative analysis of transcriptomic and ATAC-Seq datasets revealed high expression of SMARCA4, one of the subunits of the SWI/SNF complex, in T-ALL patient samples and cell lines compared to normal T cells. Loss of SMARCA protein function resulted in apoptosis induction and growth inhibition in multiple T-ALL cell lines. ATAC-Seq analysis revealed a massive reduction in chromatin accessibility across the genome after the loss of SMARCA protein function. RUNX1 interacts with SMARCA4 protein and co-occupies the same genomic regions. Importantly, the NOTCH1-MYC pathway was primarily affected when SMARCA protein function was impaired, implicating SWI/SNF as a novel therapeutic target.
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Affiliation(s)
- Hyoju Kim
- Cancer Science Institute of Singapore, National University of, Singapore, 117599, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of, Singapore, 117599, Singapore
| | - Dean Zi Yang Lee
- Cancer Science Institute of Singapore, National University of, Singapore, 117599, Singapore
| | - Xiao Zi Huang
- Cancer Science Institute of Singapore, National University of, Singapore, 117599, Singapore
| | - Jolynn Zu Lin Ong
- Cancer Science Institute of Singapore, National University of, Singapore, 117599, Singapore
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Allen Eng Juh Yeoh
- Cancer Science Institute of Singapore, National University of, Singapore, 117599, Singapore
- Department of Pediatrics, National University of, Singapore, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan.
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, National University of, Singapore, 117599, Singapore
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3
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Ramos-Rodríguez M, Subirana-Granés M, Norris R, Sordi V, Fernández Á, Fuentes-Páez G, Pérez-González B, Berenguer Balaguer C, Raurell-Vila H, Chowdhury M, Corripio R, Partelli S, López-Bigas N, Pellegrini S, Montanya E, Nacher M, Falconi M, Layer R, Rovira M, González-Pérez A, Piemonti L, Pasquali L. Implications of noncoding regulatory functions in the development of insulinomas. CELL GENOMICS 2024; 4:100604. [PMID: 38959898 PMCID: PMC11406191 DOI: 10.1016/j.xgen.2024.100604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/22/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
Insulinomas are rare neuroendocrine tumors arising from pancreatic β cells, characterized by aberrant proliferation and altered insulin secretion, leading to glucose homeostasis failure. With the aim of uncovering the role of noncoding regulatory regions and their aberrations in the development of these tumors, we coupled epigenetic and transcriptome profiling with whole-genome sequencing. As a result, we unraveled somatic mutations associated with changes in regulatory functions. Critically, these regions impact insulin secretion, tumor development, and epigenetic modifying genes, including polycomb complex components. Chromatin remodeling is apparent in insulinoma-selective domains shared across patients, containing a specific set of regulatory sequences dominated by the SOX17 binding motif. Moreover, many of these regions are H3K27me3 repressed in β cells, suggesting that tumoral transition involves derepression of polycomb-targeted domains. Our work provides a compendium of aberrant cis-regulatory elements affecting the function and fate of β cells in their progression to insulinomas and a framework to identify coding and noncoding driver mutations.
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Affiliation(s)
- Mireia Ramos-Rodríguez
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Marc Subirana-Granés
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Richard Norris
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Valeria Sordi
- Diabetes Research Institute (DRI) - IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ángel Fernández
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Department of Physiological Science, School of Medicine, Universitat de Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, Spain; Pancreas Regeneration: Pancreatic Progenitors and Their Niche Group, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; Program for Advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet de Llobregat, Barcelona, Spain
| | - Georgina Fuentes-Páez
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Beatriz Pérez-González
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Clara Berenguer Balaguer
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Helena Raurell-Vila
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Murad Chowdhury
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Raquel Corripio
- Paediatric Endocrinology Department, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Stefano Partelli
- Pancreas Translational & Research Institute, Scientific Institute San Raffaele Hospital and University Vita-Salute, Milan, Italy
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Silvia Pellegrini
- Diabetes Research Institute (DRI) - IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eduard Montanya
- Bellvitge Hospital-IDIBELL, Barcelona, Spain; Department of Clinical Sciences, University of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Montserrat Nacher
- Bellvitge Hospital-IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain
| | - Massimo Falconi
- Pancreas Translational & Research Institute, Scientific Institute San Raffaele Hospital and University Vita-Salute, Milan, Italy
| | - Ryan Layer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA; Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
| | - Meritxell Rovira
- Department of Physiological Science, School of Medicine, Universitat de Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, Spain; Pancreas Regeneration: Pancreatic Progenitors and Their Niche Group, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; Program for Advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet de Llobregat, Barcelona, Spain
| | - Abel González-Pérez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Lorenzo Piemonti
- Diabetes Research Institute (DRI) - IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lorenzo Pasquali
- Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
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Heimlich JB, Bhat P, Parker AC, Jenkins MT, Vlasschaert C, Ulloa J, Van Amburg JC, Potts CR, Olson S, Silver AJ, Ahmad A, Sharber B, Brown D, Hu N, van Galen P, Savona MR, Bick AG, Ferrell PB. Multiomic profiling of human clonal hematopoiesis reveals genotype and cell-specific inflammatory pathway activation. Blood Adv 2024; 8:3665-3678. [PMID: 38507736 DOI: 10.1182/bloodadvances.2023011445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/22/2024] Open
Abstract
ABSTRACT Clonal hematopoiesis (CH) is an age-associated phenomenon that increases the risk of hematologic malignancy and cardiovascular disease. CH is thought to enhance disease risk through inflammation in the peripheral blood.1 Here, we profile peripheral blood gene expression in 66 968 single cells from a cohort of 17 patients with CH and 7 controls. Using a novel mitochondrial DNA barcoding approach, we were able to identify and separately compare mutant Tet methylcytosine dioxygenase 2 (TET2) and DNA methyltransferase 3A (DNMT3A) cells with nonmutant counterparts. We discovered the vast majority of mutated cells were in the myeloid compartment. Additionally, patients harboring DNMT3A and TET2 CH mutations possessed a proinflammatory profile in CD14+ monocytes through previously unrecognized pathways such as galectin and macrophage inhibitory factor. We also found that T cells from patients with CH, although mostly unmutated, had decreased expression of GTPase of the immunity associated protein genes, which are critical to T-cell development, suggesting that CH impairs T-cell function.
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Affiliation(s)
- J Brett Heimlich
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Pawan Bhat
- Vanderbilt University School of Medicine, Nashville, TN
| | | | | | | | - Jessica Ulloa
- Division of Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Joseph C Van Amburg
- Division of Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Chad R Potts
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Sydney Olson
- Division of Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | | | - Ayesha Ahmad
- Division of Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Brian Sharber
- Division of Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Donovan Brown
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Ningning Hu
- Division of Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Peter van Galen
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Michael R Savona
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt-Ingram Cancer Center, Program in Cancer Biology, and Center for Immunobiology, Nashville, TN
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN
| | - Alexander G Bick
- Division of Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - P Brent Ferrell
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
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5
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Zhang Y, Liu S, Liu D, Zhao Z, Song H, Peng K. Identification and validation of GIMAP family genes as immune-related prognostic biomarkers in lung adenocarcinoma. Heliyon 2024; 10:e33111. [PMID: 38948046 PMCID: PMC11211882 DOI: 10.1016/j.heliyon.2024.e33111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 05/15/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024] Open
Abstract
Background The GIMAP family genes play a key role in immune function. Increasing evidence suggests that GIMAP genes were implicated in the tumorigenesis of lung adenocarcinoma (LUAD). This study aimed to investigate the clinical significance of GIMAP family genes in LUAD. Methods In this study, we explored the expression, mutation, prognostic value of GIMAP family genes and the correlation with immune microenvironment in LUAD. We further investigated the relationship between GIMAP family genes expression and immunotherapy response in GEO LUAD and melanoma cohorts. Results Among the GIMAP family genes, the expression levels of GIMAP1, GIMAP2, GIMAP4, GIMAP5, GIMAP6, GIMAP7, and GIMAP8 were significantly lower in LUAD tumor tissues than normal tissues. Most GIMAP genes were closely related to age, tumor grade and T stage, but not significantly related to sex, N stage and M stage. In the overall population, patients with high expression of GIMAP family genes had a significant longer overall survival (OS). GO and KEGG enrichment analysis showed that GIMAP family genes were highly enriched in immune-related biological process. The expression of GIMAP family genes was positively correlated with immune cell infiltration and immune checkpoint molecules. Furthermore, high expression of GIMAP family genes were correlated with therapeutic response to immunotherapy in LUAD and melanoma patients. Conclusion In this study, we identified that GIMAP family genes were significantly associated with immune cell infiltration and immune checkpoint molecules. They potentially play a critical role in anti-tumor immunity and serve as immunotherapy biomarkers.
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Affiliation(s)
- Yanyan Zhang
- Department of Infectious Diseases, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Shan Liu
- Department of Cardiology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Cardiovascular Disease, Guangzhou, Guangdong, China
| | - Deyi Liu
- Department of General Practice, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhuxiang Zhao
- Department of Infectious Diseases, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Haifeng Song
- Department of Oncology, Lianzhou People's Hospital, Lianzhou, Guangdong, China
| | - Kunwei Peng
- Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy & Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Oncology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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6
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O'Connor KW, Kishimoto K, Kuzma IO, Wagner KP, Selway JS, Roderick JE, Karna KK, Gallagher KM, Hu K, Liu H, Li R, Brehm MA, Zhu LJ, Curtis DJ, Tremblay CS, Kelliher MA. The role of quiescent thymic progenitors in TAL/LMO2-induced T-ALL chemotolerance. Leukemia 2024; 38:951-962. [PMID: 38553571 PMCID: PMC11073972 DOI: 10.1038/s41375-024-02232-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 05/08/2024]
Abstract
Relapse in T-cell acute lymphoblastic leukemia (T-ALL) may signify the persistence of leukemia-initiating cells (L-ICs). Ectopic TAL1/LMO expression defines the largest subset of T-ALL, but its role in leukemic transformation and its impact on relapse-driving L-ICs remain poorly understood. In TAL1/LMO mouse models, double negative-3 (DN3; CD4-CD8-CD25+CD44-) thymic progenitors harbored L-ICs. However, only a subset of DN3 leukemic cells exhibited L-IC activity, and studies linking L-ICs and chemotolerance are needed. To investigate L-IC heterogeneity, we used mouse models and applied single-cell RNA-sequencing and nucleosome labeling techniques in vivo. We identified a DN3 subpopulation with a cell cycle-restricted profile and heightened TAL1/LMO2 activity, that expressed genes associated with stemness and quiescence. This dormant DN3 subset progressively expanded throughout leukemogenesis, displaying intrinsic chemotolerance and enrichment in genes linked to minimal residual disease. Examination of TAL/LMO patient samples revealed a similar pattern in CD7+CD1a- thymic progenitors, previously recognized for their L-IC activity, demonstrating cell cycle restriction and chemotolerance. Our findings substantiate the emergence of dormant, chemotolerant L-ICs during leukemogenesis, and demonstrate that Tal1 and Lmo2 cooperate to promote DN3 quiescence during the transformation process. This study provides a deeper understanding of TAL1/LMO-induced T-ALL and its clinical implications in therapy failure.
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Affiliation(s)
- Kevin W O'Connor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Kensei Kishimoto
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Irena O Kuzma
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Kelsey P Wagner
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jonathan S Selway
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Justine E Roderick
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Keshab K Karna
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Kayleigh M Gallagher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Kai Hu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Haibo Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Michael A Brehm
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - David J Curtis
- Australian Centre for Blood Diseases (ACBD), Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Cedric S Tremblay
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0T5, Canada
- Paul Albrechtsen Research Institute CCMB, CancerCare Manitoba (CCMB), Winnipeg, MB, R3E 0V9, Canada
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
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7
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Ong JZL, Tan TK, Wang L, Tan SH, Sanda T. Regulatory mechanisms and context-dependent roles of TAL1 in T-cell acute lymphoblastic leukemia. Haematologica 2024; 109:1359-1372. [PMID: 37855064 PMCID: PMC11063860 DOI: 10.3324/haematol.2023.283450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy derived from thymic T-cell precursors. Approximately 40-60% of T-ALL cases exhibit aberrant overexpression of the TAL1 oncogenic transcription factor. Here, we provide a comprehensive view of the TAL1-induced transcriptional program in human T-ALL cells using a rapid protein degradation system coupled with integrative approaches. Our study demonstrates that TAL1 targets can be classified into several groups, each of which exhibits unique gene expression kinetics, chromatin features, and regulatory mechanisms. Group A genes are highly dependent on TAL1, many of which are not expressed in normal T cells or TAL1-negative T-ALL cells, representing an oncogenic TAL1 signature. The TAL1 complex predominantly activates group A genes. TAL1's effect is not replaceable with its regulatory partners GATA3 or RUNX1. In contrast, group B genes, many of which are generally expressed across different T-ALL subgroups, exhibit densely-connected chromatin-chromatin interactions and demonstrate the collaborative roles played by TAL1 with other transcription factors. Interestingly, TAL1 cooperates with NOTCH1 to regulate gene expression in TAL1-positive T-ALL cells, whereas it potentially antagonizes the NOTCH1-MYC pathway and leads to lethality in TAL1-negative/ TLX3-positive cells, demonstrating the context-dependent roles of TAL1.
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Affiliation(s)
- Jolynn Zu Lin Ong
- Cancer Science Institute of Singapore, National University of Singapore, 117599
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599
| | - Lu Wang
- Cancer Science Institute of Singapore, National University of Singapore, 117599
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117599; Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya.
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8
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Costa JR, Mansour MR. ToTAL1y degraded - rapid dTAG proteolysis of TAL1 in T-cell acute lymphoblastic leukemia. Haematologica 2024; 109:1325-1327. [PMID: 38105739 PMCID: PMC11063835 DOI: 10.3324/haematol.2023.284447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Affiliation(s)
| | - Marc R Mansour
- UCL Cancer Institute, University College London, United Kingdom; Department of Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health.
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9
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IL-15 Prevents the Development of T-ALL from Aberrant Thymocytes with Impaired DNA Repair Functions and Increased NOTCH1 Activation. Cancers (Basel) 2023; 15:cancers15030671. [PMID: 36765626 PMCID: PMC9913776 DOI: 10.3390/cancers15030671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
We previously reported that NOD.Scid mice lacking interleukin-15 (IL-15), or IL-15 receptor alpha-chain, develop T-acute lymphoblastic leukemia (T-ALL). To understand the mechanisms by which IL-15 signaling controls T-ALL development, we studied the thymocyte developmental events in IL-15-deficient Scid mice from NOD and C57BL/6 genetic backgrounds. Both kinds of mice develop T-ALL characterized by circulating TCR-negative cells expressing CD4, CD8 or both. Analyses of thymocytes in NOD.Scid.Il15-/- mice prior to T-ALL development revealed discernible changes within the CD4-CD8- double-negative (DN) thymocyte developmental stages and increased frequencies of CD4+CD8+ double-positive cells with a high proportion of TCR-negative CD4+ and CD8+ cells. The DN cells also showed elevated expressions of CXCR4 and CD117, molecules implicated in the expansion of DN thymocytes. T-ALL cell lines and primary leukemic cells from IL-15-deficient NOD.Scid and C57BL/6.Scid mice displayed increased NOTCH1 activation that was inhibited by NOTCH1 inhibitors and blockers of the PI3K/AKT pathway. Primary leukemic cells from NOD.Scid.Il15-/- mice survived and expanded when cultured with MS5 thymic stromal cells expressing Delta-like ligand 4 and supplemented with IL-7 and FLT3 ligand. These findings suggest that IL-15 signaling in the thymus controls T-ALL development from aberrant thymocytes with an impaired DNA repair capacity and increased NOTCH1 activation.
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10
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Yi ZN, Chen XK, Ma ACH. Modeling leukemia with zebrafish (Danio rerio): Towards precision medicine. Exp Cell Res 2022; 421:113401. [PMID: 36306826 DOI: 10.1016/j.yexcr.2022.113401] [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: 07/06/2022] [Revised: 10/06/2022] [Accepted: 10/20/2022] [Indexed: 12/29/2022]
Abstract
Leukemia is a type of blood cancer characterized by high genetic heterogeneity and fatality. While chemotherapy remains the primary form of treatment for leukemia, its effectiveness was profoundly diminished by the genetic heterogeneity and cytogenetic abnormalities of leukemic cells. Therefore, there is an unmet need to develop precision medicine for leukemia with distinct genetic backgrounds. Zebrafish (Danio rerio), a freshwater fish with exceptional feasibility in genome editing, is a powerful tool for rapid human cancer modeling. In the past decades, zebrafish have been adopted in modeling human leukemia, exploring the molecular mechanisms of underlying genetic abnormalities, and discovering novel therapeutic agents. Although many recurrent mutations of leukemia have been modeled in zebrafish for pathological study and drug discovery, its great potential in leukemia modeling was not yet fully exploited, particularly in precision medicine. In this review, we evaluated the current zebrafish models of leukemia/pre-leukemia and genetic techniques and discussed the potential of zebrafish models with novel techniques, which may contribute to the development of zebrafish as a disease model for precision medicine in treating leukemia.
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Affiliation(s)
- Zhen-Ni Yi
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Xiang-Ke Chen
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Alvin Chun-Hang Ma
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China.
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11
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Computational gene expression analysis reveals distinct molecular subgroups of T-cell prolymphocytic leukemia. PLoS One 2022; 17:e0274463. [PMID: 36129940 PMCID: PMC9491575 DOI: 10.1371/journal.pone.0274463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/29/2022] [Indexed: 11/20/2022] Open
Abstract
T-cell prolymphocytic leukemia (T-PLL) is a rare blood cancer with poor prognosis. Overexpression of the proto-oncogene TCL1A and missense mutations of the tumor suppressor ATM are putative main drivers of T-PLL development, but so far only little is known about the existence of T-PLL gene expression subtypes. We performed an in-depth computational reanalysis of 68 gene expression profiles of one of the largest currently existing T-PLL patient cohorts. Hierarchical clustering combined with bootstrapping revealed three robust T-PLL gene expression subgroups. Additional comparative analyses revealed similarities and differences of these subgroups at the level of individual genes, signaling and metabolic pathways, and associated gene regulatory networks. Differences were mainly reflected at the transcriptomic level, whereas gene copy number profiles of the three subgroups were much more similar to each other, except for few characteristic differences like duplications of parts of the chromosomes 7, 8, 14, and 22. At the network level, most of the 41 predicted potential major regulators showed subgroup-specific expression levels that differed at least in comparison to one other subgroup. Functional annotations suggest that these regulators contribute to differences between the subgroups by altering processes like immune responses, angiogenesis, cellular respiration, cell proliferation, apoptosis, or migration. Most of these regulators are known from other cancers and several of them have been reported in relation to leukemia (e.g. AHSP, CXCL8, CXCR2, ELANE, FFAR2, G0S2, GIMAP2, IL1RN, LCN2, MBTD1, PPP1R15A). The existence of the three revealed T-PLL subgroups was further validated by a classification of T-PLL patients from two other smaller cohorts. Overall, our study contributes to an improved stratification of T-PLL and the observed subgroup-specific molecular characteristics could help to develop urgently needed targeted treatment strategies.
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12
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Lim FQ, Chan ASY, Yokomori R, Huang XZ, Theardy MS, Yeoh AEJ, Tan SH, Sanda T. Targeting dual oncogenic machineries driven by TAL1 and PI3K-AKT pathways in T-cell acute lymphoblastic leukemia. Haematologica 2022; 108:367-381. [PMID: 36073513 PMCID: PMC9890034 DOI: 10.3324/haematol.2022.280761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Indexed: 02/03/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a malignancy of thymic T-cell precursors. Overexpression of oncogenic transcription factor TAL1 is observed in 40-60% of human T-ALL cases, frequently together with activation of the NOTCH1 and PI3K-AKT pathways. In this study, we performed chemical screening to identify small molecules that can inhibit the enhancer activity driven by TAL1 using the GIMAP enhancer reporter system. Among approximately 3,000 compounds, PIK- 75, a known inhibitor of PI3K and CDK, was found to strongly inhibit the enhancer activity. Mechanistic analysis demonstrated that PIK-75 blocks transcriptional activity, which primarily affects TAL1 target genes as well as AKT activity. TAL1-positive, AKT-activated T-ALL cells were very sensitive to PIK-75, as evidenced by growth inhibition and apoptosis induction, while T-ALL cells that exhibited activation of the JAK-STAT pathway were insensitive to this drug. Together, our study demonstrates a strategy targeting two types of core machineries mediated by oncogenic transcription factors and signaling pathways in T-ALL.
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Affiliation(s)
- Fang Qi Lim
- Cancer Science Institute of Singapore, National University of Singapore
| | | | - Rui Yokomori
- Cancer Science Institute of Singapore, National University of Singapore
| | - Xiao Zi Huang
- Cancer Science Institute of Singapore, National University of Singapore
| | | | - Allen Eng Juh Yeoh
- Cancer Science Institute of Singapore, National University of Singapore,VIVA-NUS CenTRAL, Department of Pediatrics, National University of Singapore
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117599.
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13
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Carr T, McGregor S, Dias S, Verykokakis M, Le Beau MM, Xue HH, Sigvardsson M, Bartom ET, Kee BL. Oncogenic and Tumor Suppressor Functions for Lymphoid Enhancer Factor 1 in E2a-/- T Acute Lymphoblastic Leukemia. Front Immunol 2022; 13:845488. [PMID: 35371057 PMCID: PMC8971981 DOI: 10.3389/fimmu.2022.845488] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/23/2022] [Indexed: 11/15/2022] Open
Abstract
T lymphocyte acute lymphoblastic leukemia (T-ALL) is a heterogeneous disease affecting T cells at multiple stages of their development and is characterized by frequent genomic alterations. The transcription factor LEF1 is inactivated through mutation in a subset of T-ALL cases but elevated LEF1 expression and activating mutations have also been identified in this disease. Here we show, in a murine model of T-ALL arising due to E2a inactivation, that the developmental timing of Lef1 mutation impacts its ability to function as a cooperative tumor suppressor or oncogene. T cell transformation in the presence of LEF1 allows leukemic cells to become addicted to its presence. In contrast, deletion prior to transformation both accelerates leukemogenesis and results in leukemic cells with altered expression of genes controlling receptor-signaling pathways. Our data demonstrate that the developmental timing of Lef1 mutations impact its apparent oncogenic or tumor suppressive characteristics and demonstrate the utility of mouse models for understanding the cooperation and consequence of mutational order in leukemogenesis.
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Affiliation(s)
- Tiffany Carr
- Committee on Immunology, The University of Chicago, Chicago, IL, United States
| | - Stephanie McGregor
- Committee on Cancer Biology, The University of Chicago, Chicago, IL, United States
| | - Sheila Dias
- Department of Pathology, The University of Chicago, Chicago, Chicago, IL, United States
| | - Mihalis Verykokakis
- Department of Pathology, The University of Chicago, Chicago, Chicago, IL, United States
| | - Michelle M. Le Beau
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, IL, United States
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, United States
| | | | - Elizabeth T. Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, United States
| | - Barbara L. Kee
- Committee on Immunology, The University of Chicago, Chicago, IL, United States
- Committee on Cancer Biology, The University of Chicago, Chicago, IL, United States
- Department of Pathology, The University of Chicago, Chicago, Chicago, IL, United States
- *Correspondence: Barbara L. Kee,
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14
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Komatsu M, Saito K, Miyamoto I, Koike K, Iyoda M, Nakashima D, Kasamatsu A, Shiiba M, Tanzawa H, Uzawa K. Aberrant GIMAP2 expression affects oral squamous cell carcinoma progression by promoting cell cycle and inhibiting apoptosis. Oncol Lett 2022; 23:49. [PMID: 34992682 PMCID: PMC8721858 DOI: 10.3892/ol.2021.13167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
GTPases of immunity-associated protein 2 (GIMAP2) is a GTPase family member associated with T cell survival. However, its mechanisms of action in oral squamous cell carcinoma (OSCC) remain largely unknown. Therefore, the present study aimed to elucidate the possible role of GIMAP2 in OSCC development by investigating its expression levels and molecular mechanisms in OSCC. Reverse transcription quantitative PCR, immunoblotting and immunohistochemistry indicated that GIMAP2 expression was significantly upregulated (P<0.05) in OSCC-derived cell lines and primary OSCC specimens compared with that in their normal counterparts. GIMAP2-knockdown OSCC cells exhibited decreased cell growth, which was associated with cyclin-dependent kinase (CDK)4, CDK6 and phosphorylated Rb downregulation and p53 and p21 upregulation. In addition to cell cycle arrest, GIMAP2 affected anti-apoptotic functions in GIMAP2-knockdown cells by upregulating Bcl-2 and downregulating Bax and Bak. These findings indicated that GIMAP2 may significantly influence OSCC development and apoptosis inhibition and thus is a potential biomarker of OSCC.
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Affiliation(s)
- Mari Komatsu
- Department of Oral Science, Chiba University, Chiba 260-8670, Japan
| | - Kengo Saito
- Department of Molecular Virology, Chiba University, Chiba 260-8670, Japan
| | - Isao Miyamoto
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Kazuyuki Koike
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Manabu Iyoda
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Dai Nakashima
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Atsushi Kasamatsu
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Masashi Shiiba
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Hideki Tanzawa
- Department of Oral Science, Chiba University, Chiba 260-8670, Japan.,Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
| | - Katsuhiro Uzawa
- Department of Oral Science, Chiba University, Chiba 260-8670, Japan.,Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University, Chiba 260-8670, Japan
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15
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Limoges MA, Cloutier M, Nandi M, Ilangumaran S, Ramanathan S. The GIMAP Family Proteins: An Incomplete Puzzle. Front Immunol 2021; 12:679739. [PMID: 34135906 PMCID: PMC8201404 DOI: 10.3389/fimmu.2021.679739] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/12/2021] [Indexed: 12/19/2022] Open
Abstract
Overview: Long-term survival of T lymphocytes in quiescent state is essential to maintain their cell numbers in secondary lymphoid organs and in peripheral circulation. In the BioBreeding diabetes-prone strain of rats (BB-DP), loss of functional GIMAP5 (GTPase of the immune associated nucleotide binding protein 5) results in profound peripheral T lymphopenia. This discovery heralded the identification of a new family of proteins initially called Immune-associated nucleotide binding protein (IAN) family. In this review we will use ‘GIMAP’ to refer to this family of proteins. Recent studies suggest that GIMAP proteins may interact with each other and also be involved in the movement of the cellular cargo along the cytoskeletal network. Here we will summarize the current knowledge on the characteristics and functions of GIMAP family of proteins.
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Affiliation(s)
- Marc-André Limoges
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Maryse Cloutier
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Madhuparna Nandi
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke and CRCHUS, Sherbrooke, QC, Canada
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16
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Xiao S, Huang Q, Ren H, Yang M. The mechanism and function of super enhancer RNA. Genesis 2021; 59:e23422. [PMID: 34028961 DOI: 10.1002/dvg.23422] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/19/2022]
Abstract
Super enhancer (SE) is a cluster of enhancers that has a stronger ability to promote transcription compared to the typical enhancer (TE). Similar to TE, which can transcribe enhancer RNA (eRNA), SE produces super enhancer RNA (seRNA). The activation of SE is cell and tissue-specific, and the SE-associated genes are mostly linked to the cell fate. This is demonstrated by the important role-played by SE in the embryonic stem cell (ESC) and multiple cancer development. SeRNA regulates transcription in both cis and trans configuration, and those located in the cytoplasm mediates various cell activities. However, the functions of seRNAs are unclear, and most of them have a synergistic effect with SE and SE-associated genes. In this mini review, we summarized the mechanisms of seRNA and functions of both SE and seRNA.
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Affiliation(s)
- Shibai Xiao
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qin Huang
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Ren
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Min Yang
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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17
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Systemic analyses of expression patterns and clinical features for GIMAPs family members in lung adenocarcinoma. Aging (Albany NY) 2020; 12:20413-20431. [PMID: 33115964 PMCID: PMC7655191 DOI: 10.18632/aging.103836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/14/2020] [Indexed: 12/22/2022]
Abstract
GTPase of immunity-associated proteins (GIMAPs) are frequently prescribed as important components of immune regulation complexes, which were known to play key roles in lung adenocarcinoma. However, little is known about the function of distinct GIMAPs in lung adenocarcinoma. To address this issue, this study investigated the biological function and pathway of GIMAPs in lung adenocarcinoma using multiple public databases. Absent expression of GIMAPs was found in lung adenocarcinoma at mRNA and protein levels. While a purity-corrected value uncovered that all GIMAPs were positively associated with the immune infiltration of lung adenocarcinoma. Furthermore, the expressions of GIMAPs were considered to be negatively associated with clinical cancer stages, patient’s gender and pathological tumor grades in patients with lung adenocarcinoma. Besides, higher mRNA expression of GIMAPs was significantly associated with longer overall survival of patients with lung adenocarcinoma. Taken together, these results may enable GIMAPs family members as diagnostic and survival biomarker candidates or even potential therapeutic targets for patients with lung adenocarcinoma.
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18
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Berg HE, Blackburn PR, Baughn LB, Ketterling RP, Xu X, Greipp PT, Hoppman NL, Smadbeck JB, Vasmatzis G, Shi M, Reichard KK, Viswanatha DS, Jevremovic D, Maher GM, Peterson JF. Identification of a novel KMT2A/GIMAP8 gene fusion in a pediatric patient with acute undifferentiated leukemia. Genes Chromosomes Cancer 2020; 60:108-111. [PMID: 33078871 DOI: 10.1002/gcc.22902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 01/05/2023] Open
Abstract
Acute undifferentiated leukemia (AUL) is a very rare hematologic neoplasm that expresses no markers specific for either myeloid or lymphoid lineages. While commonly observed in several acute leukemias, KMT2A rearrangements in AUL have been rarely reported in the literature. We report the third case to our knowledge of AUL harboring a KMT2A rearrangement. Furthermore, the KMT2A/GIMAP8 gene fusion identified in this case represents a novel KMT2A rearrangement.
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Affiliation(s)
- Holly E Berg
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Patrick R Blackburn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Xinjie Xu
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, Minnesota, USA
| | - Min Shi
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kaaren K Reichard
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - David S Viswanatha
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Dragan Jevremovic
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - George M Maher
- Divison of Pediatric Hematology/Oncology, Sanford Children's Hospital, Sioux Falls, South Dakota, USA
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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19
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Raby L, Völkel P, Le Bourhis X, Angrand PO. Genetic Engineering of Zebrafish in Cancer Research. Cancers (Basel) 2020; 12:E2168. [PMID: 32759814 PMCID: PMC7464884 DOI: 10.3390/cancers12082168] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022] Open
Abstract
Zebrafish (Danio rerio) is an excellent model to study a wide diversity of human cancers. In this review, we provide an overview of the genetic and reverse genetic toolbox allowing the generation of zebrafish lines that develop tumors. The large spectrum of genetic tools enables the engineering of zebrafish lines harboring precise genetic alterations found in human patients, the generation of zebrafish carrying somatic or germline inheritable mutations or zebrafish showing conditional expression of the oncogenic mutations. Comparative transcriptomics demonstrate that many of the zebrafish tumors share molecular signatures similar to those found in human cancers. Thus, zebrafish cancer models provide a unique in vivo platform to investigate cancer initiation and progression at the molecular and cellular levels, to identify novel genes involved in tumorigenesis as well as to contemplate new therapeutic strategies.
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Affiliation(s)
| | | | | | - Pierre-Olivier Angrand
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277–CANTHER–Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (X.L.B.)
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20
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覃 鸿, 郑 幽, 王 嫚, 张 峥, 牛 祖, 马 骊, 孙 强, 黄 红, 王 小. [Subcellular localization of GTPase of immunity-associated protein 2]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2020; 52:221-226. [PMID: 32306002 PMCID: PMC7433440 DOI: 10.19723/j.issn.1671-167x.2020.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To analyze the subcellular localization of GTPase of immunity-associated protein 2 (GIMAP2) for the further functional study. METHODS In the study, we first obtained the protein sequences of GTPase of immunity-associated protein 2 (GIMAP2) from National Center for Biotechnology Information (NCBI) database, and then performed a prediction analysis of its transmembrane structure, nuclear localization signal (NLS), nuclear export signal (NES) and subcellular localization through bioinformatics online tools. GIMAP2 gene amplified by PCR was inserted into the expression vector pQCXIP-mCherry-N1 and positive clones were selected by ampicillin resistance. After using methods to extract and purify, the sequenced recombinant plasmid pQCXIP-GIMAP2-mCherry, together with the retroviral packaging plasmids VSVG and Gag/pol, was transferred into HEK293FT cells by liposomes for virus packaging. The virus supernatant was collected 48 h after transfection and directly infected the human breast cancer cell line MDA-MB-436. Immunofluorescence staining was constructed to detect the localization of endogenous and exogenous GIMAP2 in MDA-MB-436 cells. Meanwhile, green fluorescent chemical dyes were used to label mitochondria, endoplasmic reticulum, and lipid droplets in living MDA-MB-436 cells stably expressing the GIMAP2-mCherry fusion protein. Images for the three dye-labeled organelles and GIMAP2-mCherry fusion protein were captured by super-resolution microscope N-SIM. RESULTS Bioinformatics analysis data showed that GIMAP2 protein composed of 337 amino acids might contain two transmembrane helix (TM) structures at the carboxyl terminus, of which TMs were estimated to contain 40-41 expected amino acids, followed by the residual protein structures toward the cytoplasmic side. NES was located at the 279-281 amino acids of the carboxyl terminus whereas NLS was not found. GIMAP2 might locate in the lumen of the endoplasmic reticulum. Sequencing results indicated that the expression vector pQCXIP-GIMAP2-mCherry was successfully constructed. Fluorescent staining confirmed that GIMAP2-mCherry fusion protein, co-localized well with endogenous GIMAP2, expressed successfully in the endoplasmic reticulum and on the surface of lipid droplets in MDA-MB-436 cells. CONCLUSION GIMAP2 localizes in the endoplasmic reticulum and on the surface of LDs, suggesting potential involvement of GIMAP2 in lipid metabolism.
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Affiliation(s)
- 鸿泉 覃
- 南方医科大学检验与生物技术学院分子免疫研究所,广州 510515School of Laboratory Medicine and Biotechnology, Institute of Molecular Immunology,Southern Medical University, Guangzhou 510515, China
- 军事医学研究院生物工程研究所,北京 100071Institute of Biotechnology, Academy of Military Medical Sciences, Beijing100071, China
| | - 幽 郑
- 军事医学研究院生物工程研究所,北京 100071Institute of Biotechnology, Academy of Military Medical Sciences, Beijing100071, China
| | - 嫚娜 王
- 军事医学研究院生物工程研究所,北京 100071Institute of Biotechnology, Academy of Military Medical Sciences, Beijing100071, China
| | - 峥嵘 张
- 军事医学研究院生物工程研究所,北京 100071Institute of Biotechnology, Academy of Military Medical Sciences, Beijing100071, China
| | - 祖彪 牛
- 军事医学研究院生物工程研究所,北京 100071Institute of Biotechnology, Academy of Military Medical Sciences, Beijing100071, China
| | - 骊 马
- 南方医科大学检验与生物技术学院分子免疫研究所,广州 510515School of Laboratory Medicine and Biotechnology, Institute of Molecular Immunology,Southern Medical University, Guangzhou 510515, China
| | - 强 孙
- 军事医学研究院生物工程研究所,北京 100071Institute of Biotechnology, Academy of Military Medical Sciences, Beijing100071, China
| | - 红艳 黄
- 首都医科大学附属北京世纪坛医院脑胶质瘤科,北京 100038Department of Glioma, Beijing Shijitan Hospital, Capital Medical University, Beijing100038, China
| | - 小宁 王
- 南方医科大学检验与生物技术学院分子免疫研究所,广州 510515School of Laboratory Medicine and Biotechnology, Institute of Molecular Immunology,Southern Medical University, Guangzhou 510515, China
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21
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Park G, Burroughs-Garcia J, Foster CA, Hasan A, Borga C, Frazer JK. Zebrafish B cell acute lymphoblastic leukemia: new findings in an old model. Oncotarget 2020; 11:1292-1305. [PMID: 32341750 PMCID: PMC7170496 DOI: 10.18632/oncotarget.27555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/19/2020] [Indexed: 12/22/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric, and ninth most common adult, cancer. ALL can develop in either B or T lymphocytes, but B-lineage ALL (B-ALL) exceeds T-ALL clinically. As for other cancers, animal models allow study of the molecular mechanisms driving ALL. Several zebrafish (Danio rerio) T-ALL models have been reported, but until recently, robust D. rerio B-ALL models were not described. Then, D. rerio B-ALL was discovered in two related zebrafish transgenic lines; both were already known to develop T-ALL. Here, we report new B-ALL findings in one of these models, fish expressing transgenic human MYC (hMYC). We describe B-ALL incidence in a large cohort of hMYC fish, and show B-ALL in two new lines where T-ALL does not interfere with B-ALL detection. We also demonstrate B-ALL responses to steroid and radiation treatments, which effect ALL remissions, but are usually followed by prompt relapses. Finally, we report gene expression in zebrafish B lymphocytes and B-ALL, in both bulk samples and single B- and T-ALL cells. Using these gene expression profiles, we compare differences between the two new D. rerio B-ALL models, which are both driven by transgenic mammalian MYC oncoproteins. Collectively, these new data expand the utility of this new vertebrate B-ALL model.
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Affiliation(s)
- Gilseung Park
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,These authors contributed equally to this work
| | - Jessica Burroughs-Garcia
- Department of Pediatrics, Section of Pediatric Hematology-Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,These authors contributed equally to this work
| | - Clay A Foster
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA.,These authors contributed equally to this work
| | - Ameera Hasan
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Chiara Borga
- Department of Pediatrics, Section of Pediatric Hematology-Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - J Kimble Frazer
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Department of Pediatrics, Section of Pediatric Hematology-Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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22
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Gianni F, Belver L, Ferrando A. The Genetics and Mechanisms of T-Cell Acute Lymphoblastic Leukemia. Cold Spring Harb Perspect Med 2020; 10:a035246. [PMID: 31570389 PMCID: PMC7050584 DOI: 10.1101/cshperspect.a035246] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy derived from early T-cell progenitors. The recognition of clinical, genetic, transcriptional, and biological heterogeneity in this disease has already translated into new prognostic biomarkers, improved leukemia animal models, and emerging targeted therapies. This work reviews our current understanding of the molecular mechanisms of T-ALL.
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Affiliation(s)
- Francesca Gianni
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
| | - Laura Belver
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
- Department of Pathology, Columbia University Medical Center, New York, New York 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
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23
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Jia Y, Chng WJ, Zhou J. Super-enhancers: critical roles and therapeutic targets in hematologic malignancies. J Hematol Oncol 2019; 12:77. [PMID: 31311566 PMCID: PMC6636097 DOI: 10.1186/s13045-019-0757-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022] Open
Abstract
Super-enhancers (SEs) in a broad range of human cell types are large clusters of enhancers with aberrant high levels of transcription factor binding, which are central to drive expression of genes in controlling cell identity and stimulating oncogenic transcription. Cancer cells acquire super-enhancers at oncogene and cancerous phenotype relies on these abnormal transcription propelled by SEs. Furthermore, specific inhibitors targeting SEs assembly and activation have offered potential targets for treating various tumors including hematological malignancies. Here, we first review the identification, functional significance of SEs. Next, we summarize recent findings of SEs and SE-driven gene regulation in normal hematopoiesis and hematologic malignancies. The importance and various modes of SE-mediated MYC oncogene amplification are illustrated. Finally, we highlight the progress of SEs as selective therapeutic targets in basic research and clinical trials. Some open questions regarding functional significance and future directions of targeting SEs in the clinic will be discussed too.
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Affiliation(s)
- Yunlu Jia
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore.,Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore.,Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Republic of Singapore
| | - Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore.
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24
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The enhancer RNA ARIEL activates the oncogenic transcriptional program in T-cell acute lymphoblastic leukemia. Blood 2019; 134:239-251. [PMID: 31076442 DOI: 10.1182/blood.2018874503] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/07/2019] [Indexed: 11/20/2022] Open
Abstract
The oncogenic transcription factor TAL1 regulates the transcriptional program in T-ALL. ARID5B is one of the critical downstream targets of TAL1, which further activates the oncogenic regulatory circuit in T-ALL cells. Here, we elucidated the molecular functions of the noncoding RNA, ARID5B-inducing enhancer associated long noncoding RNA (ARIEL), in T-ALL pathogenesis. We demonstrated that ARIEL is specifically activated in TAL1 + T-ALL cases, and its expression is associated with ARID5B enhancer activity. ARIEL recruits mediator proteins to the ARID5B enhancer, promotes enhancer-promoter interactions, and activates the expression of ARID5B, thereby positively regulating the TAL1-induced transcriptional program and the MYC oncogene. The TAL1 complex coordinately regulates the expression of ARIEL Knockdown of ARIEL inhibits cell growth and survival of T-ALL cells in culture and blocks disease progression in a murine xenograft model. Our results indicate that ARIEL plays an oncogenic role as an enhancer RNA in T-ALL.
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25
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He Y, Long W, Liu Q. Targeting Super-Enhancers as a Therapeutic Strategy for Cancer Treatment. Front Pharmacol 2019; 10:361. [PMID: 31105558 PMCID: PMC6499164 DOI: 10.3389/fphar.2019.00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/22/2019] [Indexed: 01/09/2023] Open
Abstract
Super-enhancers (SEs) refer to large clusters of enhancers that drive gene expressions. Recent data has provided novel insights in elucidating the roles of SEs in many diseases, including cancer. Many mechanisms involved in tumorigenesis and progression, ranging from internal gene mutation and rearrangement to external damage and inducement, have been demonstrated to be highly associated with SEs. Moreover, translocation, formation, deletion, or duplication of SEs themselves could lead to tumor development. It has been reported that various oncogenic molecules and pathways are tightly regulated by SEs. Moreover, several clinical trials on novel SEs blockers, such as BET inhibitor and CDK7i, have indicated the potential roles of SEs in cancer therapy. In this review, we highlighted the underlying mechanism of action of SEs in cancer development and the corresponding novel potential therapeutic strategies. It is speculated that targeting SEs could complement the traditional approaches and lead to more effective treatment for cancer patients.
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Affiliation(s)
- Yi He
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wenyong Long
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Qing Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
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26
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Luo M, Zhang Q, Xia M, Hu F, Ma Z, Chen Z, Guo AY. Differential Co-expression and Regulatory Network Analysis Uncover the Relapse Factor and Mechanism of T Cell Acute Leukemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:184-194. [PMID: 30195757 PMCID: PMC6023839 DOI: 10.1016/j.omtn.2018.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 04/02/2018] [Accepted: 05/04/2018] [Indexed: 01/17/2023]
Abstract
The pediatric T cell acute lymphoblastic leukemia (T-ALL) still remains a cancer with worst prognosis for high recurrence. Massive studies were conducted for the leukemia relapse based on diagnosis and relapse paired samples. However, the initially diagnostic samples may contain the relapse information and mechanism, which were rarely studied. In this study, we collected mRNA and microRNA (miRNA) data from initially diagnosed pediatric T-ALL samples with their relapse or remission status after treatment. Integrated differential co-expression and miRNA-transcription factor (TF)-gene regulatory network analyses were used to reveal the possible relapse mechanisms for pediatric T-ALL. We detected miR-1246/1248 and NOTCH2 served as key nodes in the relapse network, and they combined with TF WT1/SOX4/REL to form regulatory modules that influence the progress of T-ALL. A regulatory loop miR-429-MYCN-MFHAS1 was found potentially associated with the remission of T-ALL. Furthermore, we proved miR-1246/1248 combined with NOTCH2 could promote cell proliferation in the T-ALL cell line by experiments. Meanwhile, analysis based on the miRNA-drug relationships demonstrated that drugs 5-fluorouracil, ascorbate, and trastuzumab targeting miR-1246 could serve as potential supplements for the standard therapy. In conclusion, our findings revealed the potential molecular mechanisms of T-ALL relapse by the combination of co-expression and regulatory network, and they provide preliminary clues for precise treatment of T-ALL patients.
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Affiliation(s)
- Mei Luo
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qiong Zhang
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mengxuan Xia
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Feifei Hu
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhaowu Ma
- Laboratory of Neuronal Network and Brain Diseases Modulation, School of Medicine, Yangtze University, Jingzhou, Hubei 434023, China
| | - Zehua Chen
- Joint Laboratory for the Research of Pharmaceutics-Huazhong University of Science and Technology and Infinitus, Wuhan, China
| | - An-Yuan Guo
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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27
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Tan TK, Zhang C, Sanda T. Oncogenic transcriptional program driven by TAL1 in T-cell acute lymphoblastic leukemia. Int J Hematol 2018; 109:5-17. [PMID: 30145780 DOI: 10.1007/s12185-018-2518-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/21/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
TAL1/SCL is a prime example of an oncogenic transcription factor that is abnormally expressed in acute leukemia due to the replacement of regulator elements. This gene has also been recognized as an essential regulator of hematopoiesis. TAL1 expression is strictly regulated in a lineage- and stage-specific manner. Such precise control is crucial for the switching of the transcriptional program. The misexpression of TAL1 in immature thymocytes leads to a widespread series of orchestrated downstream events that affect several different cellular machineries, resulting in a lethal consequence, namely T-cell acute lymphoblastic leukemia (T-ALL). In this article, we will discuss the transcriptional regulatory network and downstream target genes, including protein-coding genes and non-coding RNAs, controlled by TAL1 in normal hematopoiesis and T-cell leukemogenesis.
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Affiliation(s)
- Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Chujing Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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28
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Yi K, Ju YS. Patterns and mechanisms of structural variations in human cancer. Exp Mol Med 2018; 50:1-11. [PMID: 30089796 PMCID: PMC6082854 DOI: 10.1038/s12276-018-0112-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 12/29/2017] [Indexed: 12/16/2022] Open
Abstract
Next-generation sequencing technology has enabled the comprehensive detection of genomic alterations in human somatic cells, including point mutations, chromosomal rearrangements, and structural variations (SVs). Using sophisticated bioinformatics algorithms, unbiased catalogs of SVs are emerging from thousands of human cancer genomes for the first time. Via careful examination of SV breakpoints at single-nucleotide resolution as well as local DNA copy number changes, diverse patterns of genomic rearrangements are being revealed. These "SV signatures" provide deep insight into the mutational processes that have shaped genome changes in human somatic cells. This review summarizes the characteristics of recently identified complex SVs, including chromothripsis, chromoplexy, microhomology-mediated breakage-induced replication (MMBIR), and others, to provide a holistic snapshot of the current knowledge on genomic rearrangements in somatic cells.
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Affiliation(s)
- Kijong Yi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea.
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29
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Identification of novel lncRNAs regulated by the TAL1 complex in T-cell acute lymphoblastic leukemia. Leukemia 2018; 32:2138-2151. [PMID: 29654272 DOI: 10.1038/s41375-018-0110-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 02/05/2018] [Accepted: 03/09/2018] [Indexed: 12/13/2022]
Abstract
TAL1/SCL is one of the most prevalent oncogenes in T-cell acute lymphoblastic leukemia (T-ALL). TAL1 and its regulatory partners (GATA3, RUNX1, and MYB) positively regulate each other and coordinately regulate the expression of their downstream target genes in T-ALL cells. However, long non-coding RNAs (lncRNAs) regulated by these factors are largely unknown. Here we established a bioinformatics pipeline and analyzed RNA-seq datasets with deep coverage to identify lncRNAs regulated by TAL1 in T-ALL cells. Our analysis predicted 57 putative lncRNAs that are activated by TAL1. Many of these transcripts were regulated by GATA3, RUNX1, and MYB in a coordinated manner. We identified two novel transcripts that were activated in multiple T-ALL cell samples but were downregulated in normal thymocytes. One transcript near the ARID5B gene locus was specifically expressed in TAL1-positive T-ALL cases. The other transcript located between the FAM49A and MYCN gene locus was also expressed in normal hematopoietic stem cells and T-cell progenitor cells. In addition, we identified a subset of lncRNAs that were negatively regulated by TAL1 and positively regulated by E-proteins in T-ALL cells. This included a known lncRNA (lnc-OAZ3-2:7) located near the RORC gene, which was expressed in normal thymocytes but repressed in TAL1-positive T-ALL cells.
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30
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Nakada-Tsukui K, Sekizuka T, Sato-Ebine E, Escueta-de Cadiz A, Ji DD, Tomii K, Kuroda M, Nozaki T. AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica. PLoS Pathog 2018; 14:e1006882. [PMID: 29554130 PMCID: PMC5884625 DOI: 10.1371/journal.ppat.1006882] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 04/04/2018] [Accepted: 01/17/2018] [Indexed: 11/17/2022] Open
Abstract
The disease state of amebiasis, caused by Entamoeba histolytica, varies from asymptomatic to severe manifestations that include dysentery and extraintestinal abscesses. The virulence factors of the pathogen, and host defense mechanisms, contribute to the outcomes of infection; however, the underlying genetic factors, which affect clinical outcomes, remain to be fully elucidated. To identify these genetic factors in E. histolytica, we used Illumina next-generation sequencing to conduct a comparative genomic analysis of two clinical isolates obtained from diarrheal and asymptomatic patients (strains KU50 and KU27, respectively). By mapping KU50 and KU27 reads to the genome of a reference HM-1:IMSS strain, we identified two genes (EHI_089440 and EHI_176590) that were absent in strain KU27. In KU27, a single AIG1 (avrRpt2-induced gene 1) family gene (EHI_176590) was found to be deleted, from a tandem array of three AIG1 genes, by homologous recombination between the two flanking genes. Overexpression of the EHI_176590 gene, in strain HM-1:IMSS cl6, resulted in increased formation of cell-surface protrusions and enhanced adhesion to human erythrocytes. The EHI_176590 gene was detected by PCR in 56% of stool samples from symptomatic patients infected with E. histolytica, but only in 15% of stool samples from asymptomatic individuals. This suggests that the presence of the EHI_176590 gene is correlated with the outcomes of infection. Taken together, these data strongly indicate that the AIG1 family protein plays a pivotal role in E. histolytica virulence via regulation of host cell adhesion. Our in-vivo experiments, using a hamster liver abscess model, showed that overexpression or gene silencing of EHI_176590 reduced and increased liver abscess formation, respectively. This suggests that the AIG1 genes may have contrasting roles in virulence depending on the genetic background of the parasite and host environment.
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Affiliation(s)
- Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Emi Sato-Ebine
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Dar-der Ji
- Center for Research and Diagnostics, Centers for Disease Control, Taipei, Taiwan
| | - Kentaro Tomii
- Artificial Intelligence Research Center (AIRC) and Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Makoto Kuroda
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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31
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Leong WZ, Tan SH, Ngoc PCT, Amanda S, Yam AWY, Liau WS, Gong Z, Lawton LN, Tenen DG, Sanda T. ARID5B as a critical downstream target of the TAL1 complex that activates the oncogenic transcriptional program and promotes T-cell leukemogenesis. Genes Dev 2018; 31:2343-2360. [PMID: 29326336 PMCID: PMC5795782 DOI: 10.1101/gad.302646.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/30/2017] [Indexed: 12/13/2022]
Abstract
Leong et al. identified ARID5B as a collaborating oncogenic factor involved in the transcriptional program in T-ALL. ARID5B positively regulates the expression of TAL1 and its regulatory partners and also activates the expression of the oncogene MYC. The oncogenic transcription factor TAL1/SCL induces an aberrant transcriptional program in T-cell acute lymphoblastic leukemia (T-ALL) cells. However, the critical factors that are directly activated by TAL1 and contribute to T-ALL pathogenesis are largely unknown. Here, we identified AT-rich interactive domain 5B (ARID5B) as a collaborating oncogenic factor involved in the transcriptional program in T-ALL. ARID5B expression is down-regulated at the double-negative 2–4 stages in normal thymocytes, while it is induced by the TAL1 complex in human T-ALL cells. The enhancer located 135 kb upstream of the ARID5B gene locus is activated under a superenhancer in T-ALL cells but not in normal T cells. Notably, ARID5B-bound regions are associated predominantly with active transcription. ARID5B and TAL1 frequently co-occupy target genes and coordinately control their expression. ARID5B positively regulates the expression of TAL1 and its regulatory partners. ARID5B also activates the expression of the oncogene MYC. Importantly, ARID5B is required for the survival and growth of T-ALL cells, and forced expression of ARID5B in immature thymocytes results in thymus retention, differentiation arrest, radioresistance, and tumor formation in zebrafish. Our results indicate that ARID5B reinforces the oncogenic transcriptional program by positively regulating the TAL1-induced regulatory circuit and MYC in T-ALL, thereby contributing to T-cell leukemogenesis.
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Affiliation(s)
- Wei Zhong Leong
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Phuong Cao Thi Ngoc
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Stella Amanda
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Alice Wei Yee Yam
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Wei-Siang Liau
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Zhiyuan Gong
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Lee N Lawton
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore.,Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
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32
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Tan SH, Bertulfo FC, Sanda T. Leukemia-Initiating Cells in T-Cell Acute Lymphoblastic Leukemia. Front Oncol 2017; 7:218. [PMID: 29034206 PMCID: PMC5627022 DOI: 10.3389/fonc.2017.00218] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/01/2017] [Indexed: 12/26/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a hematological malignancy characterized by the clonal proliferation of immature T-cell precursors. T-ALL has many similar pathophysiological features to acute myeloid leukemia, which has been extensively studied in the establishment of the cancer stem cell (CSC) theory, but the CSC concept in T-ALL is still debatable. Although leukemia-initiating cells (LICs), which can generate leukemia in a xenograft setting, have been found in both human T-ALL patients and animal models, the nature and origin of LICs are largely unknown. In this review, we discuss recent studies on LICs in T-ALL and the potential mechanisms of LIC emergence in this disease. We focus on the oncogenic transcription factors TAL1, LMO2, and NOTCH1 and highlight the significance of the transcriptional regulatory programs in normal hematopoietic stem cells and T-ALL.
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Affiliation(s)
- Shi Hao Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Fatima Carla Bertulfo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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33
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Sanda T, Leong WZ. TAL1 as a master oncogenic transcription factor in T-cell acute lymphoblastic leukemia. Exp Hematol 2017; 53:7-15. [PMID: 28652130 DOI: 10.1016/j.exphem.2017.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/11/2017] [Indexed: 11/29/2022]
Abstract
In hematopoietic cell development, the transcriptional program is strictly regulated in a lineage- and stage-specific manner that requires a number of transcription factors to work in a cascade or in a loop, in addition to interactions with nonhematopoietic cells in the microenvironment. Disruption of the transcriptional program alters the cellular state and may predispose cells to the acquisition of genetic abnormalities. Early studies have shown that proteins that promote cell differentiation often serve as tumor suppressors, whereas inhibitors of those proteins act as oncogenes in the context of acute leukemia. A prime example is T-cell acute lymphoblastic leukemia (T-ALL), a malignant disorder characterized by clonal proliferation of immature stage thymocytes. Although a relatively small number of genetic abnormalities are observed in T-ALL, these abnormalities are crucial for leukemogenesis. Many oncogenes and tumor suppressors in T-ALL are transcription factors that are required for normal hematopoiesis. The transformation process in T-ALL is efficient and orchestrated; the oncogene disrupts the transcriptional program directing T-cell differentiation and also uses its native ability as a master transcription factor in hematopoiesis. This imbalance in the transcriptional program is a primary determinant underlying the molecular pathogenesis of T-ALL. In this review, we focus on the oncogenic transcription factor TAL1 and the tumor-suppressor E-proteins and discuss the malignant cell state, the transcriptional circuit, and the consequence of molecular abnormalities in T-ALL.
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Affiliation(s)
- Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Wei Zhong Leong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
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