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Bandini P, Borràs N, Berrueco R, Gassiot S, Martin-Fernandez L, Sarrate E, Comes N, Ramírez L, Hobeich C, Vidal F, Corrales I. Gaining Insights into Inherited Bleeding Disorders of Complex Etiology in Pediatric Patients: Whole-Exome Sequencing as First-Line Investigation Tool. Thromb Haemost 2024; 124:628-640. [PMID: 38158197 DOI: 10.1055/s-0043-1778070] [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] [Indexed: 01/03/2024]
Abstract
INTRODUCTION Investigation of the molecular basis of inherited bleeding disorders (IBD) is mostly performed with gene panel sequencing. However, the continuous discovery of new related genes underlies the limitation of this approach. This study aimed to identify genetic variants responsible for IBD in pediatric patients using whole-exome sequencing (WES), and to provide a detailed description and reclassification of candidate variants. MATERIAL AND METHODS WES was performed for 18 pediatric patients, and variants were filtered using a first-line list of 290 genes. Variant prioritization was discussed in a multidisciplinary team based on genotype-phenotype correlation, and segregation studies were performed with available family members. RESULTS The study identified 22 candidate variants in 17 out of 18 patients (94%). Eleven patients had complete genotype-phenotype correlation, resulting in a diagnostic yield of 61%, 5 (28%) were classified as partially solved, and 2 (11%) remained unsolved. Variants were identified in platelet (ACTN1, ANKRD26, CYCS, GATA1, GFI1B, ITGA2, NBEAL2, RUNX1, SRC, TUBB1), bleeding (APOLD1), and coagulation (F7, F8, F11, VWF) genes. Notably, 9 out of 22 (41%) variants were previously unreported. Variant pathogenicity was assessed according to the American College of Medical Genetics and Genomics guidelines and reclassification of three variants based on family segregation evidence, resulting in the identification of 10 pathogenic or likely pathogenic variants, 6 variants of uncertain significance, and 6 benign or likely benign variants. CONCLUSION This study demonstrated the high potential of WES in identifying rare molecular defects causing IBD in pediatric patients, improving their management, prognosis, and treatment, particularly for patients at risk of malignancy and/or bleeding due to invasive procedures.
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Affiliation(s)
- Perla Bandini
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain
- Medicina Transfusional, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Nina Borràs
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain
- Medicina Transfusional, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
| | - Ruben Berrueco
- Servei d'Hematologia Pediàtrica, Hospital Sant Joan de Déu Barcelona, Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu de Barcelona (IRP-HSJD), Universitat de Barcelona, Barcelona, Spain
- Instituto Nacional de Investigación Biomédica en Enfermedades Raras (CIBER ER), Instituto de Salud Carlos III, Madrid, Spain
| | - Susanna Gassiot
- Servei de Diagnòstic de Laboratori, Hospital Sant Joan de Déu Barcelona, Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu de Barcelona (IRP-HSJD), Universitat de Barcelona, Barcelona, Spain
| | - Laura Martin-Fernandez
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain
- Medicina Transfusional, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
| | - Edurne Sarrate
- Servei de Diagnòstic de Laboratori, Hospital Sant Joan de Déu Barcelona, Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu de Barcelona (IRP-HSJD), Universitat de Barcelona, Barcelona, Spain
| | - Natàlia Comes
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain
- Medicina Transfusional, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
| | - Lorena Ramírez
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain
- Medicina Transfusional, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
| | - Carlos Hobeich
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain
- Medicina Transfusional, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
| | - Francisco Vidal
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain
- Medicina Transfusional, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV). Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Irene Corrales
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain
- Medicina Transfusional, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV). Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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Patnana PK, Liu L, Frank D, Nimmagadda SC, Behrens M, Ahmed H, Xie X, Liebmann M, Wei L, Gerdemann A, Thivakaran A, Humpf HU, Klotz L, Dugas M, Varghese J, Trajkovic-Arsic M, Siveke JT, Hanenberg H, Opalka B, Dührsen U, Reinhardt HC, Guenther U, von Bubnoff N, Khandanpour C. Dose-dependent expression of GFI1 alters metabolism in the haematopoietic progenitors and MLL::AF9-induced leukaemic cells. Br J Haematol 2023; 202:1033-1048. [PMID: 37423893 DOI: 10.1111/bjh.18939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023]
Abstract
Growth factor independence 1 (GFI1) is a transcriptional repressor protein that plays an essential role in the differentiation of myeloid and lymphoid progenitors. We and other groups have shown that GFI1 has a dose-dependent role in the initiation, progression, and prognosis of acute myeloid leukaemia (AML) patients by inducing epigenetic changes. We now demonstrate a novel role for dose-dependent GFI1 expression in regulating metabolism in haematopoietic progenitor and leukaemic cells. Using in-vitro and ex-vivo murine models of MLL::AF9-induced human AML and extra-cellular flux assays, we now demonstrate that a lower GFI1 expression enhances oxidative phosphorylation rate via upregulation of the FOXO1- MYC axis. Our findings underscore the significance of therapeutic exploitation in GFI1-low-expressing leukaemia cells by targeting oxidative phosphorylation and glutamine metabolism.
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Affiliation(s)
- Pradeep Kumar Patnana
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Longlong Liu
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
- Department of Hematology, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Daria Frank
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Subbaiah Chary Nimmagadda
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Matthias Behrens
- Institute of Food Chemistry, University of Muenster, Muenster, Germany
| | - Helal Ahmed
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Xiaoqing Xie
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
- Department of Hematology-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Marie Liebmann
- Department of Neurology with Institute of Translational Neurology, University Hospital Muenster, Muenster, Germany
| | - Lanying Wei
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
- Institute of Medical Informatics, University of Muenster, Muenster, Germany
| | - Andrea Gerdemann
- Institute of Food Chemistry, University of Muenster, Muenster, Germany
| | | | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Muenster, Muenster, Germany
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University Hospital Muenster, Muenster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Muenster, Muenster, Germany
| | - Marija Trajkovic-Arsic
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Jens T Siveke
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Helmut Hanenberg
- Clinic for Pediatrics III, University Hospital Essen, Essen, Germany
- Pediatric Oncology, Hematology & Immunology, Heinrich Heine University, University Hospital Düsseldorf, Dusseldorf, Germany
| | - Bertram Opalka
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Dührsen
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Guenther
- Institute of Chemistry and Metabolomics, University of Lübeck, Lübeck, Germany
| | - Nikolas von Bubnoff
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Cyrus Khandanpour
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University of Lübeck, Lübeck, Germany
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Hartung EE, Singh K, Berg T. LSD1 inhibition modulates transcription factor networks in myeloid malignancies. Front Oncol 2023; 13:1149754. [PMID: 36969082 PMCID: PMC10036816 DOI: 10.3389/fonc.2023.1149754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Acute Myeloid Leukemia (AML) is a type of cancer of the blood system that is characterized by an accumulation of immature hematopoietic cells in the bone marrow and blood. Its pathogenesis is characterized by an increase in self-renewal and block in differentiation in hematopoietic stem and progenitor cells. Underlying its pathogenesis is the acquisition of mutations in these cells. As there are many different mutations found in AML that can occur in different combinations the disease is very heterogeneous. There has been some progress in the treatment of AML through the introduction of targeted therapies and a broader application of the stem cell transplantation in its treatment. However, many mutations found in AML are still lacking defined interventions. These are in particular mutations and dysregulation in important myeloid transcription factors and epigenetic regulators that also play a crucial role in normal hematopoietic differentiation. While a direct targeting of the partial loss-of-function or change in function observed in these factors is very difficult to imagine, recent data suggests that the inhibition of LSD1, an important epigenetic regulator, can modulate interactions in the network of myeloid transcription factors and restore differentiation in AML. Interestingly, the impact of LSD1 inhibition in this regard is quite different between normal and malignant hematopoiesis. The effect of LSD1 inhibition involves transcription factors that directly interact with LSD1 such as GFI1 and GFI1B, but also transcription factors that bind to enhancers that are modulated by LSD1 such as PU.1 and C/EBPα as well as transcription factors that are regulated downstream of LSD1 such as IRF8. In this review, we are summarizing the current literature on the impact of LSD1 modulation in normal and malignant hematopoietic cells and the current knowledge how the involved transcription factor networks are altered. We are also exploring how these modulation of transcription factors play into the rational selection of combination partners with LSD1 inhibitors, which is an intense area of clinical investigation.
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Affiliation(s)
- Emily E. Hartung
- Centre for Discovery in Cancer Research, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Kanwaldeep Singh
- Centre for Discovery in Cancer Research, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Department of Oncology, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Tobias Berg
- Centre for Discovery in Cancer Research, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Department of Oncology, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Escarpment Cancer Research Institute, McMaster University, Hamilton Health Sciences, Hamilton, ON, Canada
- *Correspondence: Tobias Berg,
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He X, Xu Y, Huang D, Yu Z, Yu J, Xie L, Liu L, Yu Y, Chen C, Wan J, Zhang Y, Zheng J. P2X1 enhances leukemogenesis through PBX3-BCAT1 pathways. Leukemia 2023; 37:265-275. [PMID: 36418376 PMCID: PMC9898031 DOI: 10.1038/s41375-022-01759-y] [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: 04/20/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022]
Abstract
How bone marrow niches regulate leukemogenic activities of leukemia-initiating cells (LICs) is unclear. The present study revealed that the metabolic niche component, ATP, efficiently induced ion influx in LICs through its ligand-gated ion channel, P2X1. P2X1 deletion impaired LIC self-renewal capacities and resulted in an approximately 8-fold decrease in functional LIC numbers in a murine acute myeloid leukemia (AML) model without affecting normal hematopoiesis. P2X1 phosphorylation at specific sites of S387 and T389 was essential for sustaining its promoting effects on leukemia development. ATP-P2X1-mediated signaling upregulated the PBX3 level to transactivate BCAT1 to maintain LIC fates. P2X1 knockdown inhibited the proliferation of both human AML cell lines and primary cells. The P2X1 antagonist sufficiently suppressed AML cell proliferation. These results provided a unique perspective on how metabolic niche factor ATP fine-tunes LIC activities, which may benefit the development of strategies for targeting LICs or other cancer stem cells.
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Affiliation(s)
- Xiaoxiao He
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Yilu Xu
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Dan Huang
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Zhuo Yu
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Jing Yu
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Li Xie
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Ligen Liu
- grid.16821.3c0000 0004 0368 8293Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Ye Yu
- grid.254147.10000 0000 9776 7793School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
| | - Chiqi Chen
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jiangbo Wan
- Department of Hematology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Yaping Zhang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Junke Zheng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Research Unit of Stress and Cancer, Chinese Academy of Medical Sciences, Shanghai Cancer Institute, Renji hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200127, China.
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5
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Liu L, Patnana PK, Xie X, Frank D, Nimmagadda SC, Su M, Zhang D, Koenig T, Rosenbauer F, Liebmann M, Klotz L, Xu W, Vorwerk J, Neumann F, Hüve J, Unger A, Okun JG, Opalka B, Khandanpour C. GFI1B acts as a metabolic regulator in hematopoiesis and acute myeloid leukemia. Leukemia 2022; 36:2196-2207. [PMID: 35804097 PMCID: PMC9417998 DOI: 10.1038/s41375-022-01635-9] [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: 02/10/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
Recent studies highlighted the role of transcription factors in metabolic regulation during hematopoiesis and leukemia development. GFI1B is a transcriptional repressor that plays a critical role in hematopoiesis, and its expression is negatively related to the prognosis of acute myeloid leukemia (AML) patients. We earlier reported a change in the metabolic state of hematopoietic stem cells upon Gfi1b deletion. Here we explored the role of Gfi1b in metabolism reprogramming during hematopoiesis and leukemogenesis. We demonstrated that Gfi1b deletion remarkably activated mitochondrial respiration and altered energy metabolism dependence toward oxidative phosphorylation (OXPHOS). Mitochondrial substrate dependency was shifted from glucose to fatty acids upon Gfi1b deletion via upregulating fatty acid oxidation (FAO). On a molecular level, Gfi1b epigenetically regulated multiple FAO-related genes. Moreover, we observed that metabolic phenotypes evolved as cells progressed from preleukemia to leukemia, and the correlation between Gfi1b expression level and metabolic phenotype was affected by genetic variations in AML cells. FAO or OXPHOS inhibition significantly impeded leukemia progression of Gfi1b-KO MLL/AF9 cells. Finally, we showed that Gfi1b-deficient AML cells were more sensitive to metformin as well as drugs implicated in OXPHOS and FAO inhibition, opening new potential therapeutic strategies.
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Affiliation(s)
- Longlong Liu
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
| | - Pradeep Kumar Patnana
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany.,Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Xiaoqing Xie
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
| | - Daria Frank
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany.,Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Subbaiah Chary Nimmagadda
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
| | - Minhua Su
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 300052, Tianjin, China
| | - Donghua Zhang
- Department of Hematology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Thorsten Koenig
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Muenster, 48149, Muenster, Germany
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Muenster, 48149, Muenster, Germany
| | - Marie Liebmann
- Department of Neurology with Institute of Translational Neurology, University Hospital Muenster, 48149, Muenster, Germany
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University Hospital Muenster, 48149, Muenster, Germany
| | - Wendan Xu
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
| | - Jan Vorwerk
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
| | - Felix Neumann
- Fluorescence Microscopy Facility Muenster (FM)2, Institute of Medical Physics and Biophysics, University of Muenster, 48149, Muenster, Germany.,evorion biotechnologies GmbH, 48149, Muenster, Germany
| | - Jana Hüve
- Fluorescence Microscopy Facility Muenster (FM)2, Institute of Medical Physics and Biophysics, University of Muenster, 48149, Muenster, Germany
| | - Andreas Unger
- Institute of Physiology II, University of Muenster, 48149, Muenster, Germany
| | - Jürgen Günther Okun
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, Dietmar-Hopp-Metabolic Center, 69120, Heidelberg, Germany
| | - Bertram Opalka
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Cyrus Khandanpour
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany. .,Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University of Luebeck, 23538, Luebeck, Germany.
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Liu L, Patnana PK, Xie X, Frank D, Nimmagadda SC, Rosemann A, Liebmann M, Klotz L, Opalka B, Khandanpour C. High Metabolic Dependence on Oxidative Phosphorylation Drives Sensitivity to Metformin Treatment in MLL/AF9 Acute Myeloid Leukemia. Cancers (Basel) 2022; 14:cancers14030486. [PMID: 35158754 PMCID: PMC8833593 DOI: 10.3390/cancers14030486] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Acute myeloid leukemia is a group of metabolic heterogeneous cancers, of which the long-term overall survival is still poor, especially in elderly patients. Targeting metabolic reprogramming in leukemic cells is becoming a promising strategy. The aim of our research was to explore the relation of genetic mutations with the metabolic phenotype and potential therapeutics to target metabolic pathway dependence. We confirmed the metabolic heterogeneity in AML cell lines and found the high dependence on oxidative phosphorylation in MLL/AF9 AML cells. Metformin could significantly repress the proliferation of MLL/AF9 AML cells by inhibiting oxidative phosphorylation. Abstract Acute myeloid leukemia (AML) is a group of hematological cancers with metabolic heterogeneity. Oxidative phosphorylation (OXPHOS) has been reported to play an important role in the function of leukemic stem cells and chemotherapy-resistant cells and are associated with inferior prognosis in AML patients. However, the relationship between metabolic phenotype and genetic mutations are yet to be explored. In the present study, we demonstrate that AML cell lines have high metabolic heterogeneity, and AML cells with MLL/AF9 have upregulated mitochondrial activity and mainly depend on OXPHOS for energy production. Furthermore, we show that metformin repressed the proliferation of MLL/AF9 AML cells by inhibiting mitochondrial respiration. Together, this study demonstrates that AML cells with an MLL/AF9 genotype have a high dependency on OXPHOS and could be therapeutically targeted by metformin.
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Affiliation(s)
- Longlong Liu
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany; (L.L.); (P.K.P.); (X.X.); (D.F.); (S.C.N.)
| | - Pradeep Kumar Patnana
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany; (L.L.); (P.K.P.); (X.X.); (D.F.); (S.C.N.)
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Xiaoqing Xie
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany; (L.L.); (P.K.P.); (X.X.); (D.F.); (S.C.N.)
| | - Daria Frank
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany; (L.L.); (P.K.P.); (X.X.); (D.F.); (S.C.N.)
| | - Subbaiah Chary Nimmagadda
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany; (L.L.); (P.K.P.); (X.X.); (D.F.); (S.C.N.)
| | - Annegret Rosemann
- Department of Pediatric Hematology and Oncology, University Children’s Hospital Muenster, 48149 Muenster, Germany;
| | - Marie Liebmann
- Department of Neurology with Institute of Translational Neurology, University Hospital Muenster, 48149 Muenster, Germany; (M.L.); (L.K.)
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University Hospital Muenster, 48149 Muenster, Germany; (M.L.); (L.K.)
| | - Bertram Opalka
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Cyrus Khandanpour
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149 Muenster, Germany; (L.L.); (P.K.P.); (X.X.); (D.F.); (S.C.N.)
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University of Lübeck, 23562 Lübeck, Germany
- Correspondence:
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7
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Characterization of a genomic region 8 kb downstream of GFI1B associated with myeloproliferative neoplasms. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166259. [PMID: 34450246 DOI: 10.1016/j.bbadis.2021.166259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/07/2021] [Accepted: 08/23/2021] [Indexed: 11/23/2022]
Abstract
A genomic locus 8 kb downstream of the transcription factor GFI1B (Growth Factor Independence 1B) predisposes to clonal hematopoiesis and myeloproliferative neoplasms. One of the most significantly associated polymorphisms in this region is rs621940-G. GFI1B auto-represses GFI1B, and altered GFI1B expression contributes to myeloid neoplasms. We studied whether rs621940-G affects GFI1B expression and growth of immature cells. GFI1B ChIP-seq showed clear binding to the rs621940 locus. Preferential binding of various hematopoietic transcription factors to either the rs621940-C or -G allele was observed, but GFI1B showed no preference. In gene reporter assays the rs621940 region inhibited GFI1B promoter activity with the G-allele having less suppressive effects compared to the C-allele. However, CRISPR-Cas9 mediated deletion of the locus in K562 cells did not alter GFI1B expression nor auto-repression. In healthy peripheral blood mononuclear cells GFI1B expression did not differ consistently between the rs621940 alleles. Long range and targeted deep sequencing did not detect consistent effects of rs621940-G on allelic GFI1B expression either. Finally, we observed that myeloid colony formation was not significantly affected by either rs621940 allele in 193 healthy donors. Together, these findings show no evidence that rs621940 or its locus affect GFI1B expression, auto-repression or growth of immature myeloid cells.
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8
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Zhang L, Xin M, Wang P. Identification of a novel snoRNA expression signature associated with overall survival in patients with lung adenocarcinoma: A comprehensive analysis based on RNA sequencing dataset. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:7837-7860. [PMID: 34814278 DOI: 10.3934/mbe.2021389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Since multiple studies have reported that small nucleolar RNAs (snoRNAs) can be serve as prognostic biomarkers for cancers, however, the prognostic values of snoRNAs in lung adenocarcinoma (LUAD) remain unclear. Therefore, the main work of this study is to identify the prognostic snoRNAs of LUAD and conduct a comprehensive analysis. The Cancer Genome Atlas LUAD cohort whole-genome RNA-sequencing dataset is included in this study, prognostic analysis and multiple bioinformatics approaches are used for comprehensive analysis and identification of prognostic snoRNAs. There were seven LUAD prognostic snoRNAs were screened in current study. We also constructed a novel expression signature containing five LUAD prognostic snoRNAs (snoU109, SNORA5A, SNORA70, SNORD104 and U3). Survival analysis of this expression signature reveals that LUAD patients with high risk score was significantly related to an unfavourable overall survival (adjusted P = 0.01, adjusted hazard ratio = 1.476, 95% confidence interval = 1.096-1.987). Functional analysis indicated that LUAD patients with different risk score phenotypes had significant differences in cell cycle, apoptosis, integrin, transforming growth factor beta, ErbB, nuclear factor kappa B, mitogen-activated protein kinase, phosphatidylinositol-3-kinase and toll like receptor signaling pathway. Immune microenvironment analysis also indicated that there were significant differences in immune microenvironment scores among LUAD patients with different risk score. In conclusion, this study identified an novel expression signature containing five LUAD prognostic snoRNAs, which may be serve as an independent prognostic indicator for LUAD patients.
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Affiliation(s)
- Linbo Zhang
- Department of Health Management and Division of Physical Examination, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning 530021, China
| | - Mei Xin
- Department of Health Management and Division of Physical Examination, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning 530021, China
| | - Peng Wang
- Department of Health Management and Division of Physical Examination, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning 530021, China
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9
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Abstract
Clonal haematopoiesis (CH) is a common, age-related expansion of blood cells with somatic mutations that is associated with an increased risk of haematological malignancies, cardiovascular disease and all-cause mortality. CH may be caused by point mutations in genes associated with myeloid neoplasms, chromosomal copy number changes and loss of heterozygosity events. How inherited and environmental factors shape the incidence of CH is incompletely understood. Even though the several varieties of CH may have distinct phenotypic consequences, recent research points to an underlying genetic architecture that is highly overlapping. Moreover, there are numerous commonalities between the inherited variation associated with CH and that which has been linked to age-associated biomarkers and diseases. In this Review, we synthesize what is currently known about how inherited variation shapes the risk of CH and how this genetic architecture intersects with the biology of diseases that occur with ageing.
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Affiliation(s)
- Alexander J Silver
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander G Bick
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA.
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10
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Hui B, Lu C, Wang J, Xu Y, Yang Y, Ji H, Li X, Xu L, Wang J, Tang W, Wang K, Gu Y. Engineered exosomes for co-delivery of PGM5-AS1 and oxaliplatin to reverse drug resistance in colon cancer. J Cell Physiol 2021; 237:911-933. [PMID: 34463962 DOI: 10.1002/jcp.30566] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 02/06/2023]
Abstract
Oxaliplatin resistance inevitably occurs in almost all cases of metastatic colorectal cancer (CRC), and it is important to study the roles of lncRNAs and their specific regulatory mechanisms in oxaliplatin resistance. Exosomes are increasingly designed for drug or functional nucleic acid delivery due to their properties, thereby improving the effectiveness of cancer therapy. The results of this study show that the low expression of PGM5 antisense RNA 1 (PGM5-AS1) in colon cancer is induced by transcription inhibitor, GFI1B. PGM5-AS1 prevents proliferation, migration, and acquired oxaliplatin tolerance of colon cancer cells. Exosomes encapsulating oxaliplatin and PGM5-AS1 can reverse drug resistance. For identifying differentially expressed target genes regarding PGM5-AS1, RNA transcriptome sequencing was performed. The mechanism by which PGM5-AS1 regulates its target genes was explored by performing experiments such as fluorescent in situ hybridization assay, dual-luciferase reporter gene assay, and RNA immunoprecipitation. The results show that by recruiting SRSF3, PGM5-AS1 activates alternate splicing to downregulate PAEP expression. For hsa-miR-423-5p, PGM5-AS1 can also act as a sponge to upregulate the NME1 expression.
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Affiliation(s)
- Bingqing Hui
- Department of Oncology and Cancer Rehabilitation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chen Lu
- The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Wang
- State Key Laboratory of Reproductive Medicine, Department of Anatomy, Histology and Embryology, The Research Center for Bone and Stem Cells, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yetao Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuchen Yang
- Department of Oncology and Cancer Rehabilitation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hao Ji
- Department of Liver Surgery and Liver Transplantation Center, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaofei Li
- Department of Oncology and Cancer Rehabilitation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lingyan Xu
- Department of Oncology and Cancer Rehabilitation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiawei Wang
- Department of Oncology and Cancer Rehabilitation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weiwei Tang
- Key Laboratory of Living Donor Transplantation, Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Keming Wang
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yanhong Gu
- Department of Oncology and Cancer Rehabilitation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
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11
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Barabino SML, Citterio E, Ronchi AE. Transcription Factors, R-Loops and Deubiquitinating Enzymes: Emerging Targets in Myelodysplastic Syndromes and Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13153753. [PMID: 34359655 PMCID: PMC8345071 DOI: 10.3390/cancers13153753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The advent of DNA massive sequencing technologies has allowed for the first time an extensive look into the heterogeneous spectrum of genes and mutations underpinning myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). In this review, we wish to explore the most recent advances and the rationale for the potential therapeutic interest of three main actors in myelo-leukemic transformation: transcription factors that govern myeloid differentiation; RNA splicing factors, which ensure proper mRNA maturation and whose mutations increase R-loops formation; and deubiquitinating enzymes, which contribute to genome stability in hematopoietic stem cells (HSCs). Abstract Myeloid neoplasms encompass a very heterogeneous family of diseases characterized by the failure of the molecular mechanisms that ensure a balanced equilibrium between hematopoietic stem cells (HSCs) self-renewal and the proper production of differentiated cells. The origin of the driver mutations leading to preleukemia can be traced back to HSC/progenitor cells. Many properties typical to normal HSCs are exploited by leukemic stem cells (LSCs) to their advantage, leading to the emergence of a clonal population that can eventually progress to leukemia with variable latency and evolution. In fact, different subclones might in turn develop from the original malignant clone through accumulation of additional mutations, increasing their competitive fitness. This process ultimately leads to a complex cancer architecture where a mosaic of cellular clones—each carrying a unique set of mutations—coexists. The repertoire of genes whose mutations contribute to the progression toward leukemogenesis is broad. It encompasses genes involved in different cellular processes, including transcriptional regulation, epigenetics (DNA and histones modifications), DNA damage signaling and repair, chromosome segregation and replication (cohesin complex), RNA splicing, and signal transduction. Among these many players, transcription factors, RNA splicing proteins, and deubiquitinating enzymes are emerging as potential targets for therapeutic intervention.
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12
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Beauchemin H, Möröy T. Multifaceted Actions of GFI1 and GFI1B in Hematopoietic Stem Cell Self-Renewal and Lineage Commitment. Front Genet 2020; 11:591099. [PMID: 33193732 PMCID: PMC7649360 DOI: 10.3389/fgene.2020.591099] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/23/2020] [Indexed: 12/15/2022] Open
Abstract
Growth factor independence 1 (GFI1) and the closely related protein GFI1B are small nuclear proteins that act as DNA binding transcriptional repressors. Both recognize the same consensus DNA binding motif via their C-terminal zinc finger domains and regulate the expression of their target genes by recruiting chromatin modifiers such as histone deacetylases (HDACs) and demethylases (LSD1) by using an N-terminal SNAG domain that comprises only 20 amino acids. The only region that is different between both proteins is the region that separates the zinc finger domains and the SNAG domain. Both proteins are co-expressed in hematopoietic stem cells (HSCs) and, to some extent, in multipotent progenitors (MPPs), but expression is specified as soon as early progenitors and show signs of lineage bias. While expression of GFI1 is maintained in lymphoid primed multipotent progenitors (LMPPs) that have the potential to differentiate into both myeloid and lymphoid cells, GFI1B expression is no longer detectable in these cells. By contrast, GFI1 expression is lost in megakaryocyte precursors (MKPs) and in megakaryocyte-erythrocyte progenitors (MEPs), which maintain a high level of GFI1B expression. Consequently, GFI1 drives myeloid and lymphoid differentiation and GFI1B drives the development of megakaryocytes, platelets, and erythrocytes. How such complementary cell type- and lineage-specific functions of GFI1 and GFI1B are maintained is still an unresolved question in particular since they share an almost identical structure and very similar biochemical modes of actions. The cell type-specific accessibility of GFI1/1B binding sites may explain the fact that very similar transcription factors can be responsible for very different transcriptional programming. An additional explanation comes from recent data showing that both proteins may have additional non-transcriptional functions. GFI1 interacts with a number of proteins involved in DNA repair and lack of GFI1 renders HSCs highly susceptible to DNA damage-induced death and restricts their proliferation. In contrast, GFI1B binds to proteins of the beta-catenin/Wnt signaling pathway and lack of GFI1B leads to an expansion of HSCs and MKPs, illustrating the different impact that GFI1 or GFI1B has on HSCs. In addition, GFI1 and GFI1B are required for endothelial cells to become the first blood cells during early murine development and are among those transcription factors needed to convert adult endothelial cells or fibroblasts into HSCs. This role of GFI1 and GFI1B bears high significance for the ongoing effort to generate hematopoietic stem and progenitor cells de novo for the autologous treatment of blood disorders such as leukemia and lymphoma.
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Affiliation(s)
| | - Tarik Möröy
- Institut de recherches cliniques de Montréal, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
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13
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Brøns N, Zaninetti C, Ostrowski SR, Petersen J, Greinacher A, Rossing M, Leinøe E. A novel homozygous GFI1B variant in 2 sisters with thrombocytopenia and severe bleeding tendency. Platelets 2020; 32:701-704. [PMID: 32633597 DOI: 10.1080/09537104.2020.1786041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Genetic variants in growth factor-independent 1B (GFI1B), encoding transcription factor GFI1B, are causative of platelet-type bleeding disorder-17. Presently, 53 cases of GFI1B associated inherited thrombocytopenia (IT) have been published, however only three were homozygous. The bleeding- and platelet phenotypes of these patients depend on location and inheritance pattern of the GFI1B variant. We report a novel homozygous GFI1B (Thr174Ile) variant located in the first Zinc finger domain of GFI1B in two sisters of Palestinian ancestry born to consanguineous parents. They experienced severe bleeding tendency at moderately reduced platelet counts. Flow cytometry and immunofluorescent microscopy confirmed the diagnostic features of GFI1B associated IT: a reduced content of alpha granules and aberrant expression of the stem cell marker CD34 on platelets. Transcription factor GFI1B is differentially expressed during hemato- and lymphopoiesis. In addition, to platelet function investigations, we present results of lymphoid subgroup analyses and deformability of red cells measured by ektacytometry.
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Affiliation(s)
- Nanna Brøns
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Carlo Zaninetti
- Department of Clinical Immunology, Greifswald University Hospital, Greifswald, Germany
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Jesper Petersen
- Department of Haematology Research Laboratory, Herlev Hospital, Copenhagen University Hospital, Denmark
| | - Andreas Greinacher
- Department of Clinical Immunology, Greifswald University Hospital, Greifswald, Germany
| | - Maria Rossing
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Eva Leinøe
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Denmark
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14
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He B, Gao P, Ding YY, Chen CH, Chen G, Chen C, Kim H, Tasian SK, Hunger SP, Tan K. Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. SCIENCE ADVANCES 2020; 6:eaba3064. [PMID: 32832663 PMCID: PMC7439310 DOI: 10.1126/sciadv.aba3064] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 06/10/2020] [Indexed: 05/14/2023]
Abstract
Interpreting the function of noncoding mutations in cancer genomes remains a major challenge. Here, we developed a computational framework to identify putative causal noncoding mutations of all classes by joint analysis of mutation and gene expression data. We identified thousands of SNVs/small indels and structural variants as putative causal mutations in five major pediatric cancers. We experimentally validated the oncogenic role of CHD4 overexpression via enhancer hijacking in B-ALL. We observed a general exclusivity of coding and noncoding mutations affecting the same genes and pathways. We showed that integrated mutation profiles can help define novel patient subtypes with different clinical outcomes. Our study introduces a general strategy to systematically identify and characterize the full spectrum of noncoding mutations in cancers.
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Affiliation(s)
- Bing He
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peng Gao
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yang-Yang Ding
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chia-Hui Chen
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gregory Chen
- Medical Scientist Training Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Changya Chen
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hannah Kim
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sarah K. Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen P. Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kai Tan
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author.
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15
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DePasquale EAK, Schnell D, Dexheimer P, Ferchen K, Hay S, Chetal K, Valiente-Alandí Í, Blaxall BC, Grimes H, Salomonis N. cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes. Nucleic Acids Res 2019; 47:e138. [PMID: 31529053 PMCID: PMC6868361 DOI: 10.1093/nar/gkz789] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/01/2019] [Accepted: 09/05/2019] [Indexed: 02/03/2023] Open
Abstract
To understand the molecular pathogenesis of human disease, precision analyses to define alterations within and between disease-associated cell populations are desperately needed. Single-cell genomics represents an ideal platform to enable the identification and comparison of normal and diseased transcriptional cell populations. We created cellHarmony, an integrated solution for the unsupervised analysis, classification, and comparison of cell types from diverse single-cell RNA-Seq datasets. cellHarmony efficiently and accurately matches single-cell transcriptomes using a community-clustering and alignment strategy to compute differences in cell-type specific gene expression over potentially dozens of cell populations. Such transcriptional differences are used to automatically identify distinct and shared gene programs among cell-types and identify impacted pathways and transcriptional regulatory networks to understand the impact of perturbations at a systems level. cellHarmony is implemented as a python package and as an integrated workflow within the software AltAnalyze. We demonstrate that cellHarmony has improved or equivalent performance to alternative label projection methods, is able to identify the likely cellular origins of malignant states, stratify patients into clinical disease subtypes from identified gene programs, resolve discrete disease networks impacting specific cell-types, and illuminate therapeutic mechanisms. Thus, this approach holds tremendous promise in revealing the molecular and cellular origins of complex disease.
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Affiliation(s)
- Erica A K DePasquale
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Daniel Schnell
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Phillip Dexheimer
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kyle Ferchen
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Stuart Hay
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Íñigo Valiente-Alandí
- Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Burns C Blaxall
- Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA
| | - H Leighton Grimes
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nathan Salomonis
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA
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16
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van Bergen MGJM, van der Reijden BA. Targeting the GFI1/1B-CoREST Complex in Acute Myeloid Leukemia. Front Oncol 2019; 9:1027. [PMID: 31649884 PMCID: PMC6794713 DOI: 10.3389/fonc.2019.01027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/23/2019] [Indexed: 11/21/2022] Open
Abstract
One of the hallmarks of acute myeloid leukemia (AML) is a block in cellular differentiation. Recent studies have shown that small molecules targeting Lysine Specific Demethylase 1A (KDM1A) may force the malignant cells to terminally differentiate. KDM1A is a core component of the chromatin binding CoREST complex. Together with histone deacetylases CoREST regulates gene expression by histone 3 demethylation and deacetylation. The transcription factors GFI1 and GFI1B (for growth factor independence) are major interaction partners of KDM1A and recruit the CoREST complex to chromatin in myeloid cells. Recent studies show that the small molecules that target KDM1A disrupt the GFI1/1B-CoREST interaction and that this is key to inducing terminal differentiation of leukemia cells.
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Affiliation(s)
| | - Bert A. van der Reijden
- Laboratory of Hematology, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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17
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Möröy T, Khandanpour C. Role of GFI1 in Epigenetic Regulation of MDS and AML Pathogenesis: Mechanisms and Therapeutic Implications. Front Oncol 2019; 9:824. [PMID: 31508375 PMCID: PMC6718700 DOI: 10.3389/fonc.2019.00824] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/12/2019] [Indexed: 01/12/2023] Open
Abstract
Growth factor independence 1 (GFI1) is a DNA binding zinc finger protein, which can mediate transcriptional repression mainly by recruiting histone-modifying enzymes to its target genes. GFI1 plays important roles in hematopoiesis, in particular by regulating both the function of hematopoietic stem- and precursor cells and differentiation along myeloid and lymphoid lineages. In recent years, a number of publications have provided evidence that GFI1 is involved in the pathogenesis of acute myeloid leukemia (AML), its proposed precursor, myelodysplastic syndrome (MDS), and possibly also in the progression from MDS to AML. For instance, expression levels of the GFI1 gene correlate with patient survival and treatment response in both AML and MDS and can influence disease progression and maintenance in experimental animal models. Also, a non-synonymous single nucleotide polymorphism (SNP) of GFI1, GFI1-36N, which encodes a variant GFI1 protein with a decreased efficiency to act as a transcriptional repressor, was found to be a prognostic factor for the development of AML and MDS. Both the GFI1-36N variant as well as reduced expression of the GFI1 gene lead to genome-wide epigenetic changes at sites where GFI1 occupies target gene promoters and enhancers. These epigenetic changes alter the response of leukemic cells to epigenetic drugs such as HDAC- or HAT inhibitors, indicating that GFI1 expression levels and genetic variants of GFI1 are of clinical relevance. Based on these and other findings, specific therapeutic approaches have been proposed to treat AML by targeting some of the epigenetic changes that occur as a consequence of GFI1 expression. Here, we will review the well-known role of Gfi1 as a transcription factor and describe the more recently discovered functions of GFI1 that are independent of DNA binding and how these might affect disease progression and the choice of epigenetic drugs for therapeutic regimens of AML and MDS.
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Affiliation(s)
- Tarik Möröy
- Department of Hematopoiesis and Cancer, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Cyrus Khandanpour
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
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18
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Growth Factor Independence 1B-Mediated Transcriptional Repression and Lineage Allocation Require Lysine-Specific Demethylase 1-Dependent Recruitment of the BHC Complex. Mol Cell Biol 2019; 39:MCB.00020-19. [PMID: 30988160 DOI: 10.1128/mcb.00020-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/09/2019] [Indexed: 12/16/2022] Open
Abstract
Growth factor independence 1B (GFI1B) coordinates assembly of transcriptional repressor complexes comprised of corepressors and histone-modifying enzymes to control gene expression programs governing lineage allocation in hematopoiesis. Enforced expression of GFI1B in K562 erythroleukemia cells favors erythroid over megakaryocytic differentiation, providing a platform to define molecular determinants of binary fate decisions triggered by GFI1B. We deployed proteome-wide proximity labeling to identify factors whose inclusion in GFI1B complexes depends upon GFI1B's obligate effector, lysine-specific demethylase 1 (LSD1). We show that GFI1B preferentially recruits core and putative elements of the BRAF-histone deacetylase (HDAC) (BHC) chromatin-remodeling complex (LSD1, RCOR1, HMG20A, HMG20B, HDAC1, HDAC2, PHF21A, GSE1, ZMYM2, and ZNF217) in an LSD1-dependent manner to control acquisition of erythroid traits by K562 cells. Among these elements, depletion of both HMG20A and HMG20B or of GSE1 blocks GFI1B-mediated erythroid differentiation, phenocopying impaired differentiation brought on by LSD1 depletion or disruption of GFI1B-LSD1 binding. These findings demonstrate the central role of the GFI1B-LSD1 interaction as a determinant of BHC complex recruitment to enable cell fate decisions driven by GFI1B.
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