1
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Wang J, Han L, Liu Z, Zhang W, Zhang L, Jing J, Gao A. Targeting IGF2BP1 alleviated benzene hematotoxicity by reprogramming BCAA metabolism and fatty acid oxidation. Chem Biol Interact 2024; 398:111107. [PMID: 38866309 DOI: 10.1016/j.cbi.2024.111107] [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: 03/04/2024] [Revised: 05/30/2024] [Accepted: 06/09/2024] [Indexed: 06/14/2024]
Abstract
Benzene is the main environmental pollutant and risk factor of childhood leukemia and chronic benzene poisoning. Benzene exposure leads to hematopoietic stem and progenitor cell (HSPC) dysfunction and abnormal blood cell counts. However, the key regulatory targets and mechanisms of benzene hematotoxicity are unclear. In this study, we constructed a benzene-induced hematopoietic damage mouse model to explore the underlying mechanisms. We identified that Insulin like growth factor 2 mRNA binding protein 1 (IGF2BP1) was significantly reduced in benzene-exposed mice. Moreover, targeting IGF2BP1 effectively mitigated damages to hematopoietic function and hematopoietic molecule expression caused by benzene in mice. On the mechanics, by metabolomics and transcriptomics, we discovered that branched-chain amino acid (BCAA) metabolism and fatty acid oxidation were key metabolic pathways, and Branched-chain amino acid transaminase 1 (BCAT1) and Carnitine palmitoyltransferase 1a (CPT1A) were critical metabolic enzymes involved in IGF2BP1-mediated hematopoietic injury process. The expression of the above molecules in the benzene exposure population was also examined and consistent with animal experiments. In conclusion, targeting IGF2BP1 alleviated hematopoietic injury caused by benzene exposure, possibly due to the reprogramming of BCAA metabolism and fatty acid oxidation via BCAT1 and CPT1A metabolic enzymes. IGF2BP1 is a potential regulatory and therapeutic target for benzene hematotoxicity.
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Affiliation(s)
- Jingyu Wang
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing, 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, PR China
| | - Lin Han
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing, 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, PR China
| | - Ziyan Liu
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing, 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, PR China
| | - Wei Zhang
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing, 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, PR China
| | - Lei Zhang
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing, 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, PR China
| | - Jiaru Jing
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing, 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, PR China
| | - Ai Gao
- Department of Occupational and Environmental Health, School of Public Health, Capital Medical University, Beijing, 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, 100069, PR China.
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2
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Barwe SP, Kolb EA, Gopalakrishnapillai A. Down syndrome and leukemia: An insight into the disease biology and current treatment options. Blood Rev 2024; 64:101154. [PMID: 38016838 DOI: 10.1016/j.blre.2023.101154] [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: 09/15/2023] [Revised: 10/31/2023] [Accepted: 11/19/2023] [Indexed: 11/30/2023]
Abstract
Children with Down syndrome (DS) have a 10- to 20-fold greater predisposition to develop acute leukemia compared to the general population, with a skew towards myeloid leukemia (ML-DS). While ML-DS is known to be a subtype with good outcome, patients who relapse face a dismal prognosis. Acute lymphocytic leukemia in DS (DS-ALL) is considered to have poor prognosis. The relapse rate is high in DS-ALL compared to their non-DS counterparts. We have a better understanding about the mutational spectrum of DS leukemia. Studies using animal, embryonic stem cell- and induced pluripotent stem cell-based models have shed light on the mechanism by which these mutations contribute to disease initiation and progression. In this review, we list the currently available treatment strategies for DS-leukemias along with their outcome with emphasis on challenges with chemotherapy-related toxicities in children with DS. We focus on the mechanisms of initiation and progression of leukemia in children with DS and highlight the novel molecular targets with greater success in preclinical trials that have the potential to progress to the clinic.
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Affiliation(s)
- Sonali P Barwe
- Lisa Dean Moseley Institute for Cancer and Blood Disorders, Nemours Children's Health, Wilmington, Delaware, 19803, USA
| | - E Anders Kolb
- Lisa Dean Moseley Institute for Cancer and Blood Disorders, Nemours Children's Health, Wilmington, Delaware, 19803, USA
| | - Anilkumar Gopalakrishnapillai
- Lisa Dean Moseley Institute for Cancer and Blood Disorders, Nemours Children's Health, Wilmington, Delaware, 19803, USA.
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3
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Sharma G, Tran TM, Bansal I, Beg MS, Bhardwaj R, Bassi J, Tan Y, Jaiswal AK, Tso C, Jain A, Singh J, Chattopadhyay P, Singh A, Chopra A, Bakhshi S, Casero D, Rao DS, Palanichamy JK. RNA binding protein IGF2BP1 synergizes with ETV6-RUNX1 to drive oncogenic signaling in B-cell Acute Lymphoblastic Leukemia. J Exp Clin Cancer Res 2023; 42:231. [PMID: 37670323 PMCID: PMC10478443 DOI: 10.1186/s13046-023-02810-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/27/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is the most common pediatric hematological malignancy, with ETV6::RUNX1 being the most prevalent translocation whose exact pathogenesis remains unclear. IGF2BP1 (Insulin-like Growth Factor 2 Binding Protein 1) is an oncofetal RNA binding protein seen to be specifically overexpressed in ETV6::RUNX1 positive B-ALL. In this study, we have studied the mechanistic role of IGF2BP1 in leukemogenesis and its synergism with the ETV6::RUNX1 fusion protein. METHODS Gene expression was analyzed from patient bone marrow RNA using Real Time RT-qPCR. Knockout cell lines were created using CRISPR-Cas9 based lentiviral vectors. RNA-Seq and RNA Immunoprecipitation sequencing (RIP-Seq) after IGF2BP1 pulldown were performed using the Illumina platform. Mouse experiments were done by retroviral overexpression of donor HSCs followed by lethal irradiation of recipients using a bone marrow transplant model. RESULTS We observed specific overexpression of IGF2BP1 in ETV6::RUNX1 positive patients in an Indian cohort of pediatric ALL (n=167) with a positive correlation with prednisolone resistance. IGF2BP1 expression was essential for tumor cell survival in multiple ETV6::RUNX1 positive B-ALL cell lines. Integrated analysis of transcriptome sequencing after IGF2BP1 knockout and RIP-Seq after IGF2BP1 pulldown in Reh cell line revealed that IGF2BP1 targets encompass multiple pro-oncogenic signalling pathways including TNFα/NFκB and PI3K-Akt pathways. These pathways were also dysregulated in primary ETV6::RUNX1 positive B-ALL patient samples from our center as well as in public B-ALL patient datasets. IGF2BP1 showed binding and stabilization of the ETV6::RUNX1 fusion transcript itself. This positive feedback loop led to constitutive dysregulation of several oncogenic pathways. Enforced co-expression of ETV6::RUNX1 and IGF2BP1 in mouse bone marrow resulted in marrow hypercellularity which was characterized by multi-lineage progenitor expansion and strong Ki67 positivity. This pre-leukemic phenotype confirmed their synergism in-vivo. Clonal expansion of cells overexpressing both ETV6::RUNX1 and IGF2BP1 was clearly observed. These mice also developed splenomegaly indicating extramedullary hematopoiesis. CONCLUSION Our data suggest a combined impact of the ETV6::RUNX1 fusion protein and RNA binding protein, IGF2BP1 in activating multiple oncogenic pathways in B-ALL which makes IGF2BP1 and these pathways as attractive therapeutic targets and biomarkers.
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Affiliation(s)
- Gunjan Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Tiffany M Tran
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Ishu Bansal
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Mohammad Sabique Beg
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Ruchi Bhardwaj
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Jaspal Bassi
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Yuande Tan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Amit Kumar Jaiswal
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Christine Tso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Ayushi Jain
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Jay Singh
- Department of Laboratory Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Parthaprasad Chattopadhyay
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Archna Singh
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Anita Chopra
- Department of Laboratory Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sameer Bakhshi
- Department of Medical Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - David Casero
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Jayanth Kumar Palanichamy
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India.
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4
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Gu Z, Izraeli S. All about Down syndrome ALL. Blood 2023; 142:126-128. [PMID: 37440267 DOI: 10.1182/blood.2023020508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023] Open
Affiliation(s)
- Zhaohui Gu
- Beckman Research Institute of City of Hope
| | - Shai Izraeli
- Beckman Research Institute of City of Hope
- Schneider Children's Medical Center
- Tel Aviv University
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5
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Jin Z, MacPherson K, Liu Z, Vu LP. RNA modifications in hematological malignancies. Int J Hematol 2023; 117:807-820. [PMID: 36929506 DOI: 10.1007/s12185-023-03576-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023]
Abstract
RNA modifications play an important role in various cancers including blood cancers by controlling gene expression programs critical for survival, proliferation and differentiation of cancer cells. While hundreds of RNA modifications have been identified, many have not been functionally characterized. With development of enabling technologies to identify and map RNA modifications, tremendous advancement has been made in our understanding of the biological functions of these molecular markers in diverse cellular contexts. In the last 5 years, N6-methyladenosine (m6A), the most prevalent internal mRNA modification, has been extensively implicated in many facets of leukemogenesis. Other types of RNA modifications are also involved in the regulation of cell fate decisions and tumorigenesis. Here, we summarize existing knowledge and recent discoveries regarding the role of RNA modifications in leukemia. We choose to highlight cutting-edge techniques to characterize and profile RNA modifications while discussing critical functions of key modifiers and regulatory mechanisms in the pathogenesis of hematological malignancies and touch on therapeutic strategies targeting RNA modifications. These important advancements in the field will continue to foster a strong foundation for the development of innovative treatments for hematological malignancies.
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Affiliation(s)
- Zhen Jin
- Terry Fox Laboratory, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Kyle MacPherson
- Terry Fox Laboratory, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, Canada
| | - Zongmin Liu
- Terry Fox Laboratory, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Ly P Vu
- Terry Fox Laboratory, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, Canada. .,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.
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6
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Li W, Deng X, Chen J. RNA-binding proteins in regulating mRNA stability and translation: roles and mechanisms in cancer. Semin Cancer Biol 2022; 86:664-677. [PMID: 35381329 PMCID: PMC9526761 DOI: 10.1016/j.semcancer.2022.03.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/10/2023]
Abstract
RNA-binding proteins (RBPs) are key players in cellular physiology through posttranscriptional regulation of the expression of target RNA transcripts. By modulating the processing, stability and translation of cancer-related messenger RNA (mRNA) transcripts, a large set of RBPs play essential roles in various types of cancers. Perturbations in RBP activity have been causally associated with cancer development, tumor metabolism, drug resistance, cancer stem cell self-renewal, and tumor immune evasion. Here, we summarize the recent advances in cancer pathological roles and mechanisms of RBPs in regulating mRNA stability and translation with an emphasis on the emerging category of RNA modification-associated RBPs. The functional diversity of RBPs in different types of cancers and the therapeutic potential of targeting dysregulated RBPs for cancer treatment are also discussed.
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Affiliation(s)
- Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA.
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7
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Wu H, Xu H, Huang S, Tang Y, Tang J, Zhou H, Xie L, Qiao G. m 6A-binding protein IGF2BP1 promotes the malignant phenotypes of lung adenocarcinoma. Front Oncol 2022; 12:989817. [PMID: 36249006 PMCID: PMC9554348 DOI: 10.3389/fonc.2022.989817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/06/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD), the most common type of lung cancer, poses a significant threat to the life of patients. N6-methyladenosine modification is the most abundant epigenetic modification and may play an important role in the lung carcinogenesis. IGF2BP1 is a newly discovered m6A-binding protein, but little is known about its role in LUAD. METHODS Data from TCGA, GEO, Kaplan-Meier Plotter, and GEPIA databases were systematically analyzed to access the expression and prognostic value of IGF2BP1 on LUAD. Real-time polymerase chain reaction, Western blot, and immunohistochemistry were performed to detect the mRNA and protein level of IGF2BP1 in LUAD tissues and para-carcinoma tissues. Functional cell experiments, including Cell Counting Kit-8 assay, Transwell invasion assay, wound healing assay, Annexin V-FITC/PI double-staining assay, and TUNEL assay, were used to investigate the functions of IGF2BP1 on LUAD cell proliferation, invasion, migration, and apoptosis, respectively. The top 50 genes that were positively or negatively related to the expression of IGF2BP1 were identified, and pathway enrichment analysis was performed. m6A modification sites within IGF2BP1-related genes were predicted by SRAMP. RESULT 16 m6A regulators were significantly differentially expressed in LUAD tissues. IGF2BP1 was upregulated in LUAD tissues compared with para-carcinoma tissues. High expression of IGF2PB1 was significantly associated with higher clinical stages and poor prognosis of LUAD patients. Furthermore, our functional experiments indicated that IGF2BP1 facilitated cell proliferation, invasion, and migration and suppressed apoptosis in LUAD. Functional enrichment analysis of IGF2BP1-related genes indicated enrichment in several pathways related to oncogenesis. Additionally, m6A modification sites were detected within IGF2BP1-related genes. CONCLUSIONS Our findings demonstrate that IGF2BP1 plays a contributory role in the development and progression of LUAD. IGF2BP1 has the potential to become a prognostic predictor and therapeutic target for LUAD.
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Affiliation(s)
- Hansheng Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Haijie Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Shantou University Medical College, Shantou, China
| | - Shujie Huang
- Shantou University Medical College, Shantou, China
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yong Tang
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jiming Tang
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Haiyu Zhou
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Liang Xie
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Guibin Qiao
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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8
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Leo IR, Aswad L, Stahl M, Kunold E, Post F, Erkers T, Struyf N, Mermelekas G, Joshi RN, Gracia-Villacampa E, Östling P, Kallioniemi OP, Tamm KP, Siavelis I, Lehtiö J, Vesterlund M, Jafari R. Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines. Nat Commun 2022; 13:1691. [PMID: 35354797 PMCID: PMC8967900 DOI: 10.1038/s41467-022-29224-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 03/02/2022] [Indexed: 12/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Although standard-of-care chemotherapeutics are sufficient for most ALL cases, there are subsets of patients with poor response who relapse in disease. The biology underlying differences between subtypes and their response to therapy has only partially been explained by genetic and transcriptomic profiling. Here, we perform comprehensive multi-omic analyses of 49 readily available childhood ALL cell lines, using proteomics, transcriptomics, and pharmacoproteomic characterization. We connect the molecular phenotypes with drug responses to 528 oncology drugs, identifying drug correlations as well as lineage-dependent correlations. We also identify the diacylglycerol-analog bryostatin-1 as a therapeutic candidate in the MEF2D-HNRNPUL1 fusion high-risk subtype, for which this drug activates pro-apoptotic ERK signaling associated with molecular mediators of pre-B cell negative selection. Our data is the foundation for the interactive online Functional Omics Resource of ALL (FORALL) with navigable proteomics, transcriptomics, and drug sensitivity profiles at https://proteomics.se/forall. Childhood acute lymphoblastic leukemia is characterised by a range of genetic aberrations. Here, the authors use multi-omics profiling of ALL cell lines to connect molecular phenotypes and drug responses to provide an interactive resource of drug sensitivity.
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Affiliation(s)
- Isabelle Rose Leo
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Luay Aswad
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Matthias Stahl
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Elena Kunold
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Frederik Post
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden.,Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, 48149, Muenster, Germany
| | - Tom Erkers
- Molecular Precision Medicine, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Nona Struyf
- Molecular Precision Medicine, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Georgios Mermelekas
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Rubin Narayan Joshi
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Eva Gracia-Villacampa
- Division of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Päivi Östling
- Molecular Precision Medicine, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Olli P Kallioniemi
- Molecular Precision Medicine, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Katja Pokrovskaja Tamm
- Department of Oncology-Pathology, Karolinska Institutet, J6:140 BioClinicum, Akademiska stråket 1, 171 64, Solna, Sweden
| | - Ioannis Siavelis
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Janne Lehtiö
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Mattias Vesterlund
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden
| | - Rozbeh Jafari
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Solna, Sweden.
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9
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Zhu H, Zhang R, Li R, Wang Z, Li H, Zhong H, Yin L, Ruan X, Ye C, Yuan H, Cheng Z, Peng H. Identification of diagnosis and prognosis gene markers in B-ALL with ETV6-RUNX1 fusion by integrated bioinformatics analysis. Gene 2022; 815:146132. [PMID: 34999180 DOI: 10.1016/j.gene.2021.146132] [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: 09/23/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022]
Abstract
B-acute lymphoblastic leukemia (B-ALL) is characterized by clonal expansion of immature B-lymphocytes in the bone marrow, blood, or other tissues. Chromosomal translocations have often been reported in B-ALL, which are important for its prognosis. B-ALL patients with ETV6-RUNX1 fusion have favorable outcomes, but the mechanisms remain to be clarified. In the present study, we crossed the selected WGCNA module genes and differential expression genes to obtain core genes, and random forest algorithm, a type of supervised learning analysis, was conducted to evaluate the importance of those core genes in distinguishing B-ALL samples with ETV6-RUNX2 fusion with extracting 5 genes as gene markers for ETV6-RUNX2 fusion. Moreover, we calculated the immune infiltration profiles and screened out the ETV6-RUNX2 association immune cells using the CIBERSORT algorithm. In conclusion, combined with various solid informatics methods, we depicted the underlying molecular and immune mechanism of ETV6-RUNX2 fusion and providing potential biological targets for diagnosing and treating B-ALL in the future.
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Affiliation(s)
- Hongkai Zhu
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Rong Zhang
- National Cancer Center Exploratory Oncology Research & Clinical Trial Center, Japan
| | - Ruijuan Li
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Zhihua Wang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Heng Li
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Haiying Zhong
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Le Yin
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Xueqin Ruan
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Can Ye
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Huan Yuan
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China
| | - Zhao Cheng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China
| | - Hongling Peng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, PR China; Institute of Hematology, Central South University, Changsha, Hunan 410011, PR China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, Changsha, Hunan 410011, PR China.
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10
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Ahmadi SE, Rahimi S, Zarandi B, Chegeni R, Safa M. MYC: a multipurpose oncogene with prognostic and therapeutic implications in blood malignancies. J Hematol Oncol 2021; 14:121. [PMID: 34372899 PMCID: PMC8351444 DOI: 10.1186/s13045-021-01111-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/12/2021] [Indexed: 12/17/2022] Open
Abstract
MYC oncogene is a transcription factor with a wide array of functions affecting cellular activities such as cell cycle, apoptosis, DNA damage response, and hematopoiesis. Due to the multi-functionality of MYC, its expression is regulated at multiple levels. Deregulation of this oncogene can give rise to a variety of cancers. In this review, MYC regulation and the mechanisms by which MYC adjusts cellular functions and its implication in hematologic malignancies are summarized. Further, we also discuss potential inhibitors of MYC that could be beneficial for treating hematologic malignancies.
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Affiliation(s)
- Seyed Esmaeil Ahmadi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Rahimi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Bahman Zarandi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rouzbeh Chegeni
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL, USA.
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
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11
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Schwalbe EC, H L, Lafta F, Barrow TM, Strathdee G. Integration of genome-level data to allow identification of subtype-specific vulnerability genes as novel therapeutic targets. Oncogene 2021; 40:5213-5223. [PMID: 34230614 PMCID: PMC8376645 DOI: 10.1038/s41388-021-01923-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023]
Abstract
The identification of cancer-specific vulnerability genes is one of the most promising approaches for developing more effective and less toxic cancer treatments. Cancer genomes exhibit thousands of changes in DNA methylation and gene expression, with the vast majority likely to be passenger changes. We hypothesised that, through integration of genome-wide DNA methylation/expression data, we could exploit this inherent variability to identify cancer subtype-specific vulnerability genes that would represent novel therapeutic targets that could allow cancer-specific cell killing. We developed a bioinformatics pipeline integrating genome-wide DNA methylation/gene expression data to identify candidate subtype-specific vulnerability partner genes for the genetic drivers of individual genetic/molecular subtypes. Using acute lymphoblastic leukaemia as an initial model, 21 candidate subtype-specific vulnerability genes were identified across the five common genetic subtypes, with at least one per subtype. To confirm the approach was applicable across cancer types, we also assessed medulloblastoma, identifying 15 candidate subtype-specific vulnerability genes across three of four established subtypes. Almost all identified genes had not previously been implicated in these diseases. Functional analysis of seven candidate subtype-specific vulnerability genes across the two tumour types confirmed that siRNA-mediated knockdown induced significant inhibition of proliferation/induction of apoptosis, which was specific to the cancer subtype in which the gene was predicted to be specifically lethal. Thus, we present a novel approach that integrates genome-wide DNA methylation/expression data to identify cancer subtype-specific vulnerability genes as novel therapeutic targets. We demonstrate this approach is applicable to multiple cancer types and identifies true functional subtype-specific vulnerability genes with high efficiency.
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Affiliation(s)
- Edward C Schwalbe
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle, UK
- Department of Applied Sciences, Northumbria University, Newcastle, UK
| | - Lalchungnunga H
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle, UK
| | - Fadhel Lafta
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle, UK
- Department of Biology, College of Science, University of Baghdad, Baghdad, Iraq
| | - Timothy M Barrow
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle, UK
- Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, UK
| | - Gordon Strathdee
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle, UK.
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12
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The biological function of IGF2BPs and their role in tumorigenesis. Invest New Drugs 2021; 39:1682-1693. [PMID: 34251559 DOI: 10.1007/s10637-021-01148-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/30/2021] [Indexed: 01/09/2023]
Abstract
The insulin-like growth factor-2 mRNA-binding proteins (IGF2BPs) pertain to a highly conservative RNA-binding family that works as a post-transcriptional fine-tuner for target transcripts. Emerging evidence suggests that IGF2BPs regulate RNA processing and metabolism, including stability, translation, and localization, and are involved in various cellular functions and pathophysiologies. In this review, we summarize the roles and molecular mechanisms of IGF2BPs in cancer development and progression. We mainly discuss the functional relevance of IGF2BPs in embryo development, neurogenesis, metabolism, RNA processing, and tumorigenesis. Understanding IGF2BPs role in tumor progression will provide new insight into cancer pathophysiology.
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13
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Elcheva IA, Spiegelman VS. Targeting RNA-binding proteins in acute and chronic leukemia. Leukemia 2021; 35:360-376. [PMID: 33149266 PMCID: PMC7868134 DOI: 10.1038/s41375-020-01066-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 01/01/2023]
Abstract
RNA-binding proteins (RBPs) play a crucial role in cellular physiology by regulating RNA processing, translation, and turnover. In neoplasms, RBP support of cancer-relevant expression of alternatively spliced, modified, and stabilized mRNA transcripts is essential to self-renewal, proliferation, and adaptation to stress. In this review, we assess the impact of key families of RBPs in leukemogenesis, review progress in targeting those proteins with small molecules, and discuss how multilevel composition of posttranscriptional regulation of gene expression could be used for potential therapies in acute and chronic leukemia.
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Affiliation(s)
- Irina A Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Vladimir S Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
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14
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Neu CT, Gutschner T, Haemmerle M. Post-Transcriptional Expression Control in Platelet Biogenesis and Function. Int J Mol Sci 2020; 21:ijms21207614. [PMID: 33076269 PMCID: PMC7589263 DOI: 10.3390/ijms21207614] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023] Open
Abstract
Platelets are highly abundant cell fragments of the peripheral blood that originate from megakaryocytes. Beside their well-known role in wound healing and hemostasis, they are emerging mediators of the immune response and implicated in a variety of pathophysiological conditions including cancer. Despite their anucleate nature, they harbor a diverse set of RNAs, which are subject to an active sorting mechanism from megakaryocytes into proplatelets and affect platelet biogenesis and function. However, sorting mechanisms are poorly understood, but RNA-binding proteins (RBPs) have been suggested to play a crucial role. Moreover, RBPs may regulate RNA translation and decay following platelet activation. In concert with other regulators, including microRNAs, long non-coding and circular RNAs, RBPs control multiple steps of the platelet life cycle. In this review, we will highlight the different RNA species within platelets and their impact on megakaryopoiesis, platelet biogenesis and platelet function. Additionally, we will focus on the currently known concepts of post-transcriptional control mechanisms important for RNA fate within platelets with a special emphasis on RBPs.
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Affiliation(s)
- Carolin T. Neu
- Institute of Pathology, Section for Experimental Pathology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
| | - Tony Gutschner
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
| | - Monika Haemmerle
- Institute of Pathology, Section for Experimental Pathology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
- Correspondence: ; Tel.: +49-345-557-3964
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15
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RNA-Binding Proteins in Acute Leukemias. Int J Mol Sci 2020; 21:ijms21103409. [PMID: 32408494 PMCID: PMC7279408 DOI: 10.3390/ijms21103409] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/07/2020] [Accepted: 05/10/2020] [Indexed: 12/12/2022] Open
Abstract
Acute leukemias are genetic diseases caused by translocations or mutations, which dysregulate hematopoiesis towards malignant transformation. However, the molecular mode of action is highly versatile and ranges from direct transcriptional to post-transcriptional control, which includes RNA-binding proteins (RBPs) as crucial regulators of cell fate. RBPs coordinate RNA dynamics, including subcellular localization, translational efficiency and metabolism, by binding to their target messenger RNAs (mRNAs), thereby controlling the expression of the encoded proteins. In view of the growing interest in these regulators, this review summarizes recent research regarding the most influential RBPs relevant in acute leukemias in particular. The reported RBPs, either dysregulated or as components of fusion proteins, are described with respect to their functional domains, the pathways they affect, and clinical aspects associated with their dysregulation or altered functions.
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16
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de Barrios O, Meler A, Parra M. MYC's Fine Line Between B Cell Development and Malignancy. Cells 2020; 9:E523. [PMID: 32102485 PMCID: PMC7072781 DOI: 10.3390/cells9020523] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
The transcription factor MYC is transiently expressed during B lymphocyte development, and its correct modulation is essential in defined developmental transitions. Although temporary downregulation of MYC is essential at specific points, basal levels of expression are maintained, and its protein levels are not completely silenced until the B cell becomes fully differentiated into a plasma cell or a memory B cell. MYC has been described as a proto-oncogene that is closely involved in many cancers, including leukemia and lymphoma. Aberrant expression of MYC protein in these hematological malignancies results in an uncontrolled rate of proliferation and, thereby, a blockade of the differentiation process. MYC is not activated by mutations in the coding sequence, and, as reviewed here, its overexpression in leukemia and lymphoma is mainly caused by gene amplification, chromosomal translocations, and aberrant regulation of its transcription. This review provides a thorough overview of the role of MYC in the developmental steps of B cells, and of how it performs its essential function in an oncogenic context, highlighting the importance of appropriate MYC regulation circuitry.
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Affiliation(s)
| | | | - Maribel Parra
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, IJC Building, Campus ICO-Germans Trias i Pujol, Ctra de Can Ruti, 08916 Barcelona, Spain (A.M.)
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17
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Elcheva IA, Wood T, Chiarolanzio K, Chim B, Wong M, Singh V, Gowda CP, Lu Q, Hafner M, Dovat S, Liu Z, Muljo SA, Spiegelman VS. RNA-binding protein IGF2BP1 maintains leukemia stem cell properties by regulating HOXB4, MYB, and ALDH1A1. Leukemia 2019; 34:1354-1363. [PMID: 31768017 PMCID: PMC7196026 DOI: 10.1038/s41375-019-0656-9] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/24/2019] [Accepted: 11/13/2019] [Indexed: 02/08/2023]
Abstract
Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) is an oncofetal protein expressed in various cancers including leukemia. In this study, we assessed the role of IGF2BP1 in orchestrating leukemia stem cell properties. Tumor-initiating potential, sensitivity to chemotherapeutic agents, and expression of cancer stem cell markers were assessed in a panel of myeloid, B-, and T-cell leukemia cell lines using gain- and loss-of-function systems, cross-linking immunoprecipitation (CLIP), and photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) techniques. Here, we report that genetic or chemical inhibition of IGF2BP1 decreases leukemia cells' tumorigenicity, promotes myeloid differentiation, increases leukemia cell death, and sensitizes leukemia cells to chemotherapeutic drugs. IGF2BP1 affects proliferation and tumorigenic potential of leukemia cells through critical regulators of self-renewal HOXB4 and MYB and through regulation of expression of the aldehyde dehydrogenase, ALDH1A1. Our data indicate that IGF2BP1 maintains leukemia stem cell properties by regulating multiple pathways of stemness through transcriptional and metabolic factors.
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Affiliation(s)
- Irina A Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Tyler Wood
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kathryn Chiarolanzio
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Bryan Chim
- Integrative Immunobiology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Madeline Wong
- Integrative Immunobiology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vikash Singh
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Chethana P Gowda
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Qingli Lu
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sinisa Dovat
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Zhenqiu Liu
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.,Department of Public Health Sciences, Pennsylvania State University College of Medicine, Penn State Cancer Institute, Hershey, PA, USA
| | - Stefan A Muljo
- Integrative Immunobiology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vladimir S Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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18
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Vijayakrishnan J, Qian M, Studd JB, Yang W, Kinnersley B, Law PJ, Broderick P, Raetz EA, Allan J, Pui CH, Vora A, Evans WE, Moorman A, Yeoh A, Yang W, Li C, Bartram CR, Mullighan CG, Zimmerman M, Hunger SP, Schrappe M, Relling MV, Stanulla M, Loh ML, Houlston RS, Yang JJ. Identification of four novel associations for B-cell acute lymphoblastic leukaemia risk. Nat Commun 2019; 10:5348. [PMID: 31767839 PMCID: PMC6877561 DOI: 10.1038/s41467-019-13069-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022] Open
Abstract
There is increasing evidence for a strong inherited genetic basis of susceptibility to acute lymphoblastic leukaemia (ALL) in children. To identify new risk variants for B-cell ALL (B-ALL) we conducted a meta-analysis with four GWAS (genome-wide association studies), totalling 5321 cases and 16,666 controls of European descent. We herein describe novel risk loci for B-ALL at 9q21.31 (rs76925697, P = 2.11 × 10-8), for high-hyperdiploid ALL at 5q31.1 (rs886285, P = 1.56 × 10-8) and 6p21.31 (rs210143 in BAK1, P = 2.21 × 10-8), and ETV6-RUNX1 ALL at 17q21.32 (rs10853104 in IGF2BP1, P = 1.82 × 10-8). Particularly notable are the pleiotropic effects of the BAK1 variant on multiple haematological malignancies and specific effects of IGF2BP1 on ETV6-RUNX1 ALL evidenced by both germline and somatic genomic analyses. Integration of GWAS signals with transcriptomic/epigenomic profiling and 3D chromatin interaction data for these leukaemia risk loci suggests deregulation of B-cell development and the cell cycle as central mechanisms governing genetic susceptibility to ALL.
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Affiliation(s)
- Jayaram Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Maoxiang Qian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - James B Studd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Elizabeth A Raetz
- Division of Pediatric Hematology and Oncology, New York University Langone Health, New York, New York, USA
| | - James Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anthony Moorman
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Allen Yeoh
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- VIVA-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Claus R Bartram
- Institute of Human Genetics, University Hospital, Heidelberg, Germany
| | - Charles G Mullighan
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Martin Zimmerman
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Stephen P Hunger
- Department of Paediatrics and Centre for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Martin Schrappe
- Department of Paediatrics, University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Martin Stanulla
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK.
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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19
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VICKZ1 enhances tumor progression and metastasis in lung adenocarcinomas in mice. Oncogene 2019; 38:4169-4181. [PMID: 30700831 DOI: 10.1038/s41388-019-0715-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/18/2018] [Accepted: 01/17/2019] [Indexed: 02/06/2023]
Abstract
The VICKZ (Igf2bp) family of RNA binding proteins regulate RNA function at many levels, including intracellular RNA localization, RNA stability, and translational control. One or more of the three VICKZ paralogs are upregulated in many different types of cancers. Here, we show how VICKZ1 enhances, and dominant negative VICKZ1 inhibits, cell migration, growth in soft agar, and wound healing in a mouse lung adenocarcinoma cell line containing a constitutively active, mutant Kras. Similarly, modulation of VICKZ1 activity promotes or inhibits metastases upon implantation of these cells into syngeneic mice. To test these effects in a genetic model system, we generated a mouse with an inducible VICKZ1 transgene and found that isolated overexpression of VICKZ1 in the lungs had no noticeable effect on morphology. Although directed overexpression of mutant Kras in the lungs led to the formation of small adenomas, concurrent overexpression of VICKZ1 remarkably accelerated tumor growth and formation of pulmonary adenocarcinomas. VICKZ1-containing ribonucleoprotein complexes are highly enriched in Kras mRNA in lung adenocarcinoma cells, and Kras signaling is enhanced in these cells by overexpression of VICKZ1. Analysis of lung carcinoma patients reveals that elevated VICKZ1 expression correlates with lower overall survival; this reduction is dramatically enhanced in those patients bearing a mutant Kras gene. Our study reveals that RNA binding proteins of the VICKZ family can synergize with Kras to influence signaling and oncogenic activity.
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20
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Huang X, Zhang H, Guo X, Zhu Z, Cai H, Kong X. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) in cancer. J Hematol Oncol 2018; 11:88. [PMID: 29954406 PMCID: PMC6025799 DOI: 10.1186/s13045-018-0628-y] [Citation(s) in RCA: 312] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/06/2018] [Indexed: 12/20/2022] Open
Abstract
The insulin-like growth factor-2 mRNA-binding protein 1 (IGF2BP1) plays essential roles in embryogenesis and carcinogenesis. IGF2BP1 serves as a post-transcriptional fine-tuner regulating the expression of some essential mRNA targets required for the control of tumor cell proliferation and growth, invasion, and chemo-resistance, associating with a poor overall survival and metastasis in various types of human cancers. Therefore, IGF2BP1 has been traditionally regarded as an oncogene and potential therapeutic target for cancers. Nevertheless, a few studies have also demonstrated its tumor-suppressive role. However, the details about the contradictory functions of IGF2BP1 are unclear. The growing numbers of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been identified as its direct regulators, during tumor cell proliferation, growth, and invasion in multiple cancers. Thus, the mechanisms of post-transcriptional modulation of gene expression mediated by IGF2BP1, miRNAs, and lncRNAs in determining the fate of the development of tissues and organs, as well as tumorigenesis, need to be elucidated. In this review, we summarized the tissue distribution, expression, and roles of IGF2BP1 in embryogenesis and tumorigenesis, and focused on modulation of the interconnectivity between IGF2BP1 and its targeted mRNAs or non-coding RNAs (ncRNAs). The potential use of inhibitors of IGF2BP1 and its related pathways in cancer therapy was also discussed.
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Affiliation(s)
- Xinwei Huang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming City, 650504, Yunnan Province, China
- Medical School, Kunming University of Science and Technology, Kunming City, 650504, Yunnan Province, China
| | - Hong Zhang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu City, 610500, Sichuan Province, China
| | - Xiaoran Guo
- Medical School, Kunming University of Science and Technology, Kunming City, 650504, Yunnan Province, China
| | - Zongxin Zhu
- Medical School, Kunming University of Science and Technology, Kunming City, 650504, Yunnan Province, China
| | - Haibo Cai
- Department of Oncology, Yunfeng Hospital, Xuanwei City, 655400, Yunnan Province, China.
| | - Xiangyang Kong
- Medical School, Kunming University of Science and Technology, Kunming City, 650504, Yunnan Province, China.
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21
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Pathogenesis of ETV6/RUNX1-positive childhood acute lymphoblastic leukemia and mechanisms underlying its relapse. Oncotarget 2018; 8:35445-35459. [PMID: 28418909 PMCID: PMC5471068 DOI: 10.18632/oncotarget.16367] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/23/2017] [Indexed: 01/06/2023] Open
Abstract
ETV6/RUNX1 (E/R) is the most common fusion gene in childhood acute lymphoblastic leukemia (ALL). Multiple lines of evidence imply a “two-hit” model for the molecular pathogenesis of E/R-positive ALL, whereby E/R rearrangement is followed by a series of secondary mutations that trigger overt leukemia. The cellular framework in which E/R arises and the maintenance of a pre-leukemic condition by E/R are fundamental to the mechanism that underlies leukemogenesis. Accordingly, a variety of studies have focused on the relationship between the clones giving rise to the primary and recurrent E/R-positive ALL. We review here the most recent insights into the pathogenic mechanisms underlying E/R-positive ALL, as well as the molecular abnormalities prevailing at relapse.
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22
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Ghazavi F, De Moerloose B, Van Loocke W, Wallaert A, Helsmoortel HH, Ferster A, Bakkus M, Plat G, Delabesse E, Uyttebroeck A, Van Nieuwerburgh F, Deforce D, Van Roy N, Speleman F, Benoit Y, Lammens T, Van Vlierberghe P. Unique long non-coding RNA expression signature in ETV6/RUNX1-driven B-cell precursor acute lymphoblastic leukemia. Oncotarget 2018; 7:73769-73780. [PMID: 27650541 PMCID: PMC5342012 DOI: 10.18632/oncotarget.12063] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 09/02/2016] [Indexed: 12/19/2022] Open
Abstract
Overwhelming evidence indicates that long non-coding RNAs have essential roles in tumorigenesis. Nevertheless, their role in the molecular pathogenesis of pediatric B-cell precursor acute lymphoblastic leukemia has not been extensively explored. Here, we conducted a comprehensive analysis of the long non-coding RNA transcriptome in ETV6/RUNX1-positive BCP-ALL, one of the most frequent subtypes of pediatric leukemia. First, we used primary leukemia patient samples to identify an ETV6/RUNX1 specific expression signature consisting of 596 lncRNA transcripts. Next, integration of this lncRNA signature with RNA sequencing of BCP-ALL cell lines and lncRNA profiling of an in vitro model system of ETV6/RUNX1 knockdown, revealed that lnc-NKX2-3-1, lnc-TIMM21-5, lnc-ASTN1-1 and lnc-RTN4R-1 are truly regulated by the oncogenic fusion protein. Moreover, sustained inactivation of lnc-RTN4R-1 and lnc-NKX2-3-1 in ETV6/RUNX1 positive cells caused profound changes in gene expression. All together, our study defined a unique lncRNA expression signature associated with ETV6/RUNX1-positive BCP-ALL and identified lnc-RTN4R-1 and lnc-NKX2-3-1 as lncRNAs that might be functionally implicated in the biology of this prevalent subtype of human leukemia.
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Affiliation(s)
- Farzaneh Ghazavi
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Department of Paediatrics and Genetics, Ghent University Hospital, Ghent, Belgium
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Wouter Van Loocke
- Center for Medical Genetics, Department of Paediatrics and Genetics, Ghent University Hospital, Ghent, Belgium
| | - Annelynn Wallaert
- Center for Medical Genetics, Department of Paediatrics and Genetics, Ghent University Hospital, Ghent, Belgium
| | - Hetty H Helsmoortel
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Department of Paediatrics and Genetics, Ghent University Hospital, Ghent, Belgium
| | - Alina Ferster
- Department of Hemato-Oncology, HUDERF, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marleen Bakkus
- Department of Hematology, University Hospital Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Geneviève Plat
- Department of Hematology, Children's Hospital, Toulouse, France
| | - Eric Delabesse
- Department of Hematology, Institut Universitaire de Cancérologie de Toulouse, University Toulouse-III Paul-Sabatier, Toulouse, France
| | - Anne Uyttebroeck
- Department of Pediatric Hemato-Oncology, University Hospitals Leuven, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Nadine Van Roy
- Center for Medical Genetics, Department of Paediatrics and Genetics, Ghent University Hospital, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Department of Paediatrics and Genetics, Ghent University Hospital, Ghent, Belgium
| | - Yves Benoit
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Tim Lammens
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Center for Medical Genetics, Department of Paediatrics and Genetics, Ghent University Hospital, Ghent, Belgium
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Stoskus M, Eidukaite A, Griskevicius L. Defining the significance of IGF2BP1 overexpression in t(12;21)(p13;q22)-positive leukemia REH cells. Leuk Res 2016; 47:16-21. [DOI: 10.1016/j.leukres.2016.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/06/2016] [Accepted: 05/15/2016] [Indexed: 12/27/2022]
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