1
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González-Romero E, Martínez-Valiente C, García-García G, Rosal-Vela A, Millán JM, Sanz MÁ, Sanz G, Liquori A, Cervera JV, Vázquez-Manrique RP. PCR-Based Strategy for Introducing CRISPR/Cas9 Machinery into Hematopoietic Cell Lines. Cancers (Basel) 2023; 15:4263. [PMID: 37686539 PMCID: PMC10487029 DOI: 10.3390/cancers15174263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Acute myeloid leukemia is a complex heterogeneous disease characterized by the clonal expansion of undifferentiated myeloid precursors. Due to the difficulty in the transfection of blood cells, several hematological models have recently been developed with CRISPR/Cas9, using viral vectors. In this study, we developed an alternative strategy in order to generate CRISPR constructs by fusion PCR, which any lab equipped with basic equipment can implement. Our PCR-generated constructs were easily introduced into hard-to-transfect leukemic cells, and their function was dually validated with the addition of MYBL2 and IDH2 genes into HEK293 cells. We then successfully modified the MYBL2 gene and introduced the R172 mutation into the IDH2 gene within NB4 and HL60 cells that constitutively expressed the Cas9 nuclease. The efficiency of mutation introduction with our methodology was similar to that of ribonucleoprotein strategies, and no off-target events were detected. Overall, our strategy represents a valid and intuitive alternative for introducing desired mutations into hard-to-transfect leukemic cells without viral transduction.
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Affiliation(s)
- Elisa González-Romero
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
| | - Cristina Martínez-Valiente
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
| | - Gema García-García
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain (J.M.M.)
- CIBERER, 46010 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
| | - Antonio Rosal-Vela
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- Biomedicine, Biotechnology and Public Health Department, Cádiz University, 11002 Cádiz, Spain
- Institute of Research and Innovation in Biomedical Sciences of Cadiz (INIBICA), 11009 Cádiz, Spain
| | - José María Millán
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain (J.M.M.)
- CIBERER, 46010 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
| | - Miguel Ángel Sanz
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
| | - Guillermo Sanz
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
- Hematology Department, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain
| | - Alessandro Liquori
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
| | - José Vicente Cervera
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
- Hematology Department, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain
- Genetics Unit, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain
| | - Rafael P. Vázquez-Manrique
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain (J.M.M.)
- CIBERER, 46010 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
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2
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Rabaan AA, AlSaihati H, Bukhamsin R, Bakhrebah MA, Nassar MS, Alsaleh AA, Alhashem YN, Bukhamseen AY, Al-Ruhimy K, Alotaibi M, Alsubki RA, Alahmed HE, Al-Abdulhadi S, Alhashem FA, Alqatari AA, Alsayyah A, Farahat RA, Abdulal RH, Al-Ahmed AH, Imran M, Mohapatra RK. Application of CRISPR/Cas9 Technology in Cancer Treatment: A Future Direction. Curr Oncol 2023; 30:1954-1976. [PMID: 36826113 PMCID: PMC9955208 DOI: 10.3390/curroncol30020152] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Gene editing, especially with clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9), has advanced gene function science. Gene editing's rapid advancement has increased its medical/clinical value. Due to its great specificity and efficiency, CRISPR/Cas9 can accurately and swiftly screen the whole genome. This simplifies disease-specific gene therapy. To study tumor origins, development, and metastasis, CRISPR/Cas9 can change genomes. In recent years, tumor treatment research has increasingly employed this method. CRISPR/Cas9 can treat cancer by removing genes or correcting mutations. Numerous preliminary tumor treatment studies have been conducted in relevant fields. CRISPR/Cas9 may treat gene-level tumors. CRISPR/Cas9-based personalized and targeted medicines may shape tumor treatment. This review examines CRISPR/Cas9 for tumor therapy research, which will be helpful in providing references for future studies on the pathogenesis of malignancy and its treatment.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Hajir AlSaihati
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Rehab Bukhamsin
- Dammam Regional Laboratory and Blood Bank, Dammam 31411, Saudi Arabia
| | - Muhammed A. Bakhrebah
- Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Majed S. Nassar
- Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Abdulmonem A. Alsaleh
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Yousef N. Alhashem
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Ammar Y. Bukhamseen
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Khalil Al-Ruhimy
- Department of Public Health, Ministry of Health, Riyadh 14235, Saudi Arabia
| | - Mohammed Alotaibi
- Department of Public Health, Ministry of Health, Riyadh 14235, Saudi Arabia
| | - Roua A. Alsubki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Hejji E. Alahmed
- Department of Laboratory and Blood Bank, King Fahad Hospital, Al Hofuf 36441, Saudi Arabia
| | - Saleh Al-Abdulhadi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Riyadh 11942, Saudi Arabia
- Saleh Office for Medical Genetic and Genetic Counseling Services, The House of Expertise, Prince Sattam Bin Abdulaziz University, Dammam 32411, Saudi Arabia
| | - Fatemah A. Alhashem
- Laboratory Medicine Department, Hematopathology Division, King Fahad Hospital of the University, Al-Khobar 31441, Saudi Arabia
| | - Ahlam A. Alqatari
- Hematopathology Department, Clinical Pathology, Al-Dorr Specialist Medical Center, Qatif 31911, Saudi Arabia
| | - Ahmed Alsayyah
- Department of Pathology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | - Rwaa H. Abdulal
- Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ali H. Al-Ahmed
- Dammam Health Network, Eastern Health Cluster, Dammam 31444, Saudi Arabia
| | - Mohd. Imran
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Ranjan K. Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar 758002, India
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3
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Applications of CRISPR-Cas9 as an Advanced Genome Editing System in Life Sciences. BIOTECH 2021; 10:biotech10030014. [PMID: 35822768 PMCID: PMC9245484 DOI: 10.3390/biotech10030014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/16/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022] Open
Abstract
Targeted nucleases are powerful genomic tools to precisely change the target genome of living cells, controlling functional genes with high exactness. The clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) genome editing system has been identified as one of the most useful biological tools in genetic engineering that is taken from adaptive immune strategies for bacteria. In recent years, this system has made significant progress and it has been widely used in genome editing to create gene knock-ins, knock-outs, and point mutations. This paper summarizes the application of this system in various biological sciences, including medicine, plant science, and animal breeding.
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4
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Tejedor JR, Bueno C, Vinyoles M, Petazzi P, Agraz-Doblas A, Cobo I, Torres-Ruiz R, Bayón GF, Pérez RF, López-Tamargo S, Gutierrez-Agüera F, Santamarina-Ojeda P, Ramírez-Orellana M, Bardini M, Cazzaniga G, Ballerini P, Schneider P, Stam RW, Varela I, Fraga MF, Fernández AF, Menéndez P. Integrative methylome-transcriptome analysis unravels cancer cell vulnerabilities in infant MLL-rearranged B cell acute lymphoblastic leukemia. J Clin Invest 2021; 131:138833. [PMID: 33983906 DOI: 10.1172/jci138833] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/11/2021] [Indexed: 01/04/2023] Open
Abstract
B cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. As predicted by its prenatal origin, infant B-ALL (iB-ALL) shows an exceptionally silent DNA mutational landscape, suggesting that alternative epigenetic mechanisms may substantially contribute to its leukemogenesis. Here, we have integrated genome-wide DNA methylome and transcriptome data from 69 patients with de novo MLL-rearranged leukemia (MLLr) and non-MLLr iB-ALL leukemia uniformly treated according to the Interfant-99/06 protocol. iB-ALL methylome signatures display a plethora of common and specific alterations associated with chromatin states related to enhancer and transcriptional control in normal hematopoietic cells. DNA methylation, gene expression, and gene coexpression network analyses segregated MLLr away from non-MLLr iB-ALL and identified a coordinated and enriched expression of the AP-1 complex members FOS and JUN and RUNX factors in MLLr iB-ALL, consistent with the significant enrichment of hypomethylated CpGs in these genes. Integrative methylome-transcriptome analysis identified consistent cancer cell vulnerabilities, revealed a robust iB-ALL-specific gene expression-correlating dmCpG signature, and confirmed an epigenetic control of AP-1 and RUNX members in reshaping the molecular network of MLLr iB-ALL. Finally, pharmacological inhibition or functional ablation of AP-1 dramatically impaired MLLr-leukemic growth in vitro and in vivo using MLLr-iB-ALL patient-derived xenografts, providing rationale for new therapeutic avenues in MLLr-iB-ALL.
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Affiliation(s)
- Juan Ramón Tejedor
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and.,RICORS-TERAV Network, ISCIII, Madrid, Spain
| | - Meritxell Vinyoles
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and
| | - Paolo Petazzi
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and
| | - Antonio Agraz-Doblas
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Isabel Cobo
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Raúl Torres-Ruiz
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,RICORS-TERAV Network, ISCIII, Madrid, Spain.,Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Gustavo F Bayón
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain
| | - Raúl F Pérez
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Sara López-Tamargo
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain
| | - Francisco Gutierrez-Agüera
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,RICORS-TERAV Network, ISCIII, Madrid, Spain
| | - Pablo Santamarina-Ojeda
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain
| | - Manuel Ramírez-Orellana
- RICORS-TERAV Network, ISCIII, Madrid, Spain.,Hematology Diagnostic Laboratory, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Michela Bardini
- Centro Ricerca Tettamanti, Department of Paediatrics, University of Milano Bicocca, Fondazione MBBM, Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Department of Paediatrics, University of Milano Bicocca, Fondazione MBBM, Monza, Italy
| | - Paola Ballerini
- Pediatric Hematology, Armand Trousseau Hospital, Paris, France
| | - Pauline Schneider
- Princess Maxima Center for Paediatric Oncology, Utrecht, Netherlands
| | - Ronald W Stam
- Princess Maxima Center for Paediatric Oncology, Utrecht, Netherlands
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Mario F Fraga
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Agustín F Fernández
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Pablo Menéndez
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and.,RICORS-TERAV Network, ISCIII, Madrid, Spain.,Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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5
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González-Romero E, Martínez-Valiente C, García-Ruiz C, Vázquez-Manrique RP, Cervera J, Sanjuan-Pla A. CRISPR to fix bad blood: a new tool in basic and clinical hematology. Haematologica 2019; 104:881-893. [PMID: 30923099 PMCID: PMC6518885 DOI: 10.3324/haematol.2018.211359] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/19/2019] [Indexed: 12/13/2022] Open
Abstract
Advances in genome engineering in the last decade, particularly in the development of programmable nucleases, have made it possible to edit the genomes of most cell types precisely and efficiently. Chief among these advances, the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system is a novel, versatile and easy-to-use tool to edit genomes irrespective of their complexity, with multiple and broad applications in biomedicine. In this review, we focus on the use of CRISPR/Cas9 genome editing in the context of hematologic diseases and appraise the major achievements and challenges in this rapidly moving field to gain a clearer perspective on the potential of this technology to move from the laboratory to the clinic. Accordingly, we discuss data from studies editing hematopoietic cells to understand and model blood diseases, and to develop novel therapies for hematologic malignancies. We provide an overview of the applications of gene editing in experimental, preclinical and clinical hematology including interrogation of gene function, target identification and drug discovery and chimeric antigen receptor T-cell engineering. We also highlight current limitations of CRISPR/Cas9 and the possible strategies to overcome them. Finally, we consider what advances in CRISPR/Cas9 are needed to move the hematology field forward.
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Affiliation(s)
| | | | | | - Rafael P Vázquez-Manrique
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe, Valencia
- CIBER de Enfermedades Raras, Madrid
| | - José Cervera
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia
- CIBER de Oncología, Madrid, Spain
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6
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Ibrahim OM, As Sobeai HM, Grant SG, Latimer JJ. Nucleotide excision repair is a predictor of early relapse in pediatric acute lymphoblastic leukemia. BMC Med Genomics 2018; 11:95. [PMID: 30376844 PMCID: PMC6208034 DOI: 10.1186/s12920-018-0422-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/15/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Nucleotide Excision Repair (NER) is a major pathway of mammalian DNA repair that is associated with drug resistance and has not been well characterized in acute lymphoblastic leukemia (ALL). The objective of this study was to explore the role of NER in relapsed ALL patients. We hypothesized that increased expression of NER genes was associated with drug resistance and relapse in ALL. METHODS We performed secondary data analysis on two sets of pediatric ALL patients that all ultimately relapsed, and who had matched diagnosis-relapse gene expression microarray data (GSE28460 and GSE18497). GSE28460 included 49 precursor-B-ALL patients, and GSE18497 included 27 precursor-B-ALL and 14 T-ALL patients. Microarray data were processed using the Plier 16 algorithm and the 20 canonical NER genes were extracted. Comparisons were made between time of diagnosis and relapse, and between early and late relapsing subgroups. The Chi-square test was used to evaluate whether NER gene expression was altered at the level of the entire pathway and individual gene expression was compared using t-tests. RESULTS We found that gene expression of the NER pathway was significantly increased upon relapse in patients that took 3 years or greater to relapse (late relapsers, P = .007), whereas no such change was evident in patients that relapsed in less than 3 years (early relapsers, P = .180). Moreover, at diagnosis, the NER gene expression of the early relapsing subpopulation was already significantly elevated over that of the late relapsing group (P < .001). This pattern was validated by an 'NER score' established by averaging the relative expression of the 20 canonical NER genes. The NER score at diagnosis was found to be significantly associated with disease-free survival in precursor-B-ALL (P < .001). CONCLUSION Patients are over two times more likely to undergo early relapse if they have a high NER score at diagnosis, hazard ratio 2.008, 95% CI (1.256-3.211). The NER score may provide a underlying mechanism for "time to remission", a known prognostic factor in ALL, and a rationale for differential treatment.
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Affiliation(s)
- Omar M. Ibrahim
- Department of Pharmaceutical Sciences, College of Pharmacy, 3200 S University Drive, Fort Lauderdale, FL 33328 USA
- AutoNation Institute for Breast and Solid Tumor Cancer Research, 3301 College Avenue, Fort Lauderdale, FL 33314 USA
| | - Homood M. As Sobeai
- Department of Pharmaceutical Sciences, College of Pharmacy, 3200 S University Drive, Fort Lauderdale, FL 33328 USA
- AutoNation Institute for Breast and Solid Tumor Cancer Research, 3301 College Avenue, Fort Lauderdale, FL 33314 USA
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2475, Riyadh, 11451 Saudi Arabia
| | - Stephen G. Grant
- AutoNation Institute for Breast and Solid Tumor Cancer Research, 3301 College Avenue, Fort Lauderdale, FL 33314 USA
- Department of Public Health, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, 3200 S University Drive, Fort Lauderdale, FL 33328 USA
| | - Jean J. Latimer
- Department of Pharmaceutical Sciences, College of Pharmacy, 3200 S University Drive, Fort Lauderdale, FL 33328 USA
- AutoNation Institute for Breast and Solid Tumor Cancer Research, 3301 College Avenue, Fort Lauderdale, FL 33314 USA
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7
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Yang L, Ding L, Liang J, Chen J, Tang Y, Xue H, Gu L, Shen S, Li B, Chen J. Relatively favorable prognosis for MLL-rearranged childhood acute leukemia with reciprocal translocations. Pediatr Blood Cancer 2018; 65:e27266. [PMID: 29943896 DOI: 10.1002/pbc.27266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/16/2018] [Accepted: 05/10/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Mixed-lineage leukemia (MLL) with multifarious partner genes leads to aggressive leukemia with dismal outcomes. METHODS Using panel-based targeted sequencing, we examined 90 cases with MLL-rearranged (MLL-r) childhood acute leukemia, including 55 with acute lymphoblastic leukemia (ALL) and 35 with acute myeloid leukemia (AML). RESULTS MLL breakpoints and complete rearrangements were identified. A total of 37.8% (34/90) of patients displayed a single direct MLL fusion gene, 15.6% (14/90) carried a single reciprocal fusion, and 27.8% (25/90) had both reciprocal MLL fusion alleles. The remaining 17 MLL-r cases exhibited complex translocations with homozygous disruptions on chromosome 11 or two breakpoints on the same MLL allele with a deletion of functional regions. A total of 77 patients (45 ALL and 32 AML) received chemotherapy with a median follow-up of 2.5 years. Unexpectedly, we identified children with reciprocal MLL fusions who exhibited relatively favorable outcomes compared with those in children with complex translocations or a single direct MLL fusion allele (66.1% vs. 24.6% and 27.6%, P = 0.001). Reciprocal MLL fusion may be functionally rescued by a partially truncated MLL protein. CONCLUSION Comprehensive MLL-r analysis by targeted next-generation sequencing can provide detailed molecular information and is helpful for precise stratified treatment and clinical prognosis determination.
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Affiliation(s)
- Liu Yang
- Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lixia Ding
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianwei Liang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Chen
- Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - YanJing Tang
- Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huiliang Xue
- Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Longjun Gu
- Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuhong Shen
- Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Benshang Li
- Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Jing Chen
- Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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8
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Montaño A, Forero-Castro M, Hernández-Rivas JM, García-Tuñón I, Benito R. Targeted genome editing in acute lymphoblastic leukemia: a review. BMC Biotechnol 2018; 18:45. [PMID: 30016959 PMCID: PMC6050675 DOI: 10.1186/s12896-018-0455-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/05/2018] [Indexed: 12/18/2022] Open
Abstract
Background Genome editing technologies offers new opportunities for tackling diseases such as acute lymphoblastic leukemia (ALL) that have been beyond the reach of previous therapies. Results We show how the recent availability of genome-editing tools such as CRISPR-Cas9 are an important means of advancing functional studies of ALL through the incorporation, elimination and modification of somatic mutations and fusion genes in cell lines and mouse models. These tools not only broaden the understanding of the involvement of various genetic alterations in the pathogenesis of the disease but also identify new therapeutic targets for future clinical trials. Conclusions New approaches including CRISPR-Cas9 are crucial for functional studies of genetic aberrations driving cancer progression, and that may be responsible for treatment resistance and relapses. By using this approach, diseases can be more faithfully reproduced and new therapeutic targets and approaches found.
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Affiliation(s)
- Adrián Montaño
- IBSAL, IBMCC, University of Salamanca-CSIC, Cancer Research Center, Salamanca, Spain
| | - Maribel Forero-Castro
- School of Biological Sciences (GICBUPTC Research group), Universidad Pedagógica y Tecnológica de Colombia, Boyacá, Colombia
| | - Jesús-María Hernández-Rivas
- IBSAL, IBMCC, University of Salamanca-CSIC, Cancer Research Center, Salamanca, Spain. .,Department of Medicine, University of Salamanca, Spain, Department of Hematology, University Hospital of Salamanca, Salamanca, Spain. .,IBMCC, CIC University of Salamanca-CSIC, University Hospital of Salamanca, Salamanca, Spain.
| | - Ignacio García-Tuñón
- IBSAL, IBMCC, University of Salamanca-CSIC, Cancer Research Center, Salamanca, Spain
| | - Rocío Benito
- IBSAL, IBMCC, University of Salamanca-CSIC, Cancer Research Center, Salamanca, Spain
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9
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Efficient Recreation of t(11;22) EWSR1-FLI1 + in Human Stem Cells Using CRISPR/Cas9. Stem Cell Reports 2018; 8:1408-1420. [PMID: 28494941 PMCID: PMC5425785 DOI: 10.1016/j.stemcr.2017.04.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 04/12/2017] [Accepted: 04/12/2017] [Indexed: 12/21/2022] Open
Abstract
Efficient methodologies for recreating cancer-associated chromosome translocations are in high demand as tools for investigating how such events initiate cancer. The CRISPR/Cas9 system has been used to reconstruct the genetics of these complex rearrangements at native loci while maintaining the architecture and regulatory elements. However, the CRISPR system remains inefficient in human stem cells. Here, we compared three strategies aimed at enhancing the efficiency of the CRISPR-mediated t(11;22) translocation in human stem cells, including mesenchymal and induced pluripotent stem cells: (1) using end-joining DNA processing factors involved in repair mechanisms, or (2) ssODNs to guide the ligation of the double-strand break ends generated by CRISPR/Cas9; and (3) all-in-one plasmid or ribonucleoprotein complex-based approaches. We report that the generation of targeted t(11;22) is significantly increased by using a combination of ribonucleoprotein complexes and ssODNs. The CRISPR/Cas9-mediated generation of targeted t(11;22) in human stem cells opens up new avenues in modeling Ewing sarcoma.
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10
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Malouf C, Ottersbach K. Molecular processes involved in B cell acute lymphoblastic leukaemia. Cell Mol Life Sci 2018; 75:417-446. [PMID: 28819864 PMCID: PMC5765206 DOI: 10.1007/s00018-017-2620-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 12/19/2022]
Abstract
B cell leukaemia is one of the most frequent malignancies in the paediatric population, but also affects a significant proportion of adults in developed countries. The majority of infant and paediatric cases initiate the process of leukaemogenesis during foetal development (in utero) through the formation of a chromosomal translocation or the acquisition/deletion of genetic material (hyperdiploidy or hypodiploidy, respectively). This first genetic insult is the major determinant for the prognosis and therapeutic outcome of patients. B cell leukaemia in adults displays similar molecular features as its paediatric counterpart. However, since this disease is highly represented in the infant and paediatric population, this review will focus on this demographic group and summarise the biological, clinical and epidemiological knowledge on B cell acute lymphoblastic leukaemia of four well characterised subtypes: t(4;11) MLL-AF4, t(12;21) ETV6-RUNX1, t(1;19) E2A-PBX1 and t(9;22) BCR-ABL1.
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Affiliation(s)
- Camille Malouf
- MRC Centre for Regenerative Medicine, The University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Katrin Ottersbach
- MRC Centre for Regenerative Medicine, The University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK.
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11
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Tomasik B, Pastorczak A, Fendler W, Bartłomiejczyk M, Braun M, Mycko M, Madzio J, Polakowska E, Ulińska E, Matysiak M, Derwich K, Lejman M, Kowalczyk J, Badowska W, Kazanowska B, Szczepański T, Styczyński J, Irga-Jaworska N, Młynarski W. Heterozygous carriers of germline c.657_661del5 founder mutation in NBN gene are at risk of central nervous system relapse of B-cell precursor acute lymphoblastic leukemia. Haematologica 2018; 103:e200-e203. [PMID: 29419426 DOI: 10.3324/haematol.2017.181198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Bartłomiej Tomasik
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Poland.,Department of Biostatistics & Translational Medicine, Medical University of Lodz, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Poland
| | - Agata Pastorczak
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Poland
| | - Wojciech Fendler
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Poland.,Department of Biostatistics & Translational Medicine, Medical University of Lodz, Poland
| | - Marcin Bartłomiejczyk
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Poland
| | - Marcin Braun
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Poland.,Department of Pathology, Chair of Oncology, Medical University of Lodz, Poland
| | - Marcin Mycko
- Department of Neurology, Medical University of Lodz, Poland
| | - Joanna Madzio
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Poland
| | - Ewa Polakowska
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Poland
| | - Edyta Ulińska
- Department of Pediatric Hematology and Oncology, Medical University of Warsaw, Poland
| | - Michał Matysiak
- Department of Pediatric Hematology and Oncology, Medical University of Warsaw, Poland
| | - Katarzyna Derwich
- Department of Pediatric Oncology, Hematology and Transplantology, Medical University of Poznan, Poland
| | - Monika Lejman
- Department of Pediatric Oncology and Hematology, Medical University of Lublin, Poland
| | - Jerzy Kowalczyk
- Department of Pediatric Oncology and Hematology, Medical University of Lublin, Poland
| | - Wanda Badowska
- Division of Pediatric Hematology and Oncology, Children Hospital, Olsztyn, Poland
| | - Bernarda Kazanowska
- Department and Clinic of Pediatric Oncology, Hematology and Bone Marrow Transplantation, Wroclaw Medical University, Poland
| | - Tomasz Szczepański
- Department of Pediatric Hematology and Oncology, Medical University of Silesia, Zabrze, Poland
| | - Jan Styczyński
- Department of Pediatrics, Hematology and Oncology, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Nina Irga-Jaworska
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Poland
| | - Wojciech Młynarski
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Poland
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12
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Prieto C, Marschalek R, Kühn A, Bursen A, Bueno C, Menéndez P. The AF4-MLL fusion transiently augments multilineage hematopoietic engraftment but is not sufficient to initiate leukemia in cord blood CD34 + cells. Oncotarget 2017; 8:81936-81941. [PMID: 29137234 PMCID: PMC5669860 DOI: 10.18632/oncotarget.19567] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 04/22/2017] [Indexed: 12/25/2022] Open
Abstract
The translocation t(4;11)(q21;q23) is the hallmark genetic abnormality associated with infant pro-B acute lymphoblastic leukemia (B-ALL) and has the highest frequency of rearrangement in Mixed-lineage leukemia (MLL) leukemias. Unlike other MLL translocations, MLL-AF4-induced proB-ALL is exceptionally difficult to model in mice/humans. Previous work has investigated the relevance of the reciprocal translocation fusion protein AF4-MLL for t(4;11) leukemia, finding that AF4-MLL is capable of inducing proB-ALL without requirement for MLL-AF4 when expressed in murine hematopoietic stem/progenitor cells (HSPCs). Therefore, AF4-MLL might represent a key genetic lesion contributing to t(4;11)-driven leukemogenesis. Here, we aimed to establish a humanized mouse model by using AF4-MLL to analyze its transformation potential in human cord blood-derived CD34+ HSPCs. We show that AF4-MLL-expressing human CD34+ HSPCs provide enhanced long-term hematopoietic reconstitution in primary immunodeficient recipients but are not endowed with subsequent self-renewal ability upon serial transplantation. Importantly, expression of AF4-MLL in primary neonatal CD34+ HSPCs failed to render any phenotypic or hematological sign of disease, and was therefore not sufficient to initiate leukemia within a 36-week follow-up. Species-specific (epi)-genetic intrinsic determinants may underlie the different outcome observed when AF4-MLL is expressed in murine or human HSPCs.
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Affiliation(s)
- Cristina Prieto
- Department of Biomedicine, Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology/DCAL, Goethe-University, Frankfurt, Germany
| | - Alessa Kühn
- Institute of Pharmaceutical Biology/DCAL, Goethe-University, Frankfurt, Germany
| | - Adelheid Bursen
- Institute of Pharmaceutical Biology/DCAL, Goethe-University, Frankfurt, Germany
| | - Clara Bueno
- Department of Biomedicine, Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Barcelona, Spain
| | - Pablo Menéndez
- Department of Biomedicine, Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Barcelona, Spain.,Instituciò Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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13
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Chemical exposure and infant leukaemia: development of an adverse outcome pathway (AOP) for aetiology and risk assessment research. Arch Toxicol 2017; 91:2763-2780. [PMID: 28536863 DOI: 10.1007/s00204-017-1986-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/08/2017] [Indexed: 01/06/2023]
Abstract
Infant leukaemia (<1 year old) is a rare disease of an in utero origin at an early phase of foetal development. Rearrangements of the mixed-lineage leukaemia (MLL) gene producing abnormal fusion proteins are the most frequent genetic/molecular findings in infant B cell-acute lymphoblastic leukaemia. In small epidemiological studies, mother/foetus exposures to some chemicals including pesticides have been associated with infant leukaemia; however, the strength of evidence and power of these studies are weak at best. Experimental in vitro or in vivo models do not sufficiently recapitulate the human disease and regulatory toxicology studies are unlikely to capture this kind of hazard. Here, we develop an adverse outcome pathway (AOP) based substantially on an analogous disease-secondary acute leukaemia caused by the topoisomerase II (topo II) poison etoposide-and on cellular and animal models. The hallmark of the AOP is the formation of MLL gene rearrangements via topo II poisoning, leading to fusion genes and ultimately acute leukaemia by global (epi)genetic dysregulation. The AOP condenses molecular, pathological, regulatory and clinical knowledge in a pragmatic, transparent and weight of evidence-based framework. This facilitates the interpretation and integration of epidemiological studies in the process of risk assessment by defining the biologically plausible causative mechanism(s). The AOP identified important gaps in the knowledge relevant to aetiology and risk assessment, including the specific embryonic target cell during the short and spatially restricted period of susceptibility, and the role of (epi)genetic features modifying the initiation and progression of the disease. Furthermore, the suggested AOP informs on a potential Integrated Approach to Testing and Assessment to address the risk caused by environmental chemicals in the future.
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14
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Abstract
With the introduction of precision genome editing using CRISPR-Cas9 technology, we have entered a new era of genetic engineering and gene therapy. With RNA-guided endonucleases, such as Cas9, it is possible to engineer DNA double strand breaks (DSB) at specific genomic loci. DSB repair by the error-prone non-homologous end-joining (NHEJ) pathway can disrupt a target gene by generating insertions and deletions. Alternatively, Cas9-mediated DSBs can be repaired by homology-directed repair (HDR) using an homologous DNA repair template, thus allowing precise gene editing by incorporating genetic changes into the repair template. HDR can introduce gene sequences for protein epitope tags, delete genes, make point mutations, or alter enhancer and promoter activities. In anticipation of adapting this technology for gene therapy in human somatic cells, much focus has been placed on increasing the fidelity of CRISPR-Cas9 and increasing HDR efficiency to improve precision genome editing. In this review, we will discuss applications of CRISPR technology for gene inactivation and genome editing with a focus on approaches to enhancing CRISPR-Cas9-mediated HDR for the generation of cell and animal models, and conclude with a discussion of recent advances and challenges towards the application of this technology for gene therapy in humans.
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Affiliation(s)
- Jayme Salsman
- a Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Graham Dellaire
- a Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- b Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- c Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
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