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Coleman DJL, Keane P, Luque-Martin R, Chin PS, Blair H, Ames L, Kellaway SG, Griffin J, Holmes E, Potluri S, Assi SA, Bushweller J, Heidenreich O, Cockerill PN, Bonifer C. Gene regulatory network analysis predicts cooperating transcription factor regulons required for FLT3-ITD+ AML growth. Cell Rep 2023; 42:113568. [PMID: 38104314 PMCID: PMC10874628 DOI: 10.1016/j.celrep.2023.113568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/03/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease caused by different mutations. Previously, we showed that each mutational subtype develops its specific gene regulatory network (GRN) with transcription factors interacting within multiple gene modules, many of which are transcription factor genes themselves. Here, we hypothesize that highly connected nodes within such networks comprise crucial regulators of AML maintenance. We test this hypothesis using FLT3-ITD-mutated AML as a model and conduct an shRNA drop-out screen informed by this analysis. We show that AML-specific GRNs predict crucial regulatory modules required for AML growth. Furthermore, our work shows that all modules are highly connected and regulate each other. The careful multi-omic analysis of the role of one (RUNX1) module by shRNA and chemical inhibition shows that this transcription factor and its target genes stabilize the GRN of FLT3-ITD+ AML and that its removal leads to GRN collapse and cell death.
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Affiliation(s)
- Daniel J L Coleman
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Rosario Luque-Martin
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Paulynn S Chin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Helen Blair
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK
| | - Luke Ames
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sophie G Kellaway
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - James Griffin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Elizabeth Holmes
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - John Bushweller
- University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK; Prinses Máxima Centrum for Pediatric Oncology, Postbus 113, 3720 AC Bilthoven, Heidelberglaan 25, 3584CS Utrecht, the Netherlands.
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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2
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Ng M, Verboon L, Issa H, Bhayadia R, Vermunt MW, Winkler R, Schüler L, Alejo O, Schuschel K, Regenyi E, Borchert D, Heuser M, Reinhardt D, Yaspo ML, Heckl D, Klusmann JH. Myeloid leukemia vulnerabilities embedded in long noncoding RNA locus MYNRL15. iScience 2023; 26:107844. [PMID: 37766974 PMCID: PMC10520325 DOI: 10.1016/j.isci.2023.107844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/02/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
The noncoding genome presents a largely untapped source of new biological insights, including thousands of long noncoding RNA (lncRNA) loci. While lncRNA dysregulation has been reported in myeloid malignancies, their functional relevance remains to be systematically interrogated. We performed CRISPRi screens of lncRNA signatures from normal and malignant hematopoietic cells and identified MYNRL15 as a myeloid leukemia dependency. Functional dissection suggests an RNA-independent mechanism mediated by two regulatory elements embedded in the locus. Genetic perturbation of these elements triggered a long-range chromatin interaction and downregulation of leukemia dependency genes near the gained interaction sites, as well as overall suppression of cancer dependency pathways. Thus, this study describes a new noncoding myeloid leukemia vulnerability and mechanistic concept for myeloid leukemia. Importantly, MYNRL15 perturbation caused strong and selective impairment of leukemia cells of various genetic backgrounds over normal hematopoietic stem and progenitor cells in vitro, and depletion of patient-derived xenografts in vivo.
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Affiliation(s)
- Michelle Ng
- Department of Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Lonneke Verboon
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hasan Issa
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raj Bhayadia
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marit Willemijn Vermunt
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Robert Winkler
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Leah Schüler
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oriol Alejo
- Department of Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Konstantin Schuschel
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eniko Regenyi
- Department of Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Dorit Borchert
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Dirk Reinhardt
- Clinic for Pediatrics III, University Hospital Essen, 45147 Essen, Germany
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Dirk Heckl
- Institute for Experimental Pediatric Hematology and Oncology, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
| | - Jan-Henning Klusmann
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
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3
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Pal D, Blair H, Parker J, Hockney S, Beckett M, Singh M, Tirtakusuma R, Nelson R, McNeill H, Angel SH, Wilson A, Nizami S, Nakjang S, Zhou P, Schwab C, Sinclair P, Russell LJ, Coxhead J, Halsey C, Allan JM, Harrison CJ, Moorman AV, Heidenreich O, Vormoor J. hiPSC-derived bone marrow milieu identifies a clinically actionable driver of niche-mediated treatment resistance in leukemia. Cell Rep Med 2022; 3:100717. [PMID: 35977468 PMCID: PMC9418860 DOI: 10.1016/j.xcrm.2022.100717] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/18/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022]
Abstract
Leukemia cells re-program their microenvironment to augment blast proliferation and enhance treatment resistance. Means of clinically targeting such niche-driven treatment resistance remain ambiguous. We develop human induced pluripotent stem cell (hiPSC)-engineered niches to reveal druggable cancer-niche dependencies. We reveal that mesenchymal (iMSC) and vascular niche-like (iANG) hiPSC-derived cells support ex vivo proliferation of patient-derived leukemia cells, affect dormancy, and mediate treatment resistance. iMSCs protect dormant and cycling blasts against dexamethasone, while iANGs protect only dormant blasts. Leukemia proliferation and protection from dexamethasone-induced apoptosis is dependent on cancer-niche interactions mediated by CDH2. Consequently, we test CDH2 antagonist ADH-1 (previously in Phase I/II trials for solid tumors) in a very aggressive patient-derived xenograft leukemia mouse model. ADH-1 shows high in vivo efficacy; ADH-1/dexamethasone combination is superior to dexamethasone alone, with no ADH-1-conferred additional toxicity. These findings provide a proof-of-concept starting point to develop improved, potentially safer therapeutics targeting niche-mediated cancer dependencies in blood cancers.
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Affiliation(s)
- Deepali Pal
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK; Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST UK.
| | - Helen Blair
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Jessica Parker
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST UK
| | - Sean Hockney
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST UK
| | - Melanie Beckett
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Mankaran Singh
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Ricky Tirtakusuma
- Princess Maxima Centrum for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands
| | - Ryan Nelson
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Hesta McNeill
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Sharon H Angel
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Aaron Wilson
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Salem Nizami
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Sirintra Nakjang
- Bioinformatics Support Unit, William Leech Building, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Peixun Zhou
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Claire Schwab
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Paul Sinclair
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Lisa J Russell
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Jonathan Coxhead
- Genomics Core Facility, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Christina Halsey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1QH UK
| | - James M Allan
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Christine J Harrison
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Anthony V Moorman
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK; Princess Maxima Centrum for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands
| | - Josef Vormoor
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Herschel Building Level 6, Brewery Lane, Newcastle upon Tyne, NE1 7RU UK; Princess Maxima Centrum for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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4
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The plasma membrane H +-ATPase is critical for cell growth and pathogenicity in Penicillium digitatum. Appl Microbiol Biotechnol 2022; 106:5123-5136. [PMID: 35771244 DOI: 10.1007/s00253-022-12036-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/11/2022] [Accepted: 06/16/2022] [Indexed: 11/02/2022]
Abstract
The plasma membrane H+-ATPase (PMA1) is a major cytosolic pH regulator and a potential candidate for antifungal drug discovery due to its fungal specificity and criticality. In this study, the function of Penicillum digitatum PMA1 was characterized through RNA interference (RNAi) and overexpression technology. The results showed that silencing the PMA1 gene reduces cell growth and pathogenicity, and increases susceptibility of P. digitatum to proton pump inhibitors (PPIs). Under scanning electron microscopy (SEM) and transmission electron microscopy (TEM) examination, cell morphology was significantly altered in the PMA1- silenced mutant (si57). When compared with wild type (WT) and the overexpressed mutant (oe9), the cell walls of the si57 mutant were thicker and their cell membrane damage manifested particularly at sites of polarized growth. Consistent with the morphological change on the cell wall, chitin and glucan content of the cell wall of si57 were significantly lower and accompanied with increased activities of chitinase and glucanase. The lower ergosterol content in the si57 mutant then increased cell membrane permeability, ultimately leading to leakage of cytoplasmic contents such as ions, reduced sugars and soluble proteins. Furthermore, significantly decreased activity of cell wall degrading enzymes of si57 during citrus fruit infections indicates a reduced pathogenicity in this mutant. We conclude that PMA1 in P. digitatum plays an important role in maintaining pathogenesis and PMA1 could be a candidate novel fungicidal drug discovery for citrus green mold. KEY POINTS: Silencing PMA1 gene decreased the growth and pathogenicity of P. digitatum. Silencing PMA1 gene damaged cell wall and cell membrane integrity of P. digitatum. PMA1 appears to be a suitable fungicidal target against citrus green mold.
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5
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Wang D, Xiu J, Zhao J, Luo J. miR‐AB, a miRNA‐based shRNA viral toolkit for multicolor‐barcoded multiplex RNAi at a single‐cell level. EMBO Rep 2022; 23:e53691. [PMID: 35201651 PMCID: PMC8982575 DOI: 10.15252/embr.202153691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 01/21/2022] [Accepted: 01/30/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Dapeng Wang
- Department of Immunology Binzhou Medical University Shandong China
| | - Jianbo Xiu
- State Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences Chinese Academy of Medical Sciences Beijing China
| | - Jiangyue Zhao
- Department of Ophthalmology The 4th Affiliated Hospital of China Medical University Shenyang China
| | - Junli Luo
- Department of Molecular Medicine The Scripps Research Institute Jupiter FL USA
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6
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Hassan JJ, Lieske A, Dörpmund N, Klatt D, Hoffmann D, Kleppa MJ, Kustikova OS, Stahlhut M, Schwarzer A, Schambach A, Maetzig T. A Multiplex CRISPR-Screen Identifies PLA2G4A as Prognostic Marker and Druggable Target for HOXA9 and MEIS1 Dependent AML. Int J Mol Sci 2021; 22:ijms22179411. [PMID: 34502319 PMCID: PMC8431012 DOI: 10.3390/ijms22179411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/03/2022] Open
Abstract
HOXA9 and MEIS1 are frequently upregulated in acute myeloid leukemia (AML), including those with MLL-rearrangement. Because of their pivotal role in hemostasis, HOXA9 and MEIS1 appear non-druggable. We, thus, interrogated gene expression data of pre-leukemic (overexpressing Hoxa9) and leukemogenic (overexpressing Hoxa9 and Meis1; H9M) murine cell lines to identify cancer vulnerabilities. Through gene expression analysis and gene set enrichment analyses, we compiled a list of 15 candidates for functional validation. Using a novel lentiviral multiplexing approach, we selected and tested highly active sgRNAs to knockout candidate genes by CRISPR/Cas9, and subsequently identified a H9M cell growth dependency on the cytosolic phospholipase A2 (PLA2G4A). Similar results were obtained by shRNA-mediated suppression of Pla2g4a. Remarkably, pharmacologic inhibition of PLA2G4A with arachidonyl trifluoromethyl ketone (AACOCF3) accelerated the loss of H9M cells in bulk cultures. Additionally, AACOCF3 treatment of H9M cells reduced colony numbers and colony sizes in methylcellulose. Moreover, AACOCF3 was highly active in human AML with MLL rearrangement, in which PLA2G4A was significantly higher expressed than in AML patients without MLL rearrangement, and is sufficient as an independent prognostic marker. Our work, thus, identifies PLA2G4A as a prognostic marker and potential therapeutic target for H9M-dependent AML with MLL-rearrangement.
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MESH Headings
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- CRISPR-Cas Systems
- Cell Proliferation
- Gene Expression Regulation, Neoplastic
- Group IV Phospholipases A2/antagonists & inhibitors
- Group IV Phospholipases A2/genetics
- High-Throughput Screening Assays
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Myeloid Ecotropic Viral Integration Site 1 Protein/genetics
- Myeloid Ecotropic Viral Integration Site 1 Protein/metabolism
- Tumor Cells, Cultured
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Affiliation(s)
- Jacob Jalil Hassan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Anna Lieske
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Nicole Dörpmund
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Denise Klatt
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Dirk Hoffmann
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Marc-Jens Kleppa
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Olga S. Kustikova
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Maike Stahlhut
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
| | - Adrian Schwarzer
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Tobias Maetzig
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (J.J.H.); (A.L.); (N.D.); (D.K.); (D.H.); (M.-J.K.); (O.S.K.); (M.S.); (A.S.); (A.S.)
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
- Correspondence:
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7
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Kosanke M, Osetek K, Haase A, Wiehlmann L, Davenport C, Schwarzer A, Adams F, Kleppa MJ, Schambach A, Merkert S, Wunderlich S, Menke S, Dorda M, Martin U. Reprogramming enriches for somatic cell clones with small-scale mutations in cancer-associated genes. Mol Ther 2021; 29:2535-2553. [PMID: 33831558 DOI: 10.1016/j.ymthe.2021.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/03/2021] [Accepted: 04/02/2021] [Indexed: 02/06/2023] Open
Abstract
Cellular therapies based on induced pluripotent stem cells (iPSCs) come out of age and an increasing number of clinical trials applying iPSC-based transplants are ongoing or in preparation. Recent studies, however, demonstrated a high number of small-scale mutations in iPSCs. Although the mutational load in iPSCs seems to be largely derived from their parental cells, it is still unknown whether reprogramming may enrich for individual mutations that could lead to loss of functionality and tumor formation from iPSC derivatives. 30 hiPSC lines were analyzed by whole exome sequencing. High accuracy amplicon sequencing showed that all analyzed small-scale variants pre-existed in their parental cells and that individual mutations present in small subpopulations of parental cells become enriched among hiPSC clones during reprogramming. Among those, putatively actionable driver mutations affect genes related to cell-cycle control, cell death, and pluripotency and may confer a selective advantage during reprogramming. Finally, a short hairpin RNA (shRNA)-based experimental approach was applied to provide additional evidence for the individual impact of such genes on the reprogramming efficiency. In conclusion, we show that enriched mutations in curated onco- and tumor suppressor genes may account for an increased tumor risk and impact the clinical value of patient-derived hiPSCs.
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Affiliation(s)
- Maike Kosanke
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Katarzyna Osetek
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Alexandra Haase
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Colin Davenport
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Adrian Schwarzer
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Felix Adams
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Marc-Jens Kleppa
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Sylvia Merkert
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Stephanie Wunderlich
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Sandra Menke
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Marie Dorda
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany.
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8
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Kennedy AL, Myers KC, Bowman J, Gibson CJ, Camarda ND, Furutani E, Muscato GM, Klein RH, Ballotti K, Liu S, Harris CE, Galvin A, Malsch M, Dale D, Gansner JM, Nakano TA, Bertuch A, Vlachos A, Lipton JM, Castillo P, Connelly J, Churpek J, Edwards JR, Hijiya N, Ho RH, Hofmann I, Huang JN, Keel S, Lamble A, Lau BW, Norkin M, Stieglitz E, Stock W, Walkovich K, Boettcher S, Brendel C, Fleming MD, Davies SM, Weller EA, Bahl C, Carter SL, Shimamura A, Lindsley RC. Distinct genetic pathways define pre-malignant versus compensatory clonal hematopoiesis in Shwachman-Diamond syndrome. Nat Commun 2021; 12:1334. [PMID: 33637765 PMCID: PMC7910481 DOI: 10.1038/s41467-021-21588-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 01/29/2021] [Indexed: 12/23/2022] Open
Abstract
To understand the mechanisms that mediate germline genetic leukemia predisposition, we studied the inherited ribosomopathy Shwachman-Diamond syndrome (SDS), a bone marrow failure disorder with high risk of myeloid malignancies at an early age. To define the mechanistic basis of clonal hematopoiesis in SDS, we investigate somatic mutations acquired by patients with SDS followed longitudinally. Here we report that multiple independent somatic hematopoietic clones arise early in life, most commonly harboring heterozygous mutations in EIF6 or TP53. We show that germline SBDS deficiency establishes a fitness constraint that drives selection of somatic clones via two distinct mechanisms with different clinical consequences. EIF6 inactivation mediates a compensatory pathway with limited leukemic potential by ameliorating the underlying SDS ribosome defect and enhancing clone fitness. TP53 mutations define a maladaptive pathway with enhanced leukemic potential by inactivating tumor suppressor checkpoints without correcting the ribosome defect. Subsequent development of leukemia was associated with acquisition of biallelic TP53 alterations. These results mechanistically link leukemia predisposition to germline genetic constraints on cellular fitness, and provide a rational framework for clinical surveillance strategies.
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Affiliation(s)
- Alyssa L Kennedy
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kasiani C Myers
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - James Bowman
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Institute for Protein Innovation, Boston, MA, USA
| | - Christopher J Gibson
- Department of Medical Oncology, Division of Hematological Malignancies Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Elissa Furutani
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Robert H Klein
- Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Boston, MA, USA
| | | | - Shanshan Liu
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | | | | | | | - David Dale
- Department of Internal Medicine, University of Washington, Seattle, WA, USA
| | - John M Gansner
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Taizo A Nakano
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO, USA
| | - Alison Bertuch
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Adrianna Vlachos
- Division of Hematology/Oncology and Cellular Therapy, Cohen Children's Medical Center of New York, New Hyde Park, NY, USA
- Zucker School of Medicine at Hofstra/Northwell School of Medicine, Hempstead, NY, USA
| | - Jeffrey M Lipton
- Division of Hematology/Oncology and Cellular Therapy, Cohen Children's Medical Center of New York, New Hyde Park, NY, USA
- Zucker School of Medicine at Hofstra/Northwell School of Medicine, Hempstead, NY, USA
| | - Paul Castillo
- Shands Children's Hospital, Department of Pediatrics, Division of Pediatric Hematology Oncology, University of Florida, Gainesville, FL, USA
| | - James Connelly
- Department of Pediatrics, Division of Pediatric Hematology Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jane Churpek
- Department of Medicine, Section of Hematology, Oncology, and Palliative Care, The University of Wisconsin-Madison, Madison, WI, USA
| | - John R Edwards
- Indiana Blood and Marrow Transplantation, Indianapolis, IN, USA
| | - Nobuko Hijiya
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Richard H Ho
- Department of Pediatrics, Division of Pediatric Hematology Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Inga Hofmann
- Department of Pediatrics, Division of Pediatric Hematology/Oncology and BMT, University of Wisconsin, Madison, WI, USA
| | - James N Huang
- Department of Pediatrics, UCSF Benioff Children's Hospital, San Francisco, CA, USA
- Division of Pediatric Allergy, Immunology, and Blood & Marrow Transplantation, UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | - Siobán Keel
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Adam Lamble
- Division of Hematology-Oncology, Seattle Children's Hospital, Seattle, WA, USA
| | - Bonnie W Lau
- Dartmouth-Hitchcock Medical Center, Pediatric Hematology Oncology, Geisel School of Medicine, Lebanon, NH, USA
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Maxim Norkin
- Division of Cancer Medicine, Baptist MD Anderson Cancer Center, Jacksonville, FL, USA
| | - Elliot Stieglitz
- Department of Pediatrics, UCSF Benioff Children's Hospital, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Wendy Stock
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kelly Walkovich
- Division of Pediatric Hematology- Oncology, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Steffen Boettcher
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Christian Brendel
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Stella M Davies
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Edie A Weller
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | - Christopher Bahl
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Institute for Protein Innovation, Boston, MA, USA
| | - Scott L Carter
- Broad Institute, Boston, MA, USA
- Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, MA, USA
| | - Akiko Shimamura
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - R Coleman Lindsley
- Department of Medical Oncology, Division of Hematological Malignancies Dana-Farber Cancer Institute, Boston, MA, USA.
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9
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Zhang Q, Ma XF, Dong MZ, Tan J, Zhang J, Zhuang LK, Liu SS, Xin YN. MiR-30b-5p regulates the lipid metabolism by targeting PPARGC1A in Huh-7 cell line. Lipids Health Dis 2020; 19:76. [PMID: 32299444 PMCID: PMC7164201 DOI: 10.1186/s12944-020-01261-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND MiRNAs are a group of multifunctional non-coding RNAs which play an important role in the various physiological processes including the development of NAFLD. Recent studies have shown that miR-30b-5p tightly associated with the abnormal lipid metabolism in patients with NAFLD, but the detailed mechanism of miR-30b-5p in the lipid metabolism was remain unclear. The aim of this study was to investigate the effect of miR-30b-5p on the lipid metabolism in hepatocellular carcinoma Huh-7 cells. MATERIAL AND METHODS The correlation of intracellular fat content with the expression of miR-30b-5p in Huh-7 cells and HepG2 cells was investigated by treated cells with different concentrations of FFAs. The effect of miR-30b-5p on the lipid deposition in Huh-7 cells was tested by oil red O staining and TG concentrations measurement. qRT-PCR and western blot were used to investigate the lipid metabolism-related genes PPAR-α, SREBP-1, and GULT1 in miR-30b-5p overexpressed or inhibited Huh-7 cells. Target genes of miR-30b-5p were predicted using starBase, miRDB, and TargetScan databases and verified by qRT-PCR and western blot. RESULTS The expression of miR-30b-5p was significant decreased in the FFAs treated Huh-7 cells and HepG2 cells. Overexpressing miR-30b-5p in Huh-7 cells decreased the number and size of lipid droplets and intracellular TG concentrations in Huh-7 cells. Expression of fatty acid oxidation related gene PPAR-α was increased and expression of lipid synthesis related gene SREBP-1 was decreased in the miR-30b-5p overexpressed Huh-7 cells. In addition, miR-30b-5p regulates the intracellular lipid metabolism by targeting PPARGC1A. CONCLUSIONS Overexpression of miR-30b-5p could reduce the intracellular fat deposition in Huh-7 cells, and miR-30b-5p might regulate the intracellular lipid metabolism by targeting the PPARGC1A in Huh-7 cells.
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Affiliation(s)
- Qing Zhang
- Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266011, China
| | - Xue-Feng Ma
- Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266011, China
| | - Meng-Zhen Dong
- Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266011, China
| | - Jie Tan
- Weifang Medical University, Weifang, 261053, China
| | - Jie Zhang
- Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266011, China
| | - Li-Kun Zhuang
- Hepatology Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266011, China
| | - Shou-Sheng Liu
- Digestive Disease Key Laboratory of Qingdao, Qingdao, 266071, China.
- Central Laboratories, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China.
| | - Yong-Ning Xin
- Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266011, China.
- Hepatology Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266011, China.
- Digestive Disease Key Laboratory of Qingdao, Qingdao, 266071, China.
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10
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Zhou L, Sheng D, Deng Q, Wang D, Liu S. Development of a novel method for rapid cloning of shRNA vectors, which successfully knocked down CD44 in mesenchymal triple-negative breast cancer cells. Cancer Commun (Lond) 2018; 38:57. [PMID: 30249304 PMCID: PMC6154939 DOI: 10.1186/s40880-018-0327-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/14/2018] [Indexed: 01/02/2023] Open
Affiliation(s)
- Lei Zhou
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei, 230027, Anhui, P. R. China
| | - Dandan Sheng
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei, 230027, Anhui, P. R. China
| | - Qiaodan Deng
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Department of Breast Surgery, Fudan University, Shanghai, 200032, P. R. China
| | - Dong Wang
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science & Technology of China, Hefei, 230027, Anhui, P. R. China.,Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Department of Breast Surgery, Fudan University, Shanghai, 200032, P. R. China
| | - Suling Liu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Department of Breast Surgery, Fudan University, Shanghai, 200032, P. R. China.
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11
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Labuhn M, Adams FF, Ng M, Knoess S, Schambach A, Charpentier EM, Schwarzer A, Mateo JL, Klusmann JH, Heckl D. Refined sgRNA efficacy prediction improves large- and small-scale CRISPR-Cas9 applications. Nucleic Acids Res 2018; 46:1375-1385. [PMID: 29267886 PMCID: PMC5814880 DOI: 10.1093/nar/gkx1268] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/27/2017] [Accepted: 12/11/2017] [Indexed: 12/26/2022] Open
Abstract
Genome editing with the CRISPR-Cas9 system has enabled unprecedented efficacy for reverse genetics and gene correction approaches. While off-target effects have been successfully tackled, the effort to eliminate variability in sgRNA efficacies-which affect experimental sensitivity-is in its infancy. To address this issue, studies have analyzed the molecular features of highly active sgRNAs, but independent cross-validation is lacking. Utilizing fluorescent reporter knock-out assays with verification at selected endogenous loci, we experimentally quantified the target efficacies of 430 sgRNAs. Based on this dataset we tested the predictive value of five recently-established prediction algorithms. Our analysis revealed a moderate correlation (r = 0.04 to r = 0.20) between the predicted and measured activity of the sgRNAs, and modest concordance between the different algorithms. We uncovered a strong PAM-distal GC-content-dependent activity, which enabled the exclusion of inactive sgRNAs. By deriving nine additional predictive features we generated a linear model-based discrete system for the efficient selection (r = 0.4) of effective sgRNAs (CRISPRater). We proved our algorithms' efficacy on small and large external datasets, and provide a versatile combined on- and off-target sgRNA scanning platform. Altogether, our study highlights current issues and efforts in sgRNA efficacy prediction, and provides an easily-applicable discrete system for selecting efficient sgRNAs.
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Affiliation(s)
- Maurice Labuhn
- Pediatric Hematology & Oncology, Hannover Medical School, Hannover, Germany
| | - Felix F Adams
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Michelle Ng
- Pediatric Hematology & Oncology, Hannover Medical School, Hannover, Germany
| | - Sabine Knoess
- Pediatric Hematology & Oncology, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Emmanuelle M Charpentier
- Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin, Germany
- The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Adrian Schwarzer
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Juan L Mateo
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
- Department of Information Technology, University of Oviedo, Oviedo, Asturias, Spain
| | - Jan-Henning Klusmann
- Pediatric Hematology & Oncology, Hannover Medical School, Hannover, Germany
- Department of Pediatrics I, Pediatric Hematology and Oncology, University of Halle, Halle, Germany
| | - Dirk Heckl
- Pediatric Hematology & Oncology, Hannover Medical School, Hannover, Germany
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12
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Adams FF, Hoffmann T, Zuber J, Heckl D, Schambach A, Schwarzer A. Pooled Generation of Lentiviral Tetracycline-Regulated microRNA Embedded Short Hairpin RNA Libraries. Hum Gene Ther Methods 2018; 29:16-29. [PMID: 29325442 DOI: 10.1089/hgtb.2017.182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Short hairpin RNA (shRNA) screens are powerful tools to probe genetic dependencies in loss-of-function studies, such as the identification of therapeutic targets in cancer research. Lentivirally delivered shRNAs embedded in endogenous microRNA contexts (shRNAmiRs) mediate efficient long-term suppression of target genes suitable for numerous experimental contexts and clinical applications. Here, an easy-to-use laboratory protocol is described, covering the design and pooled assembly of focused shRNAmiR libraries into an optimized, Tet-inducible all-in-one lentiviral vector, packaging of viral particles, followed by retrieval and quantification of hairpin sequences after cellular DNA-recovery. Starting from a gene list to the identification of hits, the protocol enables shRNA screens within 6 weeks.
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Affiliation(s)
- Felix F Adams
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Thomas Hoffmann
- 2 Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Johannes Zuber
- 2 Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Dirk Heckl
- 3 Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany .,4 Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Adrian Schwarzer
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany .,5 Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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13
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Zhang Y, Li X, Xu Z, Chai Y, Wang H, Yuan R. An ultrasensitive electrochemiluminescence biosensor for multiple detection of microRNAs based on a novel dual circuit catalyzed hairpin assembly. Chem Commun (Camb) 2018; 54:10148-10151. [DOI: 10.1039/c8cc06102e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A novel double-hairpin DNA inducing a dual circuit catalyzed hairpin assembly (DC-CHA) strategy was proposed to fabricate electrochemiluminescence (ECL) biosensors for multiple target (microRNA-21 and microRNA-155) ultrasensitive detection.
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Affiliation(s)
- Yue Zhang
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Xue Li
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ziqi Xu
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yaqin Chai
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Haijun Wang
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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14
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Atanasov J, Groher F, Weigand JE, Suess B. Design and implementation of a synthetic pre-miR switch for controlling miRNA biogenesis in mammals. Nucleic Acids Res 2017; 45:e181. [PMID: 29036355 PMCID: PMC5727447 DOI: 10.1093/nar/gkx858] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/22/2017] [Accepted: 09/20/2017] [Indexed: 01/07/2023] Open
Abstract
Synthetic RNA-based systems have increasingly been used for the regulation of eukaryotic gene expression. Due to their structural properties, riboregulators provide a convenient basis for the development of ligand-dependent controllable systems. Here, we demonstrate reversible conditional control of miRNA biogenesis with an aptamer domain as a sensing unit connected to a natural miRNA precursor for the first time. For the design of the pre-miR switch, we replaced the natural terminal loop with the TetR aptamer. Thus, the TetR aptamer was positioned close to the Dicer cleavage sites, which allowed sterical control over pre-miR processing by Dicer. Our design proved to be highly versatile, allowing us to regulate the biogenesis of three structurally different miRNAs: miR-126, -34a and -199a. Dicer cleavage was inhibited up to 143-fold via co-expression of the TetR protein, yet could be completely restored upon addition of doxycycline. Moreover, we showed the functionality of the pre-miR switches for gene regulation through the interaction of the respective miRNA with its specific target sequence. Our designed device is capable of robust and reversible control of miRNA abundance. Thus, we offer a novel investigational tool for functional miRNA analysis.
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Affiliation(s)
- Janina Atanasov
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
| | - Florian Groher
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
| | - Julia E. Weigand
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
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