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A genetically modified minipig model for Alzheimer’s disease with SORL1 haploinsufficiency. Cell Rep Med 2022; 3:100740. [PMID: 36099918 PMCID: PMC9512670 DOI: 10.1016/j.xcrm.2022.100740] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/20/2022] [Accepted: 08/19/2022] [Indexed: 11/21/2022]
Abstract
The established causal genes in Alzheimer’s disease (AD), APP, PSEN1, and PSEN2, are functionally characterized using biomarkers, capturing an in vivo profile reflecting the disease’s initial preclinical phase. Mutations in SORL1, encoding the endosome recycling receptor SORLA, are found in 2%–3% of individuals with early-onset AD, and SORL1 haploinsufficiency appears to be causal for AD. To test whether SORL1 can function as an AD causal gene, we use CRISPR-Cas9-based gene editing to develop a model of SORL1 haploinsufficiency in Göttingen minipigs, taking advantage of porcine models for biomarker investigations. SORL1 haploinsufficiency in young adult minipigs is found to phenocopy the preclinical in vivo profile of AD observed with APP, PSEN1, and PSEN2, resulting in elevated levels of β-amyloid (Aβ) and tau preceding amyloid plaque formation and neurodegeneration, as observed in humans. Our study provides functional support for the theory that SORL1 haploinsufficiency leads to endosome cytopathology with biofluid hallmarks of autosomal dominant AD. Minipig model of Alzheimer’s disease by CRISPR knockout of the causal gene SORL1 Young SORL1 het minipigs phenocopy a preclinical CSF biomarker profile of individuals with AD SORL1 haploinsufficiency causes enlarged endosomes similar to neuronal AD pathology A minipig model bridging the translational gap between AD mouse models and affected individuals
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Boddu PC, Gupta AK, Kim JS, Neugebauer KM, Waldman T, Pillai MM. Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase. Commun Biol 2021; 4:1184. [PMID: 34645977 PMCID: PMC8514589 DOI: 10.1038/s42003-021-02690-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/15/2021] [Indexed: 11/09/2022] Open
Abstract
Scalable isogenic models of cancer-associated mutations are critical to studying dysregulated gene function. Nonsynonymous mutations of splicing factors, which typically affect one allele, are common in many cancers, but paradoxically confer growth disadvantage to cell lines, making their generation and expansion challenging. Here, we combine AAV-intron trap, CRISPR/Cas9, and inducible Cre-recombinase systems to achieve >90% efficiency to introduce the oncogenic K700E mutation in SF3B1, a splicing factor commonly mutated in multiple cancers. The intron-trap design of AAV vector limits editing to one allele. CRISPR/Cas9-induced double stranded DNA breaks direct homologous recombination to the desired genomic locus. Inducible Cre-recombinase allows for the expansion of cells prior to loxp excision and expression of the mutant allele. Importantly, AAV or CRISPR/Cas9 alone results in much lower editing efficiency and the edited cells do not expand due to toxicity of SF3B1-K700E. Our approach can be readily adapted to generate scalable isogenic systems where mutant oncogenes confer a growth disadvantage.
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Affiliation(s)
- Prajwal C. Boddu
- grid.47100.320000000419368710Section of Hematology, Yale Cancer Center, Yale University School of Medicine, New Haven, CT USA
| | - Abhishek K. Gupta
- grid.47100.320000000419368710Section of Hematology, Yale Cancer Center, Yale University School of Medicine, New Haven, CT USA
| | - Jung-Sik Kim
- grid.213910.80000 0001 1955 1644Department of Oncology, Molecular Biology and Genetics, Lombardi Cancer Center, Georgetown University, Washington, DC USA
| | - Karla M. Neugebauer
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT USA
| | - Todd Waldman
- grid.213910.80000 0001 1955 1644Department of Oncology, Molecular Biology and Genetics, Lombardi Cancer Center, Georgetown University, Washington, DC USA
| | - Manoj M. Pillai
- grid.47100.320000000419368710Section of Hematology, Yale Cancer Center, Yale University School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Department of Pathology, Yale University School of Medicine, New Haven, CT USA
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Shola DTN, Yang C, Kewaldar VS, Kar P, Bustos V. New Additions to the CRISPR Toolbox: CRISPR- CLONInG and CRISPR- CLIP for Donor Construction in Genome Editing. CRISPR J 2021; 3:109-122. [PMID: 32315232 PMCID: PMC7194329 DOI: 10.1089/crispr.2019.0062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
CRISPR-Cas has proven to be the most versatile genetic tinkering system of our time, predominantly as a precision genome editing tool. Here, we demonstrate two additions to the repertoire of CRISPR's application for constructing donor DNA templates: CRISPR-CLONInG and CRISPR-CLIP. CRISPR-CLONInG (CRISPR-Cutting and Ligation Of Nucleic acid In vitro via Gibson) was devised to enable efficient cut-and-paste of multiple complex DNA fragments by using CRISPR-Cas9 as a digestion alternative with precision and exclusivity features, followed by joining the digested products via Gibson Assembly, to construct double-stranded DNA and adeno-associated virus (AAV) donor vectors rapidly without cloning scars. CRISPR-CLIP (CRISPR-Clipped Long ssDNA via Incising Plasmid) was devised as a DNA clipping tool to retrieve long single-stranded DNA (lssDNA) efficiently from plasmid, up to 3.5 kbase, which can be supplied as the donor template for creating genetically engineered mice via Easi-CRISPR. We utilized two different Cas types (Cpf1 and Cas9n) to induce two distinct incisions at the respective ends of the lssDNA cassette junctions on the plasmid, yielding three independent single-stranded DNA units of unique sizes eligible for strand separation, followed by target strand clip-out through gel extraction. The retrieval of the lssDNA donor circumvents involvements of restriction enzymes and DNA polymerase-based steps. Hence, it not only retains sequence fidelity but also carries virtually no restriction on sequence composition, further mitigating limitations on the current Easi-CRISPR method. With the add-on feature of universal DNA-tag sequences of Cpf1-Cas9 duo protospacer adjacent motif, CRISPR-CLIP can be facile and applicable to generate lssDNA templates for any genomic target of choice. Additionally, we demonstrate robust gene editing efficiencies in the neuroblastoma cell line, as well as in mice attained with the AAV and lssDNA donors constructed herein.
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Affiliation(s)
- Dorjee T N Shola
- CRISPR and Genome Editing Resource Center, The Rockefeller University, New York, New York, USA
| | - Chingwen Yang
- CRISPR and Genome Editing Resource Center, The Rockefeller University, New York, New York, USA
| | - Vhy-Shelta Kewaldar
- CRISPR and Genome Editing Resource Center, The Rockefeller University, New York, New York, USA
| | - Pradip Kar
- CRISPR and Genome Editing Resource Center, The Rockefeller University, New York, New York, USA
| | - Victor Bustos
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, New York, USA
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Baxley RM, Leung W, Schmit MM, Matson JP, Yin L, Oram MK, Wang L, Taylor J, Hedberg J, Rogers CB, Harvey AJ, Basu D, Taylor JC, Pagnamenta AT, Dreau H, Craft J, Ormondroyd E, Watkins H, Hendrickson EA, Mace EM, Orange JS, Aihara H, Stewart GS, Blair E, Cook JG, Bielinsky AK. Bi-allelic MCM10 variants associated with immune dysfunction and cardiomyopathy cause telomere shortening. Nat Commun 2021; 12:1626. [PMID: 33712616 PMCID: PMC7955084 DOI: 10.1038/s41467-021-21878-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
Minichromosome maintenance protein 10 (MCM10) is essential for eukaryotic DNA replication. Here, we describe compound heterozygous MCM10 variants in patients with distinctive, but overlapping, clinical phenotypes: natural killer (NK) cell deficiency (NKD) and restrictive cardiomyopathy (RCM) with hypoplasia of the spleen and thymus. To understand the mechanism of MCM10-associated disease, we modeled these variants in human cell lines. MCM10 deficiency causes chronic replication stress that reduces cell viability due to increased genomic instability and telomere erosion. Our data suggest that loss of MCM10 function constrains telomerase activity by accumulating abnormal replication fork structures enriched with single-stranded DNA. Terminally-arrested replication forks in MCM10-deficient cells require endonucleolytic processing by MUS81, as MCM10:MUS81 double mutants display decreased viability and accelerated telomere shortening. We propose that these bi-allelic variants in MCM10 predispose specific cardiac and immune cell lineages to prematurely arrest during differentiation, causing the clinical phenotypes observed in both NKD and RCM patients.
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Affiliation(s)
- Ryan M Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wendy Leung
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Megan M Schmit
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jacob Peter Matson
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Lulu Yin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Marissa K Oram
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Liangjun Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - John Taylor
- Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jack Hedberg
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Colette B Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Adam J Harvey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Debashree Basu
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jenny C Taylor
- Wellcome Centre Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Oxford, OX3 7BN, UK
| | - Alistair T Pagnamenta
- Wellcome Centre Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Oxford, OX3 7BN, UK
| | - Helene Dreau
- Department of Haematology, University of Oxford, Oxford, OX3 7BN, UK
| | - Jude Craft
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Jordan S Orange
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
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Stroik S, Kurtz K, Hendrickson EA. CtIP is essential for telomere replication. Nucleic Acids Res 2019; 47:8927-8940. [PMID: 31378812 PMCID: PMC6755089 DOI: 10.1093/nar/gkz652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/08/2019] [Accepted: 07/16/2019] [Indexed: 01/10/2023] Open
Abstract
The maintenance of telomere length is critical to longevity and survival. Specifically, the failure to properly replicate, resect, and/or form appropriate telomeric structures drives telomere shortening and, in turn, genomic instability. The endonuclease CtIP is a DNA repair protein that is well-known to promote genome stability through the resection of endogenous DNA double-stranded breaks. Here, we describe a novel role for CtIP. We show that in the absence of CtIP, human telomeres shorten rapidly to non-viable lengths. This telomere dysfunction results in an accumulation of fusions, breaks, and frank telomere loss. Additionally, CtIP suppresses the generation of circular, extrachromosomal telomeric DNA. These latter structures appear to arise from arrested DNA replication forks that accumulate in the absence of CtIP. Hence, CtIP is required for faithful replication through telomeres via its roles at stalled replication tracts. Our findings demonstrate a new role for CtIP as a protector of human telomere integrity.
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Affiliation(s)
- Susanna Stroik
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Kevin Kurtz
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
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Ruis B, Molan A, Takasugi T, Hendrickson EA. Absence of XRCC4 and its paralogs in human cells reveal differences in outcomes for DNA repair and V(D)J recombination. DNA Repair (Amst) 2019; 85:102738. [PMID: 31731258 DOI: 10.1016/j.dnarep.2019.102738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023]
Abstract
The repair of DNA double-stranded breaks (DSBs) is an essential function performed by the Classical Non-Homologous End-Joining (C-NHEJ) pathway in higher eukaryotes. C-NHEJ, in fact, does double duty as it is also required for the repair of the intermediates formed during lymphoid B- and T-cell recombination. Consequently, the failure to properly repair DSBs leads to both genomic instability and immunodeficiency. A critical DSB protein required for C-NHEJ is the DNA Ligase IV (LIGIV) accessory factor, X-Ray Cross Complementing 4 (XRCC4). XRCC4 is believed to stabilize LIGIV, participate in LIGIV activation, and to help tether the broken DSB ends together. XRCC4's role in these processes has been muddied by the identification of two additional XRCC4 paralogs, XRCC4-Like Factor (XLF), and Paralog of XRCC4 and XLF (PAXX). The roles that these paralogs play in C-NHEJ is partially understood, but, in turn, has itself been obscured by species-specific differences observed in the absence of one or the other paralogs. In order to investigate the role(s) that XRCC4 may play, with or without XLF and/or PAXX, in lymphoid variable(diversity)joining [V(D)J] recombination as well as in DNA DSB repair in human somatic cells, we utilized gene targeting to inactivate the XRCC4 gene in both parental and XLF- HCT116 cells and then inactivated PAXX in those same cell lines. The loss of XRCC4 expression by itself led, as anticipated, to increased sensitivity to DNA damaging agents as well as an increased dependence on microhomology-mediated DNA repair whether in the context of DSB repair or during V(D)J recombination. The additional loss of XLF in these cell lines sensitized the cells even more whereas the presence or absence of PAXX was scarcely negligible. These studies demonstrate that, of the three LIG4 accessory factor paralogs, the absence of XRCC4 influences DNA repair and recombination the most in human cells.
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Affiliation(s)
- Brian Ruis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Amy Molan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Taylor Takasugi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States.
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Porter SN, Levine RM, Pruett-Miller SM. A Practical Guide to Genome Editing Using Targeted Nuclease Technologies. Compr Physiol 2019; 9:665-714. [PMID: 30873595 DOI: 10.1002/cphy.c180022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome engineering using programmable nucleases is a rapidly evolving technique that enables precise genetic manipulations within complex genomes. Although this technology first surfaced with the creation of meganucleases, zinc finger nucleases, and transcription activator-like effector nucleases, CRISPR-Cas9 has been the most widely adopted platform because of its ease of use. This comprehensive review presents a basic overview of genome engineering and discusses the major technological advances in the field. In addition to nucleases, we discuss CRISPR-derived base editors and epigenetic modifiers. We also delve into practical applications of these tools, including creating custom-edited cell and animal models as well as performing genetic screens. Finally, we discuss the potential for therapeutic applications and ethical considerations related to employing this technology in humans. © 2019 American Physiological Society. Compr Physiol 9:665-714, 2019.
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Affiliation(s)
- Shaina N Porter
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rachel M Levine
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Heczkova M, Machackova E, Macinga P, Gallmeier E, Cahova M, Spicak J, Jirsa M, Foretova L, Hucl T. Functional evaluation of variants of unknown significance in the BRCA2 gene identified in genetic testing. Cancer Biol Ther 2019; 20:633-641. [PMID: 30638113 DOI: 10.1080/15384047.2018.1550566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Heterozygous germline BRCA2 mutations predispose to breast, ovarian, pancreatic and other types of cancer. The presence of a pathogenic mutation in patients or their family members warrants close surveillance or prophylactic surgery. Besides clearly pathogenic mutations, variants leading only to a single amino acid substitution are often identified. The influence of such variants on cancer risk is often unknown, making their presence a major clinical problem. When genetic methods are insufficient to classify these variants, functional assays with various cellular models are performed. We developed and applied a new syngeneic model of human cancer cells to test all variants of unknown significance in exon 18 identified by genetic testing of high-risk cancer patients in the Czech Republic, via introduction of constructs containing each of these variants into the wild-type allele of BRCA2-heterozygous DLD1 cells (BRCA2wt/Δex11). We found unaffected DNA repair function of BRCA2 in cell lines BRCA27997G>C/Δex11, BRCA28111C>T/Δex11, BRCA28149G>T/Δex11, BRCA28182G>A/Δex11, and BRCA28182G>T/Δex11, whereas the cell line BRCA28168A>G/Δex11 and the nonsense mutation carrying line BRCA28305G>T/Δex11 did affect protein function. Targeting the BRCA2 wild-type allele with a construct carrying the variant c.7988A> G resulted in incorporation exclusively into the already defective allele in all viable clones, strongly suggesting a detrimental phenotype. Our model thus offers a valuable tool for the functional evaluation of unclassified variants in the BRCA2 gene and provides a stable and distributable cellular resource for further research.
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Affiliation(s)
- Marie Heczkova
- a Center for Experimental Medicine , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
| | - Eva Machackova
- b Department of Cancer Epidemiology and Genetics , Masaryk Memorial Cancer Institute , Brno , Czech Republic
| | - Peter Macinga
- c Department of Gastroenterology and Hepatology , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
| | - Eike Gallmeier
- d Department of Internal Medicine , Philipps University of Marburg , Marburg , Germany
| | - Monika Cahova
- a Center for Experimental Medicine , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
| | - Julius Spicak
- c Department of Gastroenterology and Hepatology , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
| | - Milan Jirsa
- a Center for Experimental Medicine , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
| | - Lenka Foretova
- b Department of Cancer Epidemiology and Genetics , Masaryk Memorial Cancer Institute , Brno , Czech Republic
| | - Tomas Hucl
- a Center for Experimental Medicine , Institute of Clinical and Experimental Medicine , Prague , Czech Republic.,c Department of Gastroenterology and Hepatology , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
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Xi Y, Niu J, Li D, He J, Qin L, Peng X. Mixed lineage kinase-4 promotes gastric carcinoma tumorigenesis through suppression of the c-Jun N-terminal kinase signaling pathway. Exp Ther Med 2018; 16:3317-3324. [PMID: 30233678 PMCID: PMC6143876 DOI: 10.3892/etm.2018.6618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/21/2017] [Indexed: 01/08/2023] Open
Abstract
Mixed lineage kinase-4 (MLK-4) is an important member of the mixed-lineage family of kinases that regulates the extracellular signal-regulated kinases and c-Jun N-terminal kinase (JNK) signaling pathways. The functions and mechanisms of MLK-4 in cancer initiation and progression have not been well understood. The present study investigated the expression, function and regulatory mechanism of MLK-4 in gastric carcinoma cells. Biochemical data indicated that normal MLK-4 was downregulated, which exerted dominant negative effects on gastric carcinoma cell viability, migration and invasion. The experimental data demonstrated that MLK-4 supplement abrogated activity of these mutants and induced inhibitory effects on gastric carcinoma cell viabilty, migration and invasion in vitro and in vivo. In addition, to determine the regulatory mechanism of MLK-4, its signaling pathway was assessed in gastric carcinoma cancer cells by regulating MLK-4. The present observations indicated that restoring MLK-4 activity by supplemental MLK-4 reduced gastric carcinoma cell colony formation in vitro and suppressed tumor viability, migration and invasion in vivo. The results of the present study indicated that MLK-4 may be a potential protein for targeting gastric carcinoma by suppressing kinases, which may lead to reduction of JNK signaling and enhance therapeutic efficacy in gastric carcinoma.
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Affiliation(s)
- Yu Xi
- Department of General Surgery, Tongji Hospital, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
| | - Jianhua Niu
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
| | - Dongmei Li
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
| | - Jiagen He
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
| | - Le Qin
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
| | - Xinyu Peng
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
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Galbraith MD, Andrysik Z, Pandey A, Hoh M, Bonner EA, Hill AA, Sullivan KD, Espinosa JM. CDK8 Kinase Activity Promotes Glycolysis. Cell Rep 2018; 21:1495-1506. [PMID: 29117556 DOI: 10.1016/j.celrep.2017.10.058] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/21/2017] [Accepted: 10/13/2017] [Indexed: 12/27/2022] Open
Abstract
Aerobic glycolysis, also known as the Warburg effect, is a hallmark of cancerous tissues. Despite its importance in cancer development, our understanding of mechanisms driving this form of metabolic reprogramming is incomplete. We report here an analysis of colorectal cancer cells engineered to carry a single point mutation in the active site of the Mediator-associated kinase CDK8, creating hypomorphic alleles sensitive to bulky ATP analogs. Transcriptome analysis revealed that CDK8 kinase activity is required for the expression of many components of the glycolytic cascade. CDK8 inhibition impairs glucose transporter expression, glucose uptake, glycolytic capacity and reserve, as well as cell proliferation and anchorage-independent growth, both in normoxia and hypoxia. Importantly, CDK8 impairment sensitizes cells to pharmacological glycolysis inhibition, a result reproduced with Senexin A, a dual inhibitor of CDK8/CDK19. Altogether, these results contribute to our understanding of CDK8 as an oncogene, and they justify investigations to target CDK8 in highly glycolytic tumors.
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Affiliation(s)
- Matthew D Galbraith
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Zdenek Andrysik
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ahwan Pandey
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Maria Hoh
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Elizabeth A Bonner
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Amanda A Hill
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kelly D Sullivan
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joaquín M Espinosa
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309, USA.
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11
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Urnov FD. Genome Editing B.C. (Before CRISPR): Lasting Lessons from the “Old Testament”. CRISPR J 2018; 1:34-46. [DOI: 10.1089/crispr.2018.29007.fyu] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Fyodor D. Urnov
- Altius Institute for Biomedical Sciences, Seattle, Washington
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12
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Thompson EL, Yeo JE, Lee EA, Kan Y, Raghunandan M, Wiek C, Hanenberg H, Schärer OD, Hendrickson EA, Sobeck A. FANCI and FANCD2 have common as well as independent functions during the cellular replication stress response. Nucleic Acids Res 2017; 45:11837-11857. [PMID: 29059323 PMCID: PMC5714191 DOI: 10.1093/nar/gkx847] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 09/16/2017] [Indexed: 11/18/2022] Open
Abstract
Fanconi anemia (FA) is an inherited cancer predisposition syndrome characterized by cellular hypersensitivity to DNA interstrand crosslinks (ICLs). To repair these lesions, the FA proteins act in a linear hierarchy: following ICL detection on chromatin, the FA core complex monoubiquitinates and recruits the central FANCI and FANCD2 proteins that subsequently coordinate ICL removal and repair of the ensuing DNA double-stranded break by homology-dependent repair (HDR). FANCD2 also functions during the replication stress response by mediating the restart of temporarily stalled replication forks thereby suppressing the firing of new replication origins. To address if FANCI is also involved in these FANCD2-dependent mechanisms, we generated isogenic FANCI-, FANCD2- and FANCI:FANCD2 double-null cells. We show that FANCI and FANCD2 are partially independent regarding their protein stability, nuclear localization and chromatin recruitment and contribute independently to cellular proliferation. Simultaneously, FANCD2—but not FANCI—plays a major role in HDR-mediated replication restart and in suppressing new origin firing. Consistent with this observation, deficiencies in HDR-mediated DNA DSB repair can be overcome by stabilizing RAD51 filament formation in cells lacking functional FANCD2. We propose that FANCI and FANCD2 have partially non-overlapping and possibly even opposing roles during the replication stress response.
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Affiliation(s)
- Elizabeth L Thompson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jung E Yeo
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Eun-A Lee
- Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Yinan Kan
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Maya Raghunandan
- Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Constanze Wiek
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, 40225 Düsseldorf, Germany.,Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Orlando D Schärer
- Center for Genomic Integrity (CGI), Institute for Basic Science (IBS), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alexandra Sobeck
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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Shim J, Poulsen CB, Hagensen MK, Larsen T, Heegaard PM, Christoffersen C, Bolund L, Schmidt M, Liu Y, Li J, Li R, Callesen H, Bentzon JF, Sørensen CB. Apolipoprotein E Deficiency Increases Remnant Lipoproteins and Accelerates Progressive Atherosclerosis, But Not Xanthoma Formation, in Gene-Modified Minipigs. ACTA ACUST UNITED AC 2017; 2:591-600. [PMID: 30062172 PMCID: PMC6058916 DOI: 10.1016/j.jacbts.2017.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 06/01/2017] [Accepted: 06/08/2017] [Indexed: 01/21/2023]
Abstract
APOE-deficient Yucatan minipigs were created by recombinant adeno-associated virus mediated gene targeting in porcine fibroblasts followed by somatic cell nuclear transfer. APOE−/− minipigs displayed increased plasma cholesterol and accumulation of APOB48-containing chylomicron remnants on low fat-diet, which was significantly accentuated upon feeding a high-fat, high-cholesterol diet. APOE−/− minipigs showed accelerated progressive atherosclerosis but not xanthoma formation indicating that remnant lipoproteinemia does not induce early lesions but is atherogenic in pre-existing atherosclerosis.
Deficiency of apolipoprotein E (APOE) causes familial dysbetalipoproteinemia in humans resulting in a higher risk of atherosclerotic disease. In mice, APOE deficiency results in a severe atherosclerosis phenotype, but it is unknown to what extent this is unique to mice. In this study, APOE was targeted in Yucatan minipigs. APOE−/− minipigs displayed increased plasma cholesterol and accumulation of apolipoprotein B-48–containing chylomicron remnants on low-fat diet, which was significantly accentuated upon feeding a high-fat, high-cholesterol diet. APOE−/− minipigs displayed accelerated progressive atherosclerosis but not xanthoma formation. This indicates that remnant lipoproteinemia does not induce early lesions but is atherogenic in pre-existing atherosclerosis.
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Key Words
- APOB, apolipoprotein B
- APOE, apolipoprotein E
- HFHC, high-fat high-cholesterol
- IDL, intermediate-density lipoprotein
- LAD, left anterior descending (coronary artery)
- LDL, low-density lipoprotein
- LDLR, low-density lipoprotein receptor
- LF, low-fat
- Neo, neomycin
- SMC, smooth muscle cell
- VLDL, very-low-density lipoprotein
- apolipoprotein E
- atherosclerosis
- cDNA, complementary DNA
- pig
- rAAV, recombinant adeno-associated virus
- remnant cholesterol dysbetalipoproteinemia
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Affiliation(s)
- Jeong Shim
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
| | - Christian Bo Poulsen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
| | - Mette K. Hagensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
| | - Torben Larsen
- Department of Animal Science, Aarhus University, Aarhus, Denmark
| | - Peter M.H. Heegaard
- National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Lars Bolund
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Mette Schmidt
- Section for Veterinary Reproduction and Obstetrics, Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ying Liu
- Department of Animal Science, Aarhus University, Aarhus, Denmark
| | - Juan Li
- Department of Animal Science, Aarhus University, Aarhus, Denmark
| | - Rong Li
- Department of Animal Science, Aarhus University, Aarhus, Denmark
| | - Henrik Callesen
- Department of Animal Science, Aarhus University, Aarhus, Denmark
| | - Jacob F. Bentzon
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Address for correspondence: Dr. Jacob F. Bentzon, CNIC, C/Melchor Fernández Almagro, 28029 Madrid, Spain.
| | - Charlotte B. Sørensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
- Dr. Charlotte B. Sørensen, Aarhus University, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark.
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14
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Choudhury SR, Hudry E, Maguire CA, Sena-Esteves M, Breakefield XO, Grandi P. Viral vectors for therapy of neurologic diseases. Neuropharmacology 2017; 120:63-80. [PMID: 26905292 PMCID: PMC5929167 DOI: 10.1016/j.neuropharm.2016.02.013] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/07/2016] [Accepted: 02/15/2016] [Indexed: 12/21/2022]
Abstract
Neurological disorders - disorders of the brain, spine and associated nerves - are a leading contributor to global disease burden with a shockingly large associated economic cost. Various treatment approaches - pharmaceutical medication, device-based therapy, physiotherapy, surgical intervention, among others - have been explored to alleviate the resulting extent of human suffering. In recent years, gene therapy using viral vectors - encoding a therapeutic gene or inhibitory RNA into a "gutted" viral capsid and supplying it to the nervous system - has emerged as a clinically viable option for therapy of brain disorders. In this Review, we provide an overview of the current state and advances in the field of viral vector-mediated gene therapy for neurological disorders. Vector tools and delivery methods have evolved considerably over recent years, with the goal of providing greater and safer genetic access to the central nervous system. Better etiological understanding of brain disorders has concurrently led to identification of improved therapeutic targets. We focus on the vector technology, as well as preclinical and clinical progress made thus far for brain cancer and various neurodegenerative and neurometabolic disorders, and point out the challenges and limitations that accompany this new medical modality. Finally, we explore the directions that neurological gene therapy is likely to evolve towards in the future. This article is part of the Special Issue entitled "Beyond small molecules for neurological disorders".
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Affiliation(s)
- Sourav R Choudhury
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Eloise Hudry
- Alzheimer's Disease Research Unit, Harvard Medical School & Massachusetts General Hospital, Charlestown, MA 02129, USA.
| | - Casey A Maguire
- Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and NeuroDiscovery Center, Harvard Medical School, Boston, MA 02114, USA.
| | - Miguel Sena-Esteves
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Xandra O Breakefield
- Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and NeuroDiscovery Center, Harvard Medical School, Boston, MA 02114, USA.
| | - Paola Grandi
- Department of Neurological Surgery, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15219, USA.
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15
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Kan Y, Batada NN, Hendrickson EA. Human somatic cells deficient for RAD52 are impaired for viral integration and compromised for most aspects of homology-directed repair. DNA Repair (Amst) 2017; 55:64-75. [PMID: 28549257 DOI: 10.1016/j.dnarep.2017.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/25/2017] [Accepted: 04/27/2017] [Indexed: 01/28/2023]
Abstract
Homology-directed repair (HDR) maintains genomic integrity by eliminating lesions such as DNA double-strand breaks (DSBs), interstrand crosslinks (ICLs) and stalled replication forks and thus a deficiency in HDR is associated with genomic instability and cancer predisposition. The mechanism of HDR is best understood and most rigorously characterized in yeast. The inactivation of the fungal radiation sensitive 52 (RAD52) gene, which has both recombination mediator and single-strand annealing (SSA) activities in vitro, leads to severe HDR defects in vivo. Confusingly, however, the inactivation of murine and chicken RAD52 genes resulted in mouse and chicken cells, respectively, that were largely aphenotypic. To clarify this issue, we have generated RAD52 knockout human cell lines. Human RAD52-null cells retain a significant level of SSA activity demonstrating perforce that additional SSA-like activities must exist in human cells. Moreover, we confirmed that the SSA activity associated with RAD52 is involved in, but not absolutely required for, most HDR subpathways. Specifically, a deficiency in RAD52 impaired the repair of DNA DSBs and intriguingly decreased the random integration of recombinant adeno-associated virus (rAAV). Finally, an analysis of pan-cancer genome data from The Cancer Genome Atlas (TCGA) revealed an association between aberrant levels of RAD52 expression and poor overall survival in multiple cancers. In toto, our work demonstrates that RAD52 contributes to the maintenance of genome stability and tumor suppression in human cells.
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Affiliation(s)
- Yinan Kan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States
| | - Nizar N Batada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Eric A Hendrickson
- BMBB Department, University of Minnesota Medical School, 6-155 Jackson Hall, 321 Church St., SE., Minneapolis, MN 55455, United States.
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16
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Hsu CW, Huang R, Khuc T, Shou D, Bullock J, Grooby S, Griffin S, Zou C, Little A, Astley H, Xia M. Identification of approved and investigational drugs that inhibit hypoxia-inducible factor-1 signaling. Oncotarget 2016; 7:8172-83. [PMID: 26882567 PMCID: PMC4884984 DOI: 10.18632/oncotarget.6995] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/01/2016] [Indexed: 11/25/2022] Open
Abstract
One of the requirements for tumor development is blood supply, most often driven by hypoxia-induced angiogenesis. Hypoxia induces the stabilization of hypoxia-inducible factor-1 alpha (HIF-1α), which induces expression of an angiogenic factor, vascular endothelial growth factor (VEGF). The purpose of this study is to validate a new screening platform combined with orthogonal assays to rapidly identify HIF-1 inhibitors and to evaluate the effectiveness of approved drugs on modulating HIF-1 signaling. We generated an endogenous HIF-1α-NanoLuc luciferase reporter allele in the human HCT116 colon cancer cell line using genome editing and screened a panel of small interfering RNAs (siRNAs) to 960 druggable targets and approximately 2,500 drugs on a quantitative high-throughput screening (qHTS) platform. Selected compounds were further investigated with secondary assays to confirm their anti-HIF activity and to study their mode of action. The qHTS assay identified over 300 drugs that inhibited HIF-1α-NanoLuc expression. The siRNA screening results supported the effectiveness of several target-specific inhibitors. Moreover, the identified HIF-1 inhibitors, such as mycophenolate mofetil, niclosamide, and trametinib, were able to suppress cancer cell proliferation and angiogenesis. Our study indicates that blocking the mitogen-activated protein kinase (MAPK) and phosphoinositol 3-kinase (PI3K) pathways effectively inhibits hypoxia-induced HIF-1α accumulation and HIF-1α transactivation and that proteasome inhibitors induce accumulation and decrease transcriptional activity of HIF-1α. These findings underline the importance of developing a battery of robust assay platforms and confirmation studies that focus on endogenous protein targets so that only relevant and reliable data will be taken into pre-clinical and clinical studies.
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Affiliation(s)
- Chia-Wen Hsu
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Ruili Huang
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Thai Khuc
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - David Shou
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Sue Griffin
- Horizon Discovery Ltd., Waterbeach, Cambridge, UK
| | - Chaozhong Zou
- American Type Culture Collection, Gaithersburg, MD, USA
| | | | - Holly Astley
- Horizon Discovery Ltd., Waterbeach, Cambridge, UK
| | - Menghang Xia
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
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17
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Bauer M, Cubizolles F, Schmidt A, Nigg EA. Quantitative analysis of human centrosome architecture by targeted proteomics and fluorescence imaging. EMBO J 2016; 35:2152-2166. [PMID: 27539480 PMCID: PMC5048348 DOI: 10.15252/embj.201694462] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/25/2016] [Indexed: 12/14/2022] Open
Abstract
Centrioles are essential for the formation of centrosomes and cilia. While numerical and/or structural centrosomes aberrations are implicated in cancer, mutations in centriolar and centrosomal proteins are genetically linked to ciliopathies, microcephaly, and dwarfism. The evolutionarily conserved mechanisms underlying centrosome biogenesis are centered on a set of key proteins, including Plk4, Sas-6, and STIL, whose exact levels are critical to ensure accurate reproduction of centrioles during cell cycle progression. However, neither the intracellular levels of centrosomal proteins nor their stoichiometry within centrosomes is presently known. Here, we have used two complementary approaches, targeted proteomics and EGFP-tagging of centrosomal proteins at endogenous loci, to measure protein abundance in cultured human cells and purified centrosomes. Our results provide a first assessment of the absolute and relative amounts of major components of the human centrosome. Specifically, they predict that human centriolar cartwheels comprise up to 16 stacked hubs and 1 molecule of STIL for every dimer of Sas-6. This type of quantitative information will help guide future studies of the molecular basis of centrosome assembly and function.
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Affiliation(s)
- Manuel Bauer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Erich A Nigg
- Biozentrum, University of Basel, Basel, Switzerland
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18
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Abstract
The unlimited proliferation of cancer cells requires a mechanism to prevent telomere shortening. Alternative Lengthening of Telomeres (ALT) is an homologous recombination-mediated mechanism of telomere elongation used in tumors, including osteosarcomas, soft tissue sarcoma subtypes, and glial brain tumors. Mutations in the ATRX/DAXX chromatin remodeling complex have been reported in tumors and cell lines that use the ALT mechanism, suggesting that ATRX may be an ALT repressor. We show here that knockout or knockdown of ATRX in mortal cells or immortal telomerase-positive cells is insufficient to activate ALT. Notably, however, in SV40-transformed mortal fibroblasts ATRX loss results in either a significant increase in the proportion of cell lines activating ALT (instead of telomerase) or in a significant decrease in the time prior to ALT activation. These data indicate that loss of ATRX function cooperates with one or more as-yet unidentified genetic or epigenetic alterations to activate ALT. Moreover, transient ATRX expression in ALT-positive/ATRX-negative cells represses ALT activity. These data provide the first direct, functional evidence that ATRX represses ALT.
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19
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Yi F, Danko T, Botelho SC, Patzke C, Pak C, Wernig M, Südhof TC. Autism-associated SHANK3 haploinsufficiency causes Ih channelopathy in human neurons. Science 2016; 352:aaf2669. [PMID: 26966193 DOI: 10.1126/science.aaf2669] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/26/2016] [Indexed: 12/13/2022]
Abstract
Heterozygous SHANK3 mutations are associated with idiopathic autism and Phelan-McDermid syndrome. SHANK3 is a ubiquitously expressed scaffolding protein that is enriched in postsynaptic excitatory synapses. Here, we used engineered conditional mutations in human neurons and found that heterozygous and homozygous SHANK3 mutations severely and specifically impaired hyperpolarization-activated cation (Ih) channels. SHANK3 mutations caused alterations in neuronal morphology and synaptic connectivity; chronic pharmacological blockage of Ih channels reproduced these phenotypes, suggesting that they may be secondary to Ih-channel impairment. Moreover, mouse Shank3-deficient neurons also exhibited severe decreases in Ih currents. SHANK3 protein interacted with hyperpolarization-activated cyclic nucleotide-gated channel proteins (HCN proteins) that form Ih channels, indicating that SHANK3 functions to organize HCN channels. Our data suggest that SHANK3 mutations predispose to autism, at least partially, by inducing an Ih channelopathy that may be amenable to pharmacological intervention.
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Affiliation(s)
- Fei Yi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Tamas Danko
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA. Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA. Department of Pathology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Salome Calado Botelho
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Christopher Patzke
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - ChangHui Pak
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA. Department of Pathology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA. Howard Hughes Medical Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA.
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20
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Karnan S, Ota A, Konishi Y, Wahiduzzaman M, Tsuzuki S, Hosokawa Y, Konishi H. Efficient AAV-mediated Gene Targeting Using 2A-based Promoter-trap System. Bio Protoc 2016. [DOI: 10.21769/bioprotoc.2058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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21
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Vandemoortele G, Gevaert K, Eyckerman S. Proteomics in the genome engineering era. Proteomics 2015; 16:177-87. [DOI: 10.1002/pmic.201500262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/22/2015] [Accepted: 10/15/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Giel Vandemoortele
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
| | - Sven Eyckerman
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
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22
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Ghosh S, Bhunia AK, Paun BC, Gilbert SF, Dhru U, Patel K, Kern SE. Genome annotation by shotgun inactivation of a native gene in hemizygous cells: application to BRCA2 with implication of hypomorphic variants. Hum Mutat 2015; 36:260-9. [PMID: 25451944 DOI: 10.1002/humu.22736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 11/19/2014] [Indexed: 12/30/2022]
Abstract
The greatest interpretive challenge of modern medicine may be to functionally annotate the vast variation of human genomes. Demonstrating a proposed approach, we created a library of BRCA2 exon 27 shotgun-mutant plasmids including solitary and multiplex mutations to generate human knockin clones using homologous recombination. This 55-mutation, 13-clone syngeneic variance library (SyVaL) comprised severely affected clones having early-stop nonsense mutations, functionally hypomorphic clones having multiple missense mutations emphasizing the potential to identify and assess hypomorphic mutations in novel proteomic and epidemiologic studies, and neutral clones having multiple missense mutations. Efficient coverage of nonessential amino acids was provided by mutation multiplexing. Severe mutations were distinguished from hypomorphic or neutral changes by chemosensitivity assays (hypersensitivity to mitomycin C and acetaldehyde), by analysis of RAD51 focus formation, and by mitotic multipolarity. A multiplex unbiased approach of generating all-human SyVaLs in medically important genes, with random mutations in native genes, would provide databases of variants that could be functionally annotated without concerns arising from exogenous cDNA constructs or interspecies interactions, as a basis for subsequent proteomic domain mapping or clinical calibration if desired. Such gene-irrelevant approaches could be scaled up for multiple genes of clinical interest, providing distributable cellular libraries linked to public-shared functional databases.
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Affiliation(s)
- Soma Ghosh
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, 21287
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23
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Castella M, Jacquemont C, Thompson EL, Yeo JE, Cheung RS, Huang JW, Sobeck A, Hendrickson EA, Taniguchi T. FANCI Regulates Recruitment of the FA Core Complex at Sites of DNA Damage Independently of FANCD2. PLoS Genet 2015; 11:e1005563. [PMID: 26430909 PMCID: PMC4592014 DOI: 10.1371/journal.pgen.1005563] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/10/2015] [Indexed: 12/31/2022] Open
Abstract
The Fanconi anemia (FA)-BRCA pathway mediates repair of DNA interstrand crosslinks. The FA core complex, a multi-subunit ubiquitin ligase, participates in the detection of DNA lesions and monoubiquitinates two downstream FA proteins, FANCD2 and FANCI (or the ID complex). However, the regulation of the FA core complex itself is poorly understood. Here we show that the FA core complex proteins are recruited to sites of DNA damage and form nuclear foci in S and G2 phases of the cell cycle. ATR kinase activity, an intact FA core complex and FANCM-FAAP24 were crucial for this recruitment. Surprisingly, FANCI, but not its partner FANCD2, was needed for efficient FA core complex foci formation. Monoubiquitination or ATR-dependent phosphorylation of FANCI were not required for the FA core complex recruitment, but FANCI deubiquitination by USP1 was. Additionally, BRCA1 was required for efficient FA core complex foci formation. These findings indicate that FANCI functions upstream of FA core complex recruitment independently of FANCD2, and alter the current view of the FA-BRCA pathway. Fanconi anemia is a genetic disease characterized by bone marrow failure, congenital malformations and cancer predisposition. Cells derived from Fanconi anemia patients have a dysfunctional FA-BRCA pathway and are deficient in the repair of a specific form of DNA damage, DNA interstrand-crosslinks, that are induced by certain chemotherapeutic drugs. Therefore, the study of FA-BRCA pathway regulation is essential for developing new treatments for Fanconi anemia patients and cancer patients in general. One of the first steps in the pathway is the detection of DNA lesions by the FA core complex. We have optimized a method to visualize the recruitment of the FA core complex to sites of DNA damage and, for the first time, explored how this process occurs. We have uncovered several factors that are required for this recruitment. Among them is a FA core complex substrate, FANCI. We report that non-phosphorylated FANCI, previously believed to be an inactive form, has an important role in the recruitment of the FA core complex and DNA interstrand-crosslink repair. Our findings change the current view of the FA-BRCA pathway and have implications for potential clinical strategies aimed at activating or inhibiting the FA-BRCA pathway.
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Affiliation(s)
- Maria Castella
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Celine Jacquemont
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Elizabeth L. Thompson
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Jung Eun Yeo
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Ronald S. Cheung
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jen-Wei Huang
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Alexandra Sobeck
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Eric A. Hendrickson
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Toshiyasu Taniguchi
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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Genome Engineering Using Adeno-associated Virus: Basic and Clinical Research Applications. Mol Ther 2015; 24:458-64. [PMID: 26373345 DOI: 10.1038/mt.2015.151] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 07/21/2015] [Indexed: 12/18/2022] Open
Abstract
In addition to their broad potential for therapeutic gene delivery, adeno-associated virus (AAV) vectors possess the innate ability to stimulate homologous recombination in mammalian cells at high efficiencies. This process--referred to as AAV-mediated gene targeting--has enabled the introduction of a diverse array of genomic modifications both in vitro and in vivo. With the recent emergence of targeted nucleases, AAV-mediated genome engineering is poised for clinical translation. Here, we review key properties of AAV vectors that underscore its unique utility in genome editing. We highlight the broad range of genome engineering applications facilitated by this technology and discuss the strong potential for unifying AAV with targeted nucleases for next-generation gene therapy.
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Pak C, Danko T, Zhang Y, Aoto J, Anderson G, Maxeiner S, Yi F, Wernig M, Südhof TC. Human Neuropsychiatric Disease Modeling using Conditional Deletion Reveals Synaptic Transmission Defects Caused by Heterozygous Mutations in NRXN1. Cell Stem Cell 2015; 17:316-28. [PMID: 26279266 DOI: 10.1016/j.stem.2015.07.017] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 03/23/2015] [Accepted: 07/22/2015] [Indexed: 10/23/2022]
Abstract
Heterozygous mutations of the NRXN1 gene, which encodes the presynaptic cell-adhesion molecule neurexin-1, were repeatedly associated with autism and schizophrenia. However, diverse clinical presentations of NRXN1 mutations in patients raise the question of whether heterozygous NRXN1 mutations alone directly impair synaptic function. To address this question under conditions that precisely control for genetic background, we generated human ESCs with different heterozygous conditional NRXN1 mutations and analyzed two different types of isogenic control and NRXN1 mutant neurons derived from these ESCs. Both heterozygous NRXN1 mutations selectively impaired neurotransmitter release in human neurons without changing neuronal differentiation or synapse formation. Moreover, both NRXN1 mutations increased the levels of CASK, a critical synaptic scaffolding protein that binds to neurexin-1. Our results show that, unexpectedly, heterozygous inactivation of NRXN1 directly impairs synaptic function in human neurons, and they illustrate the value of this conditional deletion approach for studying the functional effects of disease-associated mutations.
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Affiliation(s)
- ChangHui Pak
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Tamas Danko
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Yingsha Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Jason Aoto
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Garret Anderson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Stephan Maxeiner
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Fei Yi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA.
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Large-scale production of lentiviral vector in a closed system hollow fiber bioreactor. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2015; 2:15020. [PMID: 26151065 PMCID: PMC4470365 DOI: 10.1038/mtm.2015.20] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/07/2015] [Accepted: 04/16/2015] [Indexed: 12/20/2022]
Abstract
Lentiviral vectors are widely used in the field of gene therapy as an effective method for permanent gene delivery. While current methods of producing small scale vector batches for research purposes depend largely on culture flasks, the emergence and popularity of lentiviral vectors in translational, preclinical and clinical research has demanded their production on a much larger scale, a task that can be difficult to manage with the numbers of producer cell culture flasks required for large volumes of vector. To generate a large scale, partially closed system method for the manufacturing of clinical grade lentiviral vector suitable for the generation of induced pluripotent stem cells (iPSCs), we developed a method employing a hollow fiber bioreactor traditionally used for cell expansion. We have demonstrated the growth, transfection, and vector-producing capability of 293T producer cells in this system. Vector particle RNA titers after subsequent vector concentration yielded values comparable to lentiviral iPSC induction vector batches produced using traditional culture methods in 225 cm2 flasks (T225s) and in 10-layer cell factories (CF10s), while yielding a volume nearly 145 times larger than the yield from a T225 flask and nearly three times larger than the yield from a CF10. Employing a closed system hollow fiber bioreactor for vector production offers the possibility of manufacturing large quantities of gene therapy vector while minimizing reagent usage, equipment footprint, and open system manipulation.
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Batenburg NL, Thompson EL, Hendrickson EA, Zhu XD. Cockayne syndrome group B protein regulates DNA double-strand break repair and checkpoint activation. EMBO J 2015; 34:1399-416. [PMID: 25820262 DOI: 10.15252/embj.201490041] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 03/11/2015] [Indexed: 11/09/2022] Open
Abstract
Mutations of CSB account for the majority of Cockayne syndrome (CS), a devastating hereditary disorder characterized by physical impairment, neurological degeneration and segmental premature aging. Here we report the generation of a human CSB-knockout cell line. We find that CSB facilitates HR and represses NHEJ. Loss of CSB or a CS-associated CSB mutation abrogating its ATPase activity impairs the recruitment of BRCA1, RPA and Rad51 proteins to damaged chromatin but promotes the formation of 53BP1-Rif1 damage foci in S and G2 cells. Depletion of 53BP1 rescues the formation of BRCA1 damage foci in CSB-knockout cells. In addition, knockout of CSB impairs the ATM- and Chk2-mediated DNA damage responses, promoting a premature entry into mitosis. Furthermore, we show that CSB accumulates at sites of DNA double-strand breaks (DSBs) in a transcription-dependent manner. The kinetics of DSB-induced chromatin association of CSB is distinct from that of its UV-induced chromatin association. These results reveal novel, important functions of CSB in regulating the DNA DSB repair pathway choice as well as G2/M checkpoint activation.
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Affiliation(s)
| | - Elizabeth L Thompson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Jabalameli HR, Zahednasab H, Karimi-Moghaddam A, Jabalameli MR. Zinc finger nuclease technology: Advances and obstacles in modelling and treating genetic disorders. Gene 2015; 558:1-5. [DOI: 10.1016/j.gene.2014.12.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 12/09/2014] [Accepted: 12/19/2014] [Indexed: 12/23/2022]
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Stoimenov I, Ali MA, Pandzic T, Sjöblom T. Computational and molecular tools for scalable rAAV-mediated genome editing. Nucleic Acids Res 2014; 43:e30. [PMID: 25488813 PMCID: PMC4357690 DOI: 10.1093/nar/gku1286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The rapid discovery of potential driver mutations through large-scale mutational analyses of human cancers generates a need to characterize their cellular phenotypes. Among the techniques for genome editing, recombinant adeno-associated virus (rAAV)-mediated gene targeting is suited for knock-in of single nucleotide substitutions and to a lesser degree for gene knock-outs. However, the generation of gene targeting constructs and the targeting process is time-consuming and labor-intense. To facilitate rAAV-mediated gene targeting, we developed the first software and complementary automation-friendly vector tools to generate optimized targeting constructs for editing human protein encoding genes. By computational approaches, rAAV constructs for editing ~71% of bases in protein-coding exons were designed. Similarly, ~81% of genes were predicted to be targetable by rAAV-mediated knock-out. A Gateway-based cloning system for facile generation of rAAV constructs suitable for robotic automation was developed and used in successful generation of targeting constructs. Together, these tools enable automated rAAV targeting construct design, generation as well as enrichment and expansion of targeted cells with desired integrations.
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Affiliation(s)
- Ivaylo Stoimenov
- Science For Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Muhammad Akhtar Ali
- Science For Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Tatjana Pandzic
- Science For Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Tobias Sjöblom
- Science For Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
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Xu H, Xian J, Vire E, McKinney S, Wong J, Wei V, Tong R, Kouzarides T, Caldas C, Aparicio S. Up-regulation of the interferon-related genes in BRCA2 knockout epithelial cells. J Pathol 2014; 234:386-97. [PMID: 25043256 PMCID: PMC4882165 DOI: 10.1002/path.4404] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 07/03/2014] [Accepted: 07/06/2014] [Indexed: 12/30/2022]
Abstract
BRCA2 mutations are significantly associated with early-onset breast cancer, and the tumour-suppressing function of BRCA2 has been attributed to its involvement in homologous recombination (HR)-mediated DNA repair. In order to identify additional functions of BRCA2, we generated BRCA2-knockout HCT116 human colorectal carcinoma cells. Using genome-wide microarray analyses, we have discovered a link between the loss of BRCA2 and the up-regulation of a subset of interferon (IFN)-related genes, including APOBEC3F and APOBEC3G. The over-expression of IFN-related genes was confirmed in different human BRCA2(-/-) and mouse Brca2(-/-) tumour cell lines, and was independent of senescence and apoptosis. In isogenic wild-type BRCA2 cells, we observed over-expression of IFN-related genes after treatment with DNA-damaging agents, and following ionizing radiation. Cells with endogenous DNA damage because of defective BRCA1 or RAD51 also exhibited over-expression of IFN-related genes. Transcriptional activity of the IFN-stimulated response element (ISRE) was increased in BRCA2 knockout cells, and the expression of BRCA2 greatly decreased IFNα-stimulated ISRE reporter activity, suggesting that BRCA2 directly represses the expression of IFN-related genes through the ISRE. Finally, the colony-forming capacity of BRCA2 knockout cells was significantly reduced in the presence of either IFNβ or IFNγ, suggesting that IFNs may have potential as therapeutic agents in cancer cells with BRCA2 mutations. The GEO Accession No. for microarray analysis is GSE54830.
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Affiliation(s)
- Hong Xu
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Jian Xian
- Department of Oncology, University of Cambridge and Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Emmanuelle Vire
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Steven McKinney
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Jason Wong
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Vivien Wei
- Department of Microbiology and Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Rebecca Tong
- Department of Microbiology and Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Tony Kouzarides
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Carlos Caldas
- Department of Oncology, University of Cambridge and Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Wesbrook Mall, Vancouver, BC, V6T 2B5 Vancouver, BC
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Ballikaya S, Lee J, Warnken U, Schnölzer M, Gebert J, Kopitz J. De Novo proteome analysis of genetically modified tumor cells by a metabolic labeling/azide-alkyne cycloaddition approach. Mol Cell Proteomics 2014; 13:3446-56. [PMID: 25225355 DOI: 10.1074/mcp.m113.036665] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Activin receptor type II (ACVR2) is a member of the transforming growth factor type II receptor family and controls cell growth and differentiation, thereby acting as a tumor suppressor. ACVR2 inactivation is known to drive colorectal tumorigenesis. We used an ACVR2-deficient microsatellite unstable colon cancer cell line (HCT116) to set up a novel experimental design for comprehensive analysis of proteomic changes associated with such functional loss of a tumor suppressor. To this end we combined two existing technologies. First, the ACVR2 gene was reconstituted in an ACVR2-deficient colorectal cancer (CRC) cell line by means of recombinase-mediated cassette exchange, resulting in the generation of an inducible expression system that allowed the regulation of ACVR2 gene expression in a doxycycline-dependent manner. Functional expression in the induced cells was explicitly proven. Second, we used the methionine analog azidohomoalanine for metabolic labeling of newly synthesized proteins in our cell line model. Labeled proteins were tagged with biotin via a Click-iT chemistry approach enabling specific extraction of labeled proteins by streptavidin-coated beads. Tryptic on-bead digestion of captured proteins and subsequent ultra-high-performance LC coupled to LTQ Orbitrap XL mass spectrometry identified 513 proteins, with 25 of them differentially expressed between ACVR2-deficient and -proficient cells. Among these, several candidates that had already been linked to colorectal cancer or were known to play a key role in cell growth or apoptosis control were identified, proving the utility of the presented experimental approach. In principle, this strategy can be adapted to analyze any gene of interest and its effect on the cellular de novo proteome.
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Affiliation(s)
- Seda Ballikaya
- From the ‡Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, INF 224, 69120 Heidelberg, Germany; §Cancer Early Detection, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
| | - Jennifer Lee
- From the ‡Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, INF 224, 69120 Heidelberg, Germany; §Cancer Early Detection, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
| | - Uwe Warnken
- ‖Functional Proteome Analysis, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
| | - Martina Schnölzer
- ‖Functional Proteome Analysis, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
| | - Johannes Gebert
- From the ‡Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, INF 224, 69120 Heidelberg, Germany; §Cancer Early Detection, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
| | - Jürgen Kopitz
- From the ‡Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, INF 224, 69120 Heidelberg, Germany; §Cancer Early Detection, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany;
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Zhang L, Chen LH, Wan H, Yang R, Wang Z, Feng J, Yang S, Jones S, Wang S, Zhou W, Zhu H, Killela PJ, Zhang J, Wu Z, Li G, Hao S, Wang Y, Webb JB, Friedman HS, Friedman AH, McLendon RE, He Y, Reitman ZJ, Bigner DD, Yan H. Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas. Nat Genet 2014; 46:726-30. [PMID: 24880341 PMCID: PMC4073211 DOI: 10.1038/ng.2995] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 05/07/2014] [Indexed: 12/25/2022]
Affiliation(s)
- Liwei Zhang
- 1] Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China. [2]
| | - Lee H Chen
- 1] Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA. [2]
| | - Hong Wan
- 1] Beijing Neurosurgical Institute, Capital Medical University, Beijing, China. [2]
| | - Rui Yang
- 1] Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA. [2]
| | - Zhaohui Wang
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
| | - Jie Feng
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Shaohua Yang
- 1] Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China. [2] Beijing Neurosurgical Institute, Capital Medical University, Beijing, China. [3] Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Siân Jones
- Personal Genome Diagnostics, Inc., Baltimore, Maryland, USA
| | - Sizhen Wang
- Beijing Pangenomics Technology, Co Ltd., Beijing, China
| | - Weixin Zhou
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
| | - Huishan Zhu
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
| | - Patrick J Killela
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
| | - Junting Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhen Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guilin Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Shuyu Hao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Joseph B Webb
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
| | - Henry S Friedman
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
| | - Allan H Friedman
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
| | - Roger E McLendon
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
| | - Yiping He
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
| | - Zachary J Reitman
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
| | - Darell D Bigner
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
| | - Hai Yan
- Department of Pathology, Duke University Medical Center, The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, Durham, North Carolina, USA
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Genetic targeting of B-RafV600E affects survival and proliferation and identifies selective agents against BRAF-mutant colorectal cancer cells. Mol Cancer 2014; 13:122. [PMID: 24885690 PMCID: PMC4035728 DOI: 10.1186/1476-4598-13-122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 05/09/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Colorectal cancers carrying the B-Raf V600E-mutation are associated with a poor prognosis. The purpose of this study was to identify B-RafV600E-mediated traits of cancer cells in a genetic in vitro model and to assess the selective sensitization of B-RafV600E-mutant cancer cells towards therapeutic agents. METHODS Somatic cell gene targeting was used to generate subclones of the colorectal cancer cell line RKO containing either wild-type or V600E-mutant B-Raf kinase. Cell-biologic analyses were performed in order to link cancer cell traits to the BRAF-mutant genotype. Subsequently, the corresponding tumor cell clones were characterized pharmacogenetically to identify therapeutic agents exhibiting selective sensitivity in B-RafV600E-mutant cells. RESULTS Genetic targeting of mutant BRAF resulted in restoration of sensitivity to serum starvation-induced apoptosis and efficiently inhibited cell proliferation in the absence of growth factors. Among tested agents, the B-Raf inhibitor dabrafenib was found to induce a strong V600E-dependent shift in cell viability. In contrast, no differential sensitizing effect was observed for conventional chemotherapeutic agents (mitomycin C, oxaliplatin, paclitaxel, etoposide, 5-fluorouracil), nor for the targeted agents cetuximab, sorafenib, vemurafenib, RAF265, or for inhibition of PI3 kinase. Treatment with dabrafenib efficiently inhibited phosphorylation of the B-Raf downstream targets Mek 1/2 and Erk 1/2. CONCLUSION Mutant BRAF alleles mediate self-sufficiency of growth signals and serum starvation-induced resistance to apoptosis. Targeting of the BRAF mutation leads to a loss of these hallmarks of cancer. Dabrafenib selectively inhibits cell viability in B-RafV600E mutant cancer cells.
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Oh S, Harvey A, Zimbric J, Wang Y, Nguyen T, Jackson PJ, Hendrickson EA. DNA ligase III and DNA ligase IV carry out genetically distinct forms of end joining in human somatic cells. DNA Repair (Amst) 2014; 21:97-110. [PMID: 24837021 DOI: 10.1016/j.dnarep.2014.04.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 04/15/2014] [Accepted: 04/24/2014] [Indexed: 12/11/2022]
Abstract
Ku-dependent C-NHEJ (classic non-homologous end joining) is the primary DNA EJing (end joining) repair pathway in mammals. Recently, an additional EJing repair pathway (A-NHEJ; alternative-NHEJ) has been described. Currently, the mechanism of A-NHEJ is obscure although a dependency on LIGIII (DNA ligase III) is often implicated. To test the requirement for LIGIII in A-NHEJ we constructed a LIGIII conditionally-null human cell line using gene targeting. Nuclear EJing activity appeared unaffected by a deficiency in LIGIII as, surprisingly, so were random gene targeting integration events. In contrast, LIGIII was required for mitochondrial function and this defined the gene's essential activity. Human Ku:LIGIII and Ku:LIGIV (DNA ligase IV) double knockout cell lines, however, demonstrated that LIGIII is required for the enhanced A-NHEJ activity that is observed in Ku-deficient cells. Most unexpectedly, however, the majority of EJing events remained LIGIV-dependent. In conclusion, although human LIGIII has an essential function in mitochondrial maintenance, it is dispensable for most types of nuclear DSB repair, except for the A-NHEJ events that are normally suppressed by Ku. Moreover, we describe that a robust Ku-independent, LIGIV-dependent repair pathway exists in human somatic cells.
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Affiliation(s)
- Sehyun Oh
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States.
| | - Adam Harvey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States
| | - Jacob Zimbric
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States.
| | - Yongbao Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States.
| | - Thanh Nguyen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States
| | - Pauline J Jackson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States.
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Luo Y, Lin L, Bolund L, Sørensen CB. Efficient construction of rAAV-based gene targeting vectors by Golden Gate cloning. Biotechniques 2014; 56:263-8. [PMID: 24806227 DOI: 10.2144/000114169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 02/14/2014] [Indexed: 11/23/2022] Open
Abstract
The recombinant adeno-associated virus (rAAV) has proven to be an efficient and attractive tool for targeted genome engineering. Here we present a novel method employing the Golden Gate cloning strategy for fast and efficient construction of rAAV-based gene knockout or single-nucleotide knockin vectors. Two vectors, pGolden-Neo and pGolden-Hyg, were generated as common assembling modules to confer antibiotic resistance to the targeting vector. To validate the method, we then generated two rAAV-based targeting vectors: pAAV-pTP53-KO and pAAV-hTau(P301L)-KI. Furthermore, we generated a pGolden-AAV plasmid that allows one-step generation of an rAAV-based targeting vector. Our new methodology for rAAV targeting vector assembly is efficient, accurate, time-saving, and cost-effective.
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Affiliation(s)
- Yonglun Luo
- Department of Biomedicine, Faculty of Heath, Aarhus University, Aarhus, Denmark
| | - Lin Lin
- Department of Biomedicine, Faculty of Heath, Aarhus University, Aarhus, Denmark
| | - Lars Bolund
- Department of Biomedicine, Faculty of Heath, Aarhus University, Aarhus, Denmark
| | - Charlotte Brandt Sørensen
- Department of Biomedicine, Faculty of Heath, Aarhus University, Aarhus, Denmark; Department of Clinical Medicine, Department of Cardiological Medicine B, Aarhus University, Aarhus, Denmark
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36
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Fattah FJ, Kweon J, Wang Y, Lee EH, Kan Y, Lichter N, Weisensel N, Hendrickson EA. A role for XLF in DNA repair and recombination in human somatic cells. DNA Repair (Amst) 2014; 15:39-53. [PMID: 24461734 DOI: 10.1016/j.dnarep.2013.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 11/03/2013] [Accepted: 12/10/2013] [Indexed: 01/08/2023]
Abstract
Classic non-homologous end-joining (C-NHEJ) is required for the repair of radiation-induced DNA double-strand breaks (DSBs) in mammalian cells and plays a critical role in lymphoid V(D)J recombination. A core C-NHEJ component is the DNA ligase IV co-factor, Cernunnos/XLF (hereafter XLF). In patients, mutations in XLF cause predicted increases in radiosensitivity and deficits in immune function, but also cause other less well-understood pathologies including neural disorders. To characterize XLF function(s) in a defined genetic system, we used a recombinant adeno-associated virus-mediated gene targeting strategy to inactivate both copies of the XLF locus in the human HCT116 cell line. Analyses of XLF-null cells (which were viable) showed that they were highly sensitive to ionizing radiation and a radiomimetic DNA damaging agent, etoposide. XLF-null cells had profound DNA DSB repair defects as measured by in vivo plasmid end-joining assays and were also dramatically impaired in their ability to form either V(D)J coding or signal joints on extrachromosomal substrates. Thus, our somatic XLF-null cell line recapitulates many of the phenotypes expected from XLF patient cell lines. Subsequent structure:function experiments utilizing the expression of wild-type and mutant XLF cDNAs demonstrated that all of the phenotypes of an XLF deficiency could be rescued by the overexpression of a wild-type XLF cDNA. Unexpectedly, mutant forms of XLF bearing point mutations at amino acid positions L115 and L179, also completely complemented the null phenotype suggesting, in contrast to predictions to the contrary, that these mutations do not abrogate XLF function. Finally, we demonstrate that the absence of XLF causes a small, but significant, increase in homologous recombination, implicating XLF in DSB pathway choice regulation. We conclude that human XLF is a non-essential, but critical, C-NHEJ-repair factor.
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Affiliation(s)
- Farjana Jahan Fattah
- Departments of Pharmacology and Radiation Oncology, Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States.
| | - Junghun Kweon
- Department of Pediatrics, Section of Cardiology, University of Chicago, 900 East 57th Street, KCBD Room 5240, Chicago, IL 60637, United States.
| | - Yongbao Wang
- Cancer Diagnostics Service, Quest Diagnostics Nichols Institute, Chantilly, VA 20151, United States.
| | - Eu Han Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States
| | - Yinan Kan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States
| | - Natalie Lichter
- University of ND School of Medicine, 501 Columbia Road, Grand Forks, ND 58203, United States.
| | - Natalie Weisensel
- University of Wisconsin School of Medicine and Public Health, Health Sciences Learning Center, 750 Highland Ave., Madison, WI 53705, United States.
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, United States.
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Huang Z, Li S, Song W, Li X, Li Q, Zhang Z, Han Y, Zhang X, Miao S, Du R, Wang L. Lysine-specific demethylase 1 (LSD1/KDM1A) contributes to colorectal tumorigenesis via activation of the Wnt/β-catenin pathway by down-regulating Dickkopf-1 (DKK1) [corrected]. PLoS One 2013; 8:e70077. [PMID: 23922913 PMCID: PMC3724785 DOI: 10.1371/journal.pone.0070077] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 06/14/2013] [Indexed: 02/01/2023] Open
Abstract
We collected paired samples of tumor and adjacent normal colorectal tissues from 22 patients with colorectal carcinoma to compare the differences in the expression of lysine specific demethylase 1 (LSD1) in these two tissues. The results showed that in 19 paired samples (86.4%), LSD1 is more highly expressed in tumor tissue than in normal tissue. To explore the role of LSD1 in colorectal tumorigenesis, we used somatic cell gene targeting to generate an LSD1 knockout (KO) HCT 116 human colorectal cancer cell line as a research model. The analysis of phenotypic changes showed that LSD1 KO colorectal cancer cells are less tumorigenic, both in vivo and in vitro. The differential expression analysis of the cells by mRNA sequencing (RNA-Seq) yielded 2,663 differentially expressed genes, and 28 of these genes had highly significant differences (Q <0.01). We then selected the 4 colorectal cancer-related genes ADM, DKK1, HAS3 and SMURF2 for quantitative real-time PCR verification. The results showed that the differences in the expression of ADM, DKK1 and HAS3 were consistent with those measured using the RNA-Seq data. As DKK1 was the gene with the most significant differential expression, we analyzed the key proteins of the DKK1-related Wnt/β-catenin signaling pathway and found that, after knocking out LSD1, the amount of free β-catenin translocated to the nucleus was significantly reduced and that the transcription of the signaling pathway target gene c-Myc was down-regulated. Our studies show that LSD1 activates the Wnt/β-catenin signaling pathway by down-regulating the pathway antagonist DKK1, which may be one of the mechanisms leading to colorectal tumorigenesis.
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Affiliation(s)
- Zebin Huang
- National Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing, China
| | - Shangze Li
- Department of Cellular and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wei Song
- National Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing, China
| | - Xin Li
- Department of Cellular and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qinshan Li
- National Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing, China
| | - Zeyan Zhang
- Department of Cellular and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yongqing Han
- National Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing, China
| | - Xiaodong Zhang
- Department of Cellular and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shiying Miao
- National Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing, China
| | - Runlei Du
- Department of Cellular and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (RD); (LW)
| | - Linfang Wang
- National Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing, China
- * E-mail: (RD); (LW)
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Zhang P, Guo A, Possemato A, Wang C, Beard L, Carlin C, Markowitz SD, Polakiewicz RD, Wang Z. Identification and functional characterization of p130Cas as a substrate of protein tyrosine phosphatase nonreceptor 14. Oncogene 2013; 32:2087-95. [PMID: 22710723 PMCID: PMC3631434 DOI: 10.1038/onc.2012.220] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/01/2012] [Accepted: 05/01/2012] [Indexed: 01/12/2023]
Abstract
Protein tyrosine phosphatase nonreceptor type 14 (PTPN14) is frequently mutated in a variety of human cancers. However, the cell signaling pathways regulated by PTPN14 largely remain to be elucidated. Here, we identify a list of potential substrates of PTPN14 using a phospho-proteomic approach. We show that p130 Crk-associated substrate (p130Cas) is a direct substrate of PTPN14 and that PTPN14 specifically regulates p130Cas phosphorylation at tyrosine residue 128 (Y128) in colorectal cancer (CRC) cells. We engineered CRC cells homozygous for a p130Cas Y128F knock-in mutant and found that these cells exhibit significantly reduced migration and colony formation, impaired anchorage-independent growth, slower xenograft tumor growth in nude mice and have decreased phosphorylation of AKT. Furthermore, we demonstrate that SRC phosphorylates p130Cas Y128 and that CRC cell lines harboring high levels of pY128Cas are more sensitive to SRC family kinase inhibitor Dasatinib. These findings suggest that p130Cas Y128 phosphorylation may be exploited as a predictive marker for Dasatinib response in cancer patients. In aggregate, our studies reveal a novel signaling pathway that has an important role in colorectal tumorigenesis.
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Affiliation(s)
- Peng Zhang
- Department of Genetics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
| | - Ailan Guo
- Cell Signaling Technology Inc., 3 Trask Lane, Danvers, MA 01923
| | | | - Chao Wang
- Department of Genetics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
| | - Lydia Beard
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
- Department of Medicine, Case Medical Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
| | - Cathleen Carlin
- Department of Microbiology and Molecular Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
| | - Sanford D. Markowitz
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
- Department of Medicine, Case Medical Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
| | | | - Zhenghe Wang
- Department of Genetics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
- Department of Medicine, Case Medical Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
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Ebisawa T. Analysis of the molecular pathophysiology of sleep disorders relevant to a disturbed biological clock. Mol Genet Genomics 2013; 288:185-93. [PMID: 23546644 DOI: 10.1007/s00438-013-0745-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 03/22/2013] [Indexed: 11/26/2022]
Abstract
Genetic studies have revealed several clock gene variations/mutations involved in the manifestation of sleep disorders or interindividual differences in sleep-wake patterns, but only part of the genetic risk can be explained by the gene variations/mutations identified to date. Recent progress in research into circadian rhythm generation has provided efficient tools for eliciting the molecular basis of clock-relevant sleep disorders, complementing traditional genetic analysis. While the human master clock resides in the suprachiasmatic nucleus of the hypothalamus (central clock), peripheral tissue cells also generate self-sustained circadian oscillations of clock gene expression (peripheral clock), enabling estimation of individual human clock properties through a single collection of skin fibroblasts or venous blood cells. Some of the established cell lines exhibit autonomous circadian oscillations of clock gene expression, and introduction of clock gene variations into these cell lines by gene targeting makes it possible to investigate changes in the circadian phenotype induced by these variations/mutations without the need for generating transgenic animals. Estimation of human clock properties using peripheral tissue cells, in addition to genetic analysis, will facilitate comprehensive explication of the genetic risk of a variety of disorders relevant to biological clock disturbances, including sleep disorders, mood disorders, and metabolic diseases.
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Affiliation(s)
- Takashi Ebisawa
- Department of Psychiatry, Tokyo Metropolitan Police Hospital, 4-22-1, Nakano, Nakano-ku, Tokyo, 164-8541, Japan.
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40
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Martini M, Russo M, Lamba S, Vitiello E, Crowley EH, Sassi F, Romanelli D, Frattini M, Marchetti A, Bardelli A. Mixed Lineage Kinase MLK4 Is Activated in Colorectal Cancers Where It Synergistically Cooperates with Activated RAS Signaling in Driving Tumorigenesis. Cancer Res 2013; 73:1912-21. [DOI: 10.1158/0008-5472.can-12-3074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Oh S, Wang Y, Zimbric J, Hendrickson EA. Human LIGIV is synthetically lethal with the loss of Rad54B-dependent recombination and is required for certain chromosome fusion events induced by telomere dysfunction. Nucleic Acids Res 2012; 41:1734-49. [PMID: 23275564 PMCID: PMC3561972 DOI: 10.1093/nar/gks1326] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Classic non-homologous end joining (C-NHEJ) is the predominant DNA double-strand break repair pathway in humans. Although seven genes Ku70, Ku86, DNA-PKcs, Artemis, DNA Ligase IV (LIGIV), X-ray cross-complementing group 4 and XRCC4-like factor are required for C-NHEJ, several of them also have ancillary functions. For example, Ku70:Ku86 possesses an essential telomere maintenance activity. In contrast, LIGIV is believed to function exclusively in C-NHEJ. Moreover, a viable LIGIV-null human B-cell line and LIGIV-reduced patient cell lines have been described. Together, these observations suggest that LIGIV (and hence C-NHEJ), albeit important, is nonetheless dispensable, whereas Ku70:Ku86 and telomere maintenance are essential. To confirm this hypothesis, we inactivated LIGIV in the epithelial human cell line, HCT116. The resulting LIGIV-null cell line was viable, verifying that the gene and C-NHEJ are not essential. However, functional inactivation of RAD54B, a key homologous recombination factor, in the LIGIV-null background yielded no viable clones, suggesting that the combined absence of RAD54B/homologous recombination and C-NHEJ is synthetically lethal. Finally, we demonstrate that LIGIV is differentially required for certain chromosome fusion events induced by telomere dysfunction—used for those owing to the overexpression of a dominant negative version of telomere recognition factor 2, but not used for those owing to absence of Ku70:Ku86.
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Affiliation(s)
- Sehyun Oh
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
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42
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Kuo CHR, Xian J, Brenton JD, Franze K, Sivaniah E. Complex stiffness gradient substrates for studying mechanotactic cell migration. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:6059-6064. [PMID: 22991224 DOI: 10.1002/adma.201202520] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 08/14/2012] [Indexed: 06/01/2023]
Abstract
Polyacrylamide gels are cast upon a stiff support with controlled topography, resulting in a thin gel layer of variable height. The topographical profiles project a stiffness map onto the gel, resulting in controlled linear and non-linear 2D stiffness gradients. Fibroblasts, which migrate towards stiffer substrates, accumulate in areas with a gel thickness below 15 μm.
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Affiliation(s)
- Cheng-Hwa R Kuo
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge, UK
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43
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Song J, Hao Y, Du Z, Wang Z, Ewing RM. Identifying novel protein complexes in cancer cells using epitope-tagging of endogenous human genes and affinity-purification mass spectrometry. J Proteome Res 2012; 11:5630-41. [PMID: 23106643 DOI: 10.1021/pr300598t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Affinity-purification mass spectrometry (AP-MS) is the preeminent technique for identification of eukaryotic protein complexes in vivo. AP-MS workflows typically express epitope-tagged bait proteins, immunopurify, and then identify associated protein complexes using mass spectrometry. However, challenges of existing strategies include the construction of expression vectors for large open reading frames and the possibility that overexpression of bait proteins may result in expression of nonphysiological levels of the bait protein with concomitant perturbation of endogenous protein complexes. To address these issues, we use human cell lines with epitope-tagged endogenous genes as AP-MS substrates to develop a platform that we call "knock-in AP-MS", thereby avoiding the challenges of expression vector construction and ensuring that expression of tagged proteins is driven by endogenous regulatory mechanisms. Using three different bait genes (MRE11A, DNMT1 and APC), we show that cell lines expressing epitope-tagged endogenous genes make good substrates for sensitive and reproducible identification of protein interactions using AP-MS. In particular, we identify novel interactors of the important oncoprotein Adenomatous Polyposis Coli (APC), including an interaction with Flightless-1 homologue (FLII) that is enriched in nuclear fractions.
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Affiliation(s)
- Jing Song
- Center for Proteomics and Bioinformatics, Department of Genetics and Genome Science, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
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44
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Global identification of MLL2-targeted loci reveals MLL2's role in diverse signaling pathways. Proc Natl Acad Sci U S A 2012; 109:17603-8. [PMID: 23045699 DOI: 10.1073/pnas.1208807109] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Myeloid/lymphoid or mixed-lineage leukemia (MLL)-family genes encode histone lysine methyltransferases that play important roles in epigenetic regulation of gene transcription. MLL genes are frequently mutated in human cancers. Unlike MLL1, MLL2 (also known as ALR/MLL4) and its homolog MLL3 are not well-understood. Specifically, little is known regarding the extent of global MLL2 involvement in the regulation of gene expression and the mechanism underlying its alterations in driving tumorigenesis. Here we profile the global loci targeted by MLL2. A combinatorial analysis of the MLL2 binding profile and gene expression in MLL2 wild-type versus MLL2-null isogenic cell lines identified direct transcriptional target genes and revealed the connection of MLL2 to multiple cellular signaling pathways, including the p53 pathway, cAMP-mediated signaling, and cholestasis signaling. In particular, we demonstrate that MLL2 participates in retinoic acid receptor signaling by promoting retinoic acid-responsive gene transcription. Our results present a genome-wide integrative analysis of the MLL2 target loci and suggest potential mechanisms underlying tumorigenesis driven by MLL2 alterations.
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45
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Grassian AR, Lin F, Barrett R, Liu Y, Jiang W, Korpal M, Astley H, Gitterman D, Henley T, Howes R, Levell J, Korn JM, Pagliarini R. Isocitrate dehydrogenase (IDH) mutations promote a reversible ZEB1/microRNA (miR)-200-dependent epithelial-mesenchymal transition (EMT). J Biol Chem 2012; 287:42180-94. [PMID: 23038259 DOI: 10.1074/jbc.m112.417832] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mutations in the genes encoding isocitrate dehydrogenase 1 and 2 (IDH1/2) occur in a variety of tumor types, resulting in production of the proposed oncometabolite, 2-hydroxyglutarate (2-HG). How mutant IDH and 2-HG alter signaling pathways to promote cancer, however, remains unclear. Additionally, there exist relatively few cell lines with IDH mutations. To examine the effect of endogenous IDH mutations and 2-HG, we created a panel of isogenic epithelial cell lines with either wild-type IDH1/2 or clinically relevant IDH1/2 mutations. Differences were noted in the ability of IDH mutations to cause robust 2-HG accumulation. IDH1/2 mutants that produce high levels of 2-HG cause an epithelial-mesenchymal transition (EMT)-like phenotype, characterized by changes in EMT-related gene expression and cellular morphology. 2-HG is sufficient to recapitulate aspects of this phenotype in the absence of an IDH mutation. In the cells types examined, mutant IDH-induced EMT is dependent on up-regulation of the transcription factor ZEB1 and down-regulation of the miR-200 family of microRNAs. Furthermore, sustained knockdown of IDH1 in IDH1 R132H mutant cells is sufficient to reverse many characteristics of EMT, demonstrating that continued expression of mutant IDH is required to maintain this phenotype. These results suggest mutant IDH proteins can reversibly deregulate discrete signaling pathways that contribute to tumorigenesis.
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Affiliation(s)
- Alexandra R Grassian
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
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Duncan CG, Barwick BG, Jin G, Rago C, Kapoor-Vazirani P, Powell DR, Chi JT, Bigner DD, Vertino PM, Yan H. A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation. Genome Res 2012; 22:2339-55. [PMID: 22899282 PMCID: PMC3514664 DOI: 10.1101/gr.132738.111] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Monoallelic point mutations of the NADP+-dependent isocitrate dehydrogenases IDH1 and IDH2 occur frequently in gliomas, acute myeloid leukemias, and chondromas, and display robust association with specific DNA hypermethylation signatures. Here we show that heterozygous expression of the IDH1R132H allele is sufficient to induce the genome-wide alterations in DNA methylation characteristic of these tumors. Using a gene-targeting approach, we knocked-in a single copy of the most frequently observed IDH1 mutation, R132H, into a human cancer cell line and profiled changes in DNA methylation at over 27,000 CpG dinucleotides relative to wild-type parental cells. We find that IDH1R132H/WT mutation induces widespread alterations in DNA methylation, including hypermethylation of 2010 and hypomethylation of 842 CpG loci. We demonstrate that many of these alterations are consistent with those observed in IDH1-mutant and G-CIMP+ primary gliomas and can segregate IDH wild-type and mutated tumors as well as those exhibiting the G-CIMP phenotype in unsupervised analysis of two primary glioma cohorts. Further, we show that the direction of IDH1R132H/WT-mediated DNA methylation change is largely dependent upon preexisting DNA methylation levels, resulting in depletion of moderately methylated loci. Additionally, whereas the levels of multiple histone H3 and H4 methylation modifications were globally increased, consistent with broad inhibition of histone demethylation, hypermethylation at H3K9 in particular accompanied locus-specific DNA hypermethylation at several genes down-regulated in IDH1R132H/WT knock-in cells. These data provide insight on epigenetic alterations induced by IDH1 mutations and support a causal role for IDH1R132H/WT mutants in driving epigenetic instability in human cancer cells.
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Affiliation(s)
- Christopher G Duncan
- The Preston Robert Tisch Brain Tumor Center, The Pediatric Brain Tumor Foundation Institute, The Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA
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47
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Luo Y, Lin L, Bolund L, Jensen TG, Sørensen CB. Genetically modified pigs for biomedical research. J Inherit Metab Dis 2012; 35:695-713. [PMID: 22453682 DOI: 10.1007/s10545-012-9475-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/09/2012] [Accepted: 03/02/2012] [Indexed: 01/17/2023]
Abstract
During the last two decades, pigs have been used to develop some of the most important large animal models for biomedical research. Advances in pig genome research, genetic modification (GM) of primary pig cells and pig cloning by nuclear transfer, have facilitated the generation of GM pigs for xenotransplantation and various human diseases. This review summarizes the key technologies used for generating GM pigs, including pronuclear microinjection, sperm-mediated gene transfer, somatic cell nuclear transfer by traditional cloning, and somatic cell nuclear transfer by handmade cloning. Broadly used genetic engineering tools for porcine cells are also discussed. We also summarize the GM pig models that have been generated for xenotransplantation and human disease processes, including neurodegenerative diseases, cardiovascular diseases, eye diseases, bone diseases, cancers and epidermal skin diseases, diabetes mellitus, cystic fibrosis, and inherited metabolic diseases. Thus, this review provides an overview of the progress in GM pig research over the last two decades and perspectives for future development.
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Affiliation(s)
- Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark.
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48
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Luo Y, Kofod-Olsen E, Christensen R, Sørensen CB, Bolund L. Targeted genome editing by recombinant adeno-associated virus (rAAV) vectors for generating genetically modified pigs. J Genet Genomics 2012; 39:269-74. [PMID: 22749014 DOI: 10.1016/j.jgg.2012.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 05/10/2012] [Indexed: 12/22/2022]
Abstract
Recombinant adeno-associated virus (rAAV) vectors have been extensively used for experimental gene therapy of inherited human diseases. Several advantages, such as simple vector construction, high targeting frequency by homologous recombination, and applicability to many cell types, make rAAV an attractive approach for targeted genome editing. Combined with cloning by somatic cell nuclear transfer (SCNT), this technology has recently been successfully adapted to generate gene-targeted pigs as models for cystic fibrosis, hereditary tyrosinemia type 1, and breast cancer. This review summarizes the development of rAAV for targeted genome editing in mammalian cells and provides strategies for enhancing the rAAV-mediated targeting frequency by homologous recombination. We discuss current development and application of the rAAV vectors for targeted genome editing in porcine primary fibroblasts, which are subsequently used as donor cells for SCNT to generate cloned genetically designed pigs and provide positive perspectives for the generation of gene-targeted pigs with rAAV in the future.
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Affiliation(s)
- Yonglun Luo
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, DK-8000 Aarhus C, Denmark.
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49
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Abstract
Melanoma, the most aggressive form of skin cancer, has increased in incidence more rapidly than any other cancer. The completion of the human genome project and advancements in genomics technologies has allowed us to investigate genetic alterations of melanoma at a scale and depth that is unprecedented. Here, we survey the history of the different approaches taken to understand the genomics of melanoma - from early candidate genes, to gene families, to genome-wide studies. The new era of whole-exome and whole-genome sequencing has paved the way for an in-depth understanding of melanoma biology, identification of new therapeutic targets, and development of novel personalized therapies for melanoma.
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Affiliation(s)
- Vijay Walia
- The Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Euphemia W. Mu
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jimmy C. Lin
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Yardena Samuels
- The Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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50
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Mata JF, Lopes T, Gardner R, Jansen LET. A rapid FACS-based strategy to isolate human gene knockin and knockout clones. PLoS One 2012; 7:e32646. [PMID: 22393430 PMCID: PMC3290580 DOI: 10.1371/journal.pone.0032646] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 01/28/2012] [Indexed: 11/18/2022] Open
Abstract
Gene targeting protocols for mammalian cells remain inefficient and labor intensive. Here we describe FASTarget, a rapid, fluorescent cell sorting based strategy to isolate rare gene targeting events in human somatic cells. A fluorescent protein is used as a means for direct selection of targeted clones obviating the need for selection and outgrowth of drug resistant clones. Importantly, the use of a promoter-less, ATG-less construct greatly facilitates the recovery of correctly targeted cells. Using this method we report successful gene targeting in up to 94% of recovered human somatic cell clones. We create functional EYFP-tagged knockin clones in both transformed and non-transformed human somatic cell lines providing a valuable tool for mammalian cell biology. We further demonstrate the use of this technology to create gene knockouts. Using this generally applicable strategy we can recover gene targeted clones within approximately one month from DNA construct delivery to obtaining targeted monoclonal cell lines.
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Affiliation(s)
- João F. Mata
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Telma Lopes
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Rui Gardner
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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