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Reber S, Mechtersheimer J, Nasif S, Benitez JA, Colombo M, Domanski M, Jutzi D, Hedlund E, Ruepp MD. CRISPR-Trap: a clean approach for the generation of gene knockouts and gene replacements in human cells. Mol Biol Cell 2017; 29:75-83. [PMID: 29167381 PMCID: PMC5909934 DOI: 10.1091/mbc.e17-05-0288] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/27/2017] [Accepted: 11/16/2017] [Indexed: 01/08/2023] Open
Abstract
CRISPR/Cas9-based genome editing offers the possibility to knock out almost any gene of interest in an affordable and simple manner. The most common strategy is the introduction of a frameshift into the open reading frame (ORF) of the target gene which truncates the coding sequence (CDS) and targets the corresponding transcript for degradation by nonsense-mediated mRNA decay (NMD). However, we show that transcripts containing premature termination codons (PTCs) are not always degraded efficiently and can generate C-terminally truncated proteins which might have residual or dominant negative functions. Therefore, we recommend an alternative approach for knocking out genes, which combines CRISPR/Cas9 with gene traps (CRISPR-Trap) and is applicable to ∼50% of all spliced human protein-coding genes and a large subset of lncRNAs. CRISPR-Trap completely prevents the expression of the ORF and avoids expression of C-terminal truncated proteins. We demonstrate the feasibility of CRISPR-Trap by utilizing it to knock out several genes in different human cell lines. Finally, we also show that this approach can be used to efficiently generate gene replacements allowing for modulation of protein levels for otherwise lethal knockouts (KOs). Thus, CRISPR-Trap offers several advantages over conventional KO approaches and allows for generation of clean CRISPR/Cas9-based KOs.
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Affiliation(s)
- Stefan Reber
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Jonas Mechtersheimer
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Sofia Nasif
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | | | - Martino Colombo
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Michal Domanski
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Daniel Jutzi
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Eva Hedlund
- Department of Neuroscience, Karolinska Institutet,171 77 Stockholm, Sweden
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
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Nathanson T, Ahuja A, Rubinsteyn A, Aksoy BA, Hellmann MD, Miao D, Van Allen E, Merghoub T, Wolchok JD, Snyder A, Hammerbacher J. Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade. Cancer Immunol Res 2016; 5:84-91. [PMID: 27956380 DOI: 10.1158/2326-6066.cir-16-0019] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 01/08/2023]
Abstract
Immune checkpoint inhibitors are promising treatments for patients with a variety of malignancies. Toward understanding the determinants of response to immune checkpoint inhibitors, it was previously demonstrated that the presence of somatic mutations is associated with benefit from checkpoint inhibition. A hypothesis was posited that neoantigen homology to pathogens may in part explain the link between somatic mutations and response. To further examine this hypothesis, we reanalyzed cancer exome data obtained from our previously published study of 64 melanoma patients treated with CTLA-4 blockade and a new dataset of RNA-Seq data from 24 of these patients. We found that the ability to accurately predict patient benefit did not increase as the analysis narrowed from somatic mutation burden, to inclusion of only those mutations predicted to be MHC class I neoantigens, to only including those neoantigens that were expressed or that had homology to pathogens. The only association between somatic mutation burden and response was found when examining samples obtained prior to treatment. Neoantigen and expressed neoantigen burden were also associated with response, but neither was more predictive than somatic mutation burden. Neither the previously described tetrapeptide signature nor an updated method to evaluate neoepitope homology to pathogens was more predictive than mutation burden. Cancer Immunol Res; 5(1); 84-91. ©2016 AACR.
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Affiliation(s)
- Tavi Nathanson
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Arun Ahuja
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alexander Rubinsteyn
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bulent Arman Aksoy
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Matthew D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Diana Miao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Broad Institute of MIT and Harvard, Boston, Massachusetts.,Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eliezer Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Broad Institute of MIT and Harvard, Boston, Massachusetts.,Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Taha Merghoub
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Swim Across America-Ludwig Collaborative Research Laboratory, Immunology Program, Ludwig Center for Cancer Immunotherapy, New York, New York
| | - Jedd D Wolchok
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Swim Across America-Ludwig Collaborative Research Laboratory, Immunology Program, Ludwig Center for Cancer Immunotherapy, New York, New York
| | - Alexandra Snyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Jeff Hammerbacher
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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Andrews FH, Rogers MP, Paul LN, McLeish MJ. Perturbation of the monomer-monomer interfaces of the benzoylformate decarboxylase tetramer. Biochemistry 2014; 53:4358-67. [PMID: 24956165 PMCID: PMC4215898 DOI: 10.1021/bi500081r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The X-ray structure of benzoylformate
decarboxylase (BFDC) from Pseudomonas putida ATCC
12633 shows it to be a tetramer.
This was believed to be typical of all thiamin diphosphate-dependent
decarboxylases until recently when the structure of KdcA, a branched-chain
2-keto acid decarboxylase from Lactococcus lactis, showed it to be a homodimer. This lent credence to earlier unfolding
experiments on pyruvate decarboxylase from Saccharomyces cerevisiae that indicated that it might be active as a dimer. To investigate
this possibility in BFDC, we sought to shift the equilibrium toward
dimer formation. Point mutations were made in the noncatalytic monomer–monomer
interfaces, but these had a minimal effect on both tetramer formation
and catalytic activity. Subsequently, the R141E/Y288A/A306F variant
was shown by analytical ultracentrifugation to be partially dimeric.
It was also found to be catalytically inactive. Further experiments
revealed that just two mutations, R141E and A306F, were sufficient
to markedly alter the dimer–tetramer equilibrium and to provide
an ∼450-fold decrease in kcat.
Equilibrium denaturation studies suggested that the residual activity
was possibly due to the presence of residual tetramer. The structures
of the R141E and A306F variants, determined to <1.5 Å resolution,
hinted that disruption of the monomer interfaces will be accompanied
by movement of a loop containing Leu109 and Leu110. As these residues
contribute to the hydrophobicity of the active site and the correct
positioning of the substrate, it seems that tetramer formation may
well be critical to the catalytic activity of BFDC.
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Affiliation(s)
- Forest H Andrews
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
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