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1. Systematic analysis of factors that improve homologous direct repair (HDR) efficiency in CRISPR/Cas9 technique.

Author

Mariateresa Di Stazio, Nicola Foschi, Emmanouil Athanasakis, Paolo Gasparini, and Adamo Pio d'Adamo

Subjects
Medicine, Science
Abstract

The CRISPR/Cas9 bacterial system has proven to be an powerful tool for genetic manipulation in several organisms, but the efficiency of sequence replacement by homologous direct repair (HDR) is substantially lower than random indel creation. Many studies focused on improving HDR efficiency using double sgRNA, cell synchronization cycle, and the delivery of single-stranded oligo DNA nucleotides (ssODN) with a rational design. In this study, we evaluate these three methods' synergistic effects to improve HDR efficiency. For our tests, we have chosen the TNFα gene (NM_000594) for its crucial role in various biological processes and diseases. For the first time, our results showed how the use of two sgRNA with asymmetric donor design and triple transfection events dramatically increase the HDR efficiency from an undetectable HDR event to 39% of HDR efficiency and provide a new strategy to facilitate CRISPR/Cas9-mediated human genome editing. Besides, we demonstrated that the TNFα locus could be edited with CRISPR/Cas9 methodology, an opportunity to safely correct, in the future, the specific mutations of each patient.

Published
2021
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3. Systematic analysis of factors that improve homologous direct repair (HDR) efficiency in CRISPR/Cas9 technique

Author

Nicola Foschi, Adamo Pio D'Adamo, Paolo Gasparini, Mariateresa Di Stazio, Emmanouil Athanasakis, Di Stazio, M., Foschi, N., Athanasakis, E., Gasparini, P., and D'Adamo, A. P.

Subjects
DNA End-Joining Repair, Physiology, Computer science, Artificial Gene Amplification and Extension, Polymerase Chain Reaction, Synthetic Genome Editing, Biochemistry, Genome Engineering, law.invention, chemistry.chemical_compound, Trinucleotide Repeats, Genome editing, law, Immune Physiology, Medicine and Health Sciences, CRISPR, DNA Breaks, Double-Stranded, Nucleotide, Polymerase chain reaction, Subgenomic mRNA, Gene Editing, chemistry.chemical_classification, Innate Immune System, Multidisciplinary, Nucleotides, CRISPR/Cas9, Genome Editing, Crispr, Transfection, Nucleic acids, Medicine, Engineering and Technology, Cytokines, Synthetic Biology, Research Article, RNA, Guide, Kinetoplastida, Science, Immunology, DNA repair, DNA, Single-Stranded, Bioengineering, Genomics, Locus (genetics), Computational biology, DNA construction, Research and Analysis Methods, Genetics, Homologous chromosome, Humans, Molecular Biology Techniques, Indel, Molecular Biology, Gene, Cloning, Genome, Human, Tumor Necrosis Factor-alpha, Cas9, Rational design, Biology and Life Sciences, Recombinational DNA Repair, DNA, Synthetic Genomics, Molecular Development, HEK293 Cells, chemistry, Genetic Loci, Immune System, Plasmid Construction, Mutation, Human genome, CRISPR-Cas Systems, Developmental Biology
Abstract

The CRISPR/Cas9 bacterial system has proven to be an powerful tool for genetic manipulation in several organisms, but the efficiency of sequence replacement by homologous direct repair (HDR) is substantially lower than random indel creation. Many studies focused on improving HDR efficiency using double sgRNA, cell synchronization cycle, and the delivery of single-stranded oligo DNA nucleotides (ssODN) with a rational design. In this study, we evaluate these three methods’ synergistic effects to improve HDR efficiency. For our tests, we have chosen the TNFα gene (NM_000594) for its crucial role in various biological processes and diseases. For the first time, our results showed how the use of two sgRNA with asymmetric donor design and triple transfection events dramatically increase the HDR efficiency from an undetectable HDR event to 39% of HDR efficiency and provide a new strategy to facilitate CRISPR/Cas9-mediated human genome editing. Besides, we demonstrated that the TNFα locus could be edited with CRISPR/Cas9 methodology, an opportunity to safely correct, in the future, the specific mutations of each patient.

Published
2021

4. Modulation of Genetic Associations with Serum Urate Levels by Body-Mass-Index in Humans

Author

Huffman, Jennifer E., primary, Albrecht, Eva, additional, Teumer, Alexander, additional, Mangino, Massimo, additional, Kapur, Karen, additional, Johnson, Toby, additional, Kutalik, Zoltán, additional, Pirastu, Nicola, additional, Pistis, Giorgio, additional, Lopez, Lorna M., additional, Haller, Toomas, additional, Salo, Perttu, additional, Goel, Anuj, additional, Li, Man, additional, Tanaka, Toshiko, additional, Dehghan, Abbas, additional, Ruggiero, Daniela, additional, Malerba, Giovanni, additional, Smith, Albert V., additional, Nolte, Ilja M., additional, Portas, Laura, additional, Phipps-Green, Amanda, additional, Boteva, Lora, additional, Navarro, Pau, additional, Johansson, Asa, additional, Hicks, Andrew A., additional, Polasek, Ozren, additional, Esko, Tõnu, additional, Peden, John F., additional, Harris, Sarah E., additional, Murgia, Federico, additional, Wild, Sarah H., additional, Tenesa, Albert, additional, Tin, Adrienne, additional, Mihailov, Evelin, additional, Grotevendt, Anne, additional, Gislason, Gauti K., additional, Coresh, Josef, additional, D'Adamo, Pio, additional, Ulivi, Sheila, additional, Vollenweider, Peter, additional, Waeber, Gerard, additional, Campbell, Susan, additional, Kolcic, Ivana, additional, Fisher, Krista, additional, Viigimaa, Margus, additional, Metter, Jeffrey E., additional, Masciullo, Corrado, additional, Trabetti, Elisabetta, additional, Bombieri, Cristina, additional, Sorice, Rossella, additional, Döring, Angela, additional, Reischl, Eva, additional, Strauch, Konstantin, additional, Hofman, Albert, additional, Uitterlinden, Andre G., additional, Waldenberger, Melanie, additional, Wichmann, H-Erich, additional, Davies, Gail, additional, Gow, Alan J., additional, Dalbeth, Nicola, additional, Stamp, Lisa, additional, Smit, Johannes H., additional, Kirin, Mirna, additional, Nagaraja, Ramaiah, additional, Nauck, Matthias, additional, Schurmann, Claudia, additional, Budde, Kathrin, additional, Farrington, Susan M., additional, Theodoratou, Evropi, additional, Jula, Antti, additional, Salomaa, Veikko, additional, Sala, Cinzia, additional, Hengstenberg, Christian, additional, Burnier, Michel, additional, Mägi, Reedik, additional, Klopp, Norman, additional, Kloiber, Stefan, additional, Schipf, Sabine, additional, Ripatti, Samuli, additional, Cabras, Stefano, additional, Soranzo, Nicole, additional, Homuth, Georg, additional, Nutile, Teresa, additional, Munroe, Patricia B., additional, Hastie, Nicholas, additional, Campbell, Harry, additional, Rudan, Igor, additional, Cabrera, Claudia, additional, Haley, Chris, additional, Franco, Oscar H., additional, Merriman, Tony R., additional, Gudnason, Vilmundur, additional, Pirastu, Mario, additional, Penninx, Brenda W., additional, Snieder, Harold, additional, Metspalu, Andres, additional, Ciullo, Marina, additional, Pramstaller, Peter P., additional, van Duijn, Cornelia M., additional, Ferrucci, Luigi, additional, Gambaro, Giovanni, additional, Deary, Ian J., additional, Dunlop, Malcolm G., additional, Wilson, James F., additional, Gasparini, Paolo, additional, Gyllensten, Ulf, additional, Spector, Tim D., additional, Wright, Alan F., additional, Hayward, Caroline, additional, Watkins, Hugh, additional, Perola, Markus, additional, Bochud, Murielle, additional, Kao, W. H. Linda, additional, Caulfield, Mark, additional, Toniolo, Daniela, additional, Völzke, Henry, additional, Gieger, Christian, additional, Köttgen, Anna, additional, and Vitart, Veronique, additional

Published
2015
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5. Association Analysis of Bitter Receptor Genes in Five Isolated Populations Identifies a Significant Correlation between TAS2R43 Variants and Coffee Liking

Author

Pirastu, Nicola, primary, Kooyman, Maarten, additional, Traglia, Michela, additional, Robino, Antonietta, additional, Willems, Sara M., additional, Pistis, Giorgio, additional, d’Adamo, Pio, additional, Amin, Najaf, additional, d’Eustacchio, Angela, additional, Navarini, Luciano, additional, Sala, Cinzia, additional, Karssen, Lennart C., additional, van Duijn, Cornelia, additional, Toniolo, Daniela, additional, and Gasparini, Paolo, additional

Published
2014
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6. Correction: Genetic Structure of Europeans: A View from the North–East

Author

Nelis, Mari, primary, Esko, Tõnu, additional, Mägi, Reedik, additional, Zimprich, Fritz, additional, Zimprich, Alexander, additional, Toncheva, Draga, additional, Karachanak, Sena, additional, Piskáčková, Tereza, additional, Balaščák, Ivan, additional, Peltonen, Leena, additional, Jakkula, Eveliina, additional, Rehnström, Karola, additional, Lathrop, Mark, additional, Heath, Simon, additional, Galan, Pilar, additional, Schreiber, Stefan, additional, Meitinger, Thomas, additional, Pfeufer, Arne, additional, Wichmann, H-Erich, additional, Melegh, Béla, additional, Polgár, Noémi, additional, Toniolo, Daniela, additional, Gasparini, Paolo, additional, D'Adamo, Pio, additional, Klovins, Janis, additional, Nikitina-Zake, Liene, additional, Kučinskas, Vaidutis, additional, Kasnauskienė, Jūratė, additional, Lubinski, Jan, additional, Debniak, Tadeusz, additional, Limborska, Svetlana, additional, Khrunin, Andrey, additional, Estivill, Xavier, additional, Rabionet, Raquel, additional, Marsal, Sara, additional, Julià, Antonio, additional, Antonarakis, Stylianos E., additional, Deutsch, Samuel, additional, Borel, Christelle, additional, Attar, Homa, additional, Gagnebin, Maryline, additional, Macek, Milan, additional, Krawczak, Michael, additional, Remm, Maido, additional, and Metspalu, Andres, additional

Published
2010
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7. Genetic Structure of Europeans: A View from the North–East

Author

Nelis, Mari, primary, Esko, Tõnu, additional, Mägi, Reedik, additional, Zimprich, Fritz, additional, Zimprich, Alexander, additional, Toncheva, Draga, additional, Karachanak, Sena, additional, Piskáčková, Tereza, additional, Balaščák, Ivan, additional, Peltonen, Leena, additional, Jakkula, Eveliina, additional, Rehnström, Karola, additional, Lathrop, Mark, additional, Heath, Simon, additional, Galan, Pilar, additional, Schreiber, Stefan, additional, Meitinger, Thomas, additional, Pfeufer, Arne, additional, Wichmann, H-Erich, additional, Melegh, Béla, additional, Polgár, Noémi, additional, Toniolo, Daniela, additional, Gasparini, Paolo, additional, D'Adamo, Pio, additional, Klovins, Janis, additional, Nikitina-Zake, Liene, additional, Kučinskas, Vaidutis, additional, Kasnauskienė, Jūratė, additional, Lubinski, Jan, additional, Debniak, Tadeusz, additional, Limborska, Svetlana, additional, Khrunin, Andrey, additional, Estivill, Xavier, additional, Rabionet, Raquel, additional, Marsal, Sara, additional, Julià, Antonio, additional, Antonarakis, Stylianos E., additional, Deutsch, Samuel, additional, Borel, Christelle, additional, Attar, Homa, additional, Gagnebin, Maryline, additional, Macek, Milan, additional, Krawczak, Michael, additional, Remm, Maido, additional, and Metspalu, Andres, additional

Published
2009
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8. Association Analysis of Bitter Receptor Genes in Five Isolated Populations Identifies a Significant Correlation between TAS2R43 Variants and Coffee Liking.

Author

Pirastu, Nicola, Kooyman, Maarten, Traglia, Michela, Robino, Antonietta, Willems, Sara M., Pistis, Giorgio, d’Adamo, Pio, Amin, Najaf, d’Eustacchio, Angela, Navarini, Luciano, Sala, Cinzia, Karssen, Lennart C., van Duijn, Cornelia, Toniolo, Daniela, and Gasparini, Paolo

Subjects
OLFACTORY receptor genes, COFFEE, BIOACTIVE compounds, BITTERNESS (Taste), DIGESTIVE organs, HUMAN genetics
Abstract

Coffee, one of the most popular beverages in the world, contains many different physiologically active compounds with a potential impact on people’s health. Despite the recent attention given to the genetic basis of its consumption, very little has been done in understanding genes influencing coffee preference among different individuals. Given its markedly bitter taste, we decided to verify if bitter receptor genes (TAS2Rs) variants affect coffee liking. In this light, 4066 people from different parts of Europe and Central Asia filled in a field questionnaire on coffee liking. They have been consequently recruited and included in the study. Eighty-eight SNPs covering the 25 TAS2R genes were selected from the available imputed ones and used to run association analysis for coffee liking. A significant association was detected with three SNP: one synonymous and two functional variants (W35S and H212R) on the TAS2R43 gene. Both variants have been shown to greatly reduce in vitro protein activity. Surprisingly the wild type allele, which corresponds to the functional form of the protein, is associated to higher liking of coffee. Since the hTAS2R43 receptor is sensible to caffeine, we verified if the detected variants produced differences in caffeine bitter perception on a subsample of people coming from the FVG cohort. We found a significant association between differences in caffeine perception and the H212R variant but not with the W35S, which suggests that the effect of the TAS2R43 gene on coffee liking is mediated by caffeine and in particular by the H212R variant. No other significant association was found with other TAS2R genes. In conclusion, the present study opens new perspectives in the understanding of coffee liking. Further studies are needed to clarify the role of the TAS2R43 gene in coffee hedonics and to identify which other genes and pathways are involved in its genetics. [ABSTRACT FROM AUTHOR]

Published
2014
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9. Association analysis of bitter receptor genes in five isolated populations identifies a significant correlation between TAS2R43 variants and coffee liking

Author

Luciano Navarini, Angela D'Eustacchio, Giorgio Pistis, Michela Traglia, Cornelia M. van Duijn, Pio D'Adamo, Maarten Kooyman, Sara M. Willems, Cinzia Sala, Paolo Gasparini, Daniela Toniolo, Najaf Amin, Antonietta Robino, Nicola Pirastu, Lennart C. Karssen, Epidemiology, Pirastu, Nicola, Kooyman, M, Traglia, Michela, Robino, A, Willems, Sm, Pistis, G, D'Adamo, ADAMO PIO, Amin, N, D'Eustacchio, A, Navarini, L, Sala, C, Karssen, Lc, van Duijn, C, Toniolo, D, and Gasparini, Paolo

Subjects
Taste, Anatomy and Physiology, 030309 nutrition & dietetics, Epidemiology, lcsh:Medicine, Genome-wide association study, Single-nucleotide polymorphism, Biology, association study, Coffee, Polymorphism, Single Nucleotide, Receptors, G-Protein-Coupled, 03 medical and health sciences, chemistry.chemical_compound, Polymorphism (computer science), Genetics, SNP, Humans, lcsh:Science, Genetic Association Studies, 030304 developmental biology, Genetic association, 0303 health sciences, Multidisciplinary, Population Biology, Haplotype, lcsh:R, Human Genetics, chemistry, Genetic Epidemiology, Genetic Polymorphism, Sensory Perception, lcsh:Q, Caffeine, Digestive System, Population Genetics, Research Article, Neuroscience
Abstract

Coffee, one of the most popular beverages in the world, contains many different physiologically active compounds with a potential impact on people's health. Despite the recent attention given to the genetic basis of its consumption, very little has been done in understanding genes influencing coffee preference among different individuals. Given its markedly bitter taste, we decided to verify if bitter receptor genes (TAS2Rs) variants affect coffee liking. In this light, 4066 people from different parts of Europe and Central Asia filled in a field questionnaire on coffee liking. They have been consequently recruited and included in the study. Eighty-eight SNPs covering the 25 TAS2R genes were selected from the available imputed ones and used to run association analysis for coffee liking. A significant association was detected with three SNP: one synonymous and two functional variants (W35S and H212R) on the TAS2R43 gene. Both variants have been shown to greatly reduce in vitro protein activity. Surprisingly the wild type allele, which corresponds to the functional form of the protein, is associated to higher liking of coffee. Since the hTAS2R43 receptor is sensible to caffeine, we verified if the detected variants produced differences in caffeine bitter perception on a subsample of people coming from the FVG cohort. We found a significant association between differences in caffeine perception and the H212R variant but not with the W35S, which suggests that the effect of the TAS2R43 gene on coffee liking is mediated by caffeine and in particular by the H212R variant. No other significant association was found with other TAS2R genes. In conclusion, the present study opens new perspectives in the understanding of coffee liking. Further studies are needed to clarify the role of the TAS2R43 gene in coffee hedonics and to identify which other genes and pathways are involved in its genetics.

Published
2014

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