1
|
Adserà A, Arenas A, Boix C. Estimating the value of democracy relative to other institutional and economic outcomes among citizens in Brazil, France, and the United States. Proc Natl Acad Sci U S A 2023; 120:e2306168120. [PMID: 37983490 PMCID: PMC10691337 DOI: 10.1073/pnas.2306168120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/29/2023] [Indexed: 11/22/2023] Open
Abstract
How much do citizens value democracy? How willing are they to sacrifice their liberties and voting rights for growth, equality, or other social outcomes? We design a conjoint experiment in nationally representative surveys in Brazil, France, and the United States in which respondents choose between different societies that randomly vary in their economic outcomes (country income, income inequality, social mobility), political outcomes (democracy, public health insurance), and the level of personal income for each respondent. Our research allows us to estimate the respondents' willingness to trade off democracy for individual income (as well as other societal attributes). We find that, on average, individuals are strongly attached to democracy and a robust welfare state. They prefer to live in a country without free democratic elections only if their individual income multiplies by at least three times and in a country without public health insurance only if their individual income more than doubles. After estimating these preferences at the individual level for all respondents, we show that, although there is an authoritarian minority in all three countries, forming a nondemocratic majority (by offering more income and/or other goods to respondents) is very unlikely. Our findings imply that, contrary to a growing discussion about the crisis of democracy, liberal democratic values remain substantially robust in high and middle income democracies.
Collapse
Affiliation(s)
- Alicia Adserà
- School of Public and International Affairs, Princeton University, Princeton, NJ08544
- IZA (Institute of Labor Economics), Bonn53113, Germany
| | - Andreu Arenas
- School of Economics, University of Barcelona, Barcelona08034, Spain
- Institut d’Economia de Barcelona, Barcelona08034, Spain
| | - Carles Boix
- School of Public and International Affairs, Princeton University, Princeton, NJ08544
- School of Economics, University of Barcelona, Barcelona08034, Spain
- Department of Politics, Princeton University, Princeton, NJ08544
| |
Collapse
|
2
|
Hou L, Xiong X, Park Y, Boix C, James B, Sun N, He L, Patel A, Zhang Z, Molinie B, Van Wittenberghe N, Steelman S, Nusbaum C, Aguet F, Ardlie KG, Kellis M. Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease. Nat Genet 2023; 55:1665-1676. [PMID: 37770633 PMCID: PMC10562256 DOI: 10.1038/s41588-023-01509-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/22/2023] [Indexed: 09/30/2023]
Abstract
Genetic variants associated with complex traits are primarily noncoding, and their effects on gene-regulatory activity remain largely uncharacterized. To address this, we profile epigenomic variation of histone mark H3K27ac across 387 brain, heart, muscle and lung samples from Genotype-Tissue Expression (GTEx). We annotate 282 k active regulatory elements (AREs) with tissue-specific activity patterns. We identify 2,436 sex-biased AREs and 5,397 genetically influenced AREs associated with 130 k genetic variants (haQTLs) across tissues. We integrate genetic and epigenomic variation to provide mechanistic insights for disease-associated loci from 55 genome-wide association studies (GWAS), by revealing candidate tissues of action, driver SNPs and impacted AREs. Lastly, we build ARE-gene linking scores based on genetics (gLink scores) and demonstrate their unique ability to prioritize SNP-ARE-gene circuits. Overall, our epigenomic datasets, computational integration and mechanistic predictions provide valuable resources and important insights for understanding the molecular basis of human diseases/traits such as schizophrenia.
Collapse
Affiliation(s)
- Lei Hou
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xushen Xiong
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Yongjin Park
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Carles Boix
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Benjamin James
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Na Sun
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Liang He
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aman Patel
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Zhizhuo Zhang
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Benoit Molinie
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Scott Steelman
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chad Nusbaum
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - François Aguet
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Manolis Kellis
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| |
Collapse
|
3
|
Schreiber J, Boix C, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, Carman MJ, Pinoli P, Hong C, Yip KY, Spence JP, Batra SS, Song YS, Mahony S, Zhang Z, Tan W, Shen Y, Sun Y, Shi M, Adrian J, Sandstrom R, Farrell N, Halow J, Lee K, Jiang L, Yang X, Epstein C, Strattan JS, Bernstein B, Snyder M, Kellis M, Stafford W, Kundaje A. The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles. Genome Biol 2023; 24:79. [PMID: 37072822 PMCID: PMC10111747 DOI: 10.1186/s13059-023-02915-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/24/2023] [Indexed: 04/20/2023] Open
Abstract
A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best imputation methods and what measures meaningfully evaluate performance are open questions. We address these questions by comprehensively analyzing 23 methods from the ENCODE Imputation Challenge. We find that imputation evaluations are challenging and confounded by distributional shifts from differences in data collection and processing over time, the amount of available data, and redundancy among performance measures. Our analyses suggest simple steps for overcoming these issues and promising directions for more robust research.
Collapse
Affiliation(s)
| | - Carles Boix
- Stanford University School of Medicine, Stanford, CA, USA
| | - Jin Wook Lee
- Stanford University School of Medicine, Stanford, CA, USA
| | - Hongyang Li
- Stanford University School of Medicine, Stanford, CA, USA
| | - Yuanfang Guan
- Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | | | | | | | - Arif Canakoglu
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Luca Nanni
- Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Pietro Pinoli
- Stanford University School of Medicine, Stanford, CA, USA
| | - Chenyang Hong
- Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin Y Yip
- Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Yun S Song
- Stanford University School of Medicine, Stanford, CA, USA
| | - Shaun Mahony
- Stanford University School of Medicine, Stanford, CA, USA
| | - Zheng Zhang
- Stanford University School of Medicine, Stanford, CA, USA
| | - Wuwei Tan
- Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Shen
- Stanford University School of Medicine, Stanford, CA, USA
| | - Yuanfei Sun
- Stanford University School of Medicine, Stanford, CA, USA
| | - Minyi Shi
- Stanford University School of Medicine, Stanford, CA, USA
| | - Jessika Adrian
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Nina Farrell
- Stanford University School of Medicine, Stanford, CA, USA
| | - Jessica Halow
- Stanford University School of Medicine, Stanford, CA, USA
| | - Kristen Lee
- Stanford University School of Medicine, Stanford, CA, USA
| | - Lixia Jiang
- Stanford University School of Medicine, Stanford, CA, USA
| | - Xinqiong Yang
- Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | - Michael Snyder
- Stanford University School of Medicine, Stanford, CA, USA
| | - Manolis Kellis
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Anshul Kundaje
- Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
4
|
Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland J, Mudge J, Sisu C, Wright J, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, Calvet F, Cerdán-Vélez D, Cunningham F, Davidson C, Donaldson S, Dursun C, Fatima R, Giorgetti S, Giron C, Gonzalez J, Hardy M, Harrison P, Hourlier T, Hollis Z, Hunt T, James B, Jiang Y, Johnson R, Kay M, Lagarde J, Martin F, Gómez L, Nair S, Ni P, Pozo F, Ramalingam V, Ruffier M, Schmitt B, Schreiber J, Steed E, Suner MM, Sumathipala D, Sycheva I, Uszczynska-Ratajczak B, Wass E, Yang Y, Yates A, Zafrulla Z, Choudhary J, Gerstein M, Guigo R, Hubbard TJP, Kellis M, Kundaje A, Paten B, Tress M, Flicek P. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res 2022; 51:D942-D949. [PMID: 36420896 PMCID: PMC9825462 DOI: 10.1093/nar/gkac1071] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/15/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022] Open
Abstract
GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.
Collapse
Affiliation(s)
- Adam Frankish
- To whom correspondence should be addressed. Tel: +44 1223 494388; Fax: +44 1223 484696;
| | - Sílvia Carbonell-Sala
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cristina Sisu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Department of Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - James C Wright
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Carme Arnan
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abhimanyu Banerjee
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alexandra Bignell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carles Boix
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Ferriol Calvet
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Daniel Cerdán-Vélez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah Donaldson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cagatay Dursun
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stefano Giorgetti
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos Garcıa Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose Manuel Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Zoe Hollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Benjamin James
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Rory Johnson
- Department of Medical Oncology, Bern University Hospital, Murtenstrasse 35, 3008 Bern, Switzerland,School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
| | - Mike Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julien Lagarde
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura Martínez Gómez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Surag Nair
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Pengyu Ni
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Vivek Ramalingam
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bianca M Schmitt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jacob M Schreiber
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Emily Steed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dulika Sumathipala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Irina Sycheva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Barbara Uszczynska-Ratajczak
- Computational Biology of Noncoding RNA, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Elizabeth Wass
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yucheng T Yang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Zahoor Zafrulla
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Jyoti S Choudhary
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Roderic Guigo
- Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science andTechnology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, E-08003 Catalonia, Spain
| | - Tim J P Hubbard
- Department of Medical and Molecular Genetics, King's College London, Guys Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139,USA,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Palo Alto, CA, USA,Department of Computer Science, Stanford University, Palo Alto, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | - Michael L Tress
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| |
Collapse
|
5
|
Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Howe KL, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Riera FC, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Wolf MY, Xu J, Yang YT, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Tress ML, Flicek P. GENCODE 2021. Nucleic Acids Res 2021; 49:D916-D923. [PMID: 33270111 PMCID: PMC7778937 DOI: 10.1093/nar/gkaa1087] [Citation(s) in RCA: 475] [Impact Index Per Article: 158.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/21/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022] Open
Abstract
The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.
Collapse
Affiliation(s)
- Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cristina Sisu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.,Department of Bioscience, Brunel University London, Uxbridge UB8 3PH, UK
| | - James C Wright
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Joel Armstrong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alexandra Bignell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carles Boix
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.,Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Silvia Carbonell Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tomás Di Domenico
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sarah Donaldson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose Manuel Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tiago Grego
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Osagie G Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, University Hospital, University of Bern, Bern, Switzerland.,Department of Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura Martínez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Shamika Mohanan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Muir
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA.,Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Fabio C P Navarro
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Baikang Pei
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ferriol Calvet Riera
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bianca M Schmitt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eloise Stapleton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Irina Sycheva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Maxim Y Wolf
- Department of Biomedical Informatics at Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, MA 02115, USA
| | - Jinuri Xu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yucheng T Yang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.,Program in Computational Biology & Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Andrew Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yan Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.,Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Jyoti S Choudhary
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.,Program in Computational Biology & Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.,Department of Computer Science, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, E-08003 Catalonia, Spain
| | - Tim J P Hubbard
- Department of Medical and Molecular Genetics, King's College London, Guys Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, 32 Vassar St, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael L Tress
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| |
Collapse
|
6
|
Shim WJ, Sinniah E, Xu J, Vitrinel B, Alexanian M, Andreoletti G, Shen S, Sun Y, Balderson B, Boix C, Peng G, Jing N, Wang Y, Kellis M, Tam PPL, Smith A, Piper M, Christiaen L, Nguyen Q, Bodén M, Palpant NJ. Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity. Cell Syst 2020; 11:625-639.e13. [PMID: 33278344 PMCID: PMC7781436 DOI: 10.1016/j.cels.2020.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/31/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023]
Abstract
Determining genes that orchestrate cell differentiation in development and disease remains a fundamental goal of cell biology. This study establishes a genome-wide metric based on the gene-repressive trimethylation of histone H3 at lysine 27 (H3K27me3) across hundreds of diverse cell types to identify genetic regulators of cell differentiation. We introduce a computational method, TRIAGE, which uses discordance between gene-repressive tendency and expression to identify genetic drivers of cell identity. We apply TRIAGE to millions of genome-wide single-cell transcriptomes, diverse omics platforms, and eukaryotic cells and tissue types. Using a wide range of data, we validate the performance of TRIAGE in identifying cell-type-specific regulatory factors across diverse species including human, mouse, boar, bird, fish, and tunicate. Using CRISPR gene editing, we use TRIAGE to experimentally validate RNF220 as a regulator of Ciona cardiopharyngeal development and SIX3 as required for differentiation of endoderm in human pluripotent stem cells. A record of this paper’s transparent peer review process is included in the Supplemental Information. Perturbing genes controlling cell decisions have major implications in development or disease. However, identifying key regulatory genes from the thousands expressed in a cell is challenging. TRIAGE is a computational method that distills patterns of epigenetic repression across diverse cell types to infer regulatory genes using input gene expression data from any cell type. Demonstrating its utility, we combine single-cell RNA-seq and TRIAGE to identify and experimentally confirm novel regulators of heart development in evolutionarily distant species.
Collapse
Affiliation(s)
- Woo Jun Shim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Enakshi Sinniah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jun Xu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Burcu Vitrinel
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Michael Alexanian
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA
| | - Gaia Andreoletti
- Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, USA
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Brad Balderson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Carles Boix
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Guangdun Peng
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences and Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Naihe Jing
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences and Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yuliang Wang
- Paul G. Allen School of Computer Science and Engineering and Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA
| | | | - Patrick P L Tam
- The University of Sydney, Children's Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, Westmead, NSW 2145, Australia
| | - Aaron Smith
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia; Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
| |
Collapse
|
7
|
Sanz-Palau M, López-Sala A, Palacio-Navarro A, Turón M, Callejón-Póo L, Sans A, Póo P, Boix C, Colomé R. [Prognostic factors and profile in traumatic brain injury in the paediatric age]. Rev Neurol 2020; 70:235-245. [PMID: 32182370 DOI: 10.33588/rn.7007.2019393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Traumatic brain injury (TBI) is a common cause of death and disability in the paediatric population, although the literature on the Spanish population is scarce. From the perspective of early vulnerability, recent research findings suggest that early brain injury has worse sequelae and a higher risk of impact. AIMS To analyse the intelligence profile, executive functions and behaviour, and examine the association between age at the time of the injury, severity of the TBI and environmental factors for cognitive and behavioural outcomes. PATIENTS AND METHODS Seventy-one participants with moderate to severe TBI, from 6 to 16 years of age, were assessed with measures of intelligence (intelligence quotient), executive functions and behaviour. RESULTS Children with TBI are at increased risk of disability in all aspects of intelligence, executive functions and behaviour. Children who suffered a traumatic brain injury in infancy and the preschool period had more overall effects on intelligence quotient and some aspects of the executive functions. CONCLUSIONS Socioeconomic and cultural factors are the best predictors for intelligence quotient and behaviour. These findings contribute to a better understanding of the sequelae of TBI in children, which will help in rehabilitation planning and re-adaptation to functional life.
Collapse
Affiliation(s)
- M Sanz-Palau
- Hospital Universitari Sant Joan de Déu, Esplugues de Llobregat, España
| | - A López-Sala
- Hospital Universitari Sant Joan de Déu, Esplugues de Llobregat, España
| | - A Palacio-Navarro
- Hospital Universitari Sant Joan de Déu, Esplugues de Llobregat, España
| | - M Turón
- Hospital Universitari Sant Joan de Déu, Esplugues de Llobregat, España
| | - L Callejón-Póo
- Hospital Universitari Sant Joan de Déu, Esplugues de Llobregat, España
| | - A Sans
- Hospital Universitari Sant Joan de Déu, Esplugues de Llobregat, España
| | - P Póo
- Hospital Universitari Sant Joan de Déu, Esplugues de Llobregat, España
| | - C Boix
- Hospital Universitari Sant Joan de Déu, Esplugues de Llobregat, España
| | - R Colomé
- Hospital Universitari Sant Joan de Déu, Esplugues de Llobregat, España
| |
Collapse
|
8
|
Botero-Coy AM, Martínez-Pachón D, Boix C, Rincón RJ, Castillo N, Arias-Marín LP, Manrique-Losada L, Torres-Palma R, Moncayo-Lasso A, Hernández F. 'An investigation into the occurrence and removal of pharmaceuticals in Colombian wastewater'. Sci Total Environ 2018; 642:842-853. [PMID: 30045524 DOI: 10.1016/j.scitotenv.2018.06.088] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 06/06/2018] [Accepted: 06/08/2018] [Indexed: 05/25/2023]
Abstract
In this work, the presence of 20 pharmaceuticals in wastewater from Colombia is investigated. Several widely consumed compounds have been detected in wastewater samples from different origins and geographical areas in Colombia. The studied pharmaceuticals included antibiotics, analgesics and anti-inflammatories, cholesterol lowering statin drugs, lipid regulators, and anti-depressants. The investigated samples were urban wastewater collected during one whole week before (influent) and after treatment (effluent) in the wastewater treatment plants (WWTPs) of Bogotá and Medellin. Raw wastewater from the Hospital of Tumaco and from the city of Florencia were also collected. Analyses performed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that most of the target analytes were present in all the wastewater samples. The highest concentrations (up to 50 μg/L) corresponded to acetaminophen, but several antibiotics, such as azithromycin, ciprofloxacin and norfloxacin, and antihypertensive drugs, such as losartan and valsartan, were commonly present in influent wastewater (IWW) at levels above 1 μg/L. Moreover, the treatment applied in WWTPs seemed to not efficiently remove the compounds under study, because most pharmaceuticals were also present in effluent wastewater (EWW) at concentrations close to those of the IWW. Special emphasis was made in this work on the quality of data reported, performing a detailed study of quality control (QC) samples. The analytical approach used -direct injection of 5-fold diluted samples without any additional treatment - is simpler and faster than the commonly applied solid phase extraction (SPE). The use of 12 isotope-labelled internal standards ensured the satisfactory correction of matrix effects for the corresponding analytes. For the remaining 8 compounds, no drastic matrix effects were observed, and only four compounds (cloxacillin, doxycycline, losartan, tetracycline) presented QC recoveries near or slightly below 60%, revealing ionization suppression, particularly in the IWW. Data on the occurrence of pharmaceuticals reported in this paper are the basis for current studies that aim to develop efficient systems for the degradation/removal of these compounds from the aquatic environment.
Collapse
Affiliation(s)
- A M Botero-Coy
- Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón, Spain
| | - D Martínez-Pachón
- Grupo de Investigación en Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá D.C., Colombia
| | - C Boix
- Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón, Spain
| | - R J Rincón
- Grupo de Investigación en Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá D.C., Colombia
| | - N Castillo
- Grupo de Investigación en Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá D.C., Colombia
| | - L P Arias-Marín
- Grupo Bioprocesos Microbianos (Biomicro), Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - L Manrique-Losada
- Grupo de Investigación en Materiales, Ambiente y Desarrollo (MADE), Facultad de Ciencias Básicas, Universidad de la Amazonia, Florencia, Colombia
| | - R Torres-Palma
- Grupo de Investigación en Remediación Ambiental y Biocatálisis (GIRAB), Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - A Moncayo-Lasso
- Grupo de Investigación en Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá D.C., Colombia.
| | - F Hernández
- Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón, Spain.
| |
Collapse
|
9
|
Leventhal GE, Boix C, Kuechler U, Enke TN, Sliwerska E, Holliger C, Cordero OX. Strain-level diversity drives alternative community types in millimetre-scale granular biofilms. Nat Microbiol 2018; 3:1295-1303. [DOI: 10.1038/s41564-018-0242-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 08/07/2018] [Indexed: 01/12/2023]
|
10
|
Charpentier M, Khedher AHY, Menoret S, Brion A, Lamribet K, Dardillac E, Boix C, Perrouault L, Tesson L, Geny S, De Cian A, Itier JM, Anegon I, Lopez B, Giovannangeli C, Concordet JP. CtIP fusion to Cas9 enhances transgene integration by homology-dependent repair. Nat Commun 2018; 9:1133. [PMID: 29556040 PMCID: PMC5859065 DOI: 10.1038/s41467-018-03475-7] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 02/16/2018] [Indexed: 12/18/2022] Open
Abstract
In genome editing with CRISPR-Cas9, transgene integration often remains challenging. Here, we present an approach for increasing the efficiency of transgene integration by homology-dependent repair (HDR). CtIP, a key protein in early steps of homologous recombination, is fused to Cas9 and stimulates transgene integration by HDR at the human AAVS1 safe harbor locus. A minimal N-terminal fragment of CtIP, designated HE for HDR enhancer, is sufficient to stimulate HDR and this depends on CDK phosphorylation sites and the multimerization domain essential for CtIP activity in homologous recombination. HDR stimulation by Cas9-HE, however, depends on the guide RNA used, a limitation that may be overcome by testing multiple guides to the locus of interest. The Cas9-HE fusion is simple to use and allows obtaining twofold or more efficient transgene integration than that with Cas9 in several experimental systems, including human cell lines, iPS cells, and rat zygotes.
Collapse
Affiliation(s)
- M Charpentier
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - A H Y Khedher
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
- Translational Sciences, Sanofi, 13 Quai Jules Guesde, F-94400, Vitry-sur-Seine, France
| | - S Menoret
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, CHU de Nantes, 30 Avenue Jean Monnet, F-44093, Nantes, France
| | - A Brion
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - K Lamribet
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - E Dardillac
- Equipe Labellisée Ligue Contre le Cancer, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, CNRS UMR 8200, 114 rue Edouard Vaillant, Villejuif, F-94805, France
| | - C Boix
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - L Perrouault
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - L Tesson
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, CHU de Nantes, 30 Avenue Jean Monnet, F-44093, Nantes, France
| | - S Geny
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - A De Cian
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - J M Itier
- Translational Sciences, Sanofi, 13 Quai Jules Guesde, F-94400, Vitry-sur-Seine, France
| | - I Anegon
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, CHU de Nantes, 30 Avenue Jean Monnet, F-44093, Nantes, France
| | - B Lopez
- Equipe Labellisée Ligue Contre le Cancer, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, CNRS UMR 8200, 114 rue Edouard Vaillant, Villejuif, F-94805, France
| | - C Giovannangeli
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - J P Concordet
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France.
| |
Collapse
|
11
|
Gil Solsona R, Boix C, Ibáñez M, Sancho JV. The classification of almonds (Prunus dulcis) by country and variety using UHPLC-HRMS-based untargeted metabolomics. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2018; 35:395-403. [DOI: 10.1080/19440049.2017.1416679] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- R. Gil Solsona
- Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón, Spain
| | - C. Boix
- Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón, Spain
| | - M. Ibáñez
- Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón, Spain
| | - J. V. Sancho
- Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón, Spain
| |
Collapse
|
12
|
Ibáñez M, Borova V, Boix C, Aalizadeh R, Bade R, Thomaidis NS, Hernández F. UHPLC-QTOF MS screening of pharmaceuticals and their metabolites in treated wastewater samples from Athens. J Hazard Mater 2017; 323:26-35. [PMID: 27052479 DOI: 10.1016/j.jhazmat.2016.03.078] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/16/2016] [Accepted: 03/28/2016] [Indexed: 05/25/2023]
Abstract
After consumption, pharmaceuticals are excreted as parent compounds and/or metabolites in urine and faeces. Some are not completely removed during wastewater treatments, forcing sewage treatment plants (STPs) to apply alternative technologies to guarantee quality of treated water. To monitor the removal efficiency of STPs, not only unchanged compounds and metabolites have to be taken into account, but also formation of possible transformation products (TPs). In this work, QTOF MS has been used for screening metabolites/TPs of pharmaceuticals in effluent wastewater from Athens. A customised database was built with the exact masses of metabolites reported in literature for the parent drugs found in an initial screening. Additionally, TPs identified in previous degradation experiments performed at our laboratory were included. Up to 34 metabolites/TPs were detected for omeprazole, venlafaxine, clindamycin, clarithromycin, clopidogrel or dipyrone, among others. Seven corresponded to TPs whose reference standards were available at our lab, seven were TPs previously identified in laboratory degradation experiments, eight were TPs tentatively identified by QTOF MS without reference standards, and twelve TPs were discovered after using the common fragmentation pathway approach. Tentative identification of TPs was supported by prediction of their chromatographic retention time based on the use of advanced chemometric QSRR models.
Collapse
Affiliation(s)
- M Ibáñez
- Research Institute for Pesticides and Water, University Jaume I, Castellón 12071, Spain
| | - V Borova
- Department of Chemistry, National and Kapodistrian University of Athens, Athens 157 84, Greece
| | - C Boix
- Research Institute for Pesticides and Water, University Jaume I, Castellón 12071, Spain
| | - R Aalizadeh
- Department of Chemistry, National and Kapodistrian University of Athens, Athens 157 84, Greece
| | - R Bade
- Research Institute for Pesticides and Water, University Jaume I, Castellón 12071, Spain
| | - N S Thomaidis
- Department of Chemistry, National and Kapodistrian University of Athens, Athens 157 84, Greece
| | - F Hernández
- Research Institute for Pesticides and Water, University Jaume I, Castellón 12071, Spain.
| |
Collapse
|
13
|
Boix C, Ibáñez M, Fabregat-Safont D, Morales E, Pastor L, Sancho JV, Sánchez-Ramírez JE, Hernández F. Behaviour of emerging contaminants in sewage sludge after anaerobic digestion. Chemosphere 2016; 163:296-304. [PMID: 27543679 DOI: 10.1016/j.chemosphere.2016.07.098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/22/2016] [Accepted: 07/29/2016] [Indexed: 05/20/2023]
Abstract
Nowadays, there is an increasing concern over the presence of contaminants in the aquatic environment, where they can be introduced from wastewater after their incomplete removal in the treatment plants. In this work, degradation of selected emerging pollutants in the aqueous and solid phases of sewage sludge has been investigated after anaerobic digestion using two different digesters: mesophilic and thermophilic. Initially, sludge samples were screened by ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOF MS) for identification of emerging contaminants in the samples. In a second step, a target quantitative method based on LC coupled to tandem MS was applied for selected pollutants identified in the previous screening. The behaviour of the compounds under anaerobic conditions was studied estimating the degradation efficiency and distribution of compounds between both sludge phases. Irbesartan and benzoylecgonine seemed to be notably degraded in both phases of the sludge. Venlafaxine showed a significant concentration decrease in the aqueous phase in parallel to an increase in the solid phase. The majority of the compounds showed an increase of their concentrations in both phases after the digestion. Concentrations in the solid phase were commonly higher than in the aqueous for most contaminants, indicating that they were preferentially adsorbed onto the solid particles.
Collapse
Affiliation(s)
- C Boix
- Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat, E-12071, Castellón, Spain
| | - M Ibáñez
- Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat, E-12071, Castellón, Spain
| | - D Fabregat-Safont
- Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat, E-12071, Castellón, Spain
| | - E Morales
- Depuración de Aguas del Mediterráneo, Avda. Benjamin Franklin 21 Parque Tecnológico, Paterna, Spain
| | - L Pastor
- Depuración de Aguas del Mediterráneo, Avda. Benjamin Franklin 21 Parque Tecnológico, Paterna, Spain
| | - J V Sancho
- Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat, E-12071, Castellón, Spain
| | - J E Sánchez-Ramírez
- Depuración de Aguas del Mediterráneo, Avda. Benjamin Franklin 21 Parque Tecnológico, Paterna, Spain
| | - F Hernández
- Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat, E-12071, Castellón, Spain.
| |
Collapse
|
14
|
Boix C, Ibáñez M, Fabregat-Safont D, Morales E, Pastor L, Sancho JV, Sánchez-Ramírez JE, Hernández F. Analytical methodologies based on LC-MS/MS for monitoring selected emerging compounds in liquid and solid phases of the sewage sludge. MethodsX 2016; 3:333-42. [PMID: 27222823 PMCID: PMC4865632 DOI: 10.1016/j.mex.2016.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In this work, two analytical methodologies based on liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) were developed for quantification of emerging pollutants identified in sewage sludge after a previous wide-scope screening. The target list included 13 emerging contaminants (EC): thiabendazole, acesulfame, fenofibric acid, valsartan, irbesartan, salicylic acid, diclofenac, carbamazepine, 4-aminoantipyrine (4-AA), 4-acetyl aminoantipyrine (4-AAA), 4-formyl aminoantipyrine (4-FAA), venlafaxine and benzoylecgonine. The aqueous and solid phases of the sewage sludge were analyzed making use of Solid-Phase Extraction (SPE) and UltraSonic Extraction (USE) for sample treatment, respectively. The methods were validated at three concentration levels: 0.2, 2 and 20 μg L−1 for the aqueous phase, and 50, 500 and 2000 μg kg−1 for the solid phase of the sludge. In general, the method was satisfactorily validated, showing good recoveries (70–120%) and precision (RSD < 20%). Regarding the limit of quantification (LOQ), it was below 0.1 μg L−1 in the aqueous phase and below 50 μg kg−1 in the solid phase for the majority of the analytes. The method applicability was tested by analysis of samples from a wider study on degradation of emerging pollutants in sewage sludge under anaerobic digestion. The key benefits of these methodologies are: • SPE and USE are appropriate sample procedures to extract selected emerging contaminants from the aqueous phase of the sewage sludge and the solid residue. • LC–MS/MS is highly suitable for determining emerging contaminants in both sludge phases. • Up to our knowledge, the main metabolites of dipyrone had not been studied before in sewage sludge.
Collapse
Affiliation(s)
- C Boix
- Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat, E-12071 Castellón, Spain
| | - M Ibáñez
- Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat, E-12071 Castellón, Spain
| | - D Fabregat-Safont
- Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat, E-12071 Castellón, Spain
| | - E Morales
- Depuración de Aguas del Mediterráneo, Avda. Benjamin Franklin 21 Parque Tecnológico, Paterna, Spain
| | - L Pastor
- Depuración de Aguas del Mediterráneo, Avda. Benjamin Franklin 21 Parque Tecnológico, Paterna, Spain
| | - J V Sancho
- Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat, E-12071 Castellón, Spain
| | - J E Sánchez-Ramírez
- Depuración de Aguas del Mediterráneo, Avda. Benjamin Franklin 21 Parque Tecnológico, Paterna, Spain
| | - F Hernández
- Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat, E-12071 Castellón, Spain
| |
Collapse
|
15
|
Boix C, Ibáñez M, Zamora T, Sancho JV, Niessen WMA, Hernández F. Identification of new omeprazole metabolites in wastewaters and surface waters. Sci Total Environ 2014; 468-469:706-714. [PMID: 24061062 DOI: 10.1016/j.scitotenv.2013.08.095] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 06/02/2023]
Abstract
Omeprazole is one of the world-wide most consumed pharmaceuticals for treatment of gastric diseases. As opposed to other frequently used pharmaceuticals, omeprazole is scarcely detected in urban wastewaters and environmental waters. This was corroborated in a previous research, where parent omeprazole was not detected while four transformation products (TPs), mainly resulting from hydrolysis, were found in effluent wastewaters and surface waters. However, the low abundance of omeprazole TPs in the water samples together with the fact that omeprazole suffers an extensive metabolism, with a wide range of excretion rates (between 0.01 and 30%), suggests that human urinary metabolites should be investigated in the water environment. In this work, the results obtained in excretion tests after administration of a 40 mg omeprazole dose in three healthy volunteers are reported. Analysis by liquid chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry (LC-QTOF MS) reported low concentrations of omeprazole in urine. Up to twenty-four omeprazole metabolites (OMs) were detected and tentatively elucidated. The most relevant OM was an omeprazole isomer, which obviously presented the same exact mass (m/z 346.1225), but also shared a major common fragment at m/z 198.0589. Subsequent analyses of surface water and effluent wastewater samples by both LC-QTOF MS and LC-MS/MS with triple quadrupole revealed that this metabolite (named as OM10) was the compound most frequently detected in water samples, followed by OM14a and OM14b. Up to our knowledge, OM10 had not been used before as urinary biomarker of omeprazole in waters. On the contrary, parent omeprazole was never detected in any of the water samples. After this research, it seems clear that monitoring the presence of omeprazole in the aquatic environment should be focused on the OMs suggested in this article instead of the parent compound.
Collapse
Affiliation(s)
- C Boix
- Research Institute for Pesticides and Water, University Jaume I, Avda. Sos Baynat, E-12071 Castellón, Spain
| | | | | | | | | | | |
Collapse
|
16
|
Boix C, Ibáñez M, Sancho JV, Niessen WMA, Hernández F. Investigating the presence of omeprazole in waters by liquid chromatography coupled to low and high resolution mass spectrometry: degradation experiments. J Mass Spectrom 2013; 48:1091-100. [PMID: 24130012 DOI: 10.1002/jms.3260] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/29/2013] [Accepted: 08/04/2013] [Indexed: 05/12/2023]
Abstract
Omeprazole is one of the most consumed pharmaceuticals around the world. However, this compound is scarcely detected in urban wastewater and surface water. The absence of this pharmaceutical in the aquatic ecosystem might be due to its degradation in wastewater treatment plants, as well as in receiving water. In this work, different laboratory-controlled degradation experiments have been carried out on surface water in order to elucidate generated omeprazole transformation products (TPs). Surface water spiked with omeprazole was subjected to hydrolysis, photo-degradation under both sunlight and ultraviolet radiation and chlorination. Analyses by liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QTOF MS) permitted identification of up to 17 omeprazole TPs. In a subsequent step, the TPs identified were sought in surface water and urban wastewater by LC-QTOF MS and by LC coupled to tandem mass spectrometry with triple quadrupole. The parent omeprazole was not detected in any of the samples, but four TPs were found in several water samples. The most frequently detected compound was OTP 5 (omeprazole sulfide), which might be a reasonable candidate to be included in monitoring programs rather than the parent omeprazole.
Collapse
Affiliation(s)
- C Boix
- Research Institute for Pesticides and Water, Universitat Jaume I, Avda. Sos Baynat, E-12071, Castellon, Spain
| | | | | | | | | |
Collapse
|
17
|
López-Sala A, Palacio-Navarro A, Donaire A, García G, Colomé R, Boix C, Sans A, Campistol J, Sanmartí FX. [Predictive variables for mental retardation in a Pediatric Epilepsy Monitoring Unit. Neuropsychological assessment]. Rev Neurol 2010; 50 Suppl 3:S59-S67. [PMID: 20200849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
AIM We sought to describe the epidemiological and clinical data from our patients in the Pediatric Epilepsy Monitoring Unit (PEMU) of the Sant Joan de Deu Hospital of Barcelona, and determine the variables of risk for mental retardation. PATIENTS AND METHODS A retrospective review of PEMU reports and hospital discharge summaries from March 2005 to December 2008 was conducted. The data from patients with intelligence quotient (IQ) estimated, older than 3 years of age and with epileptic electroencephalography (EEG) activity was analyzed in 158 patients (8.8 +/- 5.2 years; 55.1% boys). Of those pediatric patients, 63 had IQ less than 70 and 47 an IQ greater than or equal to 70. Intractable epilepsy was present in all of them. RESULTS The percentage of the patients with mental retardation is significantly higher in patients with onset of epilepsy before 24 months (68.3%) than patients with later onset (27.7%). Onset of seizures, EEG findings and epilepsy etiology are significant risk factors for mental retardation. CONCLUSIONS Early age at seizure, multifocal epilepsy and cryptogenic etiology are factors of worse prognosis to normal development of cognitive functions in pediatric intractable epilepsy.
Collapse
Affiliation(s)
- A López-Sala
- Hospital Sant Joan de Déu, Esplugues de Llobregat, España.
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Gassió R, Vilaseca MA, Lambruschini N, Boix C, Fusté ME, Campistol J. Cognitive functions in patients with phenylketonuria in long-term treatment with tetrahydrobiopterin. Mol Genet Metab 2010; 99 Suppl 1:S75-8. [PMID: 20123475 DOI: 10.1016/j.ymgme.2009.10.187] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 10/27/2009] [Accepted: 10/29/2009] [Indexed: 11/24/2022]
Abstract
Cognitive functions were assessed in 9 patients with mild to moderate phenylketonuria (PKU) ranging from 6 to 18 years of age, who were in long-term treatment (>5 years) with 5-9 mg/kg/day tetrahydrobiopterin (BH4) on compassionate use, provided by Schircks Inc. An extensive study of cognitive functions (intelligence quotient (IQ), visuospatial, visual memory, fine motor, executive and attentional functions) was conducted, and behavior was assessed using the ADHD Rating Scale and the Behavior Rating Inventory of Executive Function (BRIEF). All patients had normal IQ (M=107, SD=10). The most notable area of impairment was fine motor function, but no significant difference was found between the PKU patients in BH4 treatment who participated in the current study and PKU patients in dietary treatment who participated in a previous study. These results, however, should be interpreted with caution. It is necessary to conduct further studies with a larger number of patients, using more sensitive tests of motor function and using the formulation of BH4 that is currently available.
Collapse
Affiliation(s)
- R Gassió
- Neuropediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Spain.
| | | | | | | | | | | |
Collapse
|
19
|
Colomé R, Sans A, López-Sala A, Boix C. [Non-verbal learning disorder: cognitive-behavioural characteristics and neuropsychological aspects]. Rev Neurol 2009; 48 Suppl 2:S77-S81. [PMID: 19280579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
INTRODUCTION AND DEVELOPMENT Non verbal learning disorder is a neurological condition which is considered to be a developmental disability. It is characterised by a specific dysfunction in motor, visuospatial and social skills in patients with a normal intellect and development of language. Warning signs in school are poor psychomotor coordination, arithmetic skills and drawing activities. Social judgment and social problem solving are also typically impaired. Furthermore, these patients seem to have increasing risk of emotional disorders. CONCLUSIONS Current evidence and theories suggest that dysfunction of white matter in the right hemisphere could be the cause. The clinical characteristics and the diagnostic criteria have not fully agreed on. A comprehensive neuropsychological evaluation reveals specific and heterogeneous patterns of difficulties for each child that would make possible to address and accommodate an educational program.
Collapse
Affiliation(s)
- R Colomé
- Servicio de Neurología, Unidad de Trastornos de Aprendizaje Escolar (UTAE), Hospital Sant Joan de Déu, Barcelona, España.
| | | | | | | |
Collapse
|
20
|
Sans A, Colomé R, López-Sala A, Boix C. [Neuropsychological aspects of acquired diffuse brain injury in paediatric childhood]. Rev Neurol 2009; 48 Suppl 2:S23-S26. [PMID: 19280569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
INTRODUCTION AND DEVELOPMENT Acquired brain injury is one of the most common causes of long-term disability in childhood and traumatisms are the most prevalent cause. Diffuse axonal injury is associated with poor neuropsychological outcome. In contrast to early focal lesions, young age confers no advantage in the outcome of severe diffuse brain injury. Plasticity is incomplete for structural and functional deficits in children. The traditional view of enhanced reorganization of function after localized brain injury it can't be applied in early severe diffuse brain injury. In the paediatric population where the central nervous system is in a rapid state of growth, developmental factors may mask the difficulties and deficits in certain skills may not be evident until that skill is expected to emerge at a certain age. CONCLUSION Like in adults the neuropsychological domains more affected in childhood are psychomotor speed, memory, attention and executive functioning. In childhood neuropsychological deficits will affect learning and adaptive behaviour. Sometimes deficits will be cumulative over time.
Collapse
Affiliation(s)
- A Sans
- Servicio de Neurología, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, España.
| | | | | | | |
Collapse
|
21
|
Behar G, Siberil S, Groulet A, Chames P, Pugniere M, Boix C, Sautes-Fridman C, Teillaud JL, Baty D. Isolation and characterization of anti-Fc RIII (CD16) llama single-domain antibodies that activate natural killer cells. Protein Eng Des Sel 2007; 21:1-10. [DOI: 10.1093/protein/gzm064] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
22
|
Mueller C, Boix C, Fournier E, Kwan W, Daussy C, Fridman W, Molina T. Rôle crucial des monocytes dans la survie et la prolifération des cellules lymphoïdes B humaines normales et des lymphomes diffus à grandes cellules B. Ann Pathol 2006. [DOI: 10.1016/s0242-6498(06)78451-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
23
|
Siberil S, Dutertre CA, Boix C, Teillaud JL. Anticorps monoclonaux à usage thérapeutique : un peu d'histoire, beaucoup d'ingénierie, et … quelques succès cliniques. Transfus Clin Biol 2005; 12:114-22. [PMID: 15907389 DOI: 10.1016/j.tracli.2005.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Indexed: 10/25/2022]
Abstract
Thirty years after their discovery by Milstein and Köhler, monoclonal antibodies have now come of age as therapeutics. Nineteen monoclonal antibodies are on the market and/or have got authorization to be used for the treatment of severe diseases. Many technical efforts have been devoted over the last two decades to the generation of second generation mAbs with better affinities, decreased immunogenicity and optimized effector functions. The development of molecular engineering techniques applied to antibody molecules has also made it possible to design bi-specific antibodies and fusion molecules exhibiting different modules with bi-functional activities. The use of proteomics and genomics combined with phage display allows now the rapid selection of antibodies directed against new targets at a high rate. Many efforts are currently focused on the selection of high-responder patients, the optimization of antibody delivery, schemes of infusion, antibody pharmaco-kinetics and bio-distribution, as well as on a better control of the severe side-effects generated by some antibody treatments.
Collapse
MESH Headings
- Animals
- Antibodies, Bispecific/immunology
- Antibodies, Bispecific/therapeutic use
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal/adverse effects
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibody Affinity
- Antigen-Antibody Reactions
- Cell Line, Transformed/immunology
- Clinical Trials as Topic
- Herpesvirus 4, Human
- History, 20th Century
- Humans
- Hybridomas/immunology
- Immunoglobulin Fragments/chemistry
- Immunoglobulin Fragments/immunology
- Immunotherapy/history
- Immunotherapy/methods
- Immunotherapy/trends
- Mice
- Peptide Library
- Protein Engineering
- Rats
- Recombinant Fusion Proteins/therapeutic use
- Species Specificity
Collapse
Affiliation(s)
- S Siberil
- Unité Inserm 255, université Paris-VI-Pierre-et-Marie-Curie, centre de recherches biomédicales des Cordeliers, France
| | | | | | | |
Collapse
|
24
|
Sans A, Boix C, Colomé R, Campistol J. [The contribution of the cerebellum to cognitive function in childhood]. Rev Neurol 2002; 35:235-7. [PMID: 12235585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
INTRODUCTION Cerebellum traditionally has been considered as a neural structure dedicated to motor control. Published studies in the last decades suggest that the cerebellum has an important role in behaviour and cognition specially in paediatric age. OBJECTIVE We review the cerebellum role in cognitive function in developmental and acquired cerebellar pathology.
Collapse
Affiliation(s)
- A Sans
- Unitat Integrada Clinic-Sant-Joan de Déu, Esplugues de Llobregat, Barcelona, España.
| | | | | | | |
Collapse
|
25
|
Sans A, Boix C, López-Sala A, Póo P, Abenia P, Maristany M, Campistol J. [Visuo-constructive disorders in periventricular leukomalacia]. Rev Neurol 2002; 34 Suppl 1:S34-7. [PMID: 12447787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
INTRODUCTION Cerebral palsy involves not only motor impairment but also the impairment of cognitive functions. Visuo spatial impairment has often been reported in preterm children with spastic diplegia due to periventricular leukomalacia. PATIENTS AND METHODS Eight children with periventricular leukomalacia diagnosis. When examined their ages were between 3 and 13 years. RESULTS We found visuo spatial anomalies in all subjects. These anomalies don't result in reading and writing learning difficulties. CONCLUSION Constructional dyspraxia is frequently found in children with periventricular leukomalacia and correlates with reduction of peritrigonal white matter in parietal lobe.
Collapse
Affiliation(s)
- A Sans
- Servicio de Neurología, Unitat Integrada Clínic-Sant Joan de Déu, Barcelona, Spain.
| | | | | | | | | | | | | |
Collapse
|
26
|
Boix C, Calvo A, Imeson AC, Schoorl JM, Soto S, Tiemessen IR. Properties and erosional response of soils in a degraded ecosystem in Crete (Greece). Environ Monit Assess 1995; 37:79-92. [PMID: 24197841 DOI: 10.1007/bf00546881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
To study desertification processes relating to soil erosion, a climatological and altitudinal gradient from south to north was selected in Crete (Greece) and four locations were selected along the gradient. At the locations precipitation ranged from 1400 mm/year at the highest location to 400 mm/year at the lowest. All locations are affected by the actual land use: intensive grazing, small controlled fires, and abandoned agricultural terraces. Representative soil profiles were described in the field and analyzed in the laboratory, and rainfall simulation experiments in the field measured soil erosion over different soil surfaces and land uses. Data on physical and chemical properties were obtained from the soil profiles and soil hydrology, and erosion data were obtained from the rainfall simulation experiments. Soil aggregation was studied with samples taken from the soil in the rainfall simulation plots and special attention being paid to the aggregate size distribution and the water-stable microaggregation. The interaction between climatological conditions and land use seems to be the main factor controlling soil erosion. This paper describes how the expected erosion along the gradient (from the most humid to the driest site) can be affected and disturbed by specific processes derived from land use.
Collapse
Affiliation(s)
- C Boix
- Fysisch Geografisch Bodemkundig Laboratorium, Landscape and Environmental Research Group, Universiteit van Amsterdam, Nieuwe Prinsengracht 130, 1018 VZ, Amsterdam, The Netherlands
| | | | | | | | | | | |
Collapse
|
27
|
Boix C, Calvo A, Cerdá A, Imeson A, Soriano M, Tiemessen I. Vulnerability of Mediterranean ecosystems to Climatic Change, study of soil degradation under different climatological conditions in an altitudinal transect in the south east of Spain. Studies in Environmental Science 1995. [DOI: 10.1016/s0166-1116(06)80105-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
|
28
|
Gené J, Espínola A, Cabezas C, Boix C, Comín E, Martin A, Sanz E. Do knowledge and attitudes about influenza and its immunization affect the likelihood of obtaining immunization? Fam Pract Res J 1992; 12:61-73. [PMID: 1549948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A telephone survey was conducted on 190 patients in Barcelona, Spain, at high-risk for influenza to evaluate the relationship between their knowledge and attitudes toward influenza and influenza immunization and whether they received the immunization. A discriminant function correlates (r = 0.86) with the immunization behavior and predicts the behavior before flu immunization in 84% of cases if we know the previous immunization behavior and adequately classifies the behavior in 82% if we don't know it (r = 0.75). Modifiable factors that predict immunization are self-identification as high-risk, belief that the immunization will not cause discomfort, intention to be immunized, and physician assigned. Those not immunized had a prevalent feeling that the shot is not effective, that they are not susceptible to the illness, and that the health center does not offer satisfactory organization to provide immunization. Furthermore, they felt that they had received controversial information through the mass media. We therefore believe that health education activities regarding influenza immunization should be specifically directed to increasing awareness of those who belong to a high-risk group, as well as to emphasizing susceptibility to the illness and the innocuousness of the immunization.
Collapse
Affiliation(s)
- J Gené
- Family and Community Medicine Training Program, Barcelona Primary Health Care Center, Spain
| | | | | | | | | | | | | |
Collapse
|
29
|
Cabezas C, Martín A, Comín E, Sabrià J, Boix C, Espínola A, Sanz E, Gené J. [Compliance of antibiotic treatment in primary health care. Value of the personalized prescription]. Rev Clin Esp 1989; 185:366-9. [PMID: 2695999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A controlled clinical study was carried out in order to evaluate the efficacy of a personalized prescription as a measure to improve the fulfillment of a short course antibiotic treatment. 180 patients completed the study (96 in the active group and 88 in the control group) finding no differences in selected variables between the two groups. Evaluation of treatment fulfillment was performed with an interview and counting the pills, finding with this method that 57.94% of the patients fulfilled the treatment. Except for a higher incidence of adverse side effects in the control group (p less than 0.05) no other significant differences were found between the two groups. The interview showed a 37% sensibility and a 97% specificity, which was specially usefull in the detection of nonfulfillers. The correlation coefficient between both groups was 0.66 (p less than 0.001). Our results suggest that the personalized prescription does not improve the patient compliance achieved by a good verbal information in the short course antibiotic treatment.
Collapse
|