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Kolomenski JE, Delea M, Simonetti L, Fabbro MC, Espeche LD, Taboas M, Nadra AD, Bruque CD, Dain L. An update on genetic variants of the NKX2-5. Hum Mutat 2020; 41:1187-1208. [PMID: 32369864 DOI: 10.1002/humu.24030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 04/03/2020] [Accepted: 04/26/2020] [Indexed: 12/13/2022]
Abstract
NKX2-5 is a homeodomain transcription factor that plays a crucial role in heart development. It is the first gene where a single genetic variant (GV) was found to be associated with congenital heart diseases in humans. In this study, we carried out a comprehensive survey of NKX2-5 GVs to build a unified, curated, and updated compilation of all available GVs. We retrieved a total of 1,380 unique GVs. From these, 970 had information on their frequency in the general population and 143 have been linked to pathogenic phenotypes in humans. In vitro effect was ascertained for 38 GVs. The homeodomain had the biggest cluster of pathogenic variants in the protein: 49 GVs in 60 residues, 23 in its third α-helix, where 11 missense variants may affect protein-DNA interaction or the hydrophobic core. We also pinpointed the likely location of pathogenic GVs in four linear motifs. These analyses allowed us to assign a putative explanation for the effect of 90 GVs. This study pointed to reliable pathogenicity for GVs in helix 3 of the homeodomain and may broaden the scope of functional and structural studies that can be done to better understand the effect of GVs in NKX2-5 function.
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Affiliation(s)
- Jorge E Kolomenski
- Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biología Traslacional, iB3, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marisol Delea
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | - Leandro Simonetti
- Department of Chemistry-Biomedical Centre, Uppsala University, Uppsala, Sweden
| | | | - Lucía D Espeche
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | - Melisa Taboas
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina
| | - Alejandro D Nadra
- Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biología Traslacional, iB3, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Carlos D Bruque
- Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina.,Instituto de Biología y Medicina Experimental, (IBYME-CONICET), Buenos Aires, Argentina
| | - Liliana Dain
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Instituto de Biociencias, Biotecnología y Biología Traslacional, iB3, Universidad de Buenos Aires, Buenos Aires, Argentina.,Centro Nacional de Genética Médica, ANLIS, Buenos Aires, Argentina.,Instituto de Biología y Medicina Experimental, (IBYME-CONICET), Buenos Aires, Argentina
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Carbonetto B, Fabbro MC, Sciara M, Seravalle A, Méjico G, Revale S, Romero MS, Brun B, Fay M, Fay F, Vazquez MP. Human Microbiota of the Argentine Population- A Pilot Study. Front Microbiol 2016; 7:51. [PMID: 26870014 PMCID: PMC4733923 DOI: 10.3389/fmicb.2016.00051] [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] [Received: 10/30/2015] [Accepted: 01/12/2016] [Indexed: 12/21/2022] Open
Abstract
The human microbiota is the collection of microorganisms living in or on the human body. An imbalance or dysbiosis in these microbial communities can be associated with a wide variety of human diseases (Petersen and Round, 2014; Pham and Lawley, 2014; Zaura et al., 2014). Moreover, when the microbiota of the same body sites is compared between different healthy individuals, specific microbial community features are apparent (Li et al., 2012; Yatsunenko et al., 2012; Oh et al., 2014; Relman, 2015). In addition, specific selective pressures are found at distinct body sites leading to different patterns in microbial community structure and composition (Costello et al., 2009; Consortium, 2012b; Zhou et al., 2013). Because of these natural variations, a comprehensive characterization of the healthy microbiota is critical for predicting alterations related to diseases. This characterization should be based on a broad healthy population over time, geography, and culture (Yatsunenko et al., 2012; Shetty et al., 2013; Leung et al., 2015; Ross et al., 2015). The study of healthy individuals representing different ages, cultural traditions, and ethnic origins will enable to understand how the associated microbiota varies between populations and respond to different lifestyles. It is important to address these natural variations in order to later detect variations related to disease.
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Affiliation(s)
- Belén Carbonetto
- Genomics and Bioinformatics, Instituto de Agrobiotecnología de Rosario - CONICET Rosario, Argentina
| | - Mónica C Fabbro
- Genomics and Bioinformatics, Instituto de Agrobiotecnología de Rosario - CONICET Rosario, Argentina
| | - Mariela Sciara
- Centro de Diagnostico Medico de Alta Complejidad (CIBIC) Rosario, Argentina
| | - Analía Seravalle
- Centro de Diagnostico Medico de Alta Complejidad (CIBIC) Rosario, Argentina
| | - Guadalupe Méjico
- Centro de Diagnostico Medico de Alta Complejidad (CIBIC) Rosario, Argentina
| | - Santiago Revale
- Genomics and Bioinformatics, Instituto de Agrobiotecnología de Rosario - CONICET Rosario, Argentina
| | - María S Romero
- Genomics and Bioinformatics, Instituto de Agrobiotecnología de Rosario - CONICET Rosario, Argentina
| | - Bianca Brun
- Genomics and Bioinformatics, Instituto de Agrobiotecnología de Rosario - CONICET Rosario, Argentina
| | - Marcelo Fay
- Centro de Diagnostico Medico de Alta Complejidad (CIBIC) Rosario, Argentina
| | - Fabián Fay
- Centro de Diagnostico Medico de Alta Complejidad (CIBIC) Rosario, Argentina
| | - Martin P Vazquez
- Genomics and Bioinformatics, Instituto de Agrobiotecnología de Rosario - CONICET Rosario, Argentina
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