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He C, Peng L, Xing S, Li D, Wang L, Jin T. Population Genetic Difference of Pharmacogenomic VIP Variants in the Tibetan Population. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:1027-1040. [PMID: 34429635 PMCID: PMC8379641 DOI: 10.2147/pgpm.s316711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022]
Abstract
Background Genetic variation influences drug reaction or adverse prognosis. The purpose of this research was to genotype very important pharmacogenetic (VIP) variants in the Tibetan population. Methods and Materials Blood samples from 200 Tibetans were randomly collected and 59 VIP variants were genotyped, and then compared our data to 26 other populations in the 1000 project to further analyze and identify significant difference. Results The results showed that on comparing with most of the 26 populations from the 1000 project, rs4291 (ACE), rs1051296 (SLC19A1) and rs1065852 (CYP2D6) significantly differed in the Tibetan population. Furthermore, three significant loci were related to drug response. In addition, the allele frequency of Tibetans least differed from that of East Asian populations, and most differed from that of Americans. Conclusion Three significant loci of variation ACE rs4291, SLC19A1 rs1051296 and CYP2D6 rs1065852 were associated with drug response. This result will contribute to improving the information of the Tibetan in the pharmacogenomics database, and providing a theoretical basis for clinical individualised drug use in Tibetans.
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Affiliation(s)
- Chunjuan He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People's Republic of China
| | - Linna Peng
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People's Republic of China
| | - Shishi Xing
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People's Republic of China
| | - Dandan Li
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People's Republic of China
| | - Li Wang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People's Republic of China
| | - Tianbo Jin
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People's Republic of China.,Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, Xizang Minzu University, Xianyang, Shaanxi, 712082, People's Republic of China
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Dixit R, Narasimhan C, Balekundri VI, Agrawal D, Kumar A, Mohapatra B. Functional analysis of novel genetic variants of NKX2-5 associated with nonsyndromic congenital heart disease. Am J Med Genet A 2021; 185:3644-3663. [PMID: 34214246 DOI: 10.1002/ajmg.a.62413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 01/26/2023]
Abstract
NKX2-5, a master cardiac regulatory transcription factor was the first known genetic cause of congenital heart diseases (CHDs). To further investigate its role in CHD pathogenesis, we performed mutational screening of 285 CHD probands and 200 healthy controls. Five coding sequence variants were identified in six CHD cases (2.1%), including three in the N-terminal region (p.A61G, p.R95L, and p.E131K) and one each in homeodomain (HD) (p.A148E) and tyrosine-rich domain (p.P247A). Variant-p.A148E showed tertiary structure changes and differential DNA binding affinity of mutant compared to wild type. Two N-terminal variants-p.A61G and p.E131K along with HD variant p.A148E demonstrated significantly reduced transcriptional activity of Nppa and Actc1 promoters in dual luciferase promoter assay supported by their reduced expression in qRT-PCR. Nonetheless, variant p.R95L affected the synergy of NKX2-5 with serum response factor and TBX5 leading to significantly decreased Actc1 promoter activity depicting a distinctive role of this region. The aberrant expression of other target genes-Irx4, Mef2c, Bmp10, Myh6, Myh7, and Myocd is also observed in response to NKX2-5 variants, possibly due to the defective gene regulatory network. Severely impaired downstream promoter activities and abnormal expression of target genes due to N-terminal variants supports the emerging role of this region during cardiac-developmental pathways.
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Affiliation(s)
- Ritu Dixit
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Chitra Narasimhan
- Department of Pediatric Cardiology, Sri Jayadeva Institute of Cardiovascular Sciences and Research, Bengaluru, Karnataka, India
| | - Vijayalakshmi I Balekundri
- Super Speciality Hospital, Pradhan Mantri Swasthya Suraksha Yojana (PMSSY), Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Damyanti Agrawal
- Department of Cardiothoracic and Vascular Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ashok Kumar
- Department of Pediatrics, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Bhagyalaxmi Mohapatra
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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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] [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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Kalayinia S, Ghasemi S, Mahdieh N. A comprehensive in silico analysis, distribution and frequency of human Nkx2-5 mutations; A critical gene in congenital heart disease. J Cardiovasc Thorac Res 2019; 11:287-299. [PMID: 31824610 PMCID: PMC6891041 DOI: 10.15171/jcvtr.2019.47] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 10/04/2019] [Indexed: 12/12/2022] Open
Abstract
Introduction: Congenital heart disease (CHD) affects 1% to 2 % of live births. The Nkx2-5 gene, is known as the significant heart marker during embryonic evolution and it is also necessary for the survival of cardiomyocytes and homeostasis in adulthood. In this study, Nkx2-5 mutations are investigated to identify the frequency, distribution, functional consequences of mutations by using computational tools.
Methods: A complete literature search was conducted to find Nkx2-5 mutations using the following key words: Nkx2-5 and/or CHD and mutations. The mutations were in silico analyzed using tools which predict the pathogenicity of the variants. A picture of Nkx2-5 protein and functional or structural effects of its variants were also figured using I-TASSER and STRING.
Results: A total number of 105 mutations from 18 countries were introduced. The most (24.1%) and the least (1.49%) frequency of Nkx2-5 mutations were observed in Europe and Africa, respectively. The c.73C>T and c.533C>T mutations are distributed worldwide. c.325G>T (62.5%) and c.896A>G (52.9%) had the most frequency. The most numbers of Nkx2-5 mutations were reported from Germany. The c.541C>T had the highest CADD score (Phred score = 38) and the least was for c.380C>A (Phred score=0.002). 41.9% of mutations were predicted as potentially pathogenic by all prediction tools.
Conclusion: This is the first report of the Nkx2-5 mutations evaluation in the worldwide. Given that the high frequency of mutation in Germany, and also some mutations were seen only in this country, therefore, presumably the main origin of Nkx2-5 mutations arise from Germany.
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Affiliation(s)
- Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Serwa Ghasemi
- Department of Biology, School of Basic Sciences, Islamic Azad University Research Tehran Branch, Tehran, Iran
| | - Nejat Mahdieh
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
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Liu S, Su Z, Tan S, Ni B, Pan H, Liu B, Wang J, Xiao J, Chen Q. Functional Analyses of a Novel CITED2 Nonsynonymous Mutation in Chinese Tibetan Patients with Congenital Heart Disease. Pediatr Cardiol 2017; 38:1226-1231. [PMID: 28687891 DOI: 10.1007/s00246-017-1649-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/02/2017] [Indexed: 12/22/2022]
Abstract
CITED2 gene is an important cardiac transcription factor that plays a fundamental role in the formation and development of embryonic cardiovascular. Previous studies have showed that knock-out of CITED2 in mice might result in various cardiac malformations. However, the mechanisms of CITED2 mutation on congenital heart disease (CHD) in Chinese Tibetan population are still poorly understood. In the present study, 187 unrelated Tibetan patients with CHD and 200 unrelated Tibetan healthy controls were screened for variants in the CITED2 gene; we subsequently identified one potential disease-causing mutation p.G143A in a 6-year-old girl with PDA and functional analyses of the mutation were carried out. Our study showed that the novel mutation of CITED2 significantly enhanced the expression activity of vascular endothelial growth factor (VEGF) under the role of co-receptor hypoxia inducible factor 1-aipha (HIF-1A), which is closely related with embryonic cardiac development. As a result, CITED2 gene mutation may play a significant role in the development of pediatric congenital heart disease.
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Affiliation(s)
- Shiming Liu
- Qinghai High Altitude Medical Research Institute, No.7, Zhuanchang Road, West District, Xining, 810012, China
| | - Zhaobing Su
- Department of Cardiology, The Dongguan Affiliated Hospital of Medical College of Jinan University, The Fifth People's Hospital of Dongguan, 154 Humen Road, Humen, 523900, Guangdong, China
| | - Sainan Tan
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, China
| | - Bin Ni
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, China
| | - Hong Pan
- Center for Genetics, National Research Institute for Family Planning, Beijing, 100081, China
| | - Beihong Liu
- Center for Genetics, National Research Institute for Family Planning, Beijing, 100081, China
| | - Jing Wang
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Jianmin Xiao
- Department of Cardiology, The Dongguan Affiliated Hospital of Medical College of Jinan University, The Fifth People's Hospital of Dongguan, 154 Humen Road, Humen, 523900, Guangdong, China.
| | - Qiuhong Chen
- Qinghai High Altitude Medical Research Institute, No.7, Zhuanchang Road, West District, Xining, 810012, China.
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