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Holborn MA, Ford G, Turner S, Mellet J, van Rensburg J, Joubert F, Pepper MS. The NESHIE and CP Genetics Resource (NCGR): A database of genes and variants reported in neonatal encephalopathy with suspected hypoxic ischemic encephalopathy (NESHIE) and consequential cerebral palsy (CP). Genomics 2022; 114:110508. [PMID: 36270382 PMCID: PMC9726645 DOI: 10.1016/j.ygeno.2022.110508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 01/15/2023]
Abstract
Neonatal encephalopathy (NE) with suspected hypoxic ischaemic encephalopathy (HIE) (NESHIE) is a complex syndrome occurring in newborns, characterised by altered neurological function. It has been suggested that genetic variants may influence NESHIE susceptibility and outcomes. Unlike NESHIE, for which a limited number of genetic studies have been performed, many studies have identified genetic variants associated with cerebral palsy (CP), which can develop from severe NESHIE. Identifying variants in patients with CP, as a consequence of NESHIE, may provide a starting point for the identification of genetic variants associated with NESHIE outcomes. We have constructed NCGR (NESHIE and CP Genetics Resource), a database of genes and variants reported in patients with NESHIE and CP (where relevant to NESHIE), for the purpose of collating and comparing genetic findings between the two conditions. In this paper we describe the construction and functionality of NCGR. Furthermore, we demonstrate how NCGR can be used to prioritise genes and variants of potential clinical relevance that may underlie a genetic predisposition to NESHIE and contribute to an understanding of its pathogenesis.
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Affiliation(s)
- Megan A. Holborn
- Institute for Cellular and Molecular Medicine, Department of Immunology; SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Graeme Ford
- Institute for Cellular and Molecular Medicine, Department of Immunology; SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa,Centre for Bioinformatics and Computational Biology, Genomics Research Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Sarah Turner
- Institute for Cellular and Molecular Medicine, Department of Immunology; SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa,Centre for Bioinformatics and Computational Biology, Genomics Research Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Institute for Cellular and Molecular Medicine, Department of Immunology; SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Jeanne van Rensburg
- Institute for Cellular and Molecular Medicine, Department of Immunology; SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Fourie Joubert
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Michael S. Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology; SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa,Corresponding author.
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An association study of IL2RA polymorphisms with cerebral palsy in a Chinese population. BMC Med Genomics 2022; 15:208. [PMID: 36195861 PMCID: PMC9531349 DOI: 10.1186/s12920-022-01350-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Abstract
Background Cerebral palsy (CP), the most common physical disability of childhood, is a nonprogressive movement disorder syndrome. Eighty percent of cases are considered idiopathic without a clear cause. Evidence has shown that cytokine abnormalities are widely thought to contribute to CP. Methods An association between 6 SNPs (rs12244380, rs2025345, rs12722561, rs4749926, rs2104286 and rs706778) in IL2RA (interleukin 2 receptor subunit alpha) and CP was investigated using a case–control method based on 782 CP cases and 778 controls. The allele, genotype and haplotype frequencies of SNPs were assessed using the SHEsis program. Subgroup analyses based on complications and clinical subtypes were also conducted. Results Globally, no differences in genotype or allele frequencies for any SNPs remained significant after Bonferroni correction between patients and controls, except rs706778, which deviated from Hardy–Weinberg equilibrium and was excluded from further analyses. However, subgroup analysis revealed a significant association of rs2025345 with spastic tetraplegia (P genotype = 0.048 after correction) and rs12722561 with CP accompanied by global developmental delay (P allele = 0.045 after correction), even after Bonferroni correction. Conclusions These findings indicated that genetic variations in IL2RA are significantly associated with CP susceptibility in the Chinese Han population, suggesting that IL2RA is likely involved in the pathogenesis of CP. Further investigation with a larger sample size in a multiethnic population is needed to confirm the association.
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Sharypova EB, Drachkova IA, Chadaeva IV, Ponomarenko MP, Savinkova LK. An experimental study of the effects of SNPs in the TATA boxes of the <i>GRIN1, ASCL3</i> and <i>NOS1</i> genes on interactions with the TATA-binding protein. Vavilovskii Zhurnal Genet Selektsii 2022; 26:227-233. [PMID: 35774364 PMCID: PMC9167820 DOI: 10.18699/vjgb-22-29] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 12/12/2022] Open
Abstract
The GRIN1, ASCL3, and NOS1 genes are associated with various phenotypes of neuropsychiatric disorders. For instance, these genes contribute to the development of schizophrenia, Alzheimer’s and Parkinson’s diseases, and epilepsy. These genes are also associated with various cancers. For example, ASCL3 is overexpressed in breast cancer, and NOS1, in ovarian cancer cell lines. Based on our findings and literature data, we had previously obtained results suggesting that the single-nucleotide polymorphisms (SNPs) that disrupt erythropoiesis are highly likely to be associated with cognitive and neuropsychiatric disorders in humans. In the present work, using SNP_TATA_Z-tester, we investigated the influence of unannotated SNPs in the TATA boxes of the promoters of the GRIN1, ASCL3, and NOS1 genes (which are involved in neuropsychiatric disorders and cancers) on the interaction of the TATA boxes with the TATA-binding protein (TBP). Double-stranded oligodeoxyribonucleotides identical to the TATA-containing promoter regions of the GRIN1, ASCL3, and NOS1 genes (reference and minor alleles) and recombinant human TBP were employed to study in vitro (by an electrophoretic mobility shift assay) kinetic characteristics of the formation of TBP–TATA complexes and their affinity. It was found, for example, that allele A of rs1402667001 in the GRIN1 promoter increases TBP–TATA affinity 1.4-fold, whereas allele C in the TATA box of the ASCL3 promoter decreases the affinity 1.4-fold. The lifetime of the complexes in both cases decreased by ~20 % due to changes in the rates of association and dissociation of the complexes (ka and kd, respectively). Our experimental results are consistent with the literature showing GRIN1 underexpression in schizophrenic disorders as well as an increased risk of cervical, bladder, and kidney cancers and lymphoma during ASCL3 underexpression. The effect of allele A of the –27G>A SNP (rs1195040887) in the NOS1 promoter is suggestive of an increased risk of ischemic damage to the brain in carriers. A comparison of experimental TBP–TATA affinity values (KD) of wild-type and minor alleles with predicted ones showed that the data correlate well (linear correlation coefficient r = 0.94, p < 0.01).
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Affiliation(s)
- E. B. Sharypova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - I. A. Drachkova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - I. V. Chadaeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - M. P. Ponomarenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - L. K. Savinkova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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Rathore SK, Pati P, Priyadarshini S, Dwibedi B. Association of G84A and C276T polymorphism in neuronal nitric oxide synthase (nNOS) gene with herpes simplex encephalitis in eastern Indian population. Nitric Oxide 2020; 108:8-11. [PMID: 33347982 DOI: 10.1016/j.niox.2020.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/22/2020] [Accepted: 12/16/2020] [Indexed: 10/22/2022]
Abstract
In this study, a hypothesis that genetic variations in neuronal nitric oxide synthase (nNOS) could influence the susceptibility and outcome of herpes simplex encephalitis was investigated. Polymorphic loci of nNOS gene, G84A and C276T were genotyped in 132 HSE cases (Age 8.2 ± 1.3yr) and 143 in healthy individuals (Age-9.2 ± 1.6yr) of the same ethnic background from Odisha. A significantly increased risk for HSVE was associated with the AG genotype (OR = 1.73, 95%CI = 1.03-2.9, P = 0.03) and AA genotype (OR = 2.96, 95%CI = 1.04-8.4, P = 0.04) of nNOS 84G →A locus. In case of nNOS 276C→T variation, HSVE risk was linked to CT genotype (OR = 1.79, 95%CI = 1.07-3.0, P = 0.03) and TT genotype (OR = 3.6, 95%CI = 1.2-10.8, P = 0.02). Patients with poor outcome either had homo or heterozygous genotype for both SNPs, but separate genotype analysis could not show significance. But combined genotype analysis of both SNPs confirmed that GG + CC was a risk factor for development of poor outcome. (OR = 6.3, CI-1.9-20.7, P = 0.0033). Haplotype analysis of both SNP did show that "at" haplotype was significantly higher and associated with HSVE cases (OR = 2.322,CI: 1.43-3.77, P = 0.00070). The result observed in this study suggested that variation at these loci of nNOS may have decreased its expression and caused low production of NO, which have resulted in risk of HSVE but provided good outcome in these patients.
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Affiliation(s)
- S K Rathore
- ICMR-Regional Medical Research Centre, Bhubneswar, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | - P Pati
- ICMR-Regional Medical Research Centre, Bhubneswar, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | | | - B Dwibedi
- ICMR-Regional Medical Research Centre, Bhubneswar, India; Dept of Pediatrics, AIIMS, Bhubaneswar, India.
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Wang Y, Xu Y, Fan Y, Bi D, Song J, Xia L, Shang Q, Gao C, Zhang X, Zhu D, Qiao Y, Su Y, Wang X, Zhu C, Xing Q. The Association Study of IL-23R Polymorphisms With Cerebral Palsy in Chinese Population. Front Neurosci 2020; 14:590098. [PMID: 33324152 PMCID: PMC7724030 DOI: 10.3389/fnins.2020.590098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022] Open
Abstract
Background: Cerebral palsy (CP) is a syndrome of non-progressive motor dysfunction caused by early brain development injury. Recent evidence has shown that immunological abnormalities are associated with an increased risk of CP. Methods: We recruited 782 children with CP as the case group and 770 healthy children as the control group. The association between IL-23R single nucleotide polymorphisms (SNPs; namely, rs10889657, rs6682925, rs1884444, rs17375018, rs1004819, rs11805303, and rs10889677) and CP was studied by using a case–control method and SHEsis online software. Subgroup analysis based on complications and clinical subtypes was also carried out. Results: There were differences in the allele and genotype frequencies between CP cases and controls at the rs11805303 and rs10889677 SNPs (Pallele = 0.014 and 0.048, respectively; Pgenotype = 0.023 and 0.008, respectively), and the difference in genotype frequency of rs10889677 remained significant after Bonferroni correction (Pgenotype = 0.048). Subgroup analysis revealed a more significant association of rs10889677 with CP accompanied by global developmental delay (Pgenotype = 0.024 after correction) and neonatal encephalopathy (Pgenotype = 0.024 after correction). Conclusion: The present results showed a significant association between IL-23R and CP, suggesting that IL-23R may play a potential role in CP pathogenesis.
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Affiliation(s)
- Yangong Wang
- Institutes of Biomedical Science and Children's Hospital, Fudan University, Shanghai, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury, Department of Pediatrics, The 3rd Affiliated Hospital of Zhengzhou University and Institute of Neuroscience, Zhengzhou, China
| | - Yangyi Fan
- Institutes of Biomedical Science and Children's Hospital, Fudan University, Shanghai, China
| | - Dan Bi
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Juan Song
- Henan Key Laboratory of Child Brain Injury, Department of Pediatrics, The 3rd Affiliated Hospital of Zhengzhou University and Institute of Neuroscience, Zhengzhou, China
| | - Lei Xia
- Henan Key Laboratory of Child Brain Injury, Department of Pediatrics, The 3rd Affiliated Hospital of Zhengzhou University and Institute of Neuroscience, Zhengzhou, China
| | - Qing Shang
- Department of Pediatrics, Children's Hospital of Zhengzhou University and Henan Children's Hospital, Zhengzhou, China
| | - Chao Gao
- Department of Pediatrics, Children's Hospital of Zhengzhou University and Henan Children's Hospital, Zhengzhou, China
| | - Xiaoli Zhang
- Henan Key Laboratory of Child Brain Injury, Department of Pediatrics, The 3rd Affiliated Hospital of Zhengzhou University and Institute of Neuroscience, Zhengzhou, China
| | - Dengna Zhu
- Child Rehabilitation Center, The 3rd Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yimeng Qiao
- Institutes of Biomedical Science and Children's Hospital, Fudan University, Shanghai, China
| | - Yu Su
- Institutes of Biomedical Science and Children's Hospital, Fudan University, Shanghai, China
| | - Xiaoyang Wang
- Henan Key Laboratory of Child Brain Injury, Department of Pediatrics, The 3rd Affiliated Hospital of Zhengzhou University and Institute of Neuroscience, Zhengzhou, China
| | - Changlian Zhu
- Henan Key Laboratory of Child Brain Injury, Department of Pediatrics, The 3rd Affiliated Hospital of Zhengzhou University and Institute of Neuroscience, Zhengzhou, China.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Qinghe Xing
- Institutes of Biomedical Science and Children's Hospital, Fudan University, Shanghai, China.,Shanghai Center for Women and Children's Health, Shanghai, China
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Pham R, Mol BW, Gecz J, MacLennan AH, MacLennan SC, Corbett MA, van Eyk CL, Webber DL, Palmer LJ, Berry JG. Definition and diagnosis of cerebral palsy in genetic studies: a systematic review. Dev Med Child Neurol 2020; 62:1024-1030. [PMID: 32542675 DOI: 10.1111/dmcn.14585] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2020] [Indexed: 01/01/2023]
Abstract
AIM To conduct a systematic review of phenotypic definition and case ascertainment in published genetic studies of cerebral palsy (CP) to inform guidelines for the reporting of such studies. METHOD Inclusion criteria comprised genetic studies of candidate genes, with CP as the outcome, published between 1990 and 2019 in the PubMed, Embase, and BIOSIS Citation Index databases. RESULTS Fifty-seven studies met the inclusion criteria. We appraised how CP was defined, the quality of information on case ascertainment, and compliance with international consensus guidelines. Seven studies (12%) were poorly described, 33 studies (58%) gave incomplete information, and 17 studies (30%) were well described. Missing key information precluded determining how many studies complied with the definition by Rosenbaum et al. Only 18 out of 57 studies (32%) were compliant with the Surveillance of Cerebral Palsy in Europe (SCPE) international guidelines on defining CP. INTERPRETATION Limited compliance with international consensus guidelines on phenotypic definition and mediocre reporting of CP case ascertainment hinders the comparison of results among genetic studies of CP (including meta-analyses), thereby limiting the quality, interpretability, and generalizability of study findings. Compliance with the SCPE guidelines is important for ongoing gene discovery efforts in CP, given the potential for misclassification of unrelated neurological conditions as CP.
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Affiliation(s)
- Ryan Pham
- School of Public Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Ben W Mol
- Discipline of Obstetrics & Gynaecology, University of Adelaide, Adelaide, South Australia, Australia.,Discipline of Obstetrics & Gynaecology, Monash University, Clayton, Victoria, Australia
| | - Jozef Gecz
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.,South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Alastair H MacLennan
- Discipline of Obstetrics & Gynaecology, University of Adelaide, Adelaide, South Australia, Australia.,Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Suzanna C MacLennan
- Neurology Department, Women's and Children's Hospital, North Adelaide, South Australia, Australia.,Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Mark A Corbett
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Clare L van Eyk
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Dani L Webber
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Lyle J Palmer
- School of Public Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Jesia G Berry
- Discipline of Obstetrics & Gynaecology, University of Adelaide, Adelaide, South Australia, Australia.,Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
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