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Feng H, Wei B, Xie X, Li P, Shen X. The potential up-regulation risk of 3' UTR SNP (rs10787760 G > A) for the VAX1 gene is associated with NSCLP in the northwest Chinese population. Gene 2024; 922:148458. [PMID: 38608796 DOI: 10.1016/j.gene.2024.148458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/18/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
AIMS To investigate the association between single nucleotide polymorphisms (SNPs) in 3'UTR region of VAX1, SYT14 and PAX7 genes and the risk of non-syndromic cleft palate (NSCLP) in a northwest Chinese population. MAIN METHODS A case-control study was conducted in 406 normal controls and 399 NSCLP patients. Using iMLDRTM genotyping technology, eight SNPs of three genes ((rs10787760, rs7086344 at VAX1), (rs1010113, rs851114, and rs485874 at PAX7), and (rs61820397, rs4609425, rs12133399 at SYT14)) were genotyped to investigate the differences in alleles and genotype distribution frequencies between NSCLP patients and healthy controls. RNA Folding Form software was used to predict RNA secondary structure and expression vectors were constructed to explore the function of the relevant SNP. The effect of SNP polymorphism of gene transcription and translation was assessed using qPCR and Western blot analysis. KEY FINDINGS Among the eight SNPs of three genes, rs10787760 of VAX1 gene was found to be associated with an increased risk of NSCLP (OR = 1.341, CI = 1.004-1.790) and the GA genotype of rs10787760 increased the risk of cleft lip and/or palate (CL/P) about 1.42 times (p < 0.05), and carrying the A allele might increase the risk of NSCL/P in male (OR = 1.356, 95 % CI = 1.010-1.823). But there was no association observed with cleft palate only (CPO). Cell function experiments revealed that the G to A mutation in rs10787760 up-regulated GFP-VAX1 transcriptional level by 2.39 and 3.13 times in two cell lines respectively, and enhance the protein expression of the VAX1 gene further. RNA secondary structure study showed that the rs10787760 (G > A) had two different secondary structures in 3'UTR region. SIGNIFICANCE The rs10787760 variant in the 3'UTR region of VAX1 gene is associated with CL/P in northwest Chinese population. We hypothesize that the machanism of it might be caused by the RNA differenct fold in the 3'UTR region caused by the polymorphism of the gene. LEVEL OF EVIDENCE Original Reports.
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Affiliation(s)
- Huan Feng
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Bing Wei
- Donggang Branch of the First Hospital of Lanzhou University, Lanzhou University, Lanzhou 730000, China
| | - Xiaodong Xie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Peiqiang Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xi Shen
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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Chai C, Cheng L, Jiao J, Dang J, Jin S. A Comprehensive Investigation on Potential Risk Factors for NSCL/P in a Rural District of Hebei Province, China. Cleft Palate Craniofac J 2023; 60:211-218. [PMID: 34787503 DOI: 10.1177/10556656211058833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Non syndromic cleft lip with or without palate (NSCL/P), one of the most common birth defects, is closely related to various risk factors. However, information regarding risk factors for NSCL/P in rural districts in China is very limited thus far. The objective of this study was designed to identify the potential risk factors for NSCL/P in rural districts. A comprehensive retrospective investigation including 435 NSCL/P patients and 402 healthy children was carried out in Hebei Province, China. Multiple logistic regression analysis and transmission disequilibrium test (TDT) were respectively used to identify non-genetic and genetic risk factors for NSCL/P, and then PLINK was used to explore the relationship between non-genetic and genetic risk factors. The results showed that maternal periconceptional exposure to pesticides and herbicides, as well as low parental education level were involved in the increased risk of NSCL/P, whereas maternal folic acid and multivitamin supplementation use during preconception period were associated with the reduced risk of NSCL/P. TDT analysis identified 2 single nucleotide polymorphisms (SNPs) (rs7078160 and rs4752028) in VAX1 and one SNP (rs17563) in BMP4 as the genetic risk factors for NSCL/P. Further analysis showed that the genetic risk factors were closely related with the negative non-genetic risk factors. Our study identified the potential risk factors for NSCL/P in rural districts, thus providing a theoretical basis for the prevention of NSCL/P occurrence.
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Affiliation(s)
- Congna Chai
- 595156Department of Stomatology, Handan Central Hospital, Handan, China
| | - Lei Cheng
- 595156Department of Stomatology, Handan Central Hospital, Handan, China
| | - Jianjun Jiao
- 595156Department of Stomatology, Handan Central Hospital, Handan, China
| | - Juan Dang
- Department of Orthodontics, Handan Stomatological Hospital, Handan, China
| | - Shubin Jin
- 595156Department of Stomatology, Handan Central Hospital, Handan, China
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Peng L, Niu Z, Chen J, Wan T, Wu D, Yang Y, Wang G, Yang L, Huang W, Chen Z. Association of genetic polymorphisms of VAX1, MAFB, and NTN1 with nonsyndromic cleft lip with or without cleft palate in Chinese population. Mol Genet Genomics 2022; 297:553-559. [PMID: 35212839 DOI: 10.1007/s00438-022-01871-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/08/2022] [Indexed: 12/09/2022]
Abstract
Nonsyndromic cleft lip with or without palate (NSCL/P) is a common birth defect involving genetic factors. We conducted this case-control study to verify the association of ten single-nucleotide polymorphisms (SNPs) of six genes (VAX1, MAFB, PAX7, ABCA4, NTN1, and NOG) with NSCL/P in the Chinese population. The study included 249 NSCL/P patients, 62 nonsyndromic cleft palate only (NSCPO) patients and 480 controls. Three loci, namely, VAX1 rs7078160, MAFB rs11696257, and NTN1 rs4791774, were associated with NSCL/P (Bonferroni method adjusted p values were 0.020, 0.00031, and 0.030, respectively). We also found that the disease risk of individuals carrying both VAX1 rs7078160 and NTN1 rs4791774 was higher than those carrying only one of them (p = 4.50 × 10-4 and 6.03 × 10-3, respectively). SNPs of genes VAX1 rs7078160, MAFB rs11696257, and NTN1 rs4791774 increased NSCL/P risk in the Chinese population.
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Affiliation(s)
- Li Peng
- Department of Orthodontics, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenmin Niu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
| | - Jiapei Chen
- Department of Orthodontics, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Teng Wan
- Department of Oral and Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dandan Wu
- Department of Oral and Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yusheng Yang
- Department of Oral and Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guomin Wang
- Department of Oral and Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Yang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Wei Huang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
| | - Zhenqi Chen
- Department of Orthodontics, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Wen Y, Su Z, Wang Z, Yang L, Liu G, Shang Z, Duan Y, Du H, Li Z, You Y, Li X, Yang Z, Zhang Z. Transcription Factor VAX1 Regulates the Regional Specification of the Subpallium Through Repressing Gsx2. Mol Neurobiol 2021; 58:3729-3744. [PMID: 33821423 DOI: 10.1007/s12035-021-02378-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/29/2021] [Indexed: 12/22/2022]
Abstract
Specification of the progenitors' regional identity is a pivotal step during development of the cerebral cortex and basal ganglia. The molecular mechanisms underlying progenitor regionalization, however, are poorly understood. Here we showed that the transcription factor Vax1 was highly expressed in the developing subpallium. In its absence, the RNA-Seq analysis, in situ RNA hybridization, and immunofluorescence staining results showed that the cell proliferation was increased in the subpallium, but the neuronal differentiation was blocked. Moreover, the dLGE expands ventrally, and the vLGE, MGE, and septum get smaller. Finally, overexpressed VAX1 in the LGE progenitors strongly inhibits Gsx2 expression. Taken together, our findings show that Vax1 is crucial for subpallium regionalization by repressing Gsx2.
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Affiliation(s)
- Yan Wen
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Zihao Su
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Ziwu Wang
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Lin Yang
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Guoping Liu
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Zicong Shang
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Yangyang Duan
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Heng Du
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Zhenmeiyu Li
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Yan You
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Xiaosu Li
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Zhengang Yang
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
| | - Zhuangzhi Zhang
- Department of Neurology, Institute of Pediatrics, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China.
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The risk of nonsyndromic cleft lip with or without cleft palate and Vax1 rs7078160 polymorphisms in southern Han Chinese. Braz J Otorhinolaryngol 2020; 87:718-722. [PMID: 33132092 PMCID: PMC9422622 DOI: 10.1016/j.bjorl.2020.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 02/08/2023] Open
Abstract
Introduction Non-syndromic cleft lip with or without cleft palate is a common worldwide birth defect due to a combination of environmental and genetic factors. Genome-wide association studies reported the rs7078160 of Vax1 is closely related to non-syndromic cleft lip with or without cleft palate in European populations. The following studies showed the same results in Mongolian, Japanese, Filipino, Vietnamese populations etc. However, conflicting research had been reported in Chinese population, Objective The aim of this study was to investigate the association between the rs7078160 polymorphism and non-syndromic cleft lip with or without cleft palate in Southern Chinese patients. Methods In this study, we investigated the polymorphism distribution of rs7078160 in 100 complete patient trios (39 patients with non-syndromic cleft lip and palate; 36 patients with non-syndromic cleft lip only; 25 had non-syndromic cleft palate only; and their parents) from Southern ethnic Han Chinese. 60 healthy trios were selected as control. Polymerase chain reaction and Sanger sequencing were used to genotype rs7078160 in Vax1; both case–control and family-based associations were analyzed. Results The case–control analyses revealed the rs7078160 polymorphism was significant, associated with non-syndromic cleft lip with or without cleft palate (p = 0.04) and non-syndromic cleft lip and palate (p = 0.01), but not associated with non-syndromic cleft lip only and non-syndromic cleft palate only patients. The genotype composition of rs7078160 comprises mutated homozygous AA, heterozygous AG and wild homozygous GG. Cases with AG + AA genotypes compared with GG homozygotes showed an increased risk of non-syndromic cleft lip with or without cleft palate (p = 0.04, OR = 2.05, 95% CI: 1.01–4.16) and non-syndromic cleft lip and palate (p = 0.01, OR = 3.94, 95% CI: 1.34–11.54). In addition, we did not detect any transmission-disequilibrium in rs7078160 (p = 0.68). Conclusion This study suggests that rs7078160 polymorphism is a risk factor of non-syndromic cleft lip with or without cleft palate, and Vax1 is strongly associated with non-syndromic cleft lip with or without cleft palate in Southern Chinese Han populations.
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