PUBLICATION

The functional variant of NTN1 contributes to the risk of nonsyndromic cleft lip with or without cleft palate

Authors
Li, D., Zhu, G., Lou, S., Ma, L., Zhang, C., Pan, Y., Wang, L.
ID
ZDB-PUB-191130-12
Date
2019
Source
European journal of human genetics : EJHG   28(4): 453-460 (Journal)
Registered Authors
Keywords
none
MeSH Terms
  • Bone Development
  • Zebrafish
  • Cleft Lip/genetics*
  • Polymorphism, Single Nucleotide
  • Enhancer Elements, Genetic
  • Heterozygote
  • Male
  • Animals
  • Female
  • HEK293 Cells
  • Apoptosis
  • Mice
  • Mutation*
  • Netrin-1/genetics*
  • Netrin-1/metabolism
  • Cleft Palate/genetics*
  • Cell Cycle
  • Humans
(all 18)
PubMed
31780810 Full text @ Eur. J. Hum. Genet.
Abstract
Previous genome-wide association study of nonsyndromic cleft lip with or without cleft palate (NSCL/P) identified a susceptible variant (rs4791774). We hypothesized that the functional single nucleotide polymorphism (SNP) may be in linkage disequilibrium with this lead SNP. The potential functional SNP (rs4791331) was identified by bioinformatic analysis. A case-control study with 891 orofacial cleft cases and 830 controls was designed to investigate its association with orofacial cleft. The allele-specific DNA-protein binding preference was predicted by JASPAR database. Cell proliferation, cycle and apoptosis, luciferase activity and netrin-1 (NTN1) expression were examined after transfection with the rs4791331 C/T vector in HEK-293 and HEPM cell lines. Forty-six lip tissues of NSCL/P patients were collected to detect NTN1 expression. ntn1a knockout zebrafish models were generated by CRISPR/Cas9 and observed with micro-CT. In the case-control study, the rs4791331-T allele was associated with an increased risk of nonsyndromic orofacial cleft (OR = 1.41, 95% CI = 1.19-1.68), as well as the subgroups cleft lip only (OR = 1.46, 95% CI = 1.14-1.87) and cleft lip and palate (OR = 1.58, 95% CI = 1.27-1.96). The T allele of rs4791331 exhibited anti-apoptotic effects and promoted cell cycle progression at the G1/S transition. Decreased enhancer activity and reduced NTN1 expression following transfection of the T allele were observed. Carriers of the CT/TT genotypes showed significantly lower expression of NTN1 than CC carriers. The ntn1a-/- zebrafish showed relatively wider intermaxillary fissures. These results indicate that rs4791331 (C > T) disrupted motif binding and led to abnormal expression of NTN1, which may be involved in the development of NSCL/P.
Genes / Markers
Figures
No images available
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Expression
Phenotype
Fish Conditions Stage Phenotype Figure
ntn1azf3231/zf3231standard conditionsAdult
1 - 1 of 1
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Mutations / Transgenics
Allele Construct Type Affected Genomic Region
zf3231
    		Unknown
    1 - 1 of 1
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    Human Disease / Model
    Human Disease Fish Conditions Evidence
    orofacial cleftTAS
    1 - 1 of 1
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    Sequence Targeting Reagents
    Target Reagent Reagent Type
    ntn1aCRISPR2-ntn1aCRISPR
    ntn1aCRISPR3-ntn1aCRISPR
    1 - 2 of 2
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    Fish
    Fish
    ntn1azf3231/zf3231
    1 - 1 of 1
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    Antibodies
    No data available
    Orthology
    Engineered Foreign Genes
    No data available
    Mapping
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    Citation
    Li, D., Zhu, G., Lou, S., Ma, L., Zhang, C., Pan, Y., Wang, L. (2019) The functional variant of NTN1 contributes to the risk of nonsyndromic cleft lip with or without cleft palate. European journal of human genetics : EJHG. 28(4):453-460.