Knockdown of Crispld2 in zebrafish identifies a novel network for nonsyndromic cleft lip with or without cleft palate candidate genes

Brett T. Chiquet, Qiuping Yuan, Eric C. Swindell, Lorena Maili, Robert Plant, Jeffrey Dyke, Ryan Boyer, John F. Teichgraeber, Matthew R. Greives, John B. Mulliken, Ariadne Letra, Susan H Blanton, Jacqueline T. Hecht

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Orofacial development is a multifaceted process involving tightly regulated genetic signaling networks, that when perturbed, lead to orofacial abnormalities including cleft lip and/or cleft palate. We and others have shown an association between the cysteine-rich secretory protein LCCL domain containing 2 (CRISPLD2) gene and nonsyndromic cleft lip with or without cleft palate (NSCLP). Further, we demonstrated that knockdown of Crispld2 in zebrafish alters neural crest cell migration patterns resulting in abnormal jaw and palate development. In this study, we performed RNA profiling in zebrafish embryos and identified 249 differentially expressed genes following knockdown of Crispld2. In silico pathway analysis identified a network of seven genes previously implicated in orofacial development for which differential expression was validated in three of the seven genes (CASP8, FOS, and MMP2). Single nucleotide variant (SNV) genotyping of these three genes revealed significant associations between NSCLP and FOS/rs1046117 (GRCh38 chr14:g.75746690 T > C, p = 0.0005) in our nonHispanic white (NHW) families and MMP2/rs243836 (GRCh38 chr16:g.55534236 G > A; p = 0.002) in our Hispanic families. Nominal association was found between NSCLP and CASP8/rs3769825 (GRCh38 chr2:g.202111380 C > A; p < 0.007). Overtransmission of MMP2 haplotypes were identified in the Hispanic families (p < 0.002). Significant gene–gene interactions were identified for FOS-MMP2 in the NHW families and for CASP8-FOS in the NHW simplex family subgroup (p < 0.004). Additional in silico analysis revealed a novel gene regulatory network including five of these newly identified and 23 previously reported NSCLP genes. Our results demonstrate that animal models of orofacial clefting can be powerful tools to identify novel candidate genes and gene regulatory networks underlying NSCLP.

Original languageEnglish (US)
Pages (from-to)1-10
Number of pages10
JournalEuropean Journal of Human Genetics
DOIs
StateAccepted/In press - Jun 13 2018

Fingerprint

Cleft Lip
Cleft Palate
Zebrafish
Gene Regulatory Networks
Genes
Hispanic Americans
Computer Simulation
Gene Knockdown Techniques
Palate
Neural Crest
Jaw
Haplotypes
Cell Movement
Cysteine
Embryonic Structures
Nucleotides
Animal Models
RNA

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Knockdown of Crispld2 in zebrafish identifies a novel network for nonsyndromic cleft lip with or without cleft palate candidate genes. / Chiquet, Brett T.; Yuan, Qiuping; Swindell, Eric C.; Maili, Lorena; Plant, Robert; Dyke, Jeffrey; Boyer, Ryan; Teichgraeber, John F.; Greives, Matthew R.; Mulliken, John B.; Letra, Ariadne; Blanton, Susan H; Hecht, Jacqueline T.

In: European Journal of Human Genetics, 13.06.2018, p. 1-10.

Research output: Contribution to journalArticle

Chiquet, BT, Yuan, Q, Swindell, EC, Maili, L, Plant, R, Dyke, J, Boyer, R, Teichgraeber, JF, Greives, MR, Mulliken, JB, Letra, A, Blanton, SH & Hecht, JT 2018, 'Knockdown of Crispld2 in zebrafish identifies a novel network for nonsyndromic cleft lip with or without cleft palate candidate genes', European Journal of Human Genetics, pp. 1-10. https://doi.org/10.1038/s41431-018-0192-5
Chiquet, Brett T. ; Yuan, Qiuping ; Swindell, Eric C. ; Maili, Lorena ; Plant, Robert ; Dyke, Jeffrey ; Boyer, Ryan ; Teichgraeber, John F. ; Greives, Matthew R. ; Mulliken, John B. ; Letra, Ariadne ; Blanton, Susan H ; Hecht, Jacqueline T. / Knockdown of Crispld2 in zebrafish identifies a novel network for nonsyndromic cleft lip with or without cleft palate candidate genes. In: European Journal of Human Genetics. 2018 ; pp. 1-10.
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abstract = "Orofacial development is a multifaceted process involving tightly regulated genetic signaling networks, that when perturbed, lead to orofacial abnormalities including cleft lip and/or cleft palate. We and others have shown an association between the cysteine-rich secretory protein LCCL domain containing 2 (CRISPLD2) gene and nonsyndromic cleft lip with or without cleft palate (NSCLP). Further, we demonstrated that knockdown of Crispld2 in zebrafish alters neural crest cell migration patterns resulting in abnormal jaw and palate development. In this study, we performed RNA profiling in zebrafish embryos and identified 249 differentially expressed genes following knockdown of Crispld2. In silico pathway analysis identified a network of seven genes previously implicated in orofacial development for which differential expression was validated in three of the seven genes (CASP8, FOS, and MMP2). Single nucleotide variant (SNV) genotyping of these three genes revealed significant associations between NSCLP and FOS/rs1046117 (GRCh38 chr14:g.75746690 T > C, p = 0.0005) in our nonHispanic white (NHW) families and MMP2/rs243836 (GRCh38 chr16:g.55534236 G > A; p = 0.002) in our Hispanic families. Nominal association was found between NSCLP and CASP8/rs3769825 (GRCh38 chr2:g.202111380 C > A; p < 0.007). Overtransmission of MMP2 haplotypes were identified in the Hispanic families (p < 0.002). Significant gene–gene interactions were identified for FOS-MMP2 in the NHW families and for CASP8-FOS in the NHW simplex family subgroup (p < 0.004). Additional in silico analysis revealed a novel gene regulatory network including five of these newly identified and 23 previously reported NSCLP genes. Our results demonstrate that animal models of orofacial clefting can be powerful tools to identify novel candidate genes and gene regulatory networks underlying NSCLP.",
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AU - Chiquet, Brett T.

AU - Yuan, Qiuping

AU - Swindell, Eric C.

AU - Maili, Lorena

AU - Plant, Robert

AU - Dyke, Jeffrey

AU - Boyer, Ryan

AU - Teichgraeber, John F.

AU - Greives, Matthew R.

AU - Mulliken, John B.

AU - Letra, Ariadne

AU - Blanton, Susan H

AU - Hecht, Jacqueline T.

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