Myelomeningocele exomes with canonical WNT/β-catenin pathway
genes disrupted
Out of the seventeen genes that nominally associated with risk for
myelomeningocele, eleven were from the canonical WNT pathway. A high
proportion in the canonical pathway is surprising, given that most WNT
signaling genes previously associated with myelomeningocele are from the
noncanonical PCP pathway, whose role in neural tube closure is more
established. When a WNT family protein binds FZD and low-density
lipoprotein receptor-related protein 5 or 6 (LRP5/6), the canonical WNT
signaling pathway is activated (Fig 5). The pathway involves multiple
events that influence the level of β-catenin in the target cell. If
present in sufficient amount, β-catenin translocates to the nucleus
where it displaces transducin-like enhancer/TLE family proteins from
binding T-cell factor/TCF proteins and proceeds to upregulate the
expression of downstream gene targets (Steinhart & Angers, 2018).
As mentioned in the section on PCP, DVL2 associates with
myelomeningocele in the EA population. In addition to their role in PCP,
Dishevelled (Dvl/Dsh) proteins are important for canonical Wnt
signaling, acting downstream of Wnt, Fzd, and Lrp5/6 (Klingensmith,
Nusse, & Perrimon, 1994; Tamai et al., 2000). Dvl2 is already
implicated in the cause of myelomeningocele, because two to three
percent of Dvl2 double knockout mice display spina bifida
phenotype (Hamblet et al., 2002). In humans, DVL2 is also
differentially expressed in the caudal human neural tube during closure
(Krupp et al., 2012).
DDB1 , which codes for UV damage-specific DNA-binding protein 1,
associated with subjects in the EA population as well. DDB1 is used as
an adaptor protein for the ubiquitin ligase protein, CUL4 (Angers et
al., 2006). Other E3 ubiquitin ligases from this family (CUL1 and CUL3)
target β-catenin and Disheveled for degradation (Higa & Zhang, 2007).
Although more research is needed, it is possible that a nonfunctionalDDB1 gene might decrease β-catenin degradation, consequently
increasing the β-catenin signal in WNT-targeted cells. DDB1 is
particularly interesting, because the Fisher’s exact P value for
its mutational burden analysis almost passed the strict Bonferroni
correction threshold adjusted for the 189 genes compared in the
populations of European ancestry (7.88E-4 versus 2.65E-4) andDDB1 is differentially expressed in the caudal human neural tube
during closure (Krupp et al., 2012). However, DDB1 has not been
previously associated with myelomeningocele.
As mentioned in the section on WNT trafficking, CPE associated
with myelomeningocele in the MA population with one qualifying variant
found in half of the relevant subjects. Whereas full length CPE
interacts with the Wnt ligand, CPE ’s splice variant CPE-ΔN
localizes to the nucleus, increases β-catenin expression, and induces
expression of Wnt target genes (Skalka et al., 2013). Plausibly, loss of
CPE-ΔN might indirectly lower gene expression driven by β-catenin.
Though CPE has not been previously associated with
myelomeningocele, CPE is differentially expressed in the caudal
neural tube during human neural tube closure (Krupp et al., 2012).
PPP2R1A on chromosome 19 also associated with myelomeningocele in
the MA population. Two of the three variants that created the
association were at the same location in two of three MA subjects
carrying the qualifying variants. The variant
NC_000019.9:g.52725413G>T p.(Arg527Leu) was over 34 times
more frequent in the MA population than in the gnomAD AMR exome control
population and the variant NC_000019.9:g.52725413G>A
(p.(Arg527His) was not reported in the gnomAD AMR exome controls.PPP2R1A codes for a conserved subunit of the heterotrimeric
protein PP2A, a serine/threonine protein phosphatase (Mayer-Jaekel &
Hemmings, 1994; Mumbly & Walter, 1993). Another subunit, B56, may
direct PP2A to down-regulate the expression of Wnt/β-catenin effector
genes by decreasing the amount of β-catenin in the cell (Seeling et al.,
1999). It is possible this occurs by directly complexing with Axin
(Ikeda, Kishida, Matsuura, Usui, & Kikuchi, 2000) and dephosphorylating
part of the APC complex (Seeling et al., 1999). Given these
understandings, loss of PPP2R1A function could lead to increased
expression of β-catenin effector genes. PPP2R1A is another novel
gene association with myelomeningocele.
TNRC6B codes for an Argonaut-associated RNA and shows an
association with myelomeningocele in the MA population. The Argonaut
molecule is a recognition motif-containing protein that participate in
RNA interference (Meister et al., 2005). The TNRC6B RNA serves as
one component of a RISC complex that inhibits NLK translation (K. Wang
et al., 2013) and the NLK protein participates in the WNT/β-catenin
pathway by causing the dissociation of the β-catenin complex from DNA
(Ishitani et al., 2003). Importantly, TNRC6B is differentially
expressed in closing caudal human neural tube (Krupp et al., 2012). So,
it is possible that a nonfunctional TNRC6B transcript compromises
the RISC complex and indirectly decreases β-catenin role in downstream
gene expression in myelomeningocele subjects. Our study is the first to
association TNRC6B and myelomeningocele.
SOSTDC1 on chromosome 7, which codes for sclerostin
domain-containing protein 1, associated with myelomeningocele in the EA
population. The variant NC_000007.13:g.16505280G>A
p.(Ala5Val) was found in two of three EA subjects who possessed
qualifying variants and both subjects were heterozygous for this
variant. The NC_000007.13:g.16505280G>A p.(Ala5Val)
variant was not present in any of the gnomAD NFE exome control subjects.
In mouse tooth development, the homolog Sostdc1 serves as an inhibitor
of Lrp5/6-mediated Wnt signaling (Ahn, Sanderson, Klein, & Krumlauf,
2010), but SOSTDC1 has not previously been associated with
myelomeningocele.