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Sonic Hedgehog switches on Wnt/planar cell polarity signaling in commissural axon growth cones by reducing levels of Shisa2

  1. Keisuke Onishi
  2. Yimin Zou Is a corresponding author
  1. University of California, San Diego, United States
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Cite as: eLife 2017;6:e25269 doi: 10.7554/eLife.25269

Abstract

Commissural axons switch on responsiveness to Wnt attraction during midline crossing and turn anteriorly only after exiting the floor plate. We report here that Sonic Hedgehog (Shh)-Smoothened signaling downregulates Shisa2, which inhibits the glycosylation and cell surface presentation of Frizzled3 in rodent commissural axon growth cones. Constitutive Shisa2 expression causes randomized turning of post-crossing commissural axons along the anterior–posterior (A–P) axis. Loss of Shisa2 led to precocious anterior turning of commissural axons before or during midline crossing. Post-crossing commissural axon turning is completely randomized along the A–P axis when Wntless, which is essential for Wnt secretion, is conditionally knocked out in the floor plate. This regulatory link between Shh and planar cell polarity (PCP) signaling may also occur in other developmental processes.

https://doi.org/10.7554/eLife.25269.001

Introduction

The complex neuronal network is in part assembled through the stepwise events of axon pathfinding. Many axonal growth cones follow the instruction of a set of guidance cues until they reach their intermediate targets; they then switch their responsiveness to follow new guidance cues which allow them to navigate to the next intermediate targets (or the final targets). The mechanisms of these important switches are not well understood. In the developing spinal cord, commissural axons arise from the dorsal margin, project along the dorsal–ventral axis and then turn anteriorly after they have reached and crossed the ventral midline (Bovolenta and Dodd, 1990). Wnts are expressed in a decreasing anterior-to-posterior gradient in the floor plate and direct the post-crossing commissural axons to turn anteriorly after midline crossing (Lyuksyutova et al., 2003). Previous work showed that components of the planar cell polarity (PCP) signaling pathway mediates Wnt attraction and anterior turning of commissural axons (Lyuksyutova et al., 2003; Shafer et al., 2011; Zou, 2012; Onishi et al., 2013; Onishi et al., 2014). We report here that Shh–Smoothened (Smo) signaling activates PCP signaling by inhibiting the expression of Shisa2, an inhibitor of Wnt signaling that blocks Frizzled3 (Fzd3) glycosylation and cell-surface presentation.

Results

Increased Shisa2 expression in dorsal commissural neurons in Smoothened (Smo) conditional knockout mice

As Shh is a major signaling molecule in the ventral midline, we hypothesized that Shh signaling may regulate the expression of genes relevant to the switch of responsiveness of commissural neurons during midline crossing. We, therefore, performed transcriptome analyses in the dorsal spinal cord, where the cell bodies of commissural neurons reside, from control Smofl/fl and Smo conditional KO (cKO) E11.5 embryos crossed with Wnt1-Cre. Consistent with a previous study, we observed compromised anterior turning of commissural axons in Smo cKO (Figure 1—figure supplement 1) (Yam et al., 2012). Dorsal margins of the spinal cord were dissected (50–100 μm from the dorsal edge) and lysed to extract total RNA. Stranded-mRNAs were prepared and sequenced by single-end RNA-sequencing (Figure 1A). Among a total of 15,737 identified genes, 363 genes showed significant differences in mRNA levels (Figure 1B). The expression of several functional groups related to neuronal differentiation, axon morphogenesis and synaptic function was found to be changed significantly (Figure 1C). We confirmed that Smo mRNA was indeed significantly reduced in Smo cKO (Figure 1F). We then compared the expression levels of all core PCP genes, such as Fzd3, Celsr3 and Vangl2, that are required for A–P guidance of post-crossing commissural axons (Figure 1D) (Shafer et al., 2011; Onishi et al., 2013). There was no significant difference in mRNA levels between control Smofl/fl and Smo cKO. Interestingly, a homolog of a Wnt inhibitor, Shisa2, showed a 3.68-fold increase in Smo cKO (Figure 1E) (Yamamoto et al., 2005).

Figure 1 with 1 supplement see all
Shh–Smo signaling regulates Shisa2 expression in dorsal spinal cord.

(A) Schematics of dorsal commissural neuron trajectory in mouse spinal cord at E11.5. Cell bodies of commissural neurons (red circles) are close to the dorsal margin of the spinal cord. Their axons (red line) project to the ventral midline and cross to the contralateral side of the spinal cord (dashed red line). Using an ‘Open-Book’ preparation, dorsal margins from Smofl/fl (control) or Smofl/fl; Wnt1-Cre (Smo cKO) were isolated followed by RNA extraction and RNA-sequencing. (B) Heat map of changes of mRNAs levels. (C) Gene ontology analysis. (D) Heat map of expression levels of PCP genes in control and Smo cKO. No significant changes were observed except Daam2. (E) Heat map of expression levels of Wnt pathway genes. mRNA levels of Wnt3a, Wnt7a, sFRP3 and Wif1 were decreased in Smo cKO. Shisa2 mRNA level was increased (FPKMcontrol = 1.25; FPKMcKO = 4.82; q = 0.0038). (F) Heat map of expression levels of Shh pathway genes. No significant changes were observed except for Smo itself (FPKMcontrol = 14.62; FPKMcKO = 4.63; q = 0.0038). * denotes a q-value of = 0.048, ** denotes a q-value of = 0.0039.

https://doi.org/10.7554/eLife.25269.002

We next tested whether Shisa2 mRNA level is increased in the dorsal spinal cord commissural neurons in Smo cKO using in situ hybridization (Figure 2A,B). To localize commissural neuron cell bodies, we performed combined fluorescent in situ hybridization and immunohistochemistry with a dI1 neuronal marker, Lhx2. Lhx2 is expressed in dI1 neurons derived from Atoh1-positive pdI1 progenitors. The dI1 neurons, which express high levels of Lhx2 (Lhx2high) at E11.5, project axons contralaterally (dI1c), whereas the Lhx2low (and Lhx9high) dI1 neurons, which are located ventral to the Lhx2high neurons at E11.5, project axons ipsilaterally (dI1i) (Figure 2A) (Ding et al., 2012). The axons of Lhx2high dI1 neurons reach and cross the floor plate at E11.5, whereas the Lhx2low dI1 neurons are a later population and extend axons ventrally at E12.5. We found that Shisa2 mRNA level was low in the control Smofl/fl dorsal spinal cord but increased in the Lhx2high dI1 neurons in Smo cKO (Figure 2B,C). These results suggest that the Shisa2 expression in dI1c commissural neurons is regulated by Shh–Smo signaling during midline crossing. We noticed that, in Smo cKO, a few Lhx2low neurons dorsal to the Lhx2high dI1 neurons also showed upregulated levels of Shisa2 mRNA. These may be later-born Lhx2high dI1 neurons, whose expression of Lhx2 is still usually not yet fully activated.

Shh–Smo signaling regulates mRNA level of Shisa2 in dI1 commissural neurons.

(A) A schematics of dI1 commissural neurons in dorsal spinal cord. Atoh1-positive pdI1 progenitors differentiate into dI1 neurons. After differentiation, cell bodies migrate laterally. Lhx2high neurons project axons contralaterally (dI1c), whereas Lhx2low neurons migrate more ventrally at E11.5 (dI1i). Lhx2low neurons start to extend axons at E12.5. (B) Shisa2 mRNA is elevated in Lhx2high dI1 neurons in Smo cKO dorsal spinal cord (white arrow head). Dash lines indicate the lateral margin of spinal cord. Scale bar: 50 μm.

https://doi.org/10.7554/eLife.25269.004

Shisa2 inhibits Fzd3 glycosylation and cell surface presentation

Shisa2 is a member of a family of transmembrane proteins with a single transmembrane domain. Xenopus Shisa, xShisa, interacts with xFrizzled8 and retains xFrizzled8 in the endoplasmic reticulum (ER), thus inhibiting canonical Wnt signaling (Yamamoto et al., 2005). We first tested whether mouse Shisa2 interacts with mouse Fzd3 by co-immunoprecipitation and found that Fzd3 and Shisa2 interact with each other (Figure 3A,B). As a control, we also tested interaction between Shisa2 and Insulin receptor β (IRβ), a cell-surface receptor unrelated to Fzd3, and found that IRβ was not co-immunoprecipitated with Shisa2 (Figure 3—figure supplement 1). We previously reported that mouse Fzd3 is glycosylated (Onishi et al., 2013). When expressed in HEK293 cells, Fzd3 shows three major bands, which correspond to ‘phosphorylated and glycosylated’, ‘glycosylated’ and ‘unphosphorylated and unglycosylated (unmodified)’ proteins (Figure 3B). We found that Shisa2 reduced the amount of ‘phosphorylated and glycosylated’ and ‘glycosylated’ Fzd3 (Figure 3A,B); the major form of Fzd3 that co-immunoprecipitated with Shisa2 is the ‘unmodified’ form (Figure 3B). We then analyzed the level of Fzd3 at the cell surface using a surface biotinylation assay and found that Shisa2 expression robustly decreased the amount of Fzd3 on the cell surface (Figure 3C,D); the cell surface level of IRβ is meanwhile unaffected (Figure 3C,D). GAPDH is a cytoplasmic marker and IRβ is a cell surface marker, which allow assessment of fractionation. IRβ was detected both in cell surface fraction and in total cell extract, whereas GAPDH was only found in total extract (Figure 3C,D). Finally, we performed immunocytochemistry to characterize Fzd3 localization. In the absence of Shisa2, Fzd3–EGFP is localized diffusely in the membrane compartments of the entire cytoplasmic area and on the plasma membrane (Figure 3E). In Shisa2–myc-expressing cells, Fzd3–EGFP and Shisa2–myc are colocalized with Calnexin, an ER marker, suggesting that Shisa2 blocks Fzd3–EGFP transport from ER to Golgi and cell surface (Figure 3E,F). Therefore, our results suggest that Shisa2 may inhibit Wnt/PCP signaling by inhibiting Fzd3 glycosylation and trafficking to the cell surface.

Figure 3 with 1 supplement see all
Shisa2 inhibits Frizzled3 (Fzd3) glycosylation and translocation to the plasma membrane.

(A) Shisa2 was pulled down by Fzd3 in a co-immunoprecipitation assay. (B) Fzd3 was pulled down by Shisa2 in a co-immunoprecipitation assay. The major form of co-immunoprecipitated Fzd3 is the unmodified form. Arrows indicate the bands corresponding to different forms of Fzd3. (C) Fzd3 surface expression and glycosylation are inhibited by Shisa2. Cell surface proteins were labeled with biotin and then precipitated with Neutravidin agarose. Precipitants and total lysates were subject to immunoblotting with the indicated antibodies. p+G represents ‘phosphorylated and glycosylated’, G represents ‘glycosylated’, and U represents ‘unmodified’ Fzd3. (D) Quantification of cell-surface levels of Fzd3 (left panel) and the proportion of different forms of Fzd3 (right panel). Shisa2 overexpression robustly suppresses cell-surface expression of Fzd3. Shisa2 overexpression significantly increases the amount of ‘unmodified’ Fzd3 and reduces ‘glycosylated’ Fzd3. Data are the mean ±SD from four independent experiments. * denotes p<0.05, ** denotes p<0.005. (E) Fzd3–EGFP was retained in the ER in the presence of Shisa2. In the control, Fzd3–EGFP was localized widely in the periphery as well as in the perinuclear region, as indicated by Calnexin, an ER marker. By contrast, in Shisa2-overexpressing cells, most Fzd3–EGFP was retrained in the perinuclear region, co-localized with Shisa2 and Calnexin. Scale bar: 10 μm. N: nucleus. Dashed lines indicate cell outlines. (F) A schematic of Shisa2 effects on Fzd3 trafficking. Left: in control cells, Fzd3 is glycosylated in ER and translocated to the cell surface through the Golgi/trans-Golgi network. Right: in Shisa2-expressing cells, glycosylation of Fzd3 is inhibited and Fzd3 is not translocated to the cell surface.

https://doi.org/10.7554/eLife.25269.005

Fzd3 glycosylation is required for its cell surface expression

To further test the importance of the glycosylation of Fzd3 in its trafficking, we set out to identify the glycosylation site(s) of Fzd3. A recent co-crystal structure of xWnt8 and xFz8 revealed a glycosylation site in the cysteine rich domain (CRD) region of xFz8, which is conserved among all vertebrate Frizzle proteins and which may be important for binding to Wnt ligands (Janda et al., 2012). In mouse Fzd3, this site is N42 (Figure 4A). Fzd3 and Fzd6 have an additional putative glycosylation site (N356 in mouse Fzd3; Figure 4A) in their extracellular loop II. To test whether these putative sites are glycosylated, we made two point mutants, N42Q and N356Q, and the double mutant (2NQ [or N42Q + N356Q]). These Fzd3 mutants, N42Q, N356Q and 2NQ, showed faster mobility (Figure 4B,C), suggesting that N42 and N356 are indeed glycosylation sites. The cell-surface level of Fzd3 (N42Q) is significantly reduced, whereas Fzd3 (N356) is completely undetectable (Figure 4D), suggesting that glycosylation at N356 is more crucial for Fzd3 trafficking than that at N42Q. To better characterize Fzd3 glycosylation, we enriched glycosylated proteins using the Glycoprotein Isolation Kit, WGA (Thermo Scientific) (Figure 4E). The wheat germ agglutinin (WGA) preferentially interacts with N-acetyl glucosamine (GluNAC), terminal GluNAC, and sialic acid structures, so that WGA-immobilized agarose allows us to enrich glycoproteins with modified GluNAC or sialic acid. We found that wildtype Fzd3 is detected in the glycoprotein fraction, whereas mutant Fzd3 (2NQ) is absent from the glycoprotein fraction, further confirming that N42 and N356 are glycosylation sites in Fzd3.

Figure 4 with 1 supplement see all
Frizzled3 (Fzd3) glycosylation sites required for its cell-surface expression.

(A) Putative glycosylation sites in Fzd3. N42 is in the cysteine rich domain (CRD), and N356 is in the second extracellular loop. (B) N42Q, N356Q and 2NQ mutantations affected Fzd3 glycosylation as well as its cell-surface expression. (C, D) Quantification of the cell-surface level of Fzd3 (C) and proportions of Fzd3-modification forms (D). Single mutations (N42Q, N356Q) and double mutation (2NQ) significantly reduced ‘glycosylated’ Fzd3 and increased ‘unmodified’ Fzd3. N42Q mutants showed reduced levels of cell-surface Fzd3. However, N356Q mutation completely eliminated cell-surface Fzd3. Data are the mean ±SD from four independent experiments (2NQ; three experiments). * denotes p<0.001; ** denotes p<5 × 10–7; *** denotes p<1 × 10–8. (E) Enrichment of glycosylated Fzd3 using the Glycosylation Isolation Kit, WGA (Thermo Scientific). Fzd3 WT was detected in the glycoprotein fraction but 2NQ mutant was not. (F) Fzd3 glycosylation in the dorsal spinal cord is reduced in Smo cKO. Dorsal spinal cord tissues from control and Smo cKO E11.5 embryos were collected and lysed, followed by glycoprotein isolation. Glycosylated Fzd3 was significantly decreased in Smo cKO. Data are the mean ±SD from three control and three Smo cKO embryos.

https://doi.org/10.7554/eLife.25269.007

To ask whether Shh–Smo signaling regulates Fzd3 glycosylation in vivo, we examined the glycosylation level of endogenous Fzd3 in the dorsal spinal cord in Smo cKO. We generated polyclonal anti-Fzd3 antibodies and performed western blot. We detected two bands corresponding to ‘glycosylated’ and ‘unmodified’ bands, which are both absent from Fzd3–/– lysate (Figure 4—figure supplement 1). However, we noted a non-specific band that runs at the same position as the ‘phosphorylation and glycosylation’ band (marked with an asterisk). Therefore, this antibody can be utilized to detect ‘glycosylation only’ and unmodified Fzd3, but not the ‘phosphorylation and glycosylation’ band. We isolated glycoprotein using the Glycoprotein Isolation Kit, WGA (Thermo Scientific) and performed western blot to detect how much Fzd3 is glycosylated. We found that Fzd3 glycosylation (‘glycosylation only’ band) was robustly reduced in Smo cKO (Figure 4F), suggesting that Shh–Smo signaling does indeed regulate Fzd3 glycosylation in vivo.

Forced expression of Shisa2 lead to A–P guidance defects of post-crossing commissural axons

To test whether Shisa2 downregulation is necessary for proper A–P guidance of commissural axons, we forced expression of Shisa2 using a heterologous CAG promoter in commissural neurons. We co-electroporated Shisa2-expressing plasmids with tdTomato-expressing plasmids into the dorsal spinal cord commissural neurons and analyzed their axon trajectory revealed by tdTomato in an ‘open-book’ culture (Figure 5A) (Lyuksyutova et al., 2003; Wolf et al., 2008; Shafer et al., 2011; Onishi et al., 2013). Axons expressing control plasmid extended to the midline, crossed, and turned normally anteriorly (Figure 5B,C; 85.9 ± 6.79%). By contrast, we found that axons of Shisa2-expressing neurons turned both anteriorly and posteriorly randomly after midline crossing (Figure 5B,C; 54.3 ± 7.89%). This result suggests that the downregulation of Shisa2 is necessary for proper A–P guidance of commissural axons.

Figure 5 with 1 supplement see all
Shisa2 overexpression lead to A–P guidance defects after midline crossing.

(A) Schematic of experimental design. Plasmids cocktail and Fast Green dye were injected into the ventricle of rat embryonic spinal cord (E13) and electroporated into the dorsal region. The spinal cord ‘open-book’ explants were prepared and cultured in collagen matrix for 72 hr. Axons were visualized by staining for tdTomato expressed by co-electroporated plasmid. (B) (Top) Shisa2 expression randomized the turning of post-crossing commissural axons along the A–P axis. (Bottom) Axons in the images on the top panels were traced manually. Green arrows indicate correct (anterior) turning, whereas red arrows indicate posterior turning. FP, floor plate. Scale bars, 50 μm. (C) Quantification of A–P guidance defects. The graph represents the percentage of the axons that turned anteriorly (correct turning). Gray bars indicate averages of all data points, black bars indicate standard deviations, and diamond dots indicate individual data points (Control; eight embryos, Shisa2-myc; eight embryos).

https://doi.org/10.7554/eLife.25269.009

As xShisa also binds to FGFR and as our RNA-seq data suggest that FGFR1, FGFR2 and FGFR3 are expressed in dorsal spinal cord (Figure 5—figure supplement 1A) (Yamamoto et al., 2005), we tested whether FGFRs are required for A–P guidance of commissural axons by blocking FGFR activity using pharmacological inhibitor LY2874455 (inhibits FGFR1, FGFR2, FGFR3, FGFR four and VEGFR2; Figure 5—figure supplement 1B). First, we tested whether LY2874455 can abolish FGFR autophosphorylation in our ‘open-book’ explants and found that LY2874455 suppressed phosphor-Y653/654 significantly (Figure 5—figure supplement 1C; Vehicle (DMSO), 1 (normalized); LY2874455, 0.43 ± 0.05). We then found that LY2874455 did not affect A–P guidance of commissural axons (Figure 5—figure supplement 1D,E), suggesting that FGFR activity is not required for anterior turning of post-crossing commissural axons.

Knocking down Shisa2 caused precocious anterior turning of precrossing axons through activation of Wnt-PCP signaling

To investigate whether Shisa2 prevents pre-crossing commissural axons from responding to Wnts, we developed shRNA constructs against Shisa2 (Figure 6A,B). As a control, we utilized scrambled shRNA (Shafer et al., 2011; Onishi et al., 2013). We then electroporated control and Shisa2 shRNAs into dorsal spinal cord. We found that the majority of control-shRNA-expressing commissural axons turned anteriorly after crossing the floor plate (Figure 6C,D; 84.3 ± 2.3%), while a small subset of axons turned before crossing (12.6 ± 2.3%) or in the floor plate (3.0 ± 1.0%). This is consistent with our previous finding using this ‘open-book’ explant culture system (Wolf et al., 2008). By contrast, the expressino of both Shisa2 shRNAs significantly elevated the proportion of commissural axons that turned before crossing and in the floor plate (Figure 6C,D) and decreased the proportion of those turning after crossing. To control for off-target effects of these shRNAs, we also performed rescue experiments. We introduced four silent mutations in the shRNA#1 targeting site, and two in the #2 site, and confirmed that the expression level of this mutant Shisa2 (which still encodes WT Shisa2) is not suppressed by shRNAs (Figure 6A,B). We then electroporated Shisa2 shRNAs together with the Shisa2 rescue construct and found that it rescues the phenotype of Shisa2 shRNAs (Figure 6C,D).

Figure 6 with 2 supplements see all
Shisa2 knockdown lead to precocious anterior turning before midline crossing.

(A) Two different shRNA constructs targeting rat Shisa2 can knock down WT Shisa2 but not shRNA-resistant Shisa2 (rescue construct) transfected into 293 T cells. (B) Quantification of (A). (C) Shisa2 knockdown induces precocious turning of commissural axons through premature Wnt–PCP signaling activation. Commissural axons expressing either of the two ShRNA constructs turned before crossing or in the floor plate. This ‘precocious turning’ was eliminated by co-expression of a Shisa2 rescue construct or of Vangl2 shRNA. FP: floor plate. Scale bars: 50 μm. (D) The percentage of axons that turn before or after midline crossing is quantified. Purple represents turning before entering the floor plate; orange represents turning in the floor plate; green represents turning after crossing the floor plate. Data are the mean ±SD. n represents the sample number.

https://doi.org/10.7554/eLife.25269.011

To test whether the precocious turning in Shisa2 knockdown mutants is caused by the premature activation of Wnt-PCP signaling, we performed double knockdown of Shisa2 and Vangl2, an essential component of Wnt-PCP signaling. We previously reported that Vangl2 is required for Wnt-stimulated axon outgrowth and essential for anterior turning of dorsal commissural axons (Shafer et al., 2011). We utilized the same Vangl2 shRNA and confirmed that Vangl2 knockdown led to A–P guidance defects (Figure 6—figure supplement 1). Then, we co-electroporated Shisa2 shRNA and Vangl2 shRNA into the dorsal spinal cord, and found that precocious anterior turning does not occur (Figure 6C,D), supporting our notion that the precocious turning produced by Shisa2 knockdown is due to the premature activation of Wnt–PCP signaling.

To confirm that Shisa2 regulates Fzd3 trafficking in neurons, we directly tested whether Shisa2 knockdown can change cell surface levels of Fzd3 protein in the growth cone of commissural neurons. We utilized a construct that we developed in a previous study, in which Fzd3 was tagged with tdTomato to the carboxyl domain and the FLAG epitope tag was engineered to the extracellular N-terminus (Figure 6—figure supplement 2A) (Onishi et al., 2013). We can label the cell surface Fzd3 using anti-Flag antibodies, while the total Fzd3 protein can be detected by the tdTomato signal. In neurons expressing control shRNA, only a small proportion of the Fzd3 protein was on the cell surface (Figure 6—figure supplement 2B,C). On the other hand, Shisa2 knockdown led to an increase of Fzd3 protein on the surface of the growth cones (Figure 6—figure supplement 2B,C). These results further support the conclusion that Shisa2 regulates Fzd3 cell-surface expression in the growth cones of commissural neurons.

Conditional knockout of Wntless in the floor plate lead to the A–P guidance defects of post-crossing commissural axons

Although we have obtained genetic evidence for the essential roles of several PCP components in the A–P guidance of commissural axons, the genetic evidence for a role for Wnts in this guidance is still lacking. This is in part due to the fact that at least five Wnts are expressed in a decreasing anterior-to-posterior gradient (Lyuksyutova et al., 2003; Agalliu et al., 2009) our unpublished results). As Wntless (Wls) is essential for the secretion of all Wnt proteins (Figure 7A) (Bänziger et al., 2006; Fu et al., 2009), we knocked out Wls specifically in the floor plate by crossing the Wls floxed allele with the Shh-CreERT2 line; in the resulting line, Cre is only expressed in the floor plate and can be activated by intraperitoneal injection of tamoxifen into pregnant females (Harfe et al., 2004).

Figure 7 with 1 supplement see all
Wntless (Wls) in the floor plate is essential for A–P guidance of commissural axons.

(A) Schematic of Wls function in Wnt secretion. Wls is required for Wnts secretion. (B) Schematic of experimental design. Tamoxifen (0.1 mg/g of mother) was injected intraperitoneally at E8.5. Embryos were harvested and dissected at E11.5 for immunohistochemistry (IHC), in situ hybridization (ISH) and DiI tracing experiments. (C) Cre recombination (tdTomato signal) was detected specifically in the notochord and floor plate. After intraperitoneal injection of tamoxifen (0.1 mg/g mother) at E8.5, embryos were collected at E11.5 and transverse sections were immunostained with the indicated antibodies. FoxA2 is a floor plate marker and Nkx2.2 marks the cells immediately outside the floor plate. (D) Loss of Wls mRNA in the floor plate of Wls cKO (Wls fl/fl; Shh-CreERT2). FP, floor plate. Scale bars, 50 μm. (E) Commissural axons, labeled by lipophilic DiI injection into the dorsal spinal cord, showed A–P guidance defects in Wlsfl/fl; Shh-CreERT2. FP, floor plate. Scale bars, 50 μm. (F) Quantification of A–P guidance defects in (E). The graph represents the percentage of injection sites that showed normal anterior turning (correct turning). Gray bars indicate means of all data points, black bars indicate standard deviations, and diamond dots indicate individual data points (control = 13, cKO = 11). (G) A model for the midline switch of Wnt responsiveness. Before reaching the floor plate, commissural neurons express higher levels of Shisa2. Fzd3 is not glycosylated and not translocated to the cell surface. Therefore, growth cones are not able to sense the Wnt gradient. After commissural axons reach the floor plate, Shh–Smo signaling is activated in the cell bodies of commissural neurons and Shisa2 expression is decreased, allowing Fzd3 to be glycosylated and translocated to the surface of the commissural axon growth cones. After crossing the floor plate, a sufficient amount Fzd3 is on the cell surface and the growth cones can now detect the Wnt gradient and turn anteriorly.

https://doi.org/10.7554/eLife.25269.014

First, we confirmed the specificity of Shh-CreERT2 by crossing with R26R-LSL-tdTom mice. After administration of tamoxifen at E8.5, embryos were collected at E11.5 and transverse sections were stained with floor plate and ventral spinal cord markers (Figure 7B). We observed that tdTomato expression is specifically activated in the notochord and floor plate, where endogenous Shh is expressed (Figure 7C). We also confirmed the knockout of the Wls gene from the floor plate by in situ hybridization (Figure 7D). Second, we tested whether conditional knockout of Wls in the floor plate may cause patterning and cell fate defects. At a much later stage, at E13.5, the number of Lhx3+; Islet1/2+ Median Motor Column (MMC) neurons was found to be reduced, as was that of Lhx3. Islet1/2+Hypaxial Motor Column (HMC) neurons were found to be increased in Wnt4/5 KO (Agalliu et al., 2009). We analyzed whether the cell numbers of different motor neuron pools are affected in Wls cKO spinal cord at E11.5 (Figure 7—figure supplement 1A). We did not observe any differences in the total numbers of motor neurons, marked by Islet1/2, between control and Wls cKO mice or the numbers of MMC (Lhx3+; Islet1/2+) and (HMC + PGC) (Lhx3; Islet1/2+) at this early stage (Figure 7—figure supplement 1B–D; p>0.05). In addition, the numbers of motor neuron progenitors (pMNs, marked by Oligo2) and V3 interneuron progenitors (p3, marked by Nkx2.2) were also unchanged (Figure 7—figure supplement 1B–D; p>0.05).

We then analyzed the midline pathfinding of commissural axons in the Wls cKO mice. The isolated spinal cords were prepared as ‘open-book’, and commissural axons were visualized using iontophoretic injection of DiI at a quarter of the way into the dorsal margin of the spinal cord. In control Wlsfl/fl mice (without Shh-CreERT2), commissural axons turn anteriorly after floor plate crossing (Figure 7E,F; 85.6 ± 15.7%). On the other hand, in Wls cKO mice spinal cords (with Shh-CreERT2), commissural axons turned randomly along the A–P axis after midline crossing (Figure 7E,F; 38.7 ± 17.8%), providing genetic evidence that the floor-plate-secreted Wnts are essential A–P guidance cues for post-crossing commissural axons. Due to the intrinsic features of the DiI labeling technique, DiI sometimes over diffuses to label other classes of neurons. Other normal axons tend to have a clear growth pattern and look different from misguided axons in mutants, which tend to show inconsistent wandering patterns. In Figure 7E, some neurons, probably located more ventral to the dl1 neurons, were also labeled. Some of them turned before crossing. Other labeled neurons appear to run along the A–P axis close the injection sites. This occurs in both WT control and mutants. These are not dIl commissural neurons. But in mutants, post-crossing commissural axons clearly wandered along the A–P axis and show varied patterns of growth.

Discussion

We found that Shh–Smo signaling reduces Shisa2 mRNA levels in commissural neurons during or after midline crossing. Shisa2 inhibits Fzd3 trafficking to the cell surface by blocking its glycosylation, keeping Wnt/PCP signaling inactive. Consistent with this, Shisa2 expression using a heterologous promoter led to randomized turning of commissural axons along the A–P axis after midline crossing. Furthermore, Shisa2 knockdown induced Vangl2-dependent precocious anterior turning before midline crossing. At this stage of development, Shh is expressed only in the floor plate and other Hedgehogs are not expressed in or near the spinal cord (Zhang et al., 2001). Secreted Shh has two different lipid modifications at its N-terminus and C-terminus (fatty-acid and cholesterol, respectively) that prevent it from diffusing over a long distance (Sloan et al., 2015). Therefore, we propose that Shh in the ventral midline is detected by commissural axons and signals retrogradely to inhibit Shisa2 expression in the cell body. This inhibition allows Fzd3 to be trafficked to the cell surface, resulting in the activation of Wnt/PCP signaling in commissural axon growth cones (Figure 7G). We also showed here that Wls, an essential component of Wnt secretion, is required for A–P guidance of commissural axons, providing genetic evidence for the role of Wnts in A–P guidance of post-crossing commissural axons. This regulatory link between Shh and PCP signaling pathways may also be important in other developmental processes.

The mechanisms for axon responsiveness switches are not fully understood and have attracted increasing attention in recent years. The midline is an excellent model system for addressing this fundamental question. Spinal cord commissural neurons are first guided by Netrin1 to grow from the dorsal spinal cord to the ventral midline, where they cross to the contralateral side (Kennedy et al., 1994; Serafini et al., 1994; Serafini et al., 1996; Podjaski et al., 2015; Yung et al., 2015). After midline crossing, they lose responsiveness to Netrin1 and become responsive to repellents in the floor plate and the ventral spinal cord, such as Semaphorins and Slits, which turn their trajectory from the dorsal-ventral axis to the anterior-posterior axis (Zou et al., 2000). Recent studies suggest that Netrin1 in the ventricular zone is sufficient to guide commissural axons to grow into the floor plate and that floor plate Netrin1 is not required, indicating that Netrin1 functions at a much shorter-range than previously thought (Dominici et al., 2017; Varadarajan et al., 2017). After midline crossing, commissural axons become responsive to the Wnts, which direct them to turn anteriorly (Lyuksyutova et al., 2003). Here, we show that Shh is a midline switch for Wnt/PCP signaling that operates by regulating the mRNA levels of Shisa2, which in turn regulates Fzd3 trafficking. We previously observed that it takes approximately 8 hr for commissural axons to cross the midline. This should be sufficient time to downregulate Shisa2 mRNA and protein levels and to allow Fzd3 to be glycosylated and trafficked to the cell surface. This switch mechanism may be optimal for the activation of PCP signaling after midline crossing, given the time it takes to cross the midline. We showed previously that Shh switches on repulsive responses to Semaphorin after midline crossing by inhibiting protein kinase A (PKA) (Parra and Zou, 2010). Therefore, Shh is a switch for growth cone responsiveness to both Wnts and Semaphorins. In addition to Shh, other switches in the midline have been proposed. At the Drosophila midline, Frazzled/DCC, a Netrin receptor, transcriptionally activates the expression of Commissureless, allowing attraction to be coupled to the downregulation of repulsion in precrossing commissural axons (Neuhaus-Follini and Bashaw, 2015). In the vertebrate midline, NrCAM and Gdnf activates Plexin-A1 to switch on responsiveness to Sema3B (Nawabi et al., 2010; Charoy et al., 2012). Floor-plate-derived neuropilin-2, probably functioning as a Semaphorin sink, was also proposed to be a switch mechanism for Semaphorin responsiveness (Yang et al., 2009Hernandez-Enriquez et al., 2015). In rodents, cell-intrinsic signaling proteins, namely the 14-3-3 proteins, were proposed to switch Shh-mediated attraction to repulsion during midline crossing (Yam et al., 2012). In chick, Shh binds Glypican 1 to induce the expression of Hhip, which was proposed to mediate repulsion by Shh (Bourikas et al., 2005; Wilson and Stoeckli, 2013). Our study here showed that Shh switches on Wnt/PCP signaling by removing an inhibitory mechanism involving Shisa2. Taken together, there may exist highly sophisticated and tightly regulated switch mechanisms to ensure proper changes of responsiveness for axons at intermediate targets. These switch mechanisms can involve gene expression, signal modulation and ligand distribution, which may function together to ensure fidelity.

Although a gene expression regulatory mechanism linking Shh, Tbx2/Tbx3, Shisa3 and canonical Wnt signaling has been observed recently (Lüdtke et al., 2016), our study identified a link from Shh to Shisa2 and to non-canonical Wnt/PCP signaling, which regulates cellular and tissue morphogenesis through cytoplasmic signaling. Therefore, Shh may determine the time and space of cell polarity signaling through PCP signaling, as well as by gene expression through the canonical Wnt pathway. Currently, we do not know whether Shisa2 is a direct target of Shh–Smo signaling. It is also possible that the Shisa2 mRNA level is regulated by a posttranscriptional mechanism.

In this study, we identified two glycosylation sites of Fzd3, one is in the CRD region (N42) and another is in extracellular loop II (N356). It is possible that glycosylation at N42 might be important for the binding affinity with Wnts. Interestingly, the lowest band of the N42Q mutant showed faster mobility than WT (Figure 4B), suggesting the possibility that all Fzd3 protein is glycosylated at N42. We show that glycosylation at N356 is more crucial for cell surface expression of Fzd3, this is a unique glycosylation site for Fzd3 and Fzd6, which may also be important for regulating interactions between Fzd3 and other PCP components.

This study also presents the missing genetic evidence for Wnts as axon guidance molecules in vertebrates. Owing to the high redundancy of Wnt family members (there are 19 Wnts in mammals), it has been hard to demonstrate that mutations of individual Wnts lead to axon guidance defects in vertebrates. Here, we conditionally knocked out Wls from the floor plate and thus perturbed the secretion of all Wnts from the floor plate. We found that post-crossing commissural axons completely lost directionality along the A–P axis, suggesting that Wnts are the key A–P guidance cues for commissural axons in the ventral midline.

Materials and methods

Antibodies and inhibitors

Anti-GAPDH (MAB374; 1/250000; RRID:AB_2107445) was purchased from Millipore. Anti-Nkx2.2 (DSHB, 74.5A5 (sup), 1/500, RRID:AB_531794); anti-TAG1 (DSHB, 4D7 (sup), 1/50, RRID:AB_531775); anti-Olig2 (Millipore, 211F1.1, 1/2000, RRID:AB_10807410); anti-DsRed (Clontech, #632496, 1/2000, RRID:AB_10013483); anti-HA.11 (Covance, 16B12, 1/5000, RRID:AB_291259); anti-Myc (Santa Cruz, 9E10, 1/2000, RRID:AB_627268); anti-Insulin Receptor β (Santa Cruz, sc-711, 1/2000, RRID:AB_631835); anti-Lhx2 (Santa Cruz, sc-19344, RRID:AB_2135660); anti-GFP (Abcam, ab6673, 1/2000, RRID:AB_305643); anti-Calnexin (Abcam, ab22595, 1/2000, RRID:_AB2069006); anti-phospho-FGFR (Y653/Y654, Cell Signaling, #3471, 1/2000, RRID:AB_331072); anti-FGFR1 (Cell Signaling, #9740, 1/2000, RRID:AB_11178519); and anti-Flag (SIGMA, M2, 1/2000, RRID:AB_439685) were purchased from the indicated venders. Anti-Lhx3 and Islet1/2 antibodies were kind gifts from Dr Pfaff of the Salk Institute. Alexa-conjugated secondary antibodies for mouse/rabbit/rat IgG and mouse IgM were purchased from Molecular Probes (1/500 dilution). HRP-conjugated secondary antibodies for mouse/rabbit/goat IgG were purchased from Jackson ImmunoResearch Laboratories (1/10000 dilution). LY2874455 was purchased from Selleckchem. Anti-Fzd3 rabbit polyclonal antibodies (1/2000 dilution) were generated by the Zou lab. The C-terminal cytoplasmic domain (505–666 a.a.) of mouse Fzd3 fused with glutathione S-transferase (GST) was generated using pGEX4T-1. Recombinant GST–Fzd3cyto protein was expressed in BL21 Escherichia coli and purified with glutathione sepharose 4B (GSH beads, GE Healthcare). Anti-Fzd3 polyclonal antibody was generated in rabbits by injection with recombinant GST–Fzd3cyto protein (Covance). Specificity of the anti-Fzd3 antibodies was validated using lysates from Fzd3 knockout dorsal spinal cord (Figure 4—figure supplement 1).

Plasmids

Fzd3–HA, Fzd3–EGFP and tdTomato expressing constructs were described previously (Shafer et al., 2011; Onishi et al., 2013). Shisa2 cDNA was amplified from the mouse E16.5 brain cDNA library (made by K.O.; SuperScriptIII, Invitrogen) and subcloned into pcDNA3.1-MycHis(A) (Invitrogen). After being subcloned into pcDNA3.1 vectors, Shisa2-MycHis was subcloned into pCAGEN, whereby Shisa2 expression is controlled under CAG promoter, and expressed in dorsal spinal cord commissural neurons without any effects from Shh signaling. To introduce N42Q, N356Q and 2NQ mutation in a Fzd3 background, site-directed mutagenesis against Fzd3 was performed using a QuickChange site-directed mutagenesis kit (Stratagene). Rat Shisa2 cDNA was amplified from a rat E13 dorsal spinal cord cDNA library (made by K.O.; SuperScriptIII, Invitrogen) and subcloned into pcDNA3.1-MycHis (A) (Invitrogen). After being subcloned into pcDNA3.1 vectors, Shisa2-MycHis was subcloned into pCAGEN.

The sequences of the shRNA constructs were follows: control scramble shRNA (5′- GAAACGGAAAGCAGGTACG −3′), rat Shisa2 shRNA#1 (5′- ACCGCCTGATGGAGACCAT −3′), and rat Shisa2 shRNA#2 (5′- CCACAAATTTCTCTGTACT −3′). Complementary oligonucleotides were annealed and inserted into pSuper vector (Oligoengine). To develop shRNA-resistant rShisa2 expression plasmids, we introduced four and two silent mutations in each target region, respectively. Mutant sequence in shRNA#1 is 5′- ACCGgCTcATGGAaACgAT −3′. Mutant sequence in shRNA#2 is 5′- CCACAAAcTTCTCaGTACT −3′. Lower cases represent mutated sites. Mutations were introduced using QuickChange site-directed mutagenesis kit. All constructs were verified by sequencing (Eton Biosciences, Inc).

Cell lines and transfection

COS-7 (RRID:CVCL_0224) cells and HEK293T cells (RRID:CVCL_0063) were purchased from ATCC and maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum. Transfection of both COS-7 and HEK293T cells was carried out using 1 mg/ml Polyethyleneimine MAX (Polyscience). Mycoplasma contamination was monitored by DAPI staining. These cell lines are not on the lists of Cross-contaminated or Misidentified Cell Lines from the International Cell Line Authentication Committee.

RNA isolation and RNA-seq

Control Smofl/fl or Smo cKO mouse E11.5 embryos of either sex were dissected. Isolated spinal cords were opened from the dorsal midline (‘open-book’). The dorsal margins where cell bodies of dorsal commissural neurons are located were dissected by L-shaped tungsten needle (50–100 μm from the dorsal edge) and collected into microcentrifuge tubes. Total RNA was extracted using RNeasy Plus Micro Kit (QIAGEN). We dissected a total of 14 embryos (seven for each genotype). Total RNA quality was assessed using an Agilent Tapestation. Samples had an RNA Integrity Number (RIN) of greater than 8.0. RNA libraries were generated using Illumina’s TruSeq Stranded mRNA Sample Prep Kit using 300 ng of total RNA. RNA libraries were multiplexed and sequenced with 100 base pair (bp) paired single end reads (SR100) to an average depth of approximately 35 million reads per sample on an Illumina HiSeq2500 using V4 chemistry. Sequence results were analyzed using BaseSpace Cloud Computing System (Illumina). RNA reads were aligned using TopHat Alighment App, followed by Cufflinks Assembly and DE App to determine mRNA expression level. RNA levels were quantified using FPKM (Fragment per kilobase of exon per million fragments mapped). Gene Ontology analysis was performed using GO term mapper (http://go.princeton.edu/cgi-bin/GOTermMapper).

In situ hybridization combined with immunohistochemistry

For Shisa2 and Wls mRNA, 1406–2224 bp and 414–947 bp regions, respectively, were amplified with PCR and subcloned into pCRII-TOPO vectors (Life Technologies). DIG-labeled antisense probes against each mRNA were transcribed by SP6 RNA polymerase (Roche), whereas sense probes were transcribed by T7 RNA polymerase (NEB). E11.5 mouse transverse sections were prepared on glass slides (Fisher Scientific; #12-550-15). Sections were postfixed with 4% PFA for 5 min, followed by 1 μg/ml Proteinase K treatment and acetylation. Hybridization was performed at 65°C for 20 hr, followed by washes with 0.2 × SSC at 65°C (30 min × 3 times). After SSC wash, RNA probe-hybridized sections were incubated with 10% Donkey serum/TBS for 1 hr for blocking, followed by primary antibody incubation (anti-Lhx2 (1/500) in 3% donkey serum +3% BSA/TBST (TBS +0.1% Tween-20)) at 4°C overnight. After primary antibody wash, sections were incubated with AlexaFluor 647-conjugated anti-goat antibodies (1/500) and Alkaline phosphatase (AP)-conjugated anti-DIG antibodies (Roche/SIGMA, 1/5000, RRID:AB_514497) in 3% donkey serum +3% BSA/TBST at 4°C overnight. After washing, AP activity is detected by HNPP/Fast Red (Roche/SIGMA; 11758888001). Images were taken using Leica SP5 confocal microscopy immediately after Fluoromount G became dry because Fast Red is quickly diffused in the samples. To detect Wls mRNA, sections were blocked with 10% Donkey serum/TBS for 1 hr after 0.2 × SSC wash. After blocking, sections were incubated with AP-conjugated anti-DIG antibodies, followed by NBT/BCIP (Thermo Scientific) color detection. Images were taken using Keyence BZX-700 microscope (UCSD Microscopy Core in School of Medicine).

Dorsal spinal cord extract

Mouse E11.5 embryos from control Smofl/fl or Smo cKO were dissected and isolated spinal cords were prepared as ‘open-book’. Dorsal margin of the spinal cord was collected into microcentrifuge tubes and then lysed with RIPA buffer (20 mM Tris HCl [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 5 mM NaF, 10 mM β-glycerophosphate, 1 mM Na3VO4, 1 mM DTT and protease inhibitor cocktail (SIGMA), 1% TX-100% and 0.1% SDS). Lysates were subject to immunoblotting with anti-Fzd3 and anti-GAPDH antibodies. The band intensity was quantified with ImageJ. Statistical analysis was performed with Prism7 (GraphPad Software).

Glycoprotein isolation

Isolation of glycoprotein from tissue/cell extracts was performed using a Glycoprotein Isolation Kit, WGA (ThermoScientific). For quantification of Fzd3 glycosylation, we prepared lysates from three control Smofl/fl and three Smo cKO embryos. The band intensity was quantified with ImageJ. Statistical analysis was performed using Prism7 (GraphPad Software).

Surface biotinylation assay

The surface biotinylation and NeutrAvidin pull down methods have been described previously (Shafer et al., 2011; Onishi et al., 2013). Briefly, 48 hr after transfection with indicated plasmids, HEK293T cells (seeded on 20 μg/ml PDL-coated six-well plate) cells were washed with ice-cold PBS (pH 8.0) three times and incubated with 1 mg/ml Sulfo-NHS-LC-Biotin (ThermoFisher Scientific)/PBS for 2 min at room temperature to initiate the reaction, followed by incubation on ice for 1 hr. After quenching active biotin by washing with ice-cold 100 mM Glycine/PBS twice followed by normal ice-cold PBS, the cell lysates were incubated with NeutrAvidin agarose for 2 hr and then precipitated. For quantification, three independent experiments were performed and the band intensity was quantified with ImageJ. Statistical analysis was performed with Prism7 (GraphPad Software).

Co-immunoprecipitation

48 hr after transfection with the indicated plasmids, HEK293T cells were lysed with IP buffer (20 mM Tris HCl (pH 7.5), 150 mM NaCl, 1 mM EGTA, 5 mM NaF, 10 mM β-glycerophosphate, 1 mM Na3VO4, 1 mM DTT and protease inhibitor cocktail (SIGMA), 0.1% TX-100). Lysates were immunoprecipitated with anti-HA or anti-Myc antibodies and with protein A/G agarose (Santa Cruz). Experiments were repeated four times and showed similar results.

Immunocytochemistry

COS-7 cells were plated on coverslips and cultured overnight. Cells were then transfected with 0.4 μg of total DNA. After 40–48 hr, cells were fixed with 4% PFA for 15 min at room temperature, and blocked and permeabilized with 3% normal donkey serum, 3% BSA and 0.1% Triton X-100 in phosphate-buffered saline (PBS) for 30 min and then incubated with primary antibodies at 4°C overnight. After three washes with PBS, cells were incubated with secondary antibodies for 30 min at room temperature followed by three washes with PBS and mounted in Fluoromount G.

To quantify Fzd3 cell-surface levels, rat commissural neurons expressing Flag– Fzd3–tdTomato were fixed with 4% PFA for 10 min at 37°C, followed by incubation with anti-Flag antibodies (1/5000) for 1 hr at room temperature. After PBS wash, neurons were permeabilized with 0.1% TX-100 for 3 min and blocked with 3% donkey serum +3% BSA/PBST (PBS + 0.1% Tween-20). To detect tdTomato signal, neurons were incubated with anti-DsRed antibodies (1/2000) at 4°C overnight. Neurons were washed and then incubated with secondary antibodies for 1 hr, followed by mounting. Images were taken using Leica SP5 confocal microscope. Signal intensity was quantified using ImageJ. 12 growth cones with scramble shRNA and 15 growth cones with Shisa2 shRNAs from three independent experiments were analyzed.

Animals

Mice were housed in an environment with a 12 hr light/dark cycle (7 am to 7 pm). Wnt1–Cre (#022501), Shh-CreERT2 (#005623), Smoothened floxed (#004526) and Wntless floxed (#012888) mice were purchased from The Jackson Laboratory. Genotyping of all animals was done by PCR using genomic DNA prepared from tails. Timed-pregnant wild type Sprague-Dawley rats were purchased from Charles River Laboratories International, Inc. Experiments were conducted in accordance with the NIH Guide for the Care and Use of Laboratory Animals and approved by the UCSD Animal Subjects Committee (Approved Protocol #; S06219, S06222).

‘Open-book’ preparation and DiI axon labeling

Mouse E11.5 spinal cord ‘open-books’ were prepared as described previously (Lyuksyutova et al., 2003; Wolf et al., 2008; Shafer et al., 2011; Onishi et al., 2013). Mouse spinal cord ‘open-books’ were immediately fixed with 4% PFA. To visualize the trajectory of commissural axons, DiI labeling was used in the open-book preparation. DiI injection and quantification were performed as described previously (Lyuksyutova et al., 2003; Wolf et al., 2008; Shafer et al., 2011; Onishi et al., 2013). The number of injection sites and embryos are indicated in the figures.

Ex utero electroporation

Rat E13 embryos were eviscerated and the notochord was removed. Using a pulled glass needle, plasmids were injected into the neural tube. Using 5 mm gold-plated electrodes (#45–0115; Harvard Apparatus, South Natick, MA), square-wave current was passed across the dorsal neural tubes using a BTX #ECM 830 electroporator. Electroporation conditions were three pulses, 25 V, 100 ms pulse and 1 s interval. After electroporation, the spinal cords were dissected and ‘open-book’ explants were cultured in a three-dimensional collagen matrix for 72 hr. Culture media were changed every 24 hr. Explants were then fixed with 4% PFA at 37°C and removed from collagen matrix and blocked with 3% normal donkey serum, 3% bovine serum albumin, and 0.5% Triton X-100 overnight. This was followed by incubation with anti-DsRed antibodies for two nights. Explants were then washed with PBST (PBS + 0.5% TX-100) for 1 hr × 5 times and incubated with secondary antibody anti-rabbit IgG conjugated with biotin overnight. After PBST washes, explants were incubated with Streptavidin-488 overnight followed by multiple washes and mounting in Fluoromount G between two coverslips for microscopic analysis. Images were taken using Leica SP5 confocal microscope. To quantify the effect of Shisa2 overexpression on commissural axon turning, 116 axons were counted for control, and 98 axons were counted for Shisa2 overexpression from eight different spinal cords (from four different litters). To quantify the effect of Shisa2 knockdown, 336 axons were counted for control (11 embryos), 427 axons were counted for shRNA#1 (eight embryos), 320 axons were counted for shRNA#2 (eight embryos), 92 axons were counted for Vangl2 shRNA (five embryos), 101 axons were counted for shRNA#1 + rescue (four embryos), 92 axons were counted for shRNA#2 + rescue (four embryos), 102 axons were counted for shRNA#1 + Vangl2 shRNA (four embryos) and 82 axons were counted for shRNA#2 + Vangl2 shRNA (four embryos).

Immunohistochemistry

E11.5 mouse embryos were fixed in 4% PFA for 2 hr on ice. After equilibration with 30% (w/v) sucrose in PBS, the fixed embryos were embedded in OCT compound (SAKURA) and frozen. Transverse sections were prepared with a cryostat (CM3050S, Leica) at a thickness of 20 μm and mounted on glass slides (Superfrost Plus, Fisher Scientific). Slides were washed in PBST (PBS + 0.1% TritonX-100) and incubated in 3% BSA in PBST (blocking solution) for 1 hr at room temperature. Slides were further incubated with primary antibodies diluted in blocking solution overnight at 4°C, washed three times for 10 min each time in PBST and then incubated for 2 hr with secondary antibodies diluted in blocking solution at room temperature. The slides were washed again and mounted using Fluoromount G (Southern Biotech). All fluorescence images were taken using a Leica SP5 confocal microscopy. All quantification data were obtained using ImageJ software.

Statistical analysis

Statistical analysis of multiple comparisons was performed using one-way ANOVA followed by a Tukey-Kramer post-hoc test for multiple comparisons using Prism7 (Figure 1—figure supplement 1C, Figure 4C,D, Figure 6B,D, Figure 6—figure supplement 2). To compare two groups, Student’s t test was performed (two-tailed distribution) using Prism7 (Figure 3D, Figure 4F, Figure 5C, Figure 5—figure supplement 1C, Figure 6—figure supplement 1, Figure 7F and Figure 7—figure supplement 1D). In the RNA-seq analysis, q-values (modified p-values) were used to estimate significance (consider q < 0.05 as significant).

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Decision letter

  1. Carol A Mason
    Reviewing Editor; Columbia University, United States

In the interests of transparency, eLife includes the editorial decision letter and accompanying author responses. A lightly edited version of the letter sent to the authors after peer review is shown, indicating the most substantive concerns; minor comments are not usually included.

Thank you for submitting your article "Sonic Hedgehog is a midline switch for Wnt/planar cell polarity signaling in commissural axon guidance" for consideration by eLife. Your article has been reviewed by three peer reviewers and the evaluation has been overseen by a Reviewing Editor and Didier Stainier as the Senior Editor. The reviewers have opted to remain anonymous.

The reviewers have discussed the reviews with one another and the Reviewing Editor has drafted this decision to help you prepare a revised submission.

Summary:

The reviewers and Reviewing Editor agree that your analysis of Wnt and Shh interactions on axon guidance at the spinal cord floor plate is a well-done study on how growth cones switch their response from one cue to another. The introduction of the signaling mechanisms involving a new player, Shisa2, brings together your lab's work on Wnt signaling in A-P projection of commissural neuron axons and sonic hedgehog influences at the ventral midline.

Your detailed analyses address how commissural growth cones become competent to respond to Wnt signalling as they cross the floor plate: Shh signaling down-regulates the expression of Shisa2 as commissural axons cross the floor plate. Shisa down-regulation in turn is needed to allow glycosylation and cell surface presentation of the Wnt receptor Fzd3, thereby rendering growth cones responsive to Wnt. Support for this idea includes that 1) Shisa and Fzd3 physically interact; maintenance of Shisa expression in commissural neurons randomizes the growth of commissural axons along the A-P axis, whereas its inhibition leads to premature turning; and conditional inactivation of floor plate-derived Wntless, a molecule responsible for the secretion of Wnt proteins, also randomizes the growth of commissural axons along the A-P axis.

The reviewers' positive comments are offset by requests for a number of analyses and controls that they view would strengthen the claims of the paper. None of these constitute new experiments outside of the scope of the current study, but are viewed as essential.eLife

Essential revisions:

1) More careful analysis of the timing and cell type specificity of Shisa2 expression, pre- and during floor plate crossing, since this is a key element of the 'gene expression switch' model:a) A comparison of Shisa2 levels before and after midline crossing would strengthen the role of midline Shh as a switch.b) Double labeling the Shisa2 in situs with a dorsal commissural neuron marker would more convincingly show that Shisa2 is up-regulated specifically in dorsal commissural neurons in the Smo conditional knock out.c) Better evaluation of changes in Fzd glycolsylation, Fzd3 protein localization, and visualization of myc-tagged Shisa2 to evaluate expression are also recommended.

2) Proper controls especially for the RNAi experiments, i.e. to rescue with an RNAi resistant Shisa2.

3) To further substantiate a link between Shisa2 and Shh/Wnt function in the in vivo experiments, knock down of Shisa2 in the Wntless knockout, which should suppress the premature anterior turning phenotype.

4) The reviewers struggled with comparing phenotypes with varying disruptions in anterior turning, given the difficulties with standardization of size and locus of DiI injections. The Wntless knock-out images are much more striking in terms of axons turning posteriorly than are the Smo knock outs, but the quantification works out to be the same. Please comment.

5) Textually, the paper is clearly written, but the tone and conclusions need to be modified:

– The conclusions are overstated and should more precisely reflect the experimental results.

– The claim that this is the first report of a gene-expression-based switch mechanism by a morphogen in axon guidance at an intermediate target is unfounded. Previous work on response switching at intermediate targets dependent on gene expression changes have been published by the Bashaw, Castellani and Charron labs, and their results compare to the present data.

– The evidence for a "loop" between Wnt-Shh signalling is thin. The signaling seems to be in one direction: Shh-smo signaling represses Shisa2, and Shisa2 prevents Frizzled3 cell surface expression.

– If Wnts are concluded to be the major the A-P guidance cue, complete loss of anterior turning should be expected but this is not the case, and in fact axons would be predicted to stall at the midline. Additional information, independent of Wnt, might be involved and should be acknowledged, especially with respect to the Wntless knockdown.

Reviewer # 2:

1) The main question is how Shisa2 is regulated by Shh/Smo signaling. It was suggested that this is a gene-expression-based mechanism. However, without direct evidence, it is not appropriate to say it is gene-expression based. As indicated in the discussion, Shisa2 mRNA levels could be regulated by many different mechanisms, and it may not be a Gli target.

2) The effect of Shisa2 and Shh on Fzd3 glycosylation is interesting. However, the western blot comparing endogenous Fzd3 levels used dorsal spinal cord (Figure 4E). Although it reflects the levels of Fzd3 in the cell body of commissural neurons, it may not reflect the levels of Fzd3 in the growth cone. Is it possible to measure the Fzd3 levels in the axon/growth cone of commissural neurons?

3) The format of a reference in subsection “Knocking down Shisa2 causes precocious anterior turning of precrossing axons” is wrong.

Reviewer # 3

Figure 2: It is unclear what the significance is of including the Neuropilin data.

Figure 3: In the co-immunoprecipitation experiments, better negative controls would increase confidence in the interaction. The only controls included are to show that the antibodies to the tags don't non-specifically pull down the target proteins, Ideally the authors could show that Shisa does not bind to some other membrane protein. (3E) There are insets included in the top row of images, but it's unclear why there are insets, and they're not significantly larger than the boxed area they are enlarging.

Figure 4: (E) the 'changes' in ratio of glycosylated versus unglycosylated Fzd in the Smo knock-outs is not convincing. The different forms are very poorly resolved. It would be interesting if the authors could speculate on how they think Shisa is affecting Fzd glycosylation.

Figure 5: Shisa2-myc is overexpressed in commissural neurons. Since Shisa2 is myc-tagged, what does shisa-myc expression look like in these neurons? Do the authors observe any difference in Fzd levels or localization in these conditions?

Figure 6: Shisa2 is knocked down with shRNA. The authors need to show that this phenotype can be rescued by over-expression of an RNAi-resistant Shisa2 construct.

Figure 5 and 6: Can Frizzled3 protein localization be visualized by immunofluorescence? If yes, what does Frizzled3 localization look like in commissural neurons when Shisa2 is over-expressed, or knocked down?

Figure 5—figure supplement 1: a positive control for FGF inhibition is needed.

[Editors' note: further revisions were requested prior to acceptance, as described below.]

Thank you for resubmitting your work entitled "Sonic Hedgehog switches on Wnt/planar cell polarity signaling in commissural axon growth cones by reducing levels of Shisa2" for further consideration at eLife. Your revised article has been evaluated by Didier Stainier (Senior editor), a Reviewing editor, and two reviewers.

Your manuscript linking Shh signaling and non-canonical Wnt signaling has been improved. Reviewer 2 was satisfied with your revisions but there are some remaining issues cited by reviewers 1 and 3 in their formal review and the consultation that followed that need to be addressed before acceptance. These are summarized below:

Please note that eLife usually doesn't consider multiple revisions especially when it appears that the authors did not strive to address all of the original concerns and/or produce an easily readable manuscript. Needless to say, this will be your last opportunity to fix the manuscript to an acceptable level.

Reviewer 1, on details of experiments in text and figures:

1) Figure 2B shows that in Smo mutants there is an increase of Shisa mRNA in a population of Lhx2-low neurons positioned dorsally to the dl1c population. Do these neurons project ipsilaterally? Why do they increase Shisa expression as well?

2) Figure 5B is not very convincing as it is difficult to determine from where the segments of axons indicated by arrows come from. Can the authors replace this image for a more illustrative one?

3) In Figure 6, there are many green/flag puncta outside of the growth cones with the exception of the control one. Can the authors provide better images? Such strong background staining casts doubts on the real increase of surface Fzd3.

4) In Figure 7, there are several axons that seem to project abnormally at the pre-crossing side of the floor plate. This should be explained

Reviewer 1 and 3, and the Reviewing Editor, have multiple concerns about the text:

1) The manuscript is still extremely poorly written. It suffers from errors of syntax, usage and grammar throughout, and needs to be completely rewritten.

2) There is a pervasive lack scholarly acknowledgement of the literature. Reviewer 3 pointed out in his initial review that the paper is poorly referenced and discussed beyond the authors' own data and their interpretation, yet this has not been fully addressed in the revision:a) The authors argue in point 5 of the response to Reviewer 3's initial comments that the work of Charron, Castellani, and Bashaw did not constitute a genuine gene-expression-based switch mechanism by a morphogen in axon guidance at an intermediate target. We agree with Reviewer 3 and would like to see a more cogent discussion and comparison of the work from these three labs in reference to the present data.b) New, very relevant papers on netrin were not cited: two studies have shown that Netrin is actually required in the ventricular zone, not the floor plate and these two studies should be discussed with reference to the authors' findings. Dominici et al., 2017 and Varadarajan et al., 2017. How might these findings interface with the authors' datac) While it is true that the manuscript provides novel evidence for a link between Shh signaling and non-canonical Wnt signaling, as Reviewer 1 has pointed out, there are many examples for a similar relationship with canonical Wnt signaling and these should be referenced.

3) The conclusions have been largely tempered in the revised manuscript, yet there are remaining places where the claims have not been toned down, with a number of unclear and unsubstantiated claims given special emphasis. Reviewer 3 finds this problem persistent in the revised manuscript, citing an excerpt from the discussion: "In this study, we also noticed that Shh also up regulates the mRNA level of a Semaphorin receptor Neuropilin2 (Figure 1—figure supplement 2), which may further sensitize commissural axon growth cones to Semaphorin. Therefore, Shh is a switch of growth cone responsiveness to both Wnts and Semaphorins." No experimental evidence is reported in support of this other than the change in Npn expression.

https://doi.org/10.7554/eLife.25269.017

Author response

Essential revisions:

1) More careful analysis of the timing and cell type specificity of Shisa2 expression, pre- and during floor plate crossing, since this is a key element of the 'gene expression switch' model:a) A comparison of Shisa2 levels before and after midline crossing would strengthen the role of midline Shh as a switch.

This is a very good suggestion to determine the timing of Shisa2 expression. However, we would like to point out the technical difficulty of distinguishing pre-crossing and post-crossing commissural neurons in the spinal cord. The cell bodies of pre- and post-crossing axons are all intermingled together in the dorsal spinal cord. There are no molecular markers for pre- and post-crossing commissural axons. It is not possible to use anatomical tracing for the following reason. It is true that we can label the postsynaptic axons and identify their cell bodies by injecting DiI to the post-crossing segment of the axons on the contralateral side. But we can’t selectively label the pre-crossing axons/cell bodies by injecting DiI on the ipsilateral side of the spinal cord because the post-crossing axons/cell bodies will also be labeled as the axons need to first go through pre-crossing segment. In addition, there is no good Shisa2 antibody to visualize endogenous Shisa2 protein levels. And even if there is a good Shisa2 antibody, DiI will also be diffused away when we do immunostaining, which needs detergent. Although we could not experimentally demonstrate the timing of Shisa2 protein expression, we would like to propose that Shh signaling is a switch of the Shisa2 protein level when commissural axons are crossing the midline: 1) Shisa2 mRNA is increased in the cell bodies of the dl1 commissural neurons (Lhx2-positive) in Smo cKO crossed with Wnt1-Cre (new Figure 2) Shh is expressed only in the floor plate and other Hedgehogs are not expressed around the spinal cord at this stage of development (Zhang et al., 2001); 3) Secreted (cleaved N-terminal) Shh has two different lipid modification at its N-terminal and C-terminal (fatty-acid and cholesterol, respectively). Therefore, Shh is a sticky protein and cannot diffuse over a long distance from floor plate to affect gene expression in the dorsal spinal cord (Sloan et al., 2015). We have now emphasized these points in the Discussion section.

b) Double labeling the Shisa2 in situs with a dorsal commissural neuron marker would more convincingly show that Shisa2 is up-regulated specifically in dorsal commissural neurons in the Smo conditional knock out.

For the suggestion to more carefully analyze the cell type specificity of Shisa2 expression, we were able to use a combination of in situ hybridization for Shisa2 (no Shisa2 antibody available) and immunostaining of Lhx2 (dl1 marker) to demonstrate that Shisa2 gene expression is increased in dl1 neurons in Smo cKO (new Figure 2).

In addition, we also further tested whether the gene expression level of Shisa2 may affect Frizzled3 cell surface presentation as we proposed and found that Shisa2 knockdown did resulted in increased Frizzlzed3 cell surface level (Figure 6—figure supplement 2).

Therefore, we propose Shh is a midline switch, which down regulates Shisa2 expression and in turn, lead to the increased Frizzled3 level on the surface of the growth cone membrane.

c) Better evaluation of changes in Fzd glycolsylation, Fzd3 protein localization, and visualization of myc-tagged Shisa2 to evaluate expression are also recommended.

As the glycosylated Frizzled3 band runs very close to the non-glycosylated band, it is hard to evaluate changes of glycosylation of Frizzled3. We purchased the “Glycoprotein Isolation Kit, WGA” from ThermoFisher to isolate and compare glycosylated Fzd3. And we found that Fzd3 glycosylation is significantly suppressed in Smoothened cKO. Please see new Figure 4F. To better visualize Fzd3 and Shisa2 localization (in old Figure 3E), we prepared larger images to show their localization more clearly. Please see new Figure 3E.

2) Proper controls especially for the RNAi experiments, i.e. to rescue with an RNAi resistant Shisa2.

In order to avoid off-target artifacts, we used two different Shisa2 shRNAs and found that they gave rise to very similar phenotypes, suggesting that this phenotype is not because of off-target effect. To further eliminate the possibility of off-target effect, we developed Shisa2 rescue construct, which is insensitive to both shRNA#1 and #2. Then we electroporated shRNA-expressing vector and rescue vector into dorsal spinal cord to see how commissural axons turn. We found that Shisa2 rescue construct restored the precocious turning phenotype of Shisa2 knock down, suggesting that Shisa2 knock down phenotype is due to the reduction of Shisa2 expression level. Please see new Figure 6.

3) To further substantiate a link between Shisa2 and Shh/Wnt function in the in vivo experiments, knock down of Shisa2 in the Wntless knockout, which should suppress the premature anterior turning phenotype.

This would be an excellent experiment. However, due to the limited number of Wntless mice we have this experiment would take many more months to finish. To test whether Shisa2 knockdown leas to premature activation of the Wnt/PCP signaling in commissural axons, we decided to also knockdown a key PCP component, Vangl2, as we have shown before that Vangl2 is required for anterior turning of commissural axons (Shafer et al., 2011). We found that double knock down indeed restored the precocious turning phenotype by Shisa2 knock down. This result further supports our working hypothesis. Please see new Figure 6.

4) The reviewers struggled with comparing phenotypes with varying disruptions in anterior turning, given the difficulties with standardization of size and locus of DiI injections. The Wntless knock-out images are much more striking in terms of axons turning posteriorly than are the Smo knock outs, but the quantification works out to be the same. Please comment.

We would like to clarify that we quantify these phenotypes by scoring the percentage of injections sites of DiI whether these sites display normal anterior turning. The axons in Smo cKO appear shorter, probably because this spinal cord was younger and the axons did not have enough time to grow along the anterior-posterior axis after midline crossing.

5) Textually, the paper is clearly written, but the tone and conclusions need to be modified:

– The conclusions are overstated and should more precisely reflect the experimental results.

We modified the conclusions to more precisely reflect the results.

– The claim that this is the first report of a gene-expression-based switch mechanism by a morphogen in axon guidance at an intermediate target is unfounded. Previous work on response switching at intermediate targets dependent on gene expression changes have been published by the Bashaw, Castellani and Charron labs, and their results compare to the present data.

We appreciate the reviewer bringing this up. Bashaw lab did show that Frazzled/DCC regulates Comm transcription in a netrin-independent manner. “A Frazzled:DCC-dependent Transcriptional Switch Regulates Midline Axon Guidance” from Dr. Bashaw (Science 2009). So our paper is indeed not the first gene-expression based switch, although it is the first morphogen triggered gene expression switch. We will modify the conclusion to the first Shh morphogen triggered mRNA level change.

We would like to clarify that Castellani did not show gene-expression based switch. They showed proteolysis of PlexinA1 is inhibited by NrCAM and GDNF secreted from floor plate, turning on Sema-Plexin signaling after floor plate.

We would also like to clarify that Charron showed expression level of some 14-3-3 proteins changes during in vitro culture (2 DIV vs 3DIV). However, they didn’t show whether this is regulated transcriptionally or translationally.

– The evidence for a "loop" between Wnt-Shh signalling is thin. The signaling seems to be in one direction: Shh-smo signaling represses Shisa2, and Shisa2 prevents Frizzled3 cell surface expression.

We really appreciate this. It was a misuse of the word. We meant to say “link”. We will remove the “loop” words from the text.

– If Wnts are concluded to be the major the A-P guidance cue, complete loss of anterior turning should be expected but this is not the case, and in fact axons would be predicted to stall at the midline. Additional information, independent of Wnt, might be involved and should be acknowledged, especially with respect to the Wntless knockdown.

We would like to clarify that if Wnts are the main A-P guidance cues, the phenotype should be random turn along the anterior-posterior axis, half turning anterior and the other half turning posterior. This would be the true loss of guidance. Because there are still repulsive cues from the floor plate and the ventral spinal cord, which prevent straight elongation after exiting floor plate or recrossing the midline (Zou et al., 2000), axons turn both anteriorly and posteriorly along the floor plate. If there are other cues for A-P guidance, then axons should still turn anteriorly as the other cues should still work without Wnts. If all axons turn posteriorly, then it means that there are other cues that turn axons posteriorly and Wnts normally overcome that. The fact that axons turn randomly along A-P axis supports the proposal that Wnts are the main (or only) A-P guidance cues. This is what we observed. Our finding that Shh regulate PCP signaling suggests that Shh’s role in A-P guidance is indirect. We would like to mention that after we discovered that Wnts guide axons along the A-P axis in the spinal cord, a number of studies in C. elegans showed that Wnts are A-P guidance cues and no other cues were implicated in those cases.

Reviewer # 2:

1) The main question is how Shisa2 is regulated by Shh/Smo signaling. It was suggested that this is a gene-expression-based mechanism. However, without direct evidence, it is not appropriate to say it is gene-expression based. As indicated in the discussion, Shisa2 mRNA levels could be regulated by many different mechanisms, and it may not be a Gli target.

Due to the technical limitation (no good commercial antibody to do mouse Gli ChIP experiments), we could not conclude that our findings are dependent or independent of Gli. We will not say it is gene-expression based. Instead, we will say it is Shisa2 mRNA level.

2) The effect of Shisa2 and Shh on Fzd3 glycosylation is interesting. However, the western blot comparing endogenous Fzd3 levels used dorsal spinal cord (Figure 4E). Although it reflects the levels of Fzd3 in the cell body of commissural neurons, it may not reflect the levels of Fzd3 in the growth cone. Is it possible to measure the Fzd3 levels in the axon/growth cone of commissural neurons?

Because not only commissural neurons, but also many other cell types are expressed Fzd3, so it is difficult to visualize endogenous Fzd3 in the growth cone in vivo. This is why we could only show the glycosylation level of Fzd3 using dorsal spinal cord extract to show the overall level of Frizzled3 glycosylation.

3) The format of a reference in subsection “Knocking down Shisa2 causes precocious anterior turning of precrossing axons” is wrong.

We appreciate this. We corrected this.

Reviewer # 3

Figure 2: It is unclear what the significance is of including the Neuropilin data.

Neuropilin2 was an internal control to show that our RNAseq results matches with in situ results. It is not essential and we removed them.

Figure 3: In the co-immunoprecipitation experiments, better negative controls would increase confidence in the interaction. The only controls included are to show that the antibodies to the tags don't non-specifically pull down the target proteins, Ideally the authors could show that Shisa does not bind to some other membrane protein. (3E) There are insets included in the top row of images, but it's unclear why there are insets, and they're not significantly larger than the boxed area they are enlarging.

We appreciate these suggestions. We tried IRβ, which is not sensitive to Shisa2 expression according to our result, and found that it was not co-immunoprecipitated with Shisa2 (Figure 3C). To visualize Fzd3 and Shisa2 localization (in Figure 3E), we prepared larger images to show their localization clearly.

Figure 4: (E) the 'changes' in ratio of glycosylated versus unglycosylated Fzd in the Smo knock-outs is not convincing. The different forms are very poorly resolved. It would be interesting if the authors could speculate on how they think Shisa is affecting Fzd glycosylation.

To better evaluate Fzd3 glycosylation in Smo cKO (in Figure 4E), we used “Glycoprotein Isolation Kit, WGA” from ThermoFisher to isolate and compare glycosylated Fzd3. And we found that Fzd3 glycosylation was reduced by 90% in Smo cKO.

Figure 5: Shisa2-myc is overexpressed in commissural neurons. Since Shisa2 is myc-tagged, what does shisa-myc expression look like in these neurons? Do the authors observe any difference in Fzd levels or localization in these conditions?

This is a great suggestion. In order to test whether endogenous Shisa2 regulates Fzd3 trafficking in the growth cones of commissural neurons, we utilized the construct in which Frizzled3 was tagged with tdTomato to the carboxyl domain and the FLAG epitope tag was engineered to the extracellular N-terminus (Onishi et al., 2013), and labeled cell surface Fzd3 using anti-Flag antibodies, while total Fzd3 can be detected by tdTomato signal. We electroporated this construct together with Shisa2 shRNA plasmid, and found that more Fzd3 is present on the cell surface when Shisa2 is knocked down. This further supports that Shisa2 indeed suppresses Fzd3 surface presentation in commissural neurons.

Figure 6: Shisa2 is knocked down with shRNA. The authors need to show that this phenotype can be rescued by over-expression of an RNAi-resistant Shisa2 construct.

Two different shRNAs showed very similar phenotype, suggesting that this phenotype is not because of off-target effect. To further eliminate the possibility of off-target effect, we constructed Shisa2 rescue construct, which is insensitive to both shRNA#1 and #2. We then electroporated the shRNA-expressing vector and the rescue vector into the dorsal spinal cord to see how commissural axons turn. We found that Shisa2 rescue construct restored the precocious turning phenotype of Shisa2 knock down, suggesting that Shisa2 knock down phenotype is due to the reduction of Shisa2 expression level.

Figure 5 and 6: Can Frizzled3 protein localization be visualized by immunofluorescence? If yes, what does Frizzled3 localization look like in commissural neurons when Shisa2 is over-expressed, or knocked down?

Because not only commissural neurons, but also many other cell types are expressed Fzd3, so it is difficult to visualize endogenous Fzd3 in the growth cone in vivo. In addition, the endogenous Frizzled3 level is very low. Therefore, we have tried to test exogenous Fzd3 in the commissural neuronal growth cones. However, overexpression of Fzd3 strongly suppressed axon elongation in ex vivo open book explants. All axons could not reach to the floor plate. Therefore, we tested the Frizzled3 localization in Shisa2 overepressing commissural neurons in culture (Figure 6—figure supplement 2). We found that Shisa2 does reduce the cell surface presentation of Frizzled3.

Figure 5—figure supplement 1: a positive control for FGF inhibition is needed.

We appreciate this. Both inhibitors inhibit kinase activity, so we tested whether these can inhibit autophosphorylation of FGFR in our context, and found that only LY2874455 can blocks autophosphorylation (p-Y653/Y654) significantly, so we removed the data about CH-5183284. Please see new Figure 5—figure supplement 1.

[Editors' note: further revisions were requested prior to acceptance, as described below.]

[…] Reviewer 1, on details of experiments in text and figures:

1) Figure 2B shows that in Smo mutants there is an increase of Shisa mRNA in a population of Lhx2-low neurons positioned dorsally to the dl1c population. Do these neurons project ipsilaterally? Why do they increase Shisa expression as well?

This is a very good question. These may be later-born Lhx2high dI1 neurons, whose expression of Lhx2 is still not fully activated. In this case, they should have increased Shisa2 level. However, our current goal is to test whether Shisa2 is indeed up regulated in Smo cKO and the Lhx2high dl1 neurons do show higher Shisa2 level. We have now included this discussion in the text.

2) Figure 5B is not very convincing as it is difficult to determine from where the segments of axons indicated by arrows come from. Can the authors replace this image for a more illustrative one?

We thank Reviewer 1 for this suggestion. We have now replaced this image for more illustrative ones that show the crossing and post-crossing segments. These new images have fewer axons and thus are clearer. We should clarify that due to the thickness of the spinal cord open-book explant, we are not able to show the entire trajectory to include the pre-crossing segment, which are buried in the thick gray matter of the ventral spinal cord. But we have confirmed that all these are commissural axons originated from the dorsal spinal cord, an experimental system that my lab established and used in a number of publications.

3) In Figure 6, there are many green/flag puncta outside of the growth cones with the exception of the control one. Can the authors provide better images? Such strong background staining casts doubts on the real increase of surface Fzd3.

We again appreciate this suggestion and provide new images with less background.

4) In Figure 7, there are several axons that seem to project abnormally at the pre-crossing side of the floor plate. This should be explained

This is due to the intrinsic feature of DiI labeling technique as DiI sometimes diffuses to label other classes of neurons, usually more ventral to the dl1 neurons, that turn anterior-posterior before crossing. They tend to have a clear growth pattern and look different from misguided axons, which tend to show inconsistent wondering patterns and turn anterior-posterior randomly. We now explain this in the text.

Reviewer 1 and 3, and the Reviewing Editor, have multiple concerns about the text:

1) The manuscript is still extremely poorly written. It suffers from errors of syntax, usage and grammar throughout, and needs to be completely rewritten.

Thank you for the alert. We have now rewritten the text throughout, hoping that it is much improved.

2) There is a pervasive lack scholarly acknowledgement of the literature. Reviewer 3 pointed out in his initial review that the paper is poorly referenced and discussed beyond the authors' own data and their interpretation, yet this has not been fully addressed in the revision:a) The authors argue in point 5 of the response to Reviewer 3's initial comments that the work of Charron, Castellani, and Bashaw did not constitute a genuine gene-expression-based switch mechanism by a morphogen in axon guidance at an intermediate target. We agree with Reviewer 3 and would like to see a more cogent discussion and comparison of the work from these three labs in reference to the present data.

We have now expanded our Discussion to include more completely the work done about the midline guidance and have written a comprehensive review about all the switch mechanisms reported. In paragraph # 2 in the Discussion section, we added 16 new references. This helps to put our work in the context of others.

b) New, very relevant papers on netrin were not cited: two studies have shown that Netrin is actually required in the ventricular zone, not the floor plate and these two studies should be discussed with reference to the authors' findings. Dominici et al., 2017 and Varadarajan et al., 2017. How might these findings interface with the authors' data?

These two new papers about Netrin are not directly related to our paper as our paper does not deal with switch of responsiveness to Netrin. These two Netrin papers highlight the short-range nature of Netrin function, which is very important. The Wnt gradient along the anterior-posterior axis is created by graded levels of gene expression, not by diffusion. Wnts are not very diffusible and commissural axons turn at the border of the floor plate where Wnts are produced. Therefore, the newly found mechanism of Netrin action actually fits very well with how Wnts function (also short-range). We now cite the two new papers as they provide a more precise view about axon guidance mechanisms.

c) While it is true that the manuscript provides novel evidence for a link between Shh signaling and non-canonical Wnt signaling, as Reviewer 1 has pointed out, there are many examples for a similar relationship with canonical Wnt signaling and these should be referenced.

This is a very good point. Urged by the reviewer, we also found a recent paper (2016) that reports a link from Shh to Tbx2/Tbx3 to Shisa3 to canonical Wnt signaling. Therefore, we now point out that our work extends the connection from Shh to PCP (non-canonical signaling), which leads to cellular and tissue morphogenesis, instead of gene expression. This suggests that Shh may use this link to exert precise temporal and spatial control of cell polarity signaling in the cytoplasm that leads to cellular and tissue morphology. We have now revised this part of discussion.

3) The conclusions have been largely tempered in the revised manuscript, yet there are remaining places where the claims have not been toned down, with a number of unclear and unsubstantiated claims given special emphasis. Reviewer 3 finds this problem persistent in the revised manuscript, citing an excerpt from the discussion: "In this study, we also noticed that Shh also up regulates the mRNA level of a Semaphorin receptor Neuropilin2 (Figure 1—figure supplement 2), which may further sensitize commissural axon growth cones to Semaphorin. Therefore, Shh is a switch of growth cone responsiveness to both Wnts and Semaphorins." No experimental evidence is reported in support of this other than the change in Npn expression.

We tried again to tone down conclusion everywhere in the paper. “Shh is a switch of responsiveness to both Wnts and Semaphorins” refers to a previous paper from our lab (Parra and Zou, 2009). In this study, we found that Neuroplilin2 was down regulated in commissural neurons in Smo cKO and we were using Neuropilin2 as our internal control for our RNAseq and in situ hybridization. The activation of the expression regulation of Neuropilin2 is potentially relevant to the role of Shh in activating semophorin and would be consistent with our 2009 paper. However, we semaphoring switch is not the focus of this paper and we do not provide more direct test of the role of Neuropilin2. Therefore, including Neuropilin2 as a control and discussing Neuropilin2 causes confusion. Therefore, we have removed all data about Neuropilin2 in the paper.

References

Sloan, T.F.W., Qasaimeh, M.A., Juncker, D., Yam, P.T., and Charron, F. (2015) Integration of Shallow Gradients of Shh and Netrin-1 Guides Commissural Axons. PLOS Biology DOI:10.1371/journal.pbio.1002119

Zhang, X.M., Ramalho-Santos, M. and McMahon A.P. (2001). Smoothened Mutants Reveal Redundant Roles for Shh and Ihh Signaling Inducing Regulation of L/R Asymmetry by the Mouse Node. Cell 105, 781 - 792

https://doi.org/10.7554/eLife.25269.018

Article and author information

Author details

  1. Keisuke Onishi

    Neurobiology Section, Biological Sciences Division, University of California, San Diego, San Diego, United States
    Contribution
    Data curation, Formal analysis, Investigation, Methodology, Writing—original draft, Writing—review and editing
    Competing interests
    No competing interests declared
    ORCID icon 0000-0001-9838-6332
  2. Yimin Zou

    Neurobiology Section, Biological Sciences Division, University of California, San Diego, San Diego, United States
    Contribution
    Conceptualization, Resources, Supervision, Funding acquisition, Validation, Visualization, Writing—original draft, Project administration, Writing—review and editing
    For correspondence
    yzou@ucsd.edu
    Competing interests
    No competing interests declared
    ORCID icon 0000-0002-1092-5547

Funding

National Institute of Neurological Disorders and Stroke (NS047484)

  • Yimin Zou

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Acknowledgements

This project was supported by NINDS RO1 NS047484 and R21 NS NS095615 to YZ and a postdoctoral fellowship from the Japan Society for the Promotion of Sciences to KO. RNA-sequencing was conducted at the IGM Genomics Center, University of California, San Diego, La Jolla, CA. We would like to acknowledge the UCSD School of Medicine Light Microscopy Facility (Grant P30 NS047101) and Jennifer Santini for allowing us to use and assistance with Keyence microscopy.

Ethics

Animal experimentation: Experiments were conducted in accordance with the NIH Guide for the Care and Use of Laboratory Animals and approved by the UCSD Animal Subjects Committee (Approved Protocol #: S06219, S06222).

Reviewing Editor

  1. Carol A Mason, Reviewing Editor, Columbia University, United States

Publication history

  1. Received: January 19, 2017
  2. Accepted: August 17, 2017
  3. Accepted Manuscript published: September 8, 2017 (version 1)
  4. Version of Record published: September 18, 2017 (version 2)

Copyright

© 2017, Onishi et al.

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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