Cagnetta R , Frese CK , Shigeoka T , Krijgsveld J , Holt CE .

Wellcome Trust

	Figure 1. pSILAC-SP3 Detects the Axonal Newly Synthesized Proteome within 5 min (A) Intact whole-eye primordia were cultured in compartmentalized Boyden chambers. Only the axons of RGCs exit the eye—via optic nerve head (ONH)—and extend through the 1 μm pores to grow on the laminin-coated underside of the transfilter. Cell bodies and dendrites remain in the eye on the upper surface and are removed immediately prior the experiment, leaving pure somaless axons. (B) RT-PCR confirms the purity of the axonal compartment. Actb (positive control; Leung et al., 2006), but not Actg or Brn3 (negative controls; Willis and Twiss, 2011, Yoon et al., 2012), mRNAs were detected. (C) Schematic representation of the pSILAC-SP3 methodology applied to somaless retinal axons. Axons are exposed to vehicle or cue in pSILAC medium containing either “medium” or “heavy” isotope-coded Arg and Lys. (D) Proteins identified in axons derived from 100 eye explants and NSPs identified in axons after 5 min of pSILAC. Error bars, SEM. (E) Density distribution of basal NSPs per minute relative to total protein amount. Red line indicates the median. (F) Enriched GO terms in the biological process, molecular function, and cellular composition categories for constitutive axonal NSPs (p < 0.1). (G) Enriched KEGG pathways for constitutive axonal NSPs (p < 0.1). Circle size and numbers indicate NSP counts.
	Figure 2. Guidance Molecules Trigger Rapid and Wide-Scale Up/Down Remodeling of the Nascent Axonal Proteome Hierarchical clustering of cue-induced NSP changes (log2(H/M)) at different time points (5′, 15′, 30′) derived from ≥3 independent biological replicates per each cue stimulation (derived from 5, 5, and 3 independent biological replicates for stimulation with BDNF, Netrin-1, and Sema3A, respectively). Red indicates upregulation, blue indicates downregulation, and dark gray indicates NSP quantified in <50% of biological replicates. Proteins not annotated in Xenopus laevis were blasted against Xenopus tropicalis (identity ≥ 90%, indicated in gray).
	Figure 3. Validation of the pSILAC-SP3 Approach in Axonal Growth Cones (A) Images of puro-PLA for negative controls (Figure 1B). (B and C) Puro-PLA quantification (B) and representative images (C) to validate NSPs across different functional categories, conditions, and time points (Table S1; Mann-Whitney test and one-way ANOVA with Bonferroni’s multiple comparisons test). (D and E) IF representative images (D) and quantification (E) to validate NSPs across different functional categories, conditions, and time points (Table S1; Mann-Whitney test and one-way ANOVA with Bonferroni’s multiple comparisons test). (F) Direct comparison of pSILAC and IF-derived detection of NSPs reveals excellent correlation with r = 0.81 (rpuro-PLA = 0.87; rqIF = −0.41).
	Figure 4. Nascent Axonal Proteome Changes Dynamically over the Duration of Cue Stimulation (A) Overlap of the NSP changes among different times of stimulation in response to each cue. Both common (i.e., the same NSP undergoes similar directional change with log2(H/M) ratio > |0.3|) and different (i.e., a new NSP exhibits change with log2(H/M) ratio > |0.3| or the same NSP undergoes opposite directional change) NSP changes were detected among different cue stimulation periods. Rectangles with solid lines outline KEGG pathway analysis for the NSP changes unique for each time point, and rectangles with dashed lines outline KEGG pathway analysis for the NSP changes constant among different time points (cutoff ≥ 3 proteins per pathway). Red indicates upregulated pathways, and blue indicates downregulated pathways. (B) Enriched GO terms in the biological process, molecular function, and cellular composition categories of selected categories (category count > 15; for complete table, see Figure S4). Rectangles indicate significantly enriched GO terms (p < 0.05).
	Figure 5. Different Guidance Molecules Induce Both Common and Distinct NSP Signatures (A) Principal component analysis (PCA) based on the NSP changes identified in response to the three cue stimulations and time points. (B) Hierarchical clustering of the NSP changes (averaged over the three time points) exhibiting similarity (SD < 0.5) among different cue stimulations. (C) Hierarchical clustering of the NSP changes (averaged over the three time points) exhibiting diverging behavior (SD > 0.5) among different cue stimulations. Proteins not annotated in Xenopus laevis were blasted against Xenopus tropicalis (identity ≥ 90%, indicated in gray). (D) Overlap of the three cue-induced NSP changes (averaged over the three time points). Rectangles outline the NSP changes unique per cue stimulation and their enriched GO terms in the biological process, molecular function, and cellular composition categories (p < 0.1).
	Figure 6. Repulsive Cue Gradient Elicits Proteomic Changes in RpSA and β-actin with Opposite Spatial Polarity within the Growth Cone (A) Growth cone stained for β-actin with a line dividing the near and far sides. Arrow indicates the 90° polarized gradient. (B) Asymmetric decrease of β-actin assessed by the near/far ratio method (unpaired t test). (C) Asymmetric decrease of β-actin assessed by “center of mass” method (unpaired t test). (D) Growth cone stained for RpSA with a line dividing near and far sides. Arrow indicates the 90° polarized gradient. (E) Asymmetric decrease of RpSA assessed by near/far ratio method (unpaired t test). (F) Asymmetric decrease of RpSA assessed by center of mass method (unpaired t test). (G) Repulsive model: β-actin decreases on the near-stimulus side, helping cytoskeleton deconstruction and growth cone collapse, whereas RpSA/67lr increases on the far-stimulus side, thus increasing F-actin and cell adhesion.
	Figure 7. Opposite Regulation of Shared NSPs Underlies Conversion of Netrin-1 Repulsion to Attraction (A) PCC correlation values among the different cue-induced axonal nascent proteomes. (B) Overlap of the three attractive cue-induced NSP changes following 15 min stimulation. Solid rectangles outline the NSP changes unique for each cue stimulation, and dashed rectangles outline the NSP changes in common between Sema3A and BDNF and their related enriched GO terms in the biological process, molecular function, and cellular composition categories (p < 0.1). (C) Plot showing repulsive and attractive Netrin-1 ratios. Circle size correlates with count number, and colored dots indicate commonly regulated NSPs (count > 50%, average ratio > |0.30|). Blue indicates NSPs undergoing opposite change, and red indicates NSPs undergoing the same change. Examples of NSP changes are labeled with protein name (for complete list, see Table S5). (D) Common NSP changes after converting Netrin-1 repulsion into attraction (count > 50%, average ratio > |0.30|). (E) Network-based cluster analysis of the enriched Netrin-1-induced NSP changes and their associated functional classes (p < 0.1). Blue nodes indicate NSPs undergoing opposite change, red nodes indicate NSPs undergoing same change, light blue lines indicate interactions known from databases, and purple lines indicate interactions experimentally determined. Disconnected nodes are not shown (i.e., more NSPs for each enriched functional cluster have been detected).
	Figure S1. Analysis of the basal newly synthesized proteome after 5 min pSILAC – Related to Figure 1 (A) Embryo retinal section was counterstained for the nuclear marker DAPI and the RGC marker Brn3a (Nadal-Nicolas et al., 2009), thus identifying the RGC layer. (B) Embryo retinal section was counterstained for the nuclear marker DAPI and the axonal marker Neurofilament- associated 3A10 (NF-A 3A10; Kastenhuber et al., 2009). All the axons leaving the eye through the ONH derive from the RGC layer. (C) Embryo retinal section was stained for the somatodendritic marker Glutamate Receptor 1 (GluR1; Kessler and Baude, 1999). GluR1 was not detected in the ONH. (D) Retinal explants were cultured on the boyden chamber, isolated from the eye and counterstained for DAPI, the axonal marker NF-A 3A10 and the RGC marker γ-synuclein (Sncg; Surgucheva et al., 2008). Stack image throughout the transfilter shows that no DAPI was detected and all the axons were positive to Sncg. (E) Retinal explants were cultured on the boyden chamber, isolated from the eye and stained for the axonal marker NF-A 3A10 and the somatodendritic marker GluR1. Stack image throughout the transfilter shows that all the axons were negative to GluR1. (F) RT-PCR confirms the purity of the axonal compartment. The positive control Actb (Leung et al., 2006) and the axonal marker Mapt/Tau (Litman et al., 1993) were detected. The dendritic markers Map2, GluR1 and Icam5 (Blichenberg et al., 1999; Grooms et al., 2006; Nicolaï et al., 2010) were absent in the axonal sample. (G) Multi scatter plot illustrating reproducibility for 3 independent biological replicates of 5 min pSILAC labeling. Numbers correspond to PCC. (H) Number of M/L ratio counts vs Intensity Based Absolute Quantification (IBAQ) as measure of protein abundance of preexisting proteins (Schwanhausser et al., 2011). (I) log2 ratios of constitutive axonal NSPs over pre- existing proteins vs IBAQ of preexisting proteins (Schwanhausser et al., 2011) reveals a negative correlation. (L) STRING-based interactome of the basal NSPs belonging to enriched KEGG metabolic pathways. Nodes represent NSPs acting in the histidine metabolism, selenoamino acid metabolism, biosynthesis of amino acids and glycolysis/gluconeogenesis pathways; ‘mt’ indicates proteins belonging to the GO cellular composition categories ‘mitochondrion’ and ‘mitochondrial matrix’; light blue lines indicate interactions known from databases, purple lines indicate interactions experimentally determined. RGC: Retinal ganglion cell; ONH: Optic Nerve Head; IPL: Inner Plexiform Layer; OPL: Outer Plexiform Layer. Scale bar Figure S1A-C: 25 μm, S1D-E: 50 μm.
	Figure S2. Analysis of the cue-induced newly synthesized proteome – Related to Figure 2 (A) Protein size distribution of the axonal proteome and of NSPs up-regulated in response to 5 min cue stimulation. The NSPs up-regulated within 5 min stimulation are shifted slightly towards the shorter size end (Kolmogorov-Smirnov test). (B) Analysis of the transcriptome abundance previously detected in Xenopus stage 32 growth cones (Zivraj et al., 2010) versus the cue-induced IBAQ (Schwanhausser et al., 2011) shows significant positive correlation (Spearman’s rank correlation coefficient ρ = 0.33).
	Figure S3. Validation of the pSILAC-SP3 approach – Related to Figure 3 (A) puro-PLA and IF representative images. (B) Growth cones were stimulated with Sema3A and co-treated with Ciliobrevin A, stained for Histone H4, and IF was measured. H4 total protein level does not change following 5 min Sema3A stimulation and decreases following 15 min Sema3A stimulation. This decrease is blocked by Ciliobrevin A (Mann-Whitney test and one-way ANOVA with Bonferroni’s Multiple Comparison test). (C-D) Pdi puro-PLA in response to 15 min Sema3A stimulation measured along 20 μm of the axon proximal to the growth cone. Sema3A increases Pdi axonal translation. The outcome perfectly correlates with the pSILAC outcome (Table S1) and the puro-PLA measurement in growth cones (Figure 3F) (Mann- Whitney test). (E) Percentage of overlap and abundance correlation (r) between the pSILAC- SP3 outcome in response to cues and the mRNAs detected to be associated with ribosomes in the RiboTag at different developmental stages in vivo (Chi-square test). Scale bars 5 μm.
	Figure S4. Functional enrichment analysis of the cue-induced newly synthesized proteomes after different stimulation times – Related to Figure 4 Enriched GO terms in the biological process, molecular function and cellular composition categories (category count > 15). Rectangles indicate significantly enriched GO terms (p-value < 0.05).
	Figure S5. RpSA/67lr activation promotes increase in F-actin and cell adhesion – Related to Figure 6 (A-B) Growth cones were treated with EGCG for 20 min, stained for F-actin and IF was measured. EGCG induced an increase in F-actin signal (Unpaired t-test). (C) EGCG induced an increase in the number of filopodia (Paired t-test). (D) EGCG was added at T0 and live imaging was carried out on growth cones. EGCG did not affect the number of filopodia added but decreased the number of filopodia retracted (Two-way ANOVA). (E) EGCG decreased the growth cone speed (Paired t-test). Scale bar 5 μm. Error bars s.e.m.
	Figure S6. Analysis of the nascent axonal proteome in repulsive vs attractive conditions – Related to Figure 7 (A) Principal Component Analysis (PCA) based on the common subset of NSPs identified in response to both repulsive (three time points) and attractive Netrin-1, BDNF, Sema3A. Data were plotted using the first two PCs. (B) Repulsive and attractive BDNF ratios were plotted. Dot size correlates to count number, colored dots indicate ‘commonly regulated NSPs’ (count > 50%, average ratio > |0.30|). Blue indicates NSPs undergoing opposite change, red indicates NSPs undergoing same change. Examples of NSP changes are labeled with protein name (for complete list see Table S5). Specifically, protein names indicated in blue or red indicate respectively NSPs undergoing opposite or same change in response to at least two distinct attractive cue stimulations among the three investigated. (C) Repulsive and attractive Sema3A ratios were plotted. Dot size correlates to count number, colored dots indicate ‘commonly regulated NSPs’ (count > 50%, average ratio > |0.30|). Blue indicates NSPs undergoing opposite change, red indicates NSPs undergoing same change. Examples of NSP changes are labeled with protein name (for complete list see Table S5). Specifically, protein names indicated in blue or red indicate respectively NSPs undergoing opposite or same change in response to at least two distinct attractive cue stimulations among the three investigated. (D) Common NSP changes after converting BDNF and Sema3A repulsion into attraction (count > 50%, average ratio > |0.30|). (E) Network-based cluster analysis of the enriched BDNF-induced NSP changes in common between repulsion and attraction, and their associated functional classes (p-value < 0.1). Blue nodes indicate NSPs undergoing opposite change, red nodes indicate NSPs undergoing same change, light blue lines indicate interactions known from databases, purple lines indicate interactions experimentally determined. Disconnected nodes are not shown. (F) Network-based cluster analysis of the enriched Sema3A-induced NSP changes in common between repulsion and attraction, and their associated functional classes (p-value < 0.1). Blue nodes indicate NSPs undergoing opposite change, red nodes indicate NSPs undergoing same change, light blue lines indicate interactions known from databases, purple lines indicate interactions experimentally determined. Disconnected nodes are not shown, i.e. more components for each enriched functional cluster have been detected (see also Figure S7).
	Figure S7. Network-based functional overview of cue-induced NSP changes shared between repulsion and attraction – Related to Figure 7 Network-based cluster analysis of the enriched cue-induced NSP changes in common between repulsion and attraction and their associated functional classes (p-value < 0.1). Light blue nodes indicate NSPs regulated by Netrin-1, green nodes indicate NSPs regulated by BDNF, yellow nodes indicate NSPs regulated by Sema3A, light blue lines indicate interactions known from databases, purple lines indicate interactions experimentally determined. Disconnected nodes are not shown.
	Figure 1. pSILAC-SP3 Detects the Axonal Newly Synthesized Proteome within 5 min(A) Intact whole-eye primordia were cultured in compartmentalized Boyden chambers. Only the axons of RGCs exit the eye—via optic nerve head (ONH)—and extend through the 1 μm pores to grow on the laminin-coated underside of the transfilter. Cell bodies and dendrites remain in the eye on the upper surface and are removed immediately prior the experiment, leaving pure somaless axons.(B) RT-PCR confirms the purity of the axonal compartment. Actb (positive control; Leung et al., 2006), but not Actg or Brn3 (negative controls; Willis and Twiss, 2011, Yoon et al., 2012), mRNAs were detected.(C) Schematic representation of the pSILAC-SP3 methodology applied to somaless retinal axons. Axons are exposed to vehicle or cue in pSILAC medium containing either “medium” or “heavy” isotope-coded Arg and Lys.(D) Proteins identified in axons derived from 100 eye explants and NSPs identified in axons after 5 min of pSILAC. Error bars, SEM.(E) Density distribution of basal NSPs per minute relative to total protein amount. Red line indicates the median.(F) Enriched GO terms in the biological process, molecular function, and cellular composition categories for constitutive axonal NSPs (p < 0.1).(G) Enriched KEGG pathways for constitutive axonal NSPs (p < 0.1). Circle size and numbers indicate NSP counts.See also Figure S1.
	Figure 2. Guidance Molecules Trigger Rapid and Wide-Scale Up/Down Remodeling of the Nascent Axonal ProteomeHierarchical clustering of cue-induced NSP changes (log2(H/M)) at different time points (5′, 15′, 30′) derived from ≥3 independent biological replicates per each cue stimulation (derived from 5, 5, and 3 independent biological replicates for stimulation with BDNF, Netrin-1, and Sema3A, respectively). Red indicates upregulation, blue indicates downregulation, and dark gray indicates NSP quantified in <50% of biological replicates. Proteins not annotated in Xenopus laevis were blasted against Xenopus tropicalis (identity ≥ 90%, indicated in gray). See also Figure S2.
	Figure 3. Validation of the pSILAC-SP3 Approach in Axonal Growth Cones(A) Images of puro-PLA for negative controls (Figure 1B).(B and C) Puro-PLA quantification (B) and representative images (C) to validate NSPs across different functional categories, conditions, and time points (Table S1; Mann-Whitney test and one-way ANOVA with Bonferroni’s multiple comparisons test).(D and E) IF representative images (D) and quantification (E) to validate NSPs across different functional categories, conditions, and time points (Table S1; Mann-Whitney test and one-way ANOVA with Bonferroni’s multiple comparisons test).(F) Direct comparison of pSILAC and IF-derived detection of NSPs reveals excellent correlation with r = 0.81 (rpuro-PLA = 0.87; rqIF = −0.41).Error bars, SEM. Scale bars, 5 μm. See also Figure S3.
	Figure 4. Nascent Axonal Proteome Changes Dynamically over the Duration of Cue Stimulation(A) Overlap of the NSP changes among different times of stimulation in response to each cue. Both common (i.e., the same NSP undergoes similar directional change with log2(H/M) ratio > |0.3|) and different (i.e., a new NSP exhibits change with log2(H/M) ratio > |0.3| or the same NSP undergoes opposite directional change) NSP changes were detected among different cue stimulation periods. Rectangles with solid lines outline KEGG pathway analysis for the NSP changes unique for each time point, and rectangles with dashed lines outline KEGG pathway analysis for the NSP changes constant among different time points (cutoff ≥ 3 proteins per pathway). Red indicates upregulated pathways, and blue indicates downregulated pathways.(B) Enriched GO terms in the biological process, molecular function, and cellular composition categories of selected categories (category count > 15; for complete table, see Figure S4). Rectangles indicate significantly enriched GO terms (p < 0.05).See also Figure S4.
	Figure 5. Different Guidance Molecules Induce Both Common and Distinct NSP Signatures(A) Principal component analysis (PCA) based on the NSP changes identified in response to the three cue stimulations and time points.(B) Hierarchical clustering of the NSP changes (averaged over the three time points) exhibiting similarity (SD < 0.5) among different cue stimulations.(C) Hierarchical clustering of the NSP changes (averaged over the three time points) exhibiting diverging behavior (SD > 0.5) among different cue stimulations. Proteins not annotated in Xenopus laevis were blasted against Xenopus tropicalis (identity ≥ 90%, indicated in gray).(D) Overlap of the three cue-induced NSP changes (averaged over the three time points). Rectangles outline the NSP changes unique per cue stimulation and their enriched GO terms in the biological process, molecular function, and cellular composition categories (p < 0.1).
	Figure 6. Repulsive Cue Gradient Elicits Proteomic Changes in RpSA and β-actin with Opposite Spatial Polarity within the Growth Cone(A) Growth cone stained for β-actin with a line dividing the near and far sides. Arrow indicates the 90° polarized gradient.(B) Asymmetric decrease of β-actin assessed by the near/far ratio method (unpaired t test).(C) Asymmetric decrease of β-actin assessed by “center of mass” method (unpaired t test).(D) Growth cone stained for RpSA with a line dividing near and far sides. Arrow indicates the 90° polarized gradient.(E) Asymmetric decrease of RpSA assessed by near/far ratio method (unpaired t test).(F) Asymmetric decrease of RpSA assessed by center of mass method (unpaired t test).(G) Repulsive model: β-actin decreases on the near-stimulus side, helping cytoskeleton deconstruction and growth cone collapse, whereas RpSA/67lr increases on the far-stimulus side, thus increasing F-actin and cell adhesion.Error bars, SEM. Scale bars, 5 μm. See also Figure S5.
	Figure 7. Opposite Regulation of Shared NSPs Underlies Conversion of Netrin-1 Repulsion to Attraction(A) PCC correlation values among the different cue-induced axonal nascent proteomes.(B) Overlap of the three attractive cue-induced NSP changes following 15 min stimulation. Solid rectangles outline the NSP changes unique for each cue stimulation, and dashed rectangles outline the NSP changes in common between Sema3A and BDNF and their related enriched GO terms in the biological process, molecular function, and cellular composition categories (p < 0.1).(C) Plot showing repulsive and attractive Netrin-1 ratios. Circle size correlates with count number, and colored dots indicate commonly regulated NSPs (count > 50%, average ratio > |0.30|). Blue indicates NSPs undergoing opposite change, and red indicates NSPs undergoing the same change. Examples of NSP changes are labeled with protein name (for complete list, see Table S5).(D) Common NSP changes after converting Netrin-1 repulsion into attraction (count > 50%, average ratio > |0.30|).(E) Network-based cluster analysis of the enriched Netrin-1-induced NSP changes and their associated functional classes (p < 0.1). Blue nodes indicate NSPs undergoing opposite change, red nodes indicate NSPs undergoing same change, light blue lines indicate interactions known from databases, and purple lines indicate interactions experimentally determined. Disconnected nodes are not shown (i.e., more NSPs for each enriched functional cluster have been detected).See also Figures S6 and S7.

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