ABSTRACT
Adgrg6 (Gpr126) is an adhesion class G protein-coupled receptor with a conserved role in myelination of the peripheral nervous system. In the zebrafish, mutation of adgrg6 also results in defects in the inner ear: otic tissue fails to down-regulate versican gene expression and morphogenesis is disrupted. We have designed a whole-animal screen that tests for rescue of both up- and down-regulated gene expression in mutant embryos, together with analysis of weak and strong alleles. From a screen of 3120 structurally diverse compounds, we have identified 68 that reduce versican b expression in the adgrg6 mutant ear, 41 of which also restore myelin basic protein gene expression in Schwann cells of mutant embryos. Nineteen compounds unable to rescue a strong adgrg6 allele provide candidates for molecules that interact directly with the Adgrg6 receptor. Our pipeline provides a powerful approach for identifying compounds that modulate GPCR activity, with potential impact for future drug design.
INTRODUCTION
Adgrg6 (Gpr126) is an adhesion (B2) class G protein-coupled receptor (aGPCR) with conserved roles in myelination of the vertebrate peripheral nervous system (PNS) (reviewed in (Langenhan et al., 2016; Patra et al., 2014)). In homozygous loss-of-function adgrg6 zebrafish and mouse mutants, peripheral myelination is severely impaired: Schwann cells associate with axons, but are unable to generate the myelin sheath, and show reduced expression of the myelin basic protein (mbp) gene (Glenn and Talbot, 2013; Mogha et al., 2013; Monk et al., 2009; Monk et al., 2011). Targeted disruption of Adgrg6 in the mouse results in additional abnormal phenotypes, including limb and cardiac abnormalities, axon degeneration and embryonic lethality (Monk et al., 2011; Patra et al., 2014; Waller-Evans et al., 2010). In humans, mutations in ADGRG6 are causative for congenital contracture syndrome 9, a severe type of arthrogryposis multiplex congenita (Ravenscroft et al., 2015). Peripheral nerves from affected individuals have reduced expression of myelin basic protein, suggesting that the function of ADGRG6 in myelination is evolutionarily conserved from teleosts to humans (Ravenscroft et al., 2015). Human ADGRG6 variants have also been proposed to underlie some paediatric musculoskeletal disorders, including adolescent idiopathic scoliosis (Karner et al., 2015) (and references within).
In zebrafish, homozygous loss-of-function adgrg6 mutants exhibit an inner ear defect in addition to deficiencies in myelination (Geng et al., 2013; Monk et al., 2009). In the otic vesicle, the epithelial projections that prefigure formation of the semicircular canal ducts overgrow and fail to fuse, resulting in morphological defects and ear swelling. Analysis of the zebrafish adgrg6 mutant ear shows a dramatic alteration in the expression of genes coding for several extracellular matrix (ECM) components and ECM-modifying enzymes (Geng et al., 2013) (Fig. 1A). Notably, transcripts coding for core proteins of the chondroitin sulphate proteoglycan Versican, normally transiently expressed in the outgrowing projections and then down-regulated once projection fusion has occurred, remain highly expressed in the overgrown and unfused projections of adgrg6 mutants (Geng et al., 2013). Although Adgrg6 (Gpr126) mRNA is known to be expressed in the mouse ear (Patra et al., 2013), a role in otic development in the mammal has yet to be determined.
Like all aGPCR members, the zebrafish Adgrg6 receptor consists of a long extracellular domain (ECD), a seven-pass transmembrane domain (7TM), and a short intracellular domain (reviewed in (Langenhan et al., 2016)) (Fig. 1B). The ECD includes a GPCR autoproteolysis-inducing (GAIN) domain, which incorporates the GPCR proteolytic site (GPS) and the conserved Stachel sequence (Liebscher et al., 2014; Patra et al., 2014). Proteolysis at the GPS results in two fragments, an NTF (N-terminal fragment) and a CTF (C-terminal fragment), which can remain associated with one another, or may dissociate, the NTF binding to cell surface or extracellular matrix ligands (Patra et al., 2014; Petersen et al., 2015). Dissociation of the NTF triggers binding of the Stachel sequence to the 7TM domain, thereby activating the CTF (Liebscher et al., 2014). This feature provides a variety of CTF-dependent or -independent signalling capabilities that orchestrate cell adhesion and other cell-cell or cell-matrix interactions. For example, during Schwann cell development and terminal differentiation, the Adgrg6 NTF promotes radial sorting of axons, while the CTF is thought to signal through a stimulatory Gα subunit (Gαs), leading to elevated cAMP levels and activated protein kinase A (PKA) to induce transcription of downstream target genes, such as egr2 and oct6 (Petersen et al., 2015). Compounds that act to raise intracellular cAMP levels, such as the phosphodiesterase inhibitor 3-isobutyl-1-methylxanthine (IBMX) and the adenylyl cyclase activator forskolin, can rescue phenotypic defects in both the inner ear and PNS in adgrg6 mutants (Geng et al., 2013; Monk et al., 2009).
Despite the enormous importance of GPCRs as drug targets (Hauser et al., 2017; Sriram and Insel, 2018; Wootten et al., 2018), adhesion class GPCRs remain poorly characterised, representing a valuable untapped resource as targets of future therapeutics (Hamann et al., 2015; Monk et al., 2015). The identification of specific modulators of aGPCR activity is an essential step for understanding the mechanism of aGPCR function and to inform the design of new drugs. Recent successful approaches include the use of Stachel sequence peptides as aGPCR agonists (Demberg et al., 2017), or synthetic monobodies directed against domains within the NTF (Salzman et al., 2017). A promising alternative approach lies in the potential of unbiased whole-animal screening of small molecules. In recent years, zebrafish have emerged as an important tool for in vivo phenotypic screening for new therapeutics (Brady et al., 2016) and for understanding biological mechanisms (Baxendale et al., 2017; Richter et al., 2017). Zebrafish have many advantages for drug discovery: they are a vertebrate species whose embryos can fit into individual wells of a multiwell plate, facilitating high-throughput analysis; they generate large numbers of offspring; they can absorb compounds directly added to the water, and whole-organism screening enables toxicity, absorption, metabolism and excretion of compounds to be assayed early in the screening pipeline.
To date, over one hundred drug screens using different zebrafish disease models have been conducted, some identifying lead compounds that have subsequently been tested in mammalian model systems or entered clinical trials (Chowdhury et al., 2013; Griffin et al., 2017; North et al., 2007; Owens et al., 2008) (reviewed in (Baxendale et al., 2017)). Two screens have been performed to identify compounds that promote myelination in the central nervous system (Buckley et al., 2010; Early et al., 2018). These studies used live imaging of Tg(olig2:GFP) or Tg(mbp:eGFP) fluorescent transgenic lines to screen for small molecules that increase progenitor or myelinating oligodendrocyte cell number. While elegant in design, and successful in identifying hit compounds, these screens required the use of sophisticated and costly high-resolution imaging platforms and relied on detailed quantitative assays for cell number, techniques that are not available to all labs and are potentially limiting in scalability and throughput.
In this study, we have developed an in vivo drug screening assay based on semi-automated in situ hybridisation (ISH) to identify modulators of the Adgrg6 pathway. We have used the otic expression of versican b (vcanb) as an easily-scored qualitative readout to identify compounds that can reduce vcanb overexpression back to normal levels in a hypomorphic mutant allele for adgrg6, tb233c. We used expression of mbp in the posterior lateral line ganglion of adgrg6tb233c mutants as a secondary screening assay, with the aim of identifying chemical classes capable of rescuing the expression of both genes, which may thus represent agonists of the Adgrg6 signalling pathway. To identify ligands that bind directly to Adgrg6, we then tested hit compounds for their ability to rescue a strong loss-of-function adgrg6 allele, fr24, which predicts a severely truncated protein. Several compounds were unable to rescue adgrg6fr24 mutants, including a group with similar structures from the gedunin family of compounds. Compounds able to rescue both alleles include colforsin, a known activator of adenylyl cyclase, demonstrating proof-of-principle that our screen can identify compounds that restore GPCR pathway activity downstream of the receptor. These alternative assays for both down-regulation and up-regulation of gene expression, combined with a comparison of rescue in both weak and strong alleles, have facilitated selection of a strong cohort of hit compounds that can be differentiated by the different screens used. Our approach is scalable and can be used to screen additional compound collections. In parallel, chemoinformatics analysis of the compound libraries and identified hits has enabled classification and prioritisation of selected hit compounds.
RESULTS
Choice of markers for an in situ hybridisation-based screen: otic vcanb expression as a robust readout
We set out to develop a simple assay to identify small molecule modifiers of the Adgrg6 pathway that can be used both to understand Adgrg6 function and to identify compounds that could inform the design of therapeutics. To this end, we chose to perform a drug screen based on in situ hybridisation (ISH), which has the advantage of being a simple, reproducible assay that can be semi-automated (Baxendale et al., 2012; North et al., 2007). We selected vcanb expression in the adgrg6 mutant ear for our primary screen. vcanb has a number of advantages for screening, including highly localised expression in the otic vesicle, very strong and reproducible staining intensity in adgrg6 mutant embryos, and a clear difference between staining in mutant and wild-type embryos at the stage chosen, making it ideal for manual scoring (Fig. 1A). We therefore developed a primary screen seeking compounds that can reduce vcanb levels in adgrg6 mutant embryos and rescue the mutant phenotype. We reasoned that, in addition to yielding information for the ear phenotype, compounds that can rescue vcanb expression may also rescue myelination defects in the PNS, where expression patterns of genetic markers are more complex and defects are harder to score.
We first made a careful comparison of the otic and PNS defects in weak (tb233c) and strong (fr24) alleles for the adgrg6 mutant (Fig. 1A). The tb233c allele is a missense mutation (I963N) in the fourth transmembrane domain of the receptor, whereas the fr24 allele is a nonsense mutation (L463X), predicting a severely truncated protein lacking the GAIN, 7TM and C-terminal domains (Geng et al., 2013) (Fig. 1B). Mutants for each allele have the same defect in semicircular canal formation: otic epithelial projections are enlarged, overgrow, and fail to fuse to form the three pillars that create the hubs of the semicircular canal ducts (Geng et al., 2013) (Fig. 1A). Time-lapse imaging using light-sheet microscopy reveals the dynamics of this process: even when projections make contact with each other, they fail to adhere as in the wild type. Instead, projections in the mutant ear continue to grow, roll around one another as they find space with least resistance, and fill the otic vesicle with semicircular canal projection tissue (Fig. 1C; Supplementary videos 1,2). In wild-type ears, vcanb is expressed in the growing semicircular canal projections between 44 and 72 hours post fertilisation (hpf), but is then strongly down-regulated after fusion; by 4 days post fertilisation (dpf), very little expression is detectable in the ear (Geng et al., 2013). By contrast, in adgrg6 mutants, the overgrown and unfused projections in the developing ear continue to express vcanb at high levels (Geng et al., 2013) (Fig. 1A). Both alleles show a dramatically increased level of expression over wild-type embryos, but the increase is stronger in the fr24 allele (Fig. 1A). mRNA for adgrg6 itself is expressed in mutant embryos for both alleles (Geng et al., 2013) (and unpublished data).
In addition to an upregulation of vcanb expression in the ear, the zebrafish adgrg6 mutant also shows a reduction or loss of expression of the myelin basic protein (mbp) gene in the PNS (Geng et al., 2013; Monk et al., 2009). This additional phenotype proved to be very valuable for our screen design, helping to validate hits and eliminate false positives. Expression of mbp is present in a complex pattern in wild-type embryos, and shows clear differences between the two alleles, correlating with the predicted severity of the mutations (Fig. 1B). Expression is variably reduced along the posterior (trunk) lateral line nerve in homozygous mutants for the hypomorphic tb233c allele, but in all individuals there is consistent absence of staining in cells (presumed Schwann cells) associated with the posterior lateral line ganglion (PLLg) (Geng et al., 2013) (Fig. 1A). The fr24 allele lacks nearly all mbp staining along peripheral nerves (Geng et al., 2013) (Fig. 1A). Note that expression of mbp in the central nervous system (CNS) is not affected in either allele, obscuring any reduction of mbp staining in the PNS without performing a detailed analysis. This made mbp expression unsuitable for a primary screen, but useful for a secondary screen of hit compounds identified from the vcanb screen.
Design of a screening pipeline for compounds that rescue the adgrg6tb233c mutant phenotype
Our strategy for the screening protocol and analysis pipeline is outlined in Figure 2. Both the weak (tb233c) and strong (fr24) alleles of adgrg6 mutants are homozygous viable, enabling large batches of 100% mutant embryos to be generated for each assay. We decided to use the hypomorphic allele (tb233c) in our primary screen, for four main reasons: (1) adult fish homozygous for the tb233c allele produce a larger number of healthy embryos than adults homozygous for the fr24 allele; (2) a lower concentration of our positive control compound IBMX was sufficient to rescue the phenotype in tb233c mutants compared with fr24 mutants (Geng et al., 2013), suggesting that the tb233c allele might also be easier to rescue with other compounds in the libraries screened; (3) vcanb expression, although not as dramatically affected as in fr24, is still robustly over-expressed in the tb233c allele, and (4) we predicted that any small molecules that interact with the active site of the receptor or act as allosteric modulators would be missed in a screen using fr24 mutants, which should only be able to identify compounds acting on targets downstream of the receptor. By using tb233c, we should be able to identify modulators of the pathway acting both downstream and at the level of the receptor itself.
Choice of controls
In all assay plates, we included the phosphodiesterase inhibitor IBMX (100 μM) as a positive control. We have previously shown that addition of 100 μM IBMX at 60 hpf is optimal for both down-regulation of vcanb expression and a rescue of projection fusion in the ears of adgrg6tb233c mutants (Geng et al., 2013). At this stage of development, the anterior and posterior projections in the mutant otic vesicle are extended and in close proximity to the lateral projection, to which they would fuse in the wild type (Fig. 2A). Compounds from both libraries are supplied as stocks dissolved in DMSO; we therefore used 1% DMSO as a negative control. The nacre (mitfa−/−) strain, which has reduced pigmentation, facilitating visualisation of ISH staining patterns, was used as an untreated wild-type control. Three embryos per well were treated with compounds at 25 μM in E3 medium from 60-90 hpf, after which they were fixed and analysed for expression of vcanb by whole-mount ISH. At the embryonic stage assayed by ISH (90 hpf), expression of vcanb in untreated mutant embryos is very specific to the ear, making it clearly visible as two dark spots in the head of each embryo within the well. All controls gave results as expected in all assay plates tested: DMSO-treated mutant embryos showed strong otic staining for vcanb, untreated wild-type embryos showed very little staining in the ear, and IBMX-treated mutant embryos showed rescued (down-regulated) otic vcanb expression (Fig. 2A).
Comparison of compound libraries with diverse structures
In order to test a wide range of compounds, we chose to screen two commercial small molecule libraries. The Tocriscreen Total library (‘Tocris’) consists of 1120 compounds representing known bioactive compounds with diverse structures. The Spectrum Collection (‘Spectrum’; Microsource Discovery Systems) comprises 2000 compounds, including FDA-approved drugs for repurposing, bioactive compounds and natural products. Scaffold analysis of the two libraries highlights the structural diversity present (Fig. 3—Supplemental file 1). Based on Bemis-Murcko scaffolds (Bemis and Murcko, 1996), the Tocris library of 1120 compounds has 693 (62%) scaffolds representing a single compound and only two scaffolds representing more than 10 compounds. The Spectrum library has 682 scaffolds representing unique chemical structures, but as the library consists of 2000 compounds, the proportion of scaffolds represented by a single molecule (30%) is lower than for the Tocris library. Together, the two libraries cover a wide range of chemical space, with a total of 1540 scaffolds, of which 1134 represent unique compounds. Scaffold analysis not only provides a broad overview of the chemical diversity of each library, but can also be used to select and analyse groups of similar compounds with interesting structure-activity relationships. Compounds were also clustered based on their fingerprint similarity using Ward’s method of hierarchical agglomerative clustering, which was useful for visualisation purposes (for dendrograms, see Fig. 3—Supplemental file 2).
Results of the primary screen for reduction of otic vcanb expression levels
To score the efficacy of the compounds in down-regulating vcanb mRNA levels, we used a scoring system from 0 to 3 (Fig. 3; for details, see the Materials and Methods). In the primary screen, each compound was tested against three embryos and the score for each embryo was added to give a final score out of 9. The final scores were classified into different groups according to the thresholds shown in Figure 3B, with the highest degree of rescue in Category A, representing a combined score no greater than 2. Completion of the primary vcanb screen for all 3120 compounds identified 92 (8%) compounds from the Tocris library and 205 (10%) from the Spectrum library that scored in categories A-C (Fig. 3C,E). 5% of the compounds from each library were found to be either toxic (category F; dead embryos or severe developmental abnormalities) or potentially corrosive (category G; no embryos present), while 99 (9%) compounds from Tocris and 269 (13%) from Spectrum were found to cause incomplete or partial suppression of vcanb expression (category D). The largest category (E; 2282 compounds from both libraries, 73%), as expected, represented compounds that had no rescuing or other effect at the concentration used (25 μM). To visualise the complete set of screening results and to identify any clusters of hit compounds with similar structures, compounds were displayed as individual data points on a polar scatterplot (Fig. 3D,F; Fig. 4; interactive version at https://adlvdl.github.io/visualizations/polar_scatterplot_whitfield_vcanb.html). Compound position along the circumference of the plot for each library is based on position on the respective similarity dendrogram (Fig. 3—Supplemental file 2). Data points that are clustered along radii of the plot are thus more likely to be structurally similar, although note that the juxtaposition of different branches of the dendrogram can also place compounds that differ in structure adjacent to one other. Due to the wide diversity of scaffolds found in the Tocris library, less clustering of hit compounds (A-C) can be observed compared with the molecules in the Spectrum library, where more clusters of compounds in the A-C categories are evident (Fig. 3D,F).
Validation of the primary screen: retesting, comparison with control compounds and analysis of duplicates
A large subset of the possible hit compounds categorised as A-C were selected and arrayed in a cherry-picked plate, which was tested using the same assay format. These included all the top hit compounds that scored A or B, and a selection of compounds from the lower-scoring C category. Specifically, 83 out of the 92 possible hit compounds from the Tocris library and 145 of the 205 possible hits from the Spectrum library were retested twice, again with three embryos per well. By increasing the number of embryos screened to a total of nine per compound, we aimed to eliminate any false-positive hits that had an increased average score over these two retests. In addition, after each retest, any compounds that did not show a clear rescue (score >7) were not followed through to the next stage. In total, 91 compounds from the combined list of hits (29 from Tocris, 62 from Spectrum) that showed consistent rescue of vcanb expression across the retests were taken forward for secondary assays (Supplemental Table S1).
To evaluate the success rate of the hit compound selection process, we compared the hits in each original category with the final category based on the average score for the nine embryos (and in a few cases, six embryos). We were interested to know if the hits in the original C category were less likely to be selected after the retest and therefore by choosing a threshold of A or B scores we were choosing the strongest hits. We found that of the 191 hit compounds that originally scored A or B, 184 rescreened with a score of A-C, and 7 compounds showed some toxicity (Fig. 4A-C). In comparison, of the 33 compounds with an original C score that were retested, 9 scored as B or C, 23 scored as D, and one compound scored as F (toxic). Thus, for our assay, >60% of potential hits with an original C score did not pass a hit threshold in the retest, whereas >96% of hits with an original A or B score were selected again in the retests.
To provide further validation for the hits identified in the primary screen, we used two approaches. Firstly, we compared the results of our control compounds to those of similar compounds present in the screened compound libraries. The control compound IBMX, a non-selective phosphodiesterase (PDE) inhibitor, is present in the Spectrum library and was identified as a hit in the primary screen (Fig. 2A). The most similar compound to IBMX from both libraries is 8-methoxymethyl-3-isobutyl-1-methylxanthine (MMPX), a selective PDE-1 inhibitor. MMPX is present in the Tocris library, but was not identified as a hit in our screen, most likely due to its selectivity. In previous work we also used forskolin to raise cAMP levels and rescue the adgrg6 ear phenotype (Geng et al., 2013), but forskolin requires different assay conditions with short drug incubation times to avoid toxicity. Forskolin is represented in the Tocris library, but was toxic in our screening assay. The Spectrum Collection contains two forskolin-related compounds, colforsin and desacetylcolforsin. Colforsin, a water-soluble derivative of forskolin, was identified as a hit in the primary screen, and retested positive in all subsequent tests (see also below); it appeared to be less toxic than forskolin, whereas desacetylcolforsin was toxic at the concentration used. The identification of both IBMX and colforsin as hits in the primary screen confirmed that the assay conditions used were efficient at detecting expected hit compounds.
Secondly, we compared the scores for all compounds that were duplicated in both compound libraries. Chemoinformatics analysis of the Tocris and Spectrum libraries identified 155 compounds represented in both libraries, 65% of which (100/155) had exactly the same vcanb score average from the two individual screens. 39 (25%) of the 155 duplicate compounds yielded a vcanb score average that differed by 1-2 units between the two libraries; 12 (8%) of the compounds yielded a vcanb score average that differed by 3-6 units, while only 4 (3%) compounds had a score average that differed by 7-9 units. In summary, 90% (139/155) of the compounds common to both libraries showed similar scores for the vcanb assay from each library (scores differing by ≤2 units), while 10% (16/155) of the compounds resulted in differing levels of vcanb down-regulation between the two different libraries. After retesting, the difference between the two vcanb score averages for nine of these compounds was reduced; however, for seven compounds, the scores between the two libraries remained significantly different. These discrepancies could be either due to differences in compound purity between the two suppliers, or could be due to experimental error (e.g. in the concentration used, or during the ISH protocol). In cases where the same compound was scored as toxic in one assay and not in another, the health condition of the fish in a particular well could be the underlying reason. Duplicated compounds have been included in the data for each library in the polar scatter plots (Figs 3,4).
The top 91 hit compounds from both libraries (29 from Tocris, 62 from Spectrum) that scored A-C in all three vcanb assays were combined to give a complete list of 89 unique compounds, with baicalein and gedunin present in both libraries. The list covers a wide spectrum of naturally-derived and synthetic molecules, with known and unknown functions (Supplementary Table S1). The hit compounds with known functions include calcium channel blockers, antifungal, anti-inflammatory, antihyperlipidemic, antibacterial and anthelmintic agents, as well as compounds with known antineoplastic and vasodilatory properties.
Secondary screen for rescue of mbp expression, and identification of false positives
The two retests for vcanb expression significantly reduced the possibility of false-positive results due to experimental error (e.g. in the ISH protocol), but the list of hits could still contain false-positive compounds that may generally inhibit transcription or cause developmental arrest of the embryo. In order to eliminate such compounds, we exploited the expression of mbp as a secondary screening assay, testing for rescue of expression in the posterior lateral line ganglion (PLLg) and from three small regions near the cristae of the inner ear (Fig. 4D; Materials and Methods). This counterscreen has the advantage of assessing for up-regulation (restoration) of mbp expression in mutant embryos, in contrast to the down-regulation of vcanb expression in the primary screen. All compounds that passed the first retest for vcanb (89 compounds in total) were subjected to this secondary assay for mbp expression. We used the same assay format and treatment time window as for vcanb, as we had previously found that treatment with IBMX between 60 and 90 hpf was also able to rescue mbp expression in adgrg6 mutants (not shown).
Following two experimental repeats (n=6 fish tested per drug), compounds were categorised into groups based on their average mbp score. These included groups of compounds that showed rescue of the mutant phenotype (an increase of mbp expression, specifically in the PLLg); no rescue (mbp expression equivalent to that in untreated adgrg6tb233c mutants), and those that resulted in a decrease in mbp expression, as shown in Figure 4D. We identified 41 compounds (12 from Tocris, 29 from Spectrum) that rescued mbp expression and thus represent possible modulators of Adgrg6 pathway (Fig. 4E,F; Table 1). Twenty-eight hit compounds (15 from Tocris, 13 from Spectrum) strongly down-regulated vcanb expression but did not affect mbp expression in adgrg6tb233c mutants. These could represent compounds that can rescue vcanb expression in an inner ear-specific or Adgrg6-independent manner. Alternatively, as all the assays were carried out at a single concentration (25 μM), it is possible that some or all of these compounds could rescue mbp expression at a higher concentration (as is the case for IBMX with the fr24 allele). The 28 members of this group are structurally and functionally diverse (Supplementary Table S1). Finally, 22 compounds (2 from Tocris, 20 from Spectrum) reduced the expression of both vcanb and mbp. This latter group—potential false positives in the vcanb assay—could represent general inhibitors of transcription or development, and were excluded from further analysis, resulting in a final list of 68 hit compounds (Supplementary Table S1).
Compounds that can rescue both inner ear and myelination defects
The 41 compounds that could both down-regulate vcanb expression and restore mbp expression to wild-type levels in adgrg6tb233c mutants, presumed modulators of the Adgrg6 signalling pathway (Table 1), are highlighted on the final combined polar scatter plot (Fig. 4G). Although hit compounds are scattered around the plot, some clustering is evident, and we chose two groups for further analysis (Fig. 4G; boxes at 300, 2500). These groups with five or more compounds included the pyridines (cluster 1 on the scatter plot) and the tetranortriterpenoids (gedunin derivatives) (cluster 2 on the scatter plot). The pyridine cluster included one pyrazolopyridine and six dihydropyridines, a class of L-type calcium channel blockers with vasodilatory properties (reviewed in (Tocci et al., 2018)). The gedunins are a family of naturally occurring compounds, previously attributed with antineoplastic and neuroprotective effects (Jang et al., 2010; Subramani et al., 2017).
Data from each of the screens and retests were used to cluster the compounds into groups based on their activity (displayed as a heat map in Fig. 5A), and compared with a compound network display based on structural similarity in Fig. 5B; interactive version at https://adlvdl.github.io/visualizations/network_whitfield_vcanb_mbp/index.html). A selection of compounds was chosen for further study (Figs 6–8). As many of the compounds classified as putative Adgrg6 pathway modulators were dihydropyridines (cluster 1, Fig. 4), two compounds were chosen from this class for further study (cilnidipine and nifedipine). The third compound that was chosen was tracazolate hydrochloride, a pyrazolopyridine derivative belonging to the nonbenzodiazepines and a known γ-aminobutyric acid A (GABAA) modulator (Thompson et al., 2002), which strongly down-regulated vcanb expression to wild-type levels. FPL 64176 was also chosen for further analysis, based on its potent efficacy in down-regulating vcanb, and the fact that it was the only calcium channel modulator (Liu et al., 2003) that did not rescue mbp expression efficiently. Initial experiments to repeat the rescue of the vcanb and mbp expression with freshly-sourced compounds from alternative suppliers (see Materials and Methods) confirmed that the pyridines cilnidipine, nifedipine and tracazolate hydrochloride were able to decrease otic vcanb expression and increase mbp expression in the PLLg in mutant embryos for the tb233c allele, whereas FPL 64176 was able to reduce vcanb expression but was unable to restore mbp expression to wild-type levels (Fig. 6C).
Nifedipine, cilnidipine, tracazolate hydrochloride and FPL 64176 rescue otic defects in adgrg6tb233c mutants in a dose-dependent manner
The four compounds shown in Figure 6 were also selected for dose-response assessment, by exposing adgrg6tb233c embryos to concentrations ranging from 0.3 μM to 222.2 μM between 60-110 hpf. Nine embryos were tested for each concentration, and a 1.5-fold dilution series of each drug was used. ISH analysis of the 110-hpf embryos revealed a robust, dose-dependent down-regulation of vcanb mRNA expression in response to treatment with all four drugs (Fig. 7). Expression of vcanb mRNA was assessed by annotating each embryo with two scores, one representing the intensity of the stain (score as in Fig. 3A) and the other representing the number of projections stained (Fig. 7A). All four drugs were able to reduce both the intensity of the ISH staining and the number of projections stained in the ear in a dose-dependent manner. For each of the four drugs, the intensity of the vcanb staining decreased even after treatment with low doses, whereas higher doses were needed to reduce the number of the projections stained.
In order to investigate whether other aspects of the ear phenotype in adgrg6tb233c mutants could be rescued by compound treatment, the inner ears of live treated embryos were observed with differential interference contrast (DIC) optics at 110 hpf (or 90 hpf in the case of FPL 64176, due to its toxicity). Consistent with the vcanb scores for the number of projections stained, live DIC images of the inner ear revealed a dose-dependent rescue of projection fusion and pillar formation, which was greater at higher doses (Fig. 7). As adgrg6tb233c mutants have a swollen ear phenotype (Geng et al., 2013), measurements of the ear-to-ear width, normalised for size differences between individuals, were taken from photographs of live embryos mounted dorsally. The results showed a dose-dependent reduction in ear swelling with increased concentration of the four drugs (Fig. 7C; Fig. 7— Supplemental file 1). LD50 concentrations were also determined for each of the four compounds and ranged from 19.2 μM (cilnidipine) to 51.7 μM (tracazolate hydrochloride) (Fig. 7—Supplemental file 2).
Test for rescue of vcanb expression in the fr24 allele: screen for Adgrg6-specific ligands
The initial screen was performed on the hypomorphic tb233c allele. We differentiated our hit compounds further by re-screening for vcanb expression in a strong adgrg6 allele, fr24 (Fig. 1B), to identify compounds that could potentially interact directly with the Adgrg6 receptor itself. We predicted that any compounds able to rescue both alleles (such as IBMX at higher concentrations) are likely to act downstream of the receptor. On the other hand, hits that rescued tb233c, but were not able to rescue fr24, are likely to act as putative agonistic ligands for the Adgrg6 receptor. Of the 41 hit compounds able to rescue both vcanb and mbp in the tb233c allele, we identified 10 compounds that also rescued vcanb expression in the fr24 screen (score sum 0-7 in Table 1, yellow), 12 compounds that gave a partial or inconclusive rescue (white), and 19 compounds that did not affect vcanb expression in the fr24 screen (score sum 9 in Table 1, grey). The first group (yellow) are presumed to act downstream of the Adgrg6 receptor, and include colforsin, which tested positive in all assays and is a known activator of adenylyl cyclase, supporting this interpretation (Fig. 8). The last class (grey) are of particular interest as they represent candidates for molecules that interact directly with the receptor. Examples of the difference in ability to rescue the two adgrg6 alleles between the two classes can be seen in Figure 8C.
Interestingly, four of the 19 compounds in the last group are in the cluster of gedunin derivatives identified in Figure 4 (cluster 2), with deoxygedunin being one of the top ten most potent drugs able to rescue the tb233c allele. The compound network shows that 38 compounds with structural similarity to the gedunins are represented in the two libraries (Figs 5,8). In the primary screens, 25/38 (66%) gedunin-related compounds affected vcanb expression to some extent (18 compounds in categories A-C and 7 in D), 9 compounds were inactive and 4 were toxic. The majority of the gedunin-related compounds that passed both rounds of retesting were later found also to rescue mbp expression (8/10, 80%). The shared structural characteristics of the gedunin group may give useful clues for candidate structures of agonistic ligands for Adgrg6. In summary, our study demonstrates a novel screening approach which, when combined with chemoinformatics analysis, is able to delineate both expected downstream rescuers of the Adgrg6 pathway and several candidates for drugs that may interact directly with the Adgrg6 receptor.
DISCUSSION
Adhesion GPCRs are critical regulators of development and disease, driving cell-cell and cell-ECM communications to elicit internal responses to extrinsic cues. This study set out to identify positive modulators of the Adgrg6 signalling pathway, a key regulator of myelination and inner ear development in the zebrafish embryo. Use of a whole-animal phenotypic (mutant rescue) screen gave the potential to identify compounds affecting the entire Adgrg6 pathway in the correct cellular context. We have used a simple in situ hybridisation approach to assay vcanb expression in the inner ear of adgrg6 mutants, exploiting an easily identifiable phenotype that could be scored manually. Following our primary screen of 3120 small molecules, we tested 89 hit compounds in a counter screen for rescue of the myelination defect in adgrg6 mutant embryos. We identified 41 compounds that can both rescue vcanb expression in the inner ear and mbp expression in Schwann cells of adgrg6 hypomorphic mutants, suggesting these are Adgrg6 pathway-specific modulators. Further analysis of a strong adgrg6 allele, fr24, identified a subset of 19 compounds that are potential direct interactors of the Adgrg6 receptor. This analysis, combined with chemoinformatics analysis of the identified hit compounds, has identified clusters of compounds acting at different levels of the Adgrg6 pathway.
An optimal drug screening assay design identifies the maximum number of hit compounds with the minimum number of false positives and false negatives. Chemical screening assays using zebrafish range from simple morphology screens (Yu et al., 2008) through to high-tech, automated methods for quantitative image analysis (Early et al., 2018) or behavioural analysis (Bruni et al., 2016; Rennekamp et al., 2016) (reviewed in (Kalueff et al., 2016)). We used an in situ hybridisation screen to analyse gene expression changes, as this has the advantages of being scalable to different sized projects and relatively inexpensive to perform—with results that are stable and reproducible. Spatial resolution of staining patterns can be accurately scored: expression pattern screens have recently been used to identify small molecules that can induce subtle differences in gene expression domains along the pronephros (Poureetezadi et al., 2016) and in the somites (Richter et al., 2017). Although quantification of gene expression levels is less reliable with an enzymatic reaction compared with a fluorescent signal, we utilised the strong contrast between the high vcanb expression in the ear of adgrg6 mutant fish compared with the low expression in a small dorsal region of the wild-type ear at 4 dpf to produce a robust scoring system for our phenotype rescue.
Relatively few zebrafish screens have been undertaken to identify compounds that can increase myelination (Buckley et al., 2010; Early et al., 2018) or restore myelination in neuropathy models (Zada et al., 2016), which is in part due to the complex distribution of glial cells in both the CNS and PNS. Performing the primary screen using our ear marker, vcanb, enabled us to bypass the difficulties of scoring and quantification of mbp staining on a large scale; instead, mbp expression was used as a counter screen on a limited number of cherry-picked hits. Contrary to the primary assays, which screened for down-regulation of vcanb expression, the counter screen assayed for up-regulation of mbp expression, enabling the identification of 21 false-positive compounds that down-regulate the expression of both genes (presumably by inhibiting transcription).
Determining the false-negative rate for any screen is difficult. In our assay we used only one concentration of compound (25 μM), so it is likely that we missed compounds that were toxic or where the dose was suboptimal; these may be effective at different concentrations. One possibility would be to run a parallel screen at a lower or higher concentration or use an alternative protocol with shorter incubation times, an approach that has recently proved successful at identifying different compounds influencing segmentation in zebrafish (Richter et al., 2017). Here, the compounds were found to be most active in the range of 10-50 μM, supporting our choice of 25 μM for the primary screen. However, increasing the number of replicates with different drug concentrations or assay conditions has significant implications on the cost and time taken to complete the screen, reducing the number of compounds analysed and the potential hits identified. Our minimum estimate for the false-negative rate is 5%, based on the seven compounds (out of a total of 155) that were duplicated in both libraries and had a significantly different score after retesting, being classified as a hit in one library but not in the other. It is possible that this is due to differences in chemical purity from the different suppliers. Other false-negative compounds could include those that are unable to penetrate into the ear. Neomycin, for example, is toxic to the superficial hair cells of the lateral line system, but is ineffective on inner ear hair cells unless microinjected into the ear (Buck et al., 2012). Other compounds that we will have missed could include myelination-specific compounds, as the primary assay scored for the ear phenotype only. Given that several compounds were positive hits for the rescue of vcanb in the ear and negative for mbp, it is likely that tissue-specific functions of Adgrg6 are mediated through different downstream pathways or are stimulated by different ligands.
Our positive control compound, IBMX, was identified independently through our screen as a category A hit. The hit compound colforsin was found to be more potent and less toxic than the related control compound forskolin, and had the highest score in every assay, showing full rescue of our strongest fr24 allele. Both these observations highlight the robustness of the assay and the consistency of the scoring process. In total, the final number of hit compounds identified was similar in both the compound libraries screened, with 42 compounds identified from the Spectrum library (2.1%) and 27 compounds from the Tocris library (2.4%). These hit rates are comparable to those found in other similar screens (Baxendale et al., 2012; Vettori et al., 2017). Chemoinformatics analysis and visualisation of the results provided additional context to the identified hit compounds. The polar scatter plot displayed an initial overview of the results and allowed the identification of clusters of active compounds with similar structure. The compound network focused the analysis on highly detailed similarity relationships inside each compound cluster, yielding a wealth of structure-activity relationship information that could prove very useful for any future optimisation of the identified hit compounds.
Of the 41 hit compounds able to rescue both inner ear and myelination phenotypes, 23 are grouped in six different structurally-related clusters. Seven of the 41 hit compounds that rescued vcanb and mbp expression are Ca2+-channel modulators. Six of these (nifedipine, cilnidipine, nitrendipine, nimodipine, efonidipine, niguldipine) belong to the chemical group of dihydropyridines (cluster 1), some of which have neuroprotective effects in murine models. Nimodipine, for example, has been shown to trigger remyelination in a mouse model of multiple sclerosis and to improve repair in peripheral nerve crush injuries in rats (Schampel et al., 2017; Tang et al., 2015). As dihydropyridines have been reported to inhibit cAMP phosphodiesterases (Sharma et al., 1997), protection of cAMP from degradation might be another mechanism whereby these molecules exert their ameliorating action on the adgrg6 mutant phenotype.
Phenotypic screens are advantageous for assessing models of multifactorial pathological conditions, such as hereditary neuropathies and cancer (reviewed in (Baxendale et al., 2017)). However, one of the challenges for phenotypic screening is the identification of the specific target for any hit compound, as multiple pathways and different cell types can contribute to a positive read-out in the screening assay. Our aim was to identify compounds that are likely to interact directly with the Adgrg6 receptor. We were able to separate hit compounds into different groups based on their ability to rescue otic phenotypes caused by missense (tb233c) and nonsense (fr24) mutations. In total, we found 19 hits that could rescue vcanb expression and mbp expression in the tb233c allele, but were unable to rescue the fr24 allele. We hypothesise that the fr24 allele is unable to produce the full-length Adgrg6 protein, and therefore any compounds that interact directly with the receptor would not be able to rescue this strong allele. Further analysis will be needed to determine whether any of these compounds can bind directly to the Adgrg6 receptor. However, this approach of using a combination of null and hypomorphic alleles in zebrafish whole-organism screening with the aim of identifying target-specific compounds is particularly exciting and one that the advent of CRISPR/Cas9 technology is placed to take full advantage of, since it is now possible to generate designer mutations in the zebrafish through homology-directed repair (Hruscha et al., 2013; Hwang et al., 2013; Komor et al., 2016).
It is of interest to note that one of the main groups of compounds identified as potential interactors of the receptor in the fr24 screen is a cluster of gedunin derivatives (cluster 2). One of these compounds, deoxygedunin, has previously been identified as a TrkB agonist that has neuroprotective properties (Nie et al., 2015), can promote axon regeneration after nerve injury (English et al., 2013), and, interestingly, has been found to protect the vestibular ganglion from degeneration in mice mutant for BDNF (Jang et al., 2010). More recently, gedunin derivatives, including 3-α-DOG, have been shown to act as partial agonists for the closely related aGPCR, ADGRG1 (formerly GPR56) (Stoveken et al., 2018), a key regulator of myelination in both the CNS and PNS (Ackerman et al., 2015; Ackerman et al., 2018; Giera et al., 2015; Salzman et al., 2016). While further work will be necessary to determine if gedunin-type molecules can also bind and activate zebrafish Adgrg6 by interacting directly, these studies set a precedent for this type of interaction.
GPCRs can be modulated by the membrane lipid cholesterol, where interactions with the 7TM domain can provide plasticity for the receptors by altering their stability and structure (Huang et al., 2018; Prasanna et al., 2016). In addition, cholesterol can activate the hedgehog signalling pathway directly by binding to the extracellular domain of the GPCR Smoothened (Huang et al., 2018; Luchetti et al., 2018). Although cholesterol was not identified as a hit in our primary screen, we did identify two cholesterol-lowering drugs, ezetimibe (Altmann et al., 2004) and rosuvastatin (Istvan and Deisenhofer, 2001), as putative modulators of the Adgrg6 pathway. Whether these act by altering the activity of Adgrg6 through altering cholesterol levels remains to be determined.
In addition to the dihydropyridines (cluster 1) and the tetranortriterpenoid (gedunin-derived) compounds (cluster 2), there are also clusters of steroid hormones (danazol, hydroxyprogesterone, pregnenalone succinate, hydrocortisone hemisuccinate) and flavonoid compounds (baicalein, tangeritin, nobiletin, dimethylnobiletin, hexamethylquercetagetin). The flavonoids are a group of molecules with wide ranging activities, including anti-cancer (Ma et al., 2015) and neuroprotective properties (reviewed in (Braidy et al., 2017)). All four O-methylated flavonoids that rescued vcanb and mbp expression in tb233c mutants were also able to rescue fr24 allele in our assay, suggesting that they act downstream of the Adgrg6 receptor.
Our screen identified 28 compounds that down-regulated vcanb expression but did not rescue mbp expression, which may provide useful tools to manipulate semicircular canal formation in vivo. Versican and other chondroitin sulphate proteoglycans (CSPGs) are associated with a number of human pathologies; Versican overexpression has been shown to be strongly involved in inflammation, cancer progression and the development of lung disorders (reviewed in (Andersson-Sjöland et al., 2015; Ricciardelli et al., 2009; Wight et al., 2017)). CSPGs and hyaluronan are components of the inhibitory scar that forms at the site of injury after CNS damage, preventing axon regeneration (Silver and Miller, 2004). In addition, CSPGs have been shown to inhibit the ability of oligodendrocytes to remyelinate axons, a process that is reversed by reduction of CSPG levels (Keough et al., 2016; Pendleton et al., 2013). Whether the down-regulation of CSPGs to promote remyelination occurs via a similar mechanism to that involved in Adgrg6-regulated projection fusion remains to be determined. However, it is of interest that a key regulator of myelination, Adgrg1, has also been recently shown to reduce fibronectin deposition and inhibit cell-ECM signalling to prevent metastatic melanoma growth (Millar et al., 2018).
In conclusion, our data show that vcanb expression in the adgrg6tb233c mutant ear provides a robust, easy-to-use screening tool to identify drugs that target the Adgrg6 pathway. In combination with the different alleles available for adgrg6 in zebrafish, this in vivo platform provides an excellent opportunity to find hit compounds specific for Adgrg6 in counter screens. These may provide a starting point for the development of therapeutic approaches towards human diseases where ADGRG6 or myelination is affected. We have identified groups of structurally-related compounds that can rescue adgrg6 mutant defects, including those that are likely to act downstream of the Adgrg6 pathway, and others that are candidates for interacting with the Adgrg6 receptor. The chemical analysis and structural comparison of the compounds shown to be putative Adgrg6 receptor agonists will contribute to the elucidation of the physical properties responsible for ligand binding and will provide further insight on the underlying mechanism of Adgrg6 signalling.
MATERIALS AND METHODS
Animals
Standard zebrafish husbandry methods were employed (Westerfield, 2000). To facilitate visualisation of in situ hybridisation (ISH) staining patterns, embryos of the nacre (mitfaw2/w2) strain (ZDB-GENO-990423-18), which lack melanophores (Lister et al., 1999), but are phenotypically wild-type for expression of vcanb and mbp, were used as controls for all drug screening experiments. The wild-type strain used for dose-response experiments was London Wild Type (LWT). adgrg6 mutant alleles used were lautb233c (formerly bgetb233c) and laufr24 (ZDB-GENE-070117-2161) (Geng et al., 2013; Whitfield et al., 1996), and were raised on a pigmented background. In all cases shown, mutant embryos are homozygous for the respective allele. The transgenic strain used for imaging in Fig. 1 and in the Supplemental movie was Tg(smad6b:GFP), a gift of Robert Knight (Baxendale and Whitfield, 2016). Prior to treatment, embryos were raised in E3 embryo medium (Westerfield, 2000) at 28.5°C. We have used the term embryo throughout to refer to zebrafish embryos and larvae from 0-5 days post fertilisation (dpf).
Compound library storage, aliquoting and administration to embryos
Chemical compounds from the Tocriscreen Total library (Tocris, 1120 compounds) and The Spectrum Collection (Microsource Discovery Systems, 2000 compounds) were arrayed in MultiScreen-Mesh 96-well culture receiver trays (Millipore) in columns 2-11 and diluted to 25 μM in E3 medium for drug screening. Control wells contained either IBMX (3-isobutyl-1-methylxanthine, Sigma, 50 μM and 100 μM), DMSO (Sigma, 1% in E3) or E3, in columns 1 and 12 (see diagram of the plate layout in Fig. 2). Wild-type (LWT and nacre) and homozygous adgrg6tb233c mutant embryos were raised to 50 hpf at 28.5°C in E3 medium, dechorionated manually with forceps, and then incubated at 20°C overnight to slow down development and facilitate timing of experimental treatments. This regime reduced ear swelling, but did not reduce otic vcanb levels, in mutant embryos. Embryos at the 60 hpf stage were aliquoted at three embryos per well into MultiScreen-Mesh mesh-bottomed plates (Millipore) and transferred to the drug plate (receiver tray; see above). Assay plates were incubated at 28.5°C for 28 hours and the embryos were then transferred to 4% paraformaldehyde and stored at 4°C overnight. Embryos were bleached according to the standard protocol (Thisse and Thisse, 2008) and stored at −20°C in 100% methanol until required for ISH. Hits identified in the primary screen were rescreened using the same protocol.
Scoring systems for vcanb and mbp expression
To score the efficacy of the drugs in down-regulating vcanb mRNA levels, a scoring system from 0 to 3 was used, with 0 being the score for a very efficient drug (a ‘hit’) that can suppress vcanb expression back to almost wild-type levels, and 3 the score for a drug that did not have any effect on vcanb mRNA levels expressed in the mutant ear. Scores 1 and 2 were given to drugs that showed an ability to down-regulate vcanb expression to some extent, with 1 given for a stronger down-regulation than 2 (Figure 5.2A). Drugs were then classified into categories A-E, according to the combined score from the three embryos treated with each drug (Figure 5.2B). Drugs categorised as A, B or C were considered successful, and were cherry-picked into new drug assay plates for further testing. Drugs categorised as D and E were considered to show incomplete or no inhibition of vcanb expression, respectively. Drugs from category F caused severe developmental abnormalities, heart oedema, brain oedema or death at the end of the treatment and therefore were characterised as toxic. Category G represented drugs that were potentially corrosive, as no fish were found in these wells at the end of the treatment, although this could also have resulted from death of the embryos followed by digestion by microorganisms, or through experimental error. Drugs that fell into any of the categories D-G were eliminated from the assay and were not followed further.
For the mbp counter screen (Fig. 4D,E), a score of 3 was used for embryos where mbp mRNA expression was rescued to wild-type levels, a score of 2 for embryos that showed some mbp expression in the PLLg (weaker than wild-type levels) and a score of 1 in cases where the mbp expression was identical to the one seen in untreated adgrg6tb233c mutants (i.e. lacking mbp expression in the PLLg). The fact that mbp expression is not missing altogether from other areas of the PNS in adgrg6tb233c mutants allowed us to use a score of 0 in cases where mbp expression levels were lower than those typically seen in adgrg6tb233c mutants.
Whole-mount in situ hybridisation analysis of gene expression
Digoxigenin-labelled RNA probes for vcanb (Kang et al., 2004) and mbp (mbpa) (Brösamle and Halpern, 2002) were prepared as recommended (Roche). Whole-mount ISH was performed using standard procedures (Thisse and Thisse, 2008), modified for the Biolane HTI 16V in situ robot (Intavis) and MultiScreen-Mesh mesh-bottomed plates to increase throughput (Baxendale et al., 2012). Stained embryos were scored manually by at least two people and any discrepancies between the results were re-analysed.
Dose-response and LD50 assays
Selected compounds were purchased separately from Sigma (nifedipine and cilnidipine), Cayman Chemicals (FPL 64176) and Santa Cruz Biotechnology (tracazolate hydrochloride) for testing in dose-response assays. In order to assess the ear swelling in drug-treated adgrg6tb233c mutant embryos, the ear-to-ear width was measured from photographs of live embryos mounted dorsally, and normalised for the size of the head, using CELLB software (for details, see Fig. 7—Supplemental file 2).
An LD50 curve was plotted for the adjusted exposure time (60-110 hpf), using 16 LWT wild-type embryos (biological replicates) per concentration. To avoid cross-contamination from dead embryos, each wild-type (LWT) embryo was kept in a separate well of a 96-well plate. At the end of each treatment, the number of dead embryos (no heartbeat for 10 seconds) was recorded.
Microscopy and photography
Still images of live embryos were taken using an Olympus BX51 microscope, C3030ZOOM camera and CELLB software, and assembled with Adobe Photoshop. All micrographs are lateral views with anterior towards the left and dorsal towards the top, unless otherwise stated. For archiving, fixed and stained embryos were imaged in MultiScreen-Mesh plates containing 50% glycerol, using a Nikon AZ100 microscope with an automated stage (Prior Scientific). A compressed in-focus image was generated using the NIS-Elements Extended Depth of Focus software (Nikon).
Time-lapse imaging of live embryos was performed on a Zeiss Z.1 light-sheet microscope. adgrg6fr24 homozygous mutant embryos in a Tg(smad6b:GFP) background were mounted at 60 hpf in 0.7% agarose with anaesthetic (MS-222; 160 μg/ml) and 0.003% PTU (to prevent pigment formation). Images were taken of a dorsal view of the ear every 5 minutes (200 z-slices, 1 μm sections). A control time-lapse of a wild-type sibling embryo (images taken at 10-minute intervals) was taken on a separate day. Images were cropped and a subset of z-slices through the anterior (adgrg6fr24) and posterior (phenotypically wild-type sibling) projections were used to make Maximum Intensity Projection movies of projection fusion in the wild-type sibling and the swollen projections in adgrg6fr24 mutant embryo. The two movies do not correspond exactly to the same developmental stage.
Chemoinformatics analysis and data visualisation
Chemical structures of the library compounds represented as SMILES (Weininger, 1988) were obtained from vendor catalogues. Molecules were standardised using the wash procedure of MOE (Chemical Computing Group Inc., Molecular Operating Environment (MOE), Montréal, QC, 2011), accessed through KNIME (Berthold et al., 2009). Standardised molecules were analysed using RDKit (RDKit: Open-Source Cheminformatics, http://www.rdkit.org/, accessed 06 Nov. 2018) in Python (Python Software Foundation: Python language reference, version 3, https://www.python.org/, accessed 06 Nov. 2018). Morgan fingerprints of radius 2 (equivalent to ECFP4 (Rogers and Hahn, 2010)) were computed for each compound. Compound similarity was calculated using the Tanimoto coefficient (Willett et al., 1998) of the fingerprints using the scikit-learn library (Pedregosa et al., 2011). Based on the similarity matrix between all compound pairs, a dendrogram was obtained using the SciPy library (SciPy: Open Source Scientific Tools for Python, http://www.scipy.org/, accessed 06 Nov. 2018). The polar scatterplot was created using the matplotlib library (printed version) (Hunter, 2007) and plotly (interactive version) (Plotly Technologies Inc, Collaborative data science, Plotly, Montréal, QC, 2015.). To identify duplicated molecules, the InChIKey (Heller et al., 2015) was computed for each compound and all pairs of compounds were checked for identical InChIKeys. To create the compound network, the similarity matrix computed for the dendrogram was transformed into an adjacency matrix using a threshold value of 0.5, i.e. compounds with a similarity value over 0.5 are connected with an edge. The network visualisation was created using Cytoscape (Shannon et al., 2003).
Statistical analysis
Statistical analyses were performed using GraphPad Prism version 7 for Mac, GraphPad Software, La Jolla California USA, www.graphpad.com.
Ethics statement
All animal work was performed under licence from the UK Home Office.
Funding
This work was funded by grants from the BBSRC (BB/J003050/1; BB/M01021X/1) to TTW and SB). ED was supported by a PhD studentship from the University of Sheffield (314420); AA was supported by a BBSRC White Rose National Productivity Investment Fund Doctoral Training Award (BB/R50581X/1); LA was supported by a Wellcome Trust VIP award (085441). Light-sheet imaging was carried out in the Sheffield Wolfson Light Microscopy Facility, supported by a BBSRC ALERT14 award (BB/M012522/1) to TTW and SB. The Sheffield Zebrafish Screening Unit and zebrafish aquaria were supported by grants from the MRC (G0802527, G0700091). The research leading to these results has received funding from the European Union’s Seventh Framework Programme (FP7/2007-2013) under Grant agreement no. 612347 to VJG.
Author contributions
Designed the study: TTW, SB
Performed the experiments SB, ED, AA, CJH, DB, LA
Wrote the manuscript: TTW, SB, ED
Analysed the data: SB, ED, TTW
Chemoinformatics analysis: AVL, VJG
Supervision: TW, SB, GW
Supplementary Video 1
Light-sheet microscope time-lapse movie using the Tg(smad6b:GFP) line, which marks cell membranes of the otic epithelium. Dorsal view (anterior to top) of the left inner ear of a phenotypically wild-type sibling embryo showing the anterior, lateral and posterior projections (the anterior projection is partially out of view). In the movie, the posterior projection grows and meets the posterior bulge from the lateral projection. The projection and bulge meet, fuse and resolve to form a pillar over 900 minutes (approximately 55 hpf-70 hpf). The movie shows a Maximum Intensity Projection of selected z-slices spanning approximately 6 μm, captured every 10 minutes, and played back at 10 frames per second. Selected stills from the movie, flipped horizontally to match the panels showing the mutant ear, are shown in Fig. 1C.
Supplementary Video 2
Light-sheet microscope time-lapse movie using the Tg(smad6b:GFP) line. Dorsal view of the right inner ear of an adgrg6fr24 mutant embryo showing anterior, lateral and posterior projections (the posterior projection is partially out of view). In the movie, the anterior projection and anterior bulge from the lateral projection touch, but continue to grow past one another. The unfused projections rotate around each other over 900 minutes (approximately 60 hpf-75 hpf). The movie shows a Maximum Intensity Projection of selected z-slices spanning approximately 20 μm, captured every 5 minutes, and played back at 20 frames per second. Selected stills from the movie are shown in Fig. 1C.
Supplementary figures
Figure 3—Supplemental File 2. Dendrograms representing structural similarity between library compounds
A. Dendrogram—Tocris
Dendrogram of the Tocriscreen Total library compounds based on the similarity matrix between all pairs of compounds (Ward’s method of hierarchical agglomerative clustering—see Materials and Methods). Compounds are named by their plate and well ID.
B. Dendrogram—Spectrum
Dendrogram of the Spectrum library compounds based on the similarity matrix between all pairs of compounds. Compounds are named by their plate and well ID.
C. Dendrogram—Combined
Dendrogram of the combined Spectrum and Tocriscreen Total library compounds based on the similarity matrix between all pairs of compounds. Compounds are named by their plate and well ID.
Figure 4B interactive version. Scatter plot of results from the primary screen (adgrg6tb233c vcanb rescue) of Tocris and Spectrum libraries combined. Hover over individual dots for compound identity. https://adlvdl.github.io/visualizations/polar_scatterplot_whitfield_vcanb.html
Figure 5B interactive version. Network analysis based on structural similarity, showing all 3120 compounds from the Tocris and Spectrum libraries. Compounds that rescued mbp expression are shown as larger nodes, while compounds that did not rescue mbp expression are shown as smaller nodes. The colours used for compounds/nodes correspond to categories A-G (as indicated in Figure 3) and the two clusters of structurally similar compounds highlighted in Figure 4 are also shown here. Zoom into individual nodes for Spectrum (S) and Tocris (T) plate number and well identity (cross-reference to Supplementary Table S1). https://adlvdl.github.io/visualizations/network_whitfield_vcanb_mbp/index.html.
Acknowledgements
We thank a number of undergraduate and MSc project students who contributed to early stages of the primary screens described here, especially D. Butler, who helped with establishing the mbp secondary screening protocol. F-S. Geng tested the initial screening protocol on wild-type embryos. We thank J-P. Ashton, S. Burbridge, M. Marzo and N. van Hateren for technical support, D. Lambert for discussion and the Sheffield aquarium staff for expert care of the zebrafish.