# Expanding the phenome and variome of the ROBO-SLIT pathway in congenital heart defects: toward improving the genetic testing yield of CHD

Hager Jaouadi, Chris Jopling, Fanny Bajolle, Alexis Théron, Adèle Faucherre, Hilla Gerard, Sarab Al Dybiat, Caroline Ovaert, Damien Bonnet, Jean-François Avierinos, et al.

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Hager Jaouadi, Chris Jopling, Fanny Bajolle, Alexis Théron, Adèle Faucherre, et al. Expanding the phenome and variome of the ROBO-SLIT pathway in congenital heart defects: toward improving the genetic testing yield of CHD. Journal of Translational Medicine, 2023, 21 (1), pp.160. 10.1186/s12967-023-03994-y. http://hal-04010246

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# Expanding the phenome and variome of the ROBO-SLIT pathway in congenital heart defects: toward improving the genetic testing yield of CHD

Hager Jaouadi<fnref n="1" />, Chris Jopling<fnref n="2" />, Fanny Bajolle<fnref n="3" />, Alexis Théron<fnref n="1" />,<fnref n="4" />, Adèle Faucherre<fnref n="2" />, Hilla Gerard<fnref n="5" />,
Sarab Al Dybiat<fnref n="6" />, Caroline Ovaert<fnref n="6" />, Damien Bonnet<fnref n="3" />, Jean-François Avierinos<fnref n="1" />,<fnref n="5" /> and Stéphane Zaffran<fnref n="1" />* ID

**Abstract**

**Background** Recent studies have shown the implication of the ROBO-SLIT pathway in heart development. Within this study, we aimed to further assess the implication of the *ROBO* and *SLIT* genes mainly in bicuspid aortic valve (BAV) and other human congenital heart defects (CHD).

**Methods** We have analyzed a cohort of singleton exome sequencing data comprising 40 adult BAV patients, 20 pediatric BAV patients generated by the Pediatric Cardiac Genomics Consortium, 10 pediatric cases with tetralogy of Fallot (ToF), and one case with coarctation of the aorta. A gene-centered analysis of data was performed. To further advance the interpretation of the variants, we intended to combine more than 5 prediction tools comprising the assessment of protein structure and stability.

**Results** A total of 24 variants were identified. Only 4 adult BAV patients (10%) had missense variants in the *ROBO* and *SLIT* genes. In contrast, 19 pediatric cases carried variants in *ROBO* or *SLIT* genes (61%). Three BAV patients with a severe phenotype were digenic. Segregation analysis was possible for two BAV patients. For the homozygous *ROBO4*: p.(Arg776Cys) variant, family segregation was consistent with an autosomal recessive pattern of inheritance. The *ROBO4*: c.3001 + 3G > A variant segregates with the affected family members. Interestingly, these variants were also found in two unrelated patients with ToF highlighting that the same variant in the *ROBO4* gene may underlie different cardiac phenotypes affecting the outflow tract development.

**Conclusion** Our results further reinforce the implication of the *ROBO4* gene not only in BAV but also in ToF hence the importance of its inclusion in clinical genetic testing. The remaining *ROBO* and *SLIT* genes may be screened in patients with negative or inconclusive genetic tests.

**Keywords** Congenital heart defects, Robo-Slit pathway, Genetics, Exome sequencing

<footnote>*Correspondence:
Stéphane Zaffran
stephane.zaffran@univ-amu.fr</footnote>

<footnote n="1">¹ Marseille Medical Genetics (MMG) U1251, Aix Marseille Université,
INSERM, 13005 Marseille, France</footnote>

<footnote n="2">² Institute of Functional Genomics (JGF), University of Montpellier, CNRS,
INSERM, LabEx ICST, Montpellier, France</footnote>

<footnote n="3">³ Service de Cardiologie Congénitale Et Pédiatrique, Centre de Référence
Malformations Cardiaques Congénitales Complexes - M3C, Hôpital
Necker-Enfants Malades, APHP and Université Paris Cité, Paris, France</footnote>

<footnote n="4">⁴ Department of Cardiac Surgery, La Timone Hospital, AP-HM, Marseille,
France</footnote>

<footnote n="5">⁵ Department of Cardiology, La Timone Hospital, AP-HM, Marseille, France</footnote>

<footnote n="6">⁶ Department of Pediatric Cardiology, Timone Enfant Hospital, AP-HM,
Marseille, France</footnote>
## Introduction

The secreted SLIT glycoproteins and their Roundabout (ROBO) receptors were initially known for axon guidance and dendritic branching in the developing central nervous system [1–3]. Subsequently, several studies have expanded the functional spectrum of the ROBO-SLIT pathway by reporting other functions, such as cell migration and proliferation, angiogenesis, and vascularization in different organs and tissues [3–5]. Recently, a pivotal role of the SLIT ligands and their ROBO receptors has been reported in animal heart morphogenesis and development [6–8]. These findings have been reinforced by the identification of genetic variations in *ROBO1* and *ROBO4* genes in patients with tetralogy of Fallot (ToF) and bicuspid aortic valve (BAV) disease, respectively [9, 10]. Indeed, Kruszka et al. identified loss of function variants in *ROBO1* gene in three unrelated patients with ToF and ventricular septal defects (VSD) [9]. More recently, Jaouadi et al. identified a *ROBO1* variant in a BAV family with three affected members [11].

In 2019, Gould et al. reported variants in the *ROBO4* gene in patients with BAV and ascending aortic aneurysms (AscAA). The phenotypes observed in *Robo4* animal models were consistent with patients' phenotypes with a novel endothelial etiology supporting a causative role of *ROBO4* [10]. Thereafter, additional variants in *ROBO4* have been linked to human BAV [12]. The authors have concluded that variants in *ROBO4* along with *NOTCH1*, *GATA4* and *SMAD6* are enriched in BAV-patients with early onset complications [12].

Albeit human genetic variations have been identified in *ROBO* genes, mainly *ROBO4* and *ROBO1*, data from several animal models point out the implication of the remaining *ROBO* and *SLIT* genes in CHD pathogenesis [6, 13, 14]. Moreover, Zhao et al. (2022) have underlined the clinical relevance of *SLIT3* as a promising candidate gene for further screening in patients [13].

In the present study, we aimed firstly to screen adult and pediatric patients with BAV in order to identify genetic variants in *ROBO* and *SLIT* genes using exome sequencing data combined to a thorough in silico analysis. Based on the results of this analysis, we sought to expand the pediatric cohort to include other CHD phenotypes (10 patients with ToF and one case with coarctation of the aorta (CoA)) in order to determine whether variants in *ROBO* and *SLIT* genes may be implicated in CHD other than BAV.

Of note, the study includes CHD patients with no relevant variants in known CHD-related genes such as *NOTCH1*, *NOTCH2*, *GATA5*, *GATA4*, *ACTA2*, *SMAD6*, *NKX2-5*, *FLT4*, *TGFBR1*, and *TGFBR2*.

## Patients and methods

This study was performed according to the principles of the Declaration of Helsinki and to the ethical standards of the first author's institutional review board. The patients provided their written informed consent to participate in this study (approved by the Marseille ethic committee n°13.061 and 2016-A00958-53). Personal health data and DNA from two pediatric BAV patients and their related are part of the CARREG study (http://carreg.fr/en/), which was declared to the French national committee for informatics and liberties (France; CNIL; No. 1734573V0). The CARREG study is a prospective monocenter study promoted by the "Centre de Référence des Malformations Cardiaques Congénitales Complexes (M3C)" located at the Pediatric cardiology department of the Necker-Enfants Malades Hospital, Paris, France. Clinical records were reviewed by cardiologist or pediatric-cardiologist before recruitment and cardiovascular diagnosis was obtained by echocardiography mainly. Patients with 22q11.2 deletion or other recognized syndromes were excluded.

### Patients

The starting study cohort includes a total of 71 patients with clinical diagnosis of bicuspid aortic valve (40 adult and 20 pediatric patients), tetralogy of Fallot (10 pediatric cases) and one pediatric case with coarctation of the aorta (CoA). No other defects are associated with the main clinical diagnosis with confirmed absence of structural myocardial and syndromic diseases.

### Exome sequencing

Germline DNA was extracted from blood samples and subjected to exome sequencing. Whole exome sequencing (WES) was performed by the Genomics and Bioinformatics Platform (GBiM) of the INSERM U1251 Marseille Medical Genetics facility using the NimbleGen SeqCap EZ MedExome kit (total design size 47 Mb) according to the manufacturer's protocol (Roche Sequencing Solutions, Madison, USA). All DNA and libraries preparations (KAPA HyperPrep Kits (Roche)) were performed according to the manufacturers' instructions. The DNA libraries were subjected to paired-end sequencing using the Illumina NextSeq500 sequencing platform (Illumina, San Diego, CA, USA). Raw fastQ files were aligned to the hg19 reference human genome (University of California Santa Cruz, UCSC) using BWA software [15]. Variant calling workflow was performed according to the GATK best practices [16]. Both HaplotypeCaller and BaseRecalibration tools have been used for variant calling and quality score recalibration. The output files were annotated using ANNOVAR software [17]. On average, a depth of
125X and a coverage of 97.7% of the bases at 30X have been obtained per sample.

## Variant annotation and prioritization

Variant annotation process and exome data analysis were performed using VarAFT software version 2.17–2 (http://varaft.eu/) [18]. Firstly, a patient-centered approach was applied. Thus, we excluded variants with a minor allele frequency (MAF) > 1% in gnomAD (Genome Aggregation Database) (http://gnomad.broadinstitute.org/). Then, we removed non-coding and synonymous variants with no impact on splicing with HSF-Pro tool. Subsequently, the remaining variants were filtered based on their in silico pathogenicity prediction with UMD_Predictor, SIFT and PolyPhen tools [19–21]. The prioritized variants were finally interpreted according to their clinical relevance. Indeed, patients with likely pathogenic and/or causative variants in genes linked to the NOTCH or TGFβ pathways or in cardiac transcription factors such as *GATA4/5*, *NKX2-5*, and *TBX-5* have been selected for further analysis and excluded from the present study.

As a second step, patients with no-relevant variants in CHD-related genes were re-analyzed as following: a gene-centered approach was applied to the remaining patients toward identifying variants in the ROBO-SLIT pathway. Thus, we used a gene list including *ROBO1*, *ROBO2*, *ROBO3*, *ROBO4*, *SLIT1*, *SLIT2*, and *SLIT3* genes to run the same prioritization strategy as above. The main functions of *ROBO* and *SLIT* genes are summarized in Table 1.

## Combined Annotation Dependent Depletion (CADD)

Given the lack of detailed clinical description for some patients and the family history that would allow for segregation analysis, we used the CADD computational algorithm to further assess variants pathogenicity.

For annotation, CADD used the Ensembl Variant Effect Predictor, data from the ENCODE project and information from UCSC genome browser tracks. These annotations span a wide range of data types including conservation metrics such as GERP, phastCons, and phyloP; functional genomic data like DNase hypersensitivity and transcription factor binding; transcript information like distance to exon–intron boundaries or expression levels in commonly studied cell lines; and protein-level scores like Grantham, SIFT, and PolyPhen [22, 23]. Thus, CADD algorithm simulate neutral and deleterious variants from multiple species alignments, annotate variants based on the conservation among species, genetic context and epigenetics, rank the variants by a logistic regression model and finally generate a CADD score for each variant in the human genome.

A scaled C-score of greater of equal 10 indicates that these are predicted to be the 10% most deleterious substitutions that you can do to the human genome, a score of greater or equal 20 indicates the 1% most deleterious and so on.

To identify potentially pathogenic variants, a cutoff between 10 and 20 can be set. A cutoff of 15 is recommended as it is the median value for all possible canonical splice site changes and non-synonymous variants in CADD v1.0.

<table><caption>**Table 1** The main functions of *ROBO* and *SLIT* genes</caption><thead><tr><td>Gene</td><td>Gene_name</td><td>HGNC ID</td><td>GeneRIF: Gene Reference into Function from NCBI</td></tr></thead><tbody><tr><td>ROBO1</td><td>Roundabout guidance receptor 1</td><td>HGNC:10249</td><td>Aortic valve development, axon guidance, axonogenesis, brain and heart development</td></tr><tr><td>ROBO2</td><td>Roundabout guidance receptor 2</td><td>HGNC:10250</td><td>Aortic valve development, apoptotic process involved in development, axon guidance, axonogenesis, brain and heart development, female gonad development, female sex differentiation</td></tr><tr><td>ROBO3</td><td>Roundabout guidance receptor 3</td><td>HGNC:13433</td><td>Axon guidance, axonogenesis, cell recognition, cell–cell adhesion via plasma-membrane adhesion molecules, neuron projection guidance, neuron recognition</td></tr><tr><td>ROBO4</td><td>Roundabout guidance receptor 4</td><td>HGNC:17985</td><td>Axonogenesis, cell recognition, cell–cell adhesion via plasma-membrane adhesion molecules, neuron projection guidance, neuron recognition</td></tr><tr><td>SLIT1</td><td>Slit guidance ligand 1</td><td>HGNC:11085</td><td>Axon extension, axon guidance, axonogenesis, brain development, central nervous system neuron development</td></tr><tr><td>SLIT2</td><td>Slit guidance ligand 2</td><td>HGNC:11086</td><td>Actin filament polymerization, aortic valve development, apoptotic process involved in development, axon extension, axon guidance, axonogenesis, brain development</td></tr><tr><td>SLIT3</td><td>Slit guidance ligand 3</td><td>HGNC:11087</td><td>Aortic valve development, apoptotic process involved in development, axon extension, axon guidance, axonogenesis, brain development, cardiac chamber development and morphogenesis</td></tr></tbody></table>
## In silico assessment of protein stability and interactions

### I-mutant

In order to aid the annotation process, an in silico prediction of protein stability free energy change (DDG) was performed using I-Mutant3.0 software (http://gpcr.biocomp.unibo.it/cgi/predictors/I-Mutant3.0/I-Mutant3.0.cgi) [24]. The substitutions are ranked according to a three-state classification system: destabilizing mutations (DDG < -0.5 kcal/mol), stabilizing mutations (DDG > 0.5 kcal/mol) and neutral mutations (-0.5 < DDG <= 0.5 kcal/mol).

### Project HOPE

The project HOPE tool (https://www3.cmbi.umcn.nl/hope) is a web service that analyses the structural and physicochemical effects of point mutations in a protein sequence using PDB file when the corresponding protein structure has been solved experimentally (95–100% match). Whenever this is not the case, HOPE will build a homology model using an existing template (between 30 and 95% match). As an estimation, HOPE uses information obtained from the 3D-structure in 60–70% of the cases [25].

## Results

From a cohort of 40 BAV adult patients [26] and 20 BAV pediatric cases, we sought to determine the implication of the ROBO-SLIT pathway in patients with no relevant variants in known BAV-related genes. Interestingly, the yield of rare variants in ROBO and SLIT genes was greater in the pediatric cohort (13/20, 65%) compared to only 4 out 40 BAV cases (10%) from the adult cohort (Table 2).

Family segregation was performed for two BAV patients only, both with ROBO4 variants.

The first patient (BAV-PED-10) is a male pediatric case with BAV. His medical records include small aortic insufficiency in the posterior commissure, fusion of the anterior commissure, right anterior leaflet prolapse, aortic annulus dilatation and dilated ascending aorta (z score 3.2 and 3.3). The patient had a positive family history of aortic valve defects. His paternal and maternal grandmothers underwent aortic valve replacement.

The patient (BAV-PED-10) carried a homozygous ROBO4 variant (p. Arg776Cys) (Table 3). His parents were found heterozygous for the variant (Fig. 1). The MAF of this variant (rs138481093) is 0.004699 in gnomAD with a total number of homozygotes equal to 8. Of

<table><caption>**Table 2** List of the identified variants and patients' phenotypes</caption><thead><tr><th>Gene</th><th>HGVSc</th><th>HGVSp</th><th>Patient phenotype</th><th>Patient ID</th><th>Sex</th></tr></thead><tbody><tr><td>ROBO1</td><td>c.1828G > A</td><td>p.Val610Ile</td><td>BAV-adult</td><td>BAV-AD-1</td><td>M</td></tr><tr><td>ROBO2</td><td>c.639C > G</td><td>p.Asp213Glu</td><td>BAV-adult</td><td>BAV-AD-2</td><td>F</td></tr><tr><td>ROBO2</td><td>c.2431C > T</td><td>p.Arg811Trp</td><td>BAV-Ped</td><td>BAV-PED-1</td><td>M</td></tr><tr><td>ROBO3</td><td>c.968C > T</td><td>p.Thr323Met</td><td>ToF</td><td>ToF-PED-2</td><td>M</td></tr><tr><td>ROBO3</td><td>c.1615C > T</td><td>p.Arg539Trp</td><td>ToF</td><td>ToF-PED-3</td><td>F</td></tr><tr><td>ROBO3</td><td>c.2576C > A</td><td>p.Pro859Gln</td><td>BAV-Ped</td><td>BAV-PED-4</td><td>M</td></tr><tr><td>ROBO3</td><td>c.2993G > T</td><td>p.Gly998Val</td><td>CoA-Ped</td><td>CoA-PED-5</td><td>M</td></tr><tr><td>ROBO3</td><td>c.3478C > T</td><td>p.Pro1160Ser</td><td>ToF</td><td>ToF-PED-6</td><td>F</td></tr><tr><td>ROBO4</td><td>c.908C > A</td><td>p.Ala303Asp</td><td>BAV-Ped</td><td>BAV-PED-7</td><td>F</td></tr><tr><td>ROBO4</td><td>c.1337C > A</td><td>p.Ala446Asp</td><td>BAV-Ped</td><td>BAV-PED-8</td><td>M</td></tr><tr><td>ROBO4</td><td>c.2326C > T</td><td>p.Arg776Cys</td><td>ToF / BAV-Ped (unrelated patients)</td><td>ToF-PED-9</td><td>F</td></tr><tr><td>ROBO4</td><td>c.2723G > A</td><td>p.Arg908Gln</td><td>BAV-Ped</td><td>BAV-PED-1</td><td>M</td></tr><tr><td>ROBO4</td><td>c.3001 + 3G > A</td><td>-</td><td>ToF / BAV-Ped (unrelated patients)</td><td>ToF-PED-11</td><td>M</td></tr><tr><td>SLIT1</td><td>c.446C > T</td><td>p.Pro149Leu</td><td>BAV-Ped</td><td>BAV-PED-13</td><td>M</td></tr><tr><td>SLIT1</td><td>c.789C > A</td><td>p.Cys263Ter</td><td>BAV-Ped</td><td>BAV-PED-14</td><td>F</td></tr><tr><td>SLIT1</td><td>c.1363C > A</td><td>p.Arg455Ser</td><td>BAV-Ped</td><td>BAV-PED-15</td><td>M</td></tr><tr><td>SLIT1</td><td>c.3757G > A</td><td>p.Ala1253Thr</td><td>BAV-Ped</td><td>BAV-PED-16</td><td>M</td></tr><tr><td>SLIT1</td><td>c.4020A > C</td><td>p.Glu1340Asp</td><td>BAV-Ped</td><td>BAV-PED-7</td><td>F</td></tr><tr><td>SLIT1</td><td>c.4145A > G</td><td>p.His1382Arg</td><td>BAV-adult</td><td>BAV-AD-3</td><td>F</td></tr><tr><td>SLIT1</td><td>c.4202G > T</td><td>p.Cys1401Phe</td><td>BAV-Ped</td><td>BAV-PED-17</td><td>M</td></tr><tr><td>SLIT2</td><td>c.3877C > A</td><td>p.Leu1293Met</td><td>BAV-Ped</td><td>BAV-PED-13</td><td>M</td></tr><tr><td>SLIT3</td><td>c.1481G > C</td><td>p.Arg494Thr</td><td>BAV-Ped</td><td>BAV-PED-18</td><td>F</td></tr><tr><td>SLIT3</td><td>c.1886G > A</td><td>p.Ser629Asn</td><td>BAV-adult</td><td>BAV-AD-4</td><td>F</td></tr><tr><td>SLIT3</td><td>c.4086C > A</td><td>p.Cys1355Ter</td><td>BAV-Ped</td><td>BAV-PED-19</td><td>M</td></tr></tbody></table>
<table><caption>**Table 3** Variants coordinates</caption><thead><tr><th>Location</th><th>Gene</th><th>RefSeq Match</th><th>cDNA position</th><th>CDS position</th><th>Protein position</th><th>Amino acids</th><th>Codons</th><th>Read depth</th><th>Exon</th><th>Variant type</th><th>gnomAD Allele Freq</th><th>Rs_number</th></tr></thead><tbody><tr><td>3:78717171-78717171</td><td>ROBO1</td><td>NM_002941</td><td>1942</td><td>1828</td><td>610</td><td>V/I</td><td>Gta/Ata</td><td>84</td><td>14</td><td>Missense</td><td>0.0005077</td><td>rs141178745</td></tr><tr><td>3:77530342-77530342</td><td>ROBO2</td><td>NM_002942</td><td>695</td><td>639</td><td>213</td><td>D/E</td><td>gaC/gaG</td><td>101</td><td>4</td><td>Missense</td><td>0.0003215</td><td>rs184080216</td></tr><tr><td>3:77629200-77629200</td><td>ROBO2</td><td>NM_002942</td><td>3331</td><td>2431</td><td>811</td><td>R/W</td><td>Cgg/Tgg</td><td>200</td><td>16</td><td>Missense</td><td>0.008396</td><td>rs188582283</td></tr><tr><td>11:1247,740,559-1247,740,559</td><td>ROBO3</td><td>NM_022370</td><td>1160</td><td>968</td><td>323</td><td>T/M</td><td>aCg/aTg</td><td>55</td><td>6</td><td>Missense</td><td>0.002300</td><td>rs151168595</td></tr><tr><td>11:124743284-124743284</td><td>ROBO3</td><td>NM_022370</td><td>1807</td><td>1615</td><td>539</td><td>R/W</td><td>Cgg/Tgg</td><td>171</td><td>10</td><td>Missense</td><td>0.003234</td><td>rs139930558</td></tr><tr><td>11:124746004-124746004</td><td>ROBO3</td><td>NM_022370</td><td>2768</td><td>2576</td><td>859</td><td>P/Q</td><td>cCa/cAa</td><td>55</td><td>16</td><td>Missense</td><td>-</td><td>-</td></tr><tr><td>11:124747839-124747839</td><td>ROBO3</td><td>NM_022370</td><td>3185</td><td>2993</td><td>998</td><td>G/V</td><td>gGa/gTa</td><td>40</td><td>21</td><td>Missense</td><td>0.001755</td><td>rs75098003</td></tr><tr><td>11:124748637-124748637</td><td>ROBO3</td><td>NM_022370</td><td>3670</td><td>3478</td><td>1160</td><td>P/S</td><td>Cct/Tct</td><td>259</td><td>23</td><td>Missense</td><td>-</td><td>-</td></tr><tr><td>11:124765481-124765481</td><td>ROBO4</td><td>NM_019055</td><td>1394</td><td>908</td><td>303</td><td>A/D</td><td>cGg/cTg</td><td>71</td><td>6</td><td>Missense</td><td>-</td><td>-</td></tr><tr><td>11:124763923-124763923</td><td>ROBO4</td><td>NM_019055</td><td>1823</td><td>1337</td><td>446</td><td>A/D</td><td>cGg/cTg</td><td>43</td><td>9</td><td>Missense</td><td>0.000</td><td>rs1287612263</td></tr><tr><td>11:124756982-124756982</td><td>ROBO4</td><td>NM_019055</td><td>2812</td><td>2326</td><td>776</td><td>R/C</td><td>Gcg/Acg</td><td>96</td><td>15</td><td>Missense</td><td>0.004699</td><td>rs138481093</td></tr><tr><td>11:124756431-124756431</td><td>ROBO4</td><td>NM_019055</td><td>3209</td><td>2723</td><td>908</td><td>R/Q</td><td>gCc/gTc</td><td>77</td><td>16</td><td>Missense</td><td>3.891e-05</td><td>rs747627515</td></tr><tr><td>11:124754934-124754934</td><td>ROBO4</td><td>NM_019055</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>270</td><td>-</td><td>Splice_donor_region</td><td>0.009486</td><td>rs145918924</td></tr><tr><td>10:98825811-98825811</td><td>SLIT1</td><td>NM_003061</td><td>692</td><td>446</td><td>149</td><td>P/L</td><td>gGg/gAg</td><td>257</td><td>5</td><td>Missense</td><td>0.000</td><td>rs1459814303</td></tr><tr><td>10:98823216-98823216</td><td>SLIT1</td><td>NM_003061</td><td>1035</td><td>789</td><td>263</td><td>C/*</td><td>acG/acT</td><td>67</td><td>8</td><td>Stop_gained</td><td>-</td><td>-</td></tr><tr><td>10:98808814-98808814</td><td>SLIT1</td><td>NM_003061</td><td>1609</td><td>1363</td><td>455</td><td>R/S</td><td>Gcg/Tcg</td><td>72</td><td>14</td><td>Missense</td><td>-</td><td>-</td></tr><tr><td>10:98763933-98763933</td><td>SLIT1</td><td>NM_003061</td><td>4003</td><td>3757</td><td>1253</td><td>A/T</td><td>Cgg/Tgg</td><td>49</td><td>34</td><td>Missense</td><td>8.131e-05</td><td>rs751020526</td></tr><tr><td>10:98762595-98762595</td><td>SLIT1</td><td>NM_003061</td><td>4266</td><td>4020</td><td>1340</td><td>E/D</td><td>ctT/ctG</td><td>70</td><td>35</td><td>Missense</td><td>0.002267</td><td>rs747965419</td></tr><tr><td>10:98762470-98762470</td><td>SLIT1</td><td>NM_003061</td><td>4391</td><td>4145</td><td>1382</td><td>H/R</td><td>cAt/cGt</td><td>539</td><td>35</td><td>Missense</td><td>1.773e-05</td><td>rs768287574</td></tr><tr><td>10:98762079-98762079</td><td>SLIT1</td><td>NM_003061</td><td>4448</td><td>4202</td><td>1401</td><td>C/F</td><td>aCg/aAg</td><td>52</td><td>36</td><td>Missense</td><td>-</td><td>-</td></tr><tr><td>4:20618562-20618562</td><td>SLIT2</td><td>NM_004787</td><td>4129</td><td>3877</td><td>1293</td><td>L/M</td><td>Ctg/Atg</td><td>67</td><td>35</td><td>Missense</td><td>-</td><td>-</td></tr><tr><td>5:168189673-168189673</td><td>SLIT3</td><td>NM_003062</td><td>1901</td><td>1481</td><td>494</td><td>R/T</td><td>tCc/tGc</td><td>85</td><td>15</td><td>Missense</td><td>0.0009129</td><td>rs147560182</td></tr><tr><td>5:168180047-168180047</td><td>SLIT3</td><td>NM_003062</td><td>2306</td><td>1886</td><td>629</td><td>S/N</td><td>tCa/tTa</td><td>144</td><td>18</td><td>Missense</td><td>0.007048</td><td>rs34260167</td></tr><tr><td>5:168098265-168098265</td><td>SLIT3</td><td>NM_003062</td><td>4485</td><td>4065</td><td>1355</td><td>C/*</td><td>acG/acT</td><td>88</td><td>34</td><td>Stop_gained</td><td>-</td><td>-</td></tr></tbody></table>

Last check of allele frequencies was performed using gnomAD browser on 24 November 2022
<figure><img src="image_3.png" /><figcaption>**Fig. 1** Family segregation of the *ROBO4*: p.Arg776Cys variant. Darkened left upper quadrant: Affected child with BAV</figcaption></figure>

<figure><img src="image_4.png" /><figcaption>**Fig. 2** Family segregation of the *ROBO4*: c.3001 + 3G > A variant. The index-case (BAV-PED-12) is marked with a star</figcaption></figure>

note, our patient is of white European non-Finnish ethnic group which represents the highest MAF population (0.007781).

The second case (BAV-PED-12) is a male pediatric case with BAV. The analysis of his WES data allowed us to identify a splice site heterozygous variant in *ROBO4* (c.3001+3G>A). The patient's father was found to have hypoplastic left coronary artery and his brother had VSD. His mother and sister are healthy.

The *ROBO4*: c.(3001+3G>A) variant was found in the patient's father (I-1) and brother (II-2). The mother (I-2) and sister (II-3) do not carry the variant.

Family pedigree and segregation are shown in Fig. 2.

As for the first patient (BAV-PED-10), this case is European non-Finnish also. The MAF of the *ROBO4*: c.3001+3G>A variant in this population is 0.01448. The highest population MAF of this variant (rs145918924) is 0.02831 in the Ashkenazi Jewish population.

Of note, Gould et al. reported a heterozygous splice site variant *ROBO4*: c.2056+1G>T in a multigenerational BAV-family. Interestingly, seven of eight affected cases were male [10]. These findings underline the intrafamilial variability as well as the phenotypic pleiotropy of *ROBO4* variants.

As we mentioned above, the identification of more *ROBO* and *SLIT* variants in the pediatric BAV cases than in the adult cohort prompted us to investigate the implication of this pathway in another CHD phenotype. Thus, we analyzed 10 ToF patients and one CoA case. Five out 10 ToF patients carried variants in *ROBO* and *SLIT* genes. Three patients carried variants in the *ROBO3* gene and strikingly, the two other patients (ToF-PED-9 and ToF-PED11) were carrying the aforementioned *ROBO4* variants (p.(Arg776Cys) and c.3001+3G>A) at a heterozygous state (Table 2).

The clinical resume of the ToF-patient (ToF-PED-9) carrying the *ROBO4*: p.Arg776Cys variant is as following: Pregnancy was complicated by gestational diabetes. Pulmonary atresia and VSD as well as partial corpus callosum agenesis were prenatally diagnosed. Amniocentesis was refused by the parents. The anatomy was confirmed after birth. Pulmonary arteries were noted to be extremely hypoplastic (2 mm, z-value -5, birth weight 4 kg). A malformation of the arterial duct was noted, with no signs of spontaneous closure. At the age of 27 months, a total cardiac repair was performed.

The clinical resume of the ToF-patient (ToF-PED-11) carrying the *ROBO4*: c.3001+3G>A splicing variant is as following: Severe ToF and thoraco-abdominal situs inversus was prenatally diagnosed. Birth weight was small for gestational age (2.4 kg, 38W). Anatomy was confirmed after birth. Pulmonary annulus was very hypoplastic (Z value – 3.7) as well as pulmonary arteries (Z value RPA – 2.4, LPA – 2). The complete cardiac repair (closure VSD and patch enlargement of pulmonary valve and artery) was performed 11 months later.

ToF is defined by the presence of four cardiac defects namely; ventricular septal defect (VSD), pulmonary valve stenosis, right ventricular hypertrophy and overriding aorta, which potentially arise from a misalignment of the great arteries [27, 28]. The identification of the same *ROBO4* variants in BAV and ToF patients points out the pleiotropic role of this gene with its implication in several CHD entities with different pattern of inheritance. This pleiotropy can be explained by the potential contribution of *ROBO4* gene in different cardiac cell populations
[8, 13, 29], but also by the difference of the genetic background of each individual and epigenetics mechanisms acting during heart morphogenesis.

Three additional *ROBO4* variants were identified in the present study. The *ROBO4* variant (p. Arg908Gln) was identified in a BAV patient with aortic stenosis (BAV-PED-1). This patient carried a second missense variant in *ROBO2* gene (p. Arg811Trp). The *ROBO4*: p.(Ala303Asp) has been identified in a pediatric BAV-case (BAV-PED-7) with aneurysm. Similarly, this patient carried a second variant in the *SLIT1* gene (p.Glu1340Asp). The third *ROBO4*: p.(Ala446Asp) variant was found in BAV-PED-8 case (Table 2). No BAV-related complications were noted for this patient.

In regards to BAV adult patients with variants in *ROBO1*, *ROBO2*, *SLIT1* and *SLIT3* genes, the presence of BAV-related complications such as aortic regurgitation, aortic stenosis, and AscAA was checked. Only the patient (BAV-AD-1) with the *ROBO1*: p.(Val610Ile) variant had AscAA.

Within this study, we report two stop-gain variants in *SLIT1* (p.Cys263Ter) and *SLIT3* (p.Cys1355Ter) genes.

The patient carrying the *SLIT3* stop-gain variant had BAV with mitral regurgitation.

Collectively, a total of 24 rare variants were identified including 21 missense, 2 stop-gain, and 1 splice site variants (Table 2). The majority of variants were found in the pediatric cohort. Indeed, 19 pediatric cases carried variants in *ROBO* and *SLIT* genes (19/31 CHD-patients; 61%), whereas, only 4 adult patients (10%) had missense variants in *ROBO1*, *ROBO2*, *SLIT1* and *SLIT3* genes.

It should be noted that, all the patients carried heterozygous variants except a BAV- patient (BAV-PED-10) with the homozygous *ROBO4* variant (p. Arg776Cys).

Overall, the in-silico predictions of variant pathogenicity are quite consistent among the different software tools, specifically, variants in *ROBO1*, *ROBO3*, and *SLIT* genes, were predicted to have a large decrease of protein stability and high CADD scores (Table 4). Indeed, except for *SLIT1* (p.Cys263Ter) and *SLIT3* (p.Cys1355Ter) stop-gain variant with a very high CADD-scores (36 and 42, respectively) which is mainly due to the truncating type of the variants, the highest scores (≥ 30) are attributed to variants located in the fibronectin type III-3 domain of

<table><caption>**Table 4** In silico prediction of variants pathogenicity</caption><thead><tr><th colspan="4">Variant prediction</th><th colspan="2">I-Mutant 3.0</th></tr><tr><th>Variant</th><th>CADD_PHRED</th><th>SIFT</th><th>PolyPhen</th><th>UMD_Prediction</th><th>DDG Value prediction</th><th>SVM3 prediction effect</th></tr></thead><tbody><tr><td>ROBO1: p.Val610Ile</td><td>25.3</td><td>Deleterious</td><td>Probably_damaging</td><td>Probably pathogenic</td><td>- 0.07 kcal/mol</td><td>Large decrease</td></tr><tr><td>ROBO2: p.Asp213Glu</td><td>20.7</td><td>Tolerated</td><td>Benign</td><td>Probably pathogenic</td><td>- 0.24 kcal/mol</td><td>Large increase</td></tr><tr><td>ROBO2: p.Arg811Trp</td><td>31</td><td>Deleterious</td><td>Probably_damaging</td><td>Pathogenic</td><td>- 0.31 kcal/mol</td><td>Neutral</td></tr><tr><td>ROBO3: p.Thr323Met</td><td>25.4</td><td>Deleterious</td><td>Probably_damaging</td><td>Pathogenic</td><td>- 1.73 kcal/mol</td><td>Large decrease</td></tr><tr><td>ROBO3: p.Arg539Trp</td><td>23.7</td><td>Deleterious</td><td>Probably_damaging</td><td>Pathogenic</td><td>- 0.03 kcal/mol</td><td>Neutral</td></tr><tr><td>ROBO3: p.Pro859Gln</td><td>32</td><td>Deleterious</td><td>Probably_damaging</td><td>Pathogenic</td><td>- 1.33 kcal/mol</td><td>Large decrease</td></tr><tr><td>ROBO3: p.Gly998Val</td><td>24.8</td><td>Deleterious</td><td>Benign</td><td>Pathogenic</td><td>- 0.46 kcal/mol</td><td>Large decrease</td></tr><tr><td>ROBO3: p.Pro1160Ser</td><td>26.1</td><td>Deleterious</td><td>Probably_damaging</td><td>Pathogenic</td><td>- 1.06 kcal/mol</td><td>Large decrease</td></tr><tr><td>ROBO4: p.Ala303Asp</td><td>14.37</td><td>Tolerated</td><td>Benign</td><td>Pathogenic</td><td>- 0.52 kcal/mol</td><td>Neutral</td></tr><tr><td>ROBO4: p.Ala446Asp</td><td>23</td><td>Deleterious</td><td>Benign</td><td>Probably pathogenic</td><td>- 0.61 kcal/mol</td><td>Large decrease</td></tr><tr><td>ROBO4: p.Arg776Cys</td><td>22.9</td><td>Tolerated</td><td>Benign</td><td>Probably pathogenic</td><td>- 0.59 kcal/mol</td><td>Neutral</td></tr><tr><td>ROBO4: p.Arg908Gln</td><td>16.15</td><td>Tolerated</td><td>Benign</td><td>Pathogenic</td><td>- 0.67 kcal/mol</td><td>Neutral</td></tr><tr><td>ROBO4: c.3001 + 3G > A</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>SLIT1: p.Pro149Leu</td><td>24.7</td><td>Deleterious</td><td>Probably_damaging</td><td>Pathogenic</td><td>- 0.30 kcal/mol</td><td>Neutral</td></tr><tr><td>SLIT1: p.Cys263Ter</td><td>36</td><td>-</td><td>-</td><td>Pathogenic</td><td>-</td><td>-</td></tr><tr><td>SLIT1: p.Arg455Ser</td><td>27.1</td><td>Deleterious</td><td>Probably_damaging</td><td>Pathogenic</td><td>- 1.30 kcal/mol</td><td>Large decrease</td></tr><tr><td>SLIT1: p.Ala1253Thr</td><td>19.47</td><td>Tolerated</td><td>Benign</td><td>Probably pathogenic</td><td>- 0.78 kcal/mol</td><td>Large decrease</td></tr><tr><td>SLIT1: p.Glu1340Asp</td><td>15.21</td><td>Tolerated</td><td>Benign</td><td>Probably pathogenic</td><td>- 0.29 kcal/mol</td><td>Large decrease</td></tr><tr><td>SLIT1: p.His1382Arg</td><td>14.47</td><td>Tolerated</td><td>Benign</td><td>Probably pathogenic</td><td>0.11 kcal/mol</td><td>Neutral</td></tr><tr><td>SLIT1: p.Cys1401Phe</td><td>29.9</td><td>Deleterious</td><td>Probably_damaging</td><td>Pathogenic</td><td>- 0.35 kcal/mol</td><td>Large decrease</td></tr><tr><td>SLIT2: p.Leu1293Met</td><td>24.8</td><td>Deleterious</td><td>Probably_damaging</td><td>Probably pathogenic</td><td>- 1.17 kcal/mol</td><td>Large decrease</td></tr><tr><td>SLIT3: p.Arg494Thr</td><td>23.3</td><td>Deleterious</td><td>Probably_damaging</td><td>Pathogenic</td><td>- 1.10 kcal/mol</td><td>Large decrease</td></tr><tr><td>SLIT3: p.Ser629Asn</td><td>21.8</td><td>Tolerated</td><td>Benign</td><td>Pathogenic</td><td>- 0.75 kcal/mol</td><td>Neutral</td></tr><tr><td>SLIT3: p.Cys1355Ter</td><td>42</td><td>-</td><td>-</td><td>Pathogenic</td><td>-</td><td>-</td></tr></tbody></table>
ROBO genes. As an example, the *ROBO2*: p. (Arg811Trp) and the *ROBO3*: p.(Pro859Gln) variants, with CADD-scores 31 and 32, respectively, are located within the Fibronectin type-III 3 domain of each gene (Additional file 1).

A more detailed description of variant localization and their predicted impact on protein structure, interaction and physicochemical properties is provided in the Additional file 1. Sanger confirmation of the prioritized variants is provided in Additional file 2.

## Discussion

ROBO receptors and their SLIT ligands play versatile roles during heart development across species and have been associated with congenital cardiac defects (CHD) in humans [3, 7, 30]. With the exception of the mammalian ROBO4 receptor, the extracellular domain of ROBO contains 5 Ig-like domains and 3 fibronectin repeats [3, 31]. SLIT are the main ligands of ROBO receptors, which bind through their LRR2 domain to the first Ig domain of ROBO proteins [3]. Of note, SLIT ligands bind also to a wide range of extracellular matrix molecules such as type IV collagens. On the other hand heparin sulfate proteoglycans binds to both SLIT and ROBO [3]. Moreover, ROBO and SLIT proteins are involved in heart tube development of Drosophila and zebrafish and in neural crest migration and adhesion in mice. The absence of ROBO1 receptor has been linked to septal and outflow tract defects [7, 29, 32]. The knockdown of *Robo1* in zebrafish resulted in an inhibition of endocardial and myocardial migration leading to an unfused heart fields [7, 33].

In vertebrates, ROBO4 is selectively expressed in endothelial cells and plays a key role in angiogenesis and blood vessel permeability [34]. Similarly, ROBO1/2 receptors and SLIT are also expressed in endothelial cells and contribute to cell motility and polarity [35]. Functional studies have suggested that *ROBO4* mutations disrupt endothelial cells performance and impair barrier function leading to abnormal aorta remodeling [10]. Furthermore, *Robo4* knockout mice showed severe cardiovascular defects such as aortic valve thickening combined with, in some cases, BAV, aortic regurgitation, aortic stenosis and AscAA [10].

It has been shown that the SLIT-ROBO pathway is involved in the guidance of cranial neural crest cell migration [36]. Additionally, SLIT-ROBO signaling is crucial for organizing neural crest cells and placode derived neurons to form ganglion [37]. Neural crest cells contribute to aortic valve development as well as aortico-pulmonary septation [38–40]. Our previous results indicated that SLIT-ROBO signaling might be involved in regulating earlier events during cardiac neural crest cell

migration that are associated to outflow tract and aortic valve development [8].

In zebrafish models, both *Slit2* and *Slit3* are expressed in the heart during chamber formation. *Slit2* is particularly expressed in endocardial cells, while *Robo1* and *Slit3* are expressed in the myocardial, endocardial and endothelial cells [7]. *Slit3* is the predominant ligand transcribed in the early mouse heart. Indeed, its expression is detected in the ventral wall of the linear heart tube and subsequently in the heart chamber but not in the atrio-ventricular canal myocardium [8].

Functional studies using Drosophila, zebrafish, and mouse models have reported a significant role of each Robo-Slit member in heart chamber, lumen, and valve formation [3, 7, 10, 13, 14, 41]. Indeed, in *Robo1/Robo2* and *Slit3* knockout mice, the ventricular septum is absent, whereas in Slit2 mutants septum anomalies were less severe [14]. Using zebrafish models, it has been shown that *Slit3* plays a crucial role in vascular development. Similarly, in mice, *Slit3* is the earliest gene to be expressed with a strong expression in the myocardium. It is also expressed in the outflow tract, atrial and sinus horn myocardium, cardiac neural crest, the second heart field and later in the epicardium [6, 7, 13, 14]. Moreover, it has been shown that *Slit3* also still expressed in the adult ventricle [13, 14].

The phenotypic analysis of mice mutants showed that *Robo1/Robo2* mutants have developed highly penetrant BAV with two entire leaflets and one partial or absent leaflet. However *Slit2* mutants have displayed less penetrant BAV phenotype and *Slit3* mutants have thickened atrioventricular valves and hypoplastic non-coronary aortic valve [13, 14].

Additionally, it has been shown that Robo-Slit are related to the Notch and vascular endothelial growth factor signaling pathways [6, 13]. Both pathways are known to be involved in heart formation and development. Furthermore, genetic variations in *NOTCH* and *VEGF* genes have been found in patients with CHD [42, 43]. In the present study, we sought to identify genetic variants in *ROBO* and *SLIT* genes in patients with different CHD. We have identified (i) several variants with a consistent in silico prediction of pathogenicity, (ii) patients with digenic variants who have a more severe phenotype and (iii) two segregating variants, one with an autosomal recessive pattern of inheritance and one segregating with the disease in the family.

## Limitations

There may be some possible limitations in this study. The first is the limited access to detailed clinical data for the majority of patients. The second limitation concerns family segregation. Indeed, family co-segregation was
possible for two cases only. Parental samples were not
available for the other index-cases.

Conclusion

Although CHD newborns are treated as soon as the dis-
ease is diagnosed, CHD persists among the most lead-
ing causes of mortality in the developed world [44]. The
specific causative genetic variant remains unknown for
a significant number of patients. The identification of
novel variants in the ROBO and SLIT genes, as a recent
associated pathway with CHD, will aid to improve the
genetic testing yield of CHD. The functional effect of
variants of unknown or uncertain significance remains
to be elucidated as well as genotype-phenotype
correlations.

Our study contributes to expand the phenotypic and allelic heterogeneity of CHD by reporting several variants in the ROBO-SLIT signaling pathway. Albeit the majority of the prioritized variants are predicted pathogenic with a consistency across different in silico predictions tools and the identification of ROBO4 variants segregating in families, functional studies are needed to assess their clinical relevance.

**Supplementary Information**

The online version contains supplementary material available at https://doi.
org/10.1186/s12967-023-03994-y.

**Additional file 1.** Figure S1: Overview of ROBO1 protein in ribbon presentation. The protein is colored by element: α-helix=blue, β-strand = red, turn=green, 3/10helix=yellow, and random coil=cyan. **Figure S2:** Close-up of the **ROBO1**: p.Val610lle variant. The protein is colored in grey, the side chain of the mutated residue is in magenta and shown as small balls. The protein is colored grey, the side chains of both the wild-type and the mutant residue are shown and colored green and red respectively **Figure S3:** Overview of ROBO2 protein in ribbon presentation. The protein is colored by element: α-helix=blue, β-strand = red, turn=green, 3/10 helix=yellow, and random coil=cyan. Other molecules in the complex are colored grey when present. **Figure S4:** Close-up of the **ROBO2**: p.Arg811Trp variant. The protein is colored grey, and the side chains of both the wild-type and the mutant residue are shown and colored green and red respectively. **Figure S5:** Overview of ROBO3 protein in ribbon presentation. The protein is colored by element: α-helix=blue, β-strand = red, turn=green, 3/10helix=yellow, and random coil=cyan. **Figure S6:** Close-up of the **ROBO3**: p.Thr323Met variant. The protein is colored grey, and the side chain of the mutated residue is colored magenta and shown as small balls. The side chains of both the wild-type and the mutant residue are shown and colored green and red respectively. **Figure S7:** Close-up of the **ROBO3**: p.Arg539Trp variant. **Figure S8:** Close-up of the **ROBO3**: p.Pro859Gln variant. **Figure S9:** Overview of ROBO4 protein in ribbon presentation. The protein is colored by element: α-helix=blue, β-strand = red, turn=green, 3/10helix=yellow, and random coil=cyan. **Figure S10:** Close-up of the **ROBO4**: p.Ala303Asp variant. The protein is colored grey and the side chains of both the wild-type and the mutant residue are shown and colored green and red respectively. The side chain of the mutated residue is colored magenta and shown as small balls. **Figure S11:** Overview of SLIT1 protein in ribbon presentation. The protein is colored by element: α-helix=blue, β-strand = red, turn=green, 3/10helix=yellow, and random coil=cyan. **Figure S12:** Close-up of the **SLIT1**: p.Pro149Leu variant. The side chain of the mutated residue is colored magenta and shown as small balls **Figure S13:** Close-up of the **SLIT1**: p.Arg455Ser

variant. The side chain of the mutated residue is colored magenta and shown as small balls. **Figure S14:** Overview of SLIT3 protein in ribbon presentation. The protein is colored by element: α-helix=blue, β-strand = red, turn=green, 3/10helix=yellow, and random coil=cyan. **Figure S15:** Close-up of the SLIT3: p.Ser629Asn variant. The side chain of the mutated residue is colored magenta and shown as small balls.

**Additional file 2:** Sanger sequencing of the prioritized variants.

Acknowledgements

Part of this data was generated by the Pediatric Cardiac Genomics Consortium (PCGC), under the auspices of the National Heart, Lung, and Blood Institute's Bench to Bassinet Program <http://www.benchtobassinet.org/>. The Pediatric Cardiac Genomics Consortium (PCGC) program is funded by the National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services through grants U01HL098123, U01HL098147, U01HL098153, U01HL098162, U01HL098163, and U01HL098188. This manuscript was not prepared in collaboration with investigators of the PCGC, has not been reviewed and/or approved by the PCGC, and does not necessarily reflect the opinions of the PCGC investigators or the NHLBI. H.J. received postdoctoral fellowship from the AFM-Telethon. S.Z. is a Research Director at the INSERM.

Author contributions

Conceptualization, SZ and HJ; Methodology, HJ; Validation, SZ; CJ; Clinical
Investigation of the patients and family members; AT; FB; AF; HG; SD; DB; CO;
JFA; Analysis and interpretation of data: HJ; CO; CJ Molecular investigation and
in silico analysis: HJ; writing—original draft preparation, HJ; Writing—Review
and Editing, HJ; SZ. All authors have read and agreed to the published version
of the manuscript.

Funding

This research received a grant from the Fédération Française de Cardiologie (FFC-Equipe 2019).

Availability of data and materials

All data generated or analyzed during this study are included in this published
article and its additional files.

Declarations

Ethics approval and consent to participate

This study was approved by the Marseille ethic committee no 13.061 and the
patients provided their written informed consent to participate.

Consent for publication

Informed consent for publication was obtained from all subjects involved in
the study.

Competing interests

The authors declare that they have no conflict of interest.

Received: 15 December 2022 Accepted: 15 February 2023

Published online: 28 February 2023

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