Laetitia Lagoutte

PNPLA1 mutations cause autosomal recessive congenital ichthyosis in golden retriever dogs and humans

Ichthyoses comprise a heterogeneous group of genodermatoses characterized by abnormal desquamation over the whole body, for which the genetic causes of several human forms remain unknown. We used a spontaneous dog model in the golden retriever breed, which is affected by a lamellar ichthyosis resembling human autosomal recessive congenital ichthyoses (ARCI), to carry out a genome-wide association study. We identified a homozygous insertion-deletion (indel) mutation in PNPLA1 that leads to a premature stop codon in all affected golden retriever dogs. We subsequently found one missense and one nonsense mutation in the catalytic domain of human PNPLA1 in six individuals with ARCI from two families. Further experiments highlighted the importance of PNPLA1 in the formation of the epidermal lipid barrier. This study identifies a new gene involved in human ichthyoses and provides insights into the localization and function of this yet uncharacterized member of the PNPLA protein family.

FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome

Abstract Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames. Benchmarking versus five state-of-the-art tools shows that FEELnc achieves similar or better classification performance on GENCODE and NONCODE data sets. The program also provides specific modules that enable the user to fine-tune classification accuracy, to formalize the annotation of lncRNA classes and to identify lncRNAs even in the absence of a training set of non-coding RNAs. We used FEELnc on a real data set comprising 20 canine RNA-seq samples produced by the European LUPA consortium to substantially expand the canine genome annotation to include 10 374 novel lncRNAs and 58 640 mRNA transcripts. FEELnc moves beyond conventional coding potential classifiers by providing a standardized and complete solution for annotating lncRNAs and is freely available at https://github.com/tderrien/FEELnc.

Evidence of Coat Color Variation Sheds New Light on Ancient Canids

We have used a paleogenetics approach to investigate the genetic landscape of coat color variation in ancient Eurasian dog and wolf populations. We amplified DNA fragments of two genes controlling coat color, Mc1r (Melanocortin 1 Receptor) and CBD103 (canine-β-defensin), in respectively 15 and 19 ancient canids (dogs and wolf morphotypes) from 14 different archeological sites, throughout Asia and Europe spanning from ca. 12 000 B.P. (end of Upper Palaeolithic) to ca. 4000 B.P. (Bronze Age). We provide evidence of a new variant (R301C) of the Melanocortin 1 receptor (Mc1r) and highlight the presence of the beta-defensin melanistic mutation (CDB103-K locus) on ancient DNA from dog-and wolf-morphotype specimens. We show that the dominant KB allele (CBD103), which causes melanism, and R301C (Mc1r), the variant that may cause light hair color, are present as early as the beginning of the Holocene, over 10 000 years ago. These results underline the genetic diversity of prehistoric dogs. This diversity may have partly stemmed not only from the wolf gene pool captured by domestication but also from mutations very likely linked to the relaxation of natural selection pressure occurring in-line with this process.

Comparison of buccal and blood-derived canine DNA, either native or whole genome amplified, for array-based genome-wide association studies.

BackgroundThe availability of array-based genotyping platforms for single nucleotide polymorphisms (SNPs) for the canine genome has expanded the opportunities to undertake genome-wide association (GWA) studies to identify the genetic basis for Mendelian and complex traits. Whole blood as the source of high quality DNA is undisputed but often proves impractical for collection of the large numbers of samples necessary to discover the loci underlying complex traits. Further, many countries prohibit the collection of blood from dogs unless medically necessary thereby restricting access to critical control samples from healthy dogs. Alternate sources of DNA, typically from buccal cytobrush extractions, while convenient, have been suggested to have low yield and perform poorly in GWA. Yet buccal cytobrushes provide a cost-effective means of collecting DNA, are readily accepted by dog owners, and represent a large resource base in many canine genetics laboratories. To increase the DNA quantities, whole genome amplification (WGA) can be performed. Thus, the present study assessed the utility of buccal-derived DNA as well as whole genome amplification in comparison to blood samples for use on the most recent iteration of the canine HD SNP array (Illumina).FindingsIn both buccal and blood samples, whether whole genome amplified or not, 97% of the samples had SNP call rates in excess of 80% indicating that the vast majority of the SNPs would be suitable to perform association studies regardless of the DNA source. Similarly, there were no significant differences in marker intensity measurements between buccal and blood samples for copy number variations (CNV) analysis.ConclusionsAll DNA samples assayed, buccal or blood, native or whole genome amplified, are appropriate for use in array-based genome-wide association studies. The concordance between subsets of dogs for which both buccal and blood samples, or those samples whole genome amplified, was shown to average >99%. Thus, the two DNA sources were comparable in the generation of SNP genotypes and intensity values to estimate structural variation indicating the utility for the use of buccal cytobrush samples and the reliability of whole genome amplification for genome-wide association and CNV studies.

Amy2B copy number variation reveals starch diet adaptations in ancient European dogs

Extant dog and wolf DNA indicates that dog domestication was accompanied by the selection of a series of duplications on the Amy2B gene coding for pancreatic amylase. In this study, we used a palaeogenetic approach to investigate the timing and expansion of the Amy2B gene in the ancient dog populations of Western and Eastern Europe and Southwest Asia. Quantitative polymerase chain reaction was used to estimate the copy numbers of this gene for 13 ancient dog samples, dated to between 15 000 and 4000 years before present (cal. BP). This evidenced an increase of Amy2B copies in ancient dogs from as early as the 7th millennium cal. BP in Southeastern Europe. We found that the gene expansion was not fixed across all dogs within this early farming context, with ancient dogs bearing between 2 and 20 diploid copies of the gene. The results also suggested that selection for the increased Amy2B copy number started 7000 years cal. BP, at the latest. This expansion reflects a local adaptation that allowed dogs to thrive on a starch rich diet, especially within early farming societies, and suggests a biocultural coevolution of dog genes and human culture.

A Spontaneous KRT16 Mutation in a Dog Breed: A Model for Human Focal Non-Epidermolytic Palmoplantar Keratoderma (FNEPPK)

TO THE EDITOR The keratin 16 gene (KRT16) encodes an intermediate filament protein mainly expressed in palmoplantar epidermis. In humans, mutations in KRT16 are responsible for pachyonychia congenita and focal non-epidermolytic palmoplantar keratoderma (FNEPPK; Smith et al., 2000; McLean and Moore, 2011). One of the main symptoms is a painful thickening of the palms and soles. To understand molecular mechanisms involved in this keratoderma, Krt16 mutant mouse models have been developed, but only one reproduces fully the palmoplantar phenotype (Lessard and Coulombe, 2012). In this study, we present a spontaneous canine model of FNEPPK inherited as an autosomal recessive disorder in the Dogue de Bordeaux breed. Because of its population structure, which features genetic isolates, the purebred dog model has recently proven its utility in understanding the molecular mechanisms of hereditary cornification disorders, notably in humans and dog Autosomal Recessive Congenital Ichthyosis (Grall et al., 2012). We investigated a family of 130 dogs including 28 affected animals; no sex bias was observed among the 13 males and 15 females analyzed. The onset usually occurred between 10 weeks and 1 year of age. First described by Paradis (1992), affected dogs exhibit a painful thickening of the footpads with severe keratinous proliferations and fissures only at the ground contact locations similar to those observed in FNEPPK patients (Figure 1). Cracks predispose the dogs to secondary infections, leading to lameness, causing the dog to be reluctant to walk. Nails did not seem to be affected, as reported in some human FNEPPK patients and in Krt16-null mice models (Shamsher et al., 1995; Smith et al., 2000; Liao et al., 2007; Lessard and Coulombe, 2012). Similarly, no other cutaneous sign such as oral leukoplakia, cysts, or follicular keratosis was reported. This is concordant with our results of quantitative reverse transcription PCR of messsengerRNA from unaffected dog biopsies, showing strong and specific expression of KRT16 in the footpad, nose, and keratinocytes but not in body skin, oral mucosa, or other organs (data not shown). Histopathological examinations of footpad biopsies revealed thick hyperkeratotic digital epidermis that was roughened by marked conical papillae with a prominent ‘‘church spire’’ appearance (Figure 1e). On the top of this, there is a thin compact column of parakeratotic cells with absent or decreased underlying granular layer and cytoplasmic vacuolization of superficial corneocytes at their base (Figure 1f and g). Outside the conical papillae, the epidermis exhibited a well-developed granular layer and compact orthohyperkeratosis. Between the conical papillae, small valleys were observed that presented dyskeratosis, an irregular and prominent granular layer, and light to moderate keratotic plugging (Figure 1h). No epidermolytic changes were noticed. Chronic superficial perivascular dermal infiltrate was sometimes observed. Immunohistochemistry and immunofluorescence staining were performed on FFPE skin biopsies from four affected and four unaffected dogs. The Ki67 proliferation index showed that, as expected, keratinocytes in affected footpads were not proliferating. Expression of keratin 1, 6, and 16 was investigated in normal footpad biopsies (Figure 2). As previously described (Bowden et al., 2009), keratin 1, 6, and 16 are coexpressed in the suprabasal layer of the footpad epidermis, with K16 located in the center of the rete ridges. No differences were observed in the expression of K1 and K6 between cases and controls. However, immunostaining revealed an abnormal distribution of K16 in affected samples: although K16 expression was diffuse and suprabasal all over the thickness of the epithelial layer of control dogs, its expression was not detected in affected samples (Figure 2). In affected dogs, discrete aggregates of K16 could be observed in the cornified layer in footpads not in contact with the ground (Supplementary Figure S1a online). In parallel, we performed a genetic linkage study on the Dogue de Bordeaux family using 14 affected and 54 unaffected dogs genotyped on the canine 173,000 SNP array Q3 . We identified a 20 Mb locus corresponding to the dog type I keratin cluster. We carried out mutation screening on several keratins in 14 affected dogs and 16 controls and identified a complex mutation in KRT16 corresponding to an insertion/ deletion (indel) of four nucleotides and a separate 1 bp deletion 15 nucleotides downstream in exon 6 (Supplementary Figure S2 online). This complex indel results in an insertion of 1 bp in affected dogs and introduces a frameshift changing the sequence of 10 amino acids and creating a premature stop codon (p.Glu392*) in the open reading frame of the gene. This stop codon located in the 2B domain leads to the loss of the last 85 amino acids of K16, including the helix termination motif LETTER TO THE EDITOR

A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies

Human Hereditary Sensory Autonomic Neuropathies (HSANs) are characterized by insensitivity to pain, sometimes combined with self-mutilation. Strikingly, several sporting dog breeds are particularly affected by such neuropathies. Clinical signs appear in young puppies and consist of acral analgesia, with or without sudden intense licking, biting and severe self-mutilation of the feet, whereas proprioception, motor abilities and spinal reflexes remain intact. Through a Genome Wide Association Study (GWAS) with 24 affected and 30 unaffected sporting dogs using the Canine HD 170K SNP array (Illumina), we identified a 1.8 Mb homozygous locus on canine chromosome 4 (adj. p-val = 2.5x10-6). Targeted high-throughput sequencing of this locus in 4 affected and 4 unaffected dogs identified 478 variants. Only one variant perfectly segregated with the expected recessive inheritance in 300 sporting dogs of known clinical status, while it was never present in 900 unaffected dogs from 130 other breeds. This variant, located 90 kb upstream of the GDNF gene, a highly relevant neurotrophic factor candidate gene, lies in a long intergenic non-coding RNAs (lincRNA), GDNF-AS. Using human comparative genomic analysis, we observed that the canine variant maps onto an enhancer element. Quantitative RT-PCR of dorsal root ganglia RNAs of affected dogs showed a significant decrease of both GDNF mRNA and GDNF-AS expression levels (respectively 60% and 80%), as compared to unaffected dogs. We thus performed gel shift assays (EMSA) that reveal that the canine variant significantly alters the binding of regulatory elements. Altogether, these results allowed the identification in dogs of GDNF as a relevant candidate for human HSAN and insensitivity to pain, but also shed light on the regulation of GDNF transcription. Finally, such results allow proposing these sporting dog breeds as natural models for clinical trials with a double benefit for human and veterinary medicine.

Discovery of human-similar gene fusions in canine cancers

Canine cancers represent a tremendous natural resource due to their incidence and striking similarities to human cancers, sharing similar clinical and pathologic features as well as oncogenic events, including identical somatic mutations. Considering the importance of gene fusions as driver alterations, we explored their relevance in canine cancers. We focused on three distinct human-comparable canine cancers representing different tissues and embryonic origins. Through RNA-Seq, we discovered similar gene fusions as those found in their human counterparts: IGK-CCND3 in B-cell lymphoma, MPB-BRAF in glioma, and COL3A1-PDGFB in dermatofibrosarcoma protuberans-like. We showed not only similar partner genes but also identical breakpoints leading to oncogene overexpression. This study demonstrates similar gene fusion partners and mechanisms in human-dog corresponding tumors and allows for selection of targeted therapies in preclinical and clinical trials with pet dogs prior to human trials, within the framework of personalized medicine. Cancer Res; 77(21); 5721-7. ©2017 AACR.

Characterisation and functional predictions of canine long non-coding RNAs

Long non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and human through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.

A spontaneous dog model for a human sensory neuropathy: identification of a mutation in the upstream region of a neurotrophic factor

In this study, we sought the genetic cause of self-mutilation syndrome in sporting dogs, which corresponds to human Hereditary Sensory and Autonomic Neuropathies (HSAN). We have identified a genetic mutation upstream of the gene encoding Glial cell line-Derived Neurotrophic Factor (GDNF). This mutation is responsible for insensitivity to pain in four sporting dog breeds and it perfectly segregates with the disease in 250 sporting dogs of known clinical status. Moreover, it was not found in any of the 900 unaffected dogs from 130 different breeds. Since this mutation is localized in a long non-coding RNA, we performed an in-depth analysis of the genomic region (locus) as well as gene expression analyses to understand its role in the pathophysiology of the disease. Thus, in addition to the discovery of a novel candidate gene for HSAN in humans, we propose a transcriptional regulation mechanism based on a “partnership” between GDNF and a long non-coding RNA (lncRNA).