Biology subjects

Lohi, H.

Publications and source records attributed to Lohi, H..

12 recordsLinked to original sources

bioRxiv2026

The DoGA Consortium Atlas of Canine Enhancers and Promoters Across Tissues and Development

The domestic dog is a powerful genetic model for complex traits, disease and behaviours relevant to human biology, yet the canine genome still lacks a systematic transcription-defined atlas of regulatory elements. Existing resources have improved annotation but largely infer regulatory activity from chromatin features rather than directly mapping transcription initiation at promoters and enhancers. Here, we address this gap using 114 CAGE-seq libraries spanning 56 tissues and developmental stages from 9 dogs. We identify 68,446 promoters and 46,661 active enhancers, and define their tissue-enriched activity across the canine body. Regulatory programmes are organized around shared transcription factor motif infrastructures, with prominent enrichment of KLF family motifs across tissues. The cerebellum emerges as a major regulatory hub, showing the highest density of enhancer-promoter interactions among brain regions. During embryogenesis, enhancer activity shifts from early neurodevelopmental patterning programmes, including OTX2 and ZIC1/4, towards regulators of functional maturation and synaptic organization, including AQP4 and NLGN3. Comparative analyses revealed 69 enhancers with highly similar regulatory structures linked to potential orthologous genes in dog and human. Together, these data establish a tissue-resolved transcription-based atlas of the canine regulatory genome that advances functional annotation and improves interpretation of non-coding variation in comparative and disease genomics.

genomics↗

bioRxiv2025

Obesity and sarcopenia affect the metabolite profiles of pet dogs

Overweight and reduced muscle mass significantly affect canine health, yet their metabolic implications in dogs require further investigation. This study aimed to characterize metabolic alterations associated with overweight, obesity, and reduced muscle mass in dogs. An observational, cross-sectional study was conducted to evaluate differences in metabolite concentrations among pet dogs with varying body and muscle conditions. Dogs older than two years were included in the Body Condition Score (BCS) analysis (n=186), while only dogs older than eight years were included in the Muscle Condition Score (MCS) analysis due to age-related sarcopenia (n=99). Metabolomic analyses were performed using a validated, canine-specific nuclear magnetic resonance (NMR) platform. Associations between metabolite concentrations and body or muscle condition were examined independently using generalized linear models, adjusting statistically for age and health status. Increasing overweight status correlated with notable disruptions in lipid and glucose metabolism, alongside elevated inflammation markers. Specifically, several lipid metabolites increased linearly with increasing overweight, as did citrate, lactate, pyruvate, and the inflammatory biomarker GlycA. Conversely, decreased muscle mass showed relatively modest independent metabolic effects, including elevated GlycA, an increased phenylalanine-to-tyrosine ratio, and alterations in VLDL subclass composition. Muscle mass was closely associated with age and overall health status, with health status emerging as the primary determinant of metabolite concentrations. Moderate to severe muscle loss was predominantly observed in dogs with underlying diseases. The metabolic consequences of overweight and sarcopenia, particularly increased inflammation common to both conditions, could significantly impact a dogs overall health. These findings reinforce existing evidence regarding the detrimental health effects associated with overweight and sarcopenia in dogs. Furthermore, the study suggests that underlying disease should be suspected in older dogs presenting highly abnormal metabolite profiles or moderate to severe muscle loss.

physiology↗

bioRxiv2025

A nonsense mutation in the PRKG2 gene in Dalmatian dogs with chondrodysplasia

Skeletal dysplasias encompass a diverse group of genetic disorders characterized by short stature and dwarfism. In humans, 771 types of skeletal dysplasia have been documented. Similar forms of these disorders have also been observed in dogs. The first cases of documented skeletal dysplasia in Dalmatian dogs were reported in the early 1980s, with additional affected dogs observed in subsequent years. Careful radiological and histopathological examinations at the time revealed severe limb deformities, including shortened radii and ulnae, irregular growth plates and disrupted endochondral ossification. In this study, we applied whole-genome sequencing on samples collected in 1992 and identified a genetic variant in the PRKG2 gene, introducing a premature stop codon (XM_038582312: c.T1601G, p.L534X). Genetic variants in PRKG2 have previously been implicated in human acromesomelic dysplasia, a disorder affecting limb growth in young children. The PRKG2-encoded protein plays a crucial role in endochondral ossification, and if translated, the identified nonsense variant would result in a truncated protein lacking most of the catalytic domain. Extended screening of the genetic variant revealed its continued segregation in the current Dalmatian population. Furthermore, three recent cases of dwarfism in Dalmatians were found to be homozygous for the identified PRKG2 nonsense variant. These findings provide compelling evidence for the role of PRKG2 in Dalmatian dwarfism, resolving a decades-old genetic mystery in the breed.

genetics↗

bioRxiv2024

A feline model of human LDLR-related atherosclerosis

BackgroundAtherosclerosis, a chronic inflammatory vascular disease driven by the accumulation of LDL-derived cholesterol on arterial walls, is the leading cause of mortality worldwide but is rare in animals. We recently identified spontaneous atherosclerosis in the Korat cat breed, characterized by severe hypercholesterolemia and clinical signs of congestive heart failure, ultimately leading to death. Histopathological examination revealed lesions similar to those observed in human atherosclerosis. Given the close genetic relationship among affected cats, we hypothesized a genetic basis for the condition. MethodsWe expanded our sample recruitment and employed whole genome sequencing to identify genetic variants associated with the condition. ResultsWe identified a homozygous XM_003981898.6:c.2406G>A variant specific to the cases in the LDLR gene. This variant is predicted to result in a premature stop codon, XP_003981947.3:p.Trp758*, leading to a truncated LDLR protein that lacks the last 108 amino acids, including the transmembrane and intracellular C-terminal domains. Genotyping this LDLR variant in an additional cohort of 309 Korat cats confirmed its segregation and revealed new affected cats for clinical follow-up. In silico analyses demonstrated that the identified variant appears optimal for gene-editing-based therapeutics. ConclusionsThis is the first report of a spontaneous atherosclerosis animal model with an LDLR variant, the most common gene associated with familial hypercholesterolemia in humans. Given that PCSK9, another known hypercholesterolemia gene, has been lost in many mammalian genomes, including cats, our study provides an exciting double knockout model for human atherosclerosis. The affected Korats may also serve as a valuable model for DNA base editing therapeutics.

genetics↗

bioRxiv2024

A genotype-first approach identifies variants for orofacial clefts and other phenotypes in dogs

Dog breeding promotes within-group homogeneity through conformation to strict breed standards, and also drives between-group heterogeneity in pursuit of characteristic breed traits. There are over 350 recognized dog breeds that provide the foundation for investigating the genetic basis of phenotypic diversity. Typically, breed standard phenotypes such as stature, fur length, and craniofacial structure are analyzed in genetic association studies. However, such analyses are limited to the assayed phenotypes, leaving difficult to measure phenotypic subtleties potentially overlooked. In this study, the genotype-first approach was adapted to the dog genome to investigate coding variation from over 2000 dogs, leading to discoveries of new mutations related to craniofacial morphology and stature. Breed-enriched variants were prioritized according to gene constraint, which was calculated using a mutation model derived from trinucleotide substitution probabilities in the dog. Among the discovered variants was a splice-acceptor mutation in PDGFRA associated with bifid nose, a characteristic trait of Catalburun dogs, implicating the genes role in midline closure, and a frameshift mutation in LCORL associated with large canine body size, thus highlighting the importance of allelic heterogeneity in selection for breed traits. Most priority variants were not associated with genomic signatures for breed differentiation, as these regions were enriched for constrained genes intolerant to nonsynonymous variation, suggesting a model of breed phenotype diversification based on regulatory changes to essential genes. Identification of trait-associated variants in dogs informs new biological roles for genes. Improved collection of breed disease risk data, along with increased breed representation, will drive further discoveries.

genomics↗

bioRxiv2024

Determinants of de novo mutations in extended pedigrees of 43 dog breeds

Intensive breeding of dogs has had dramatic effects on genetic variants underlying phenotypes. To investigate whether this also affected mutation rates, we deep-sequenced pedigrees from 43 different dog breeds representing 404 trios. We find that the mutation rate is remarkably stable across breeds and is predominantly influenced by variation in parental ages. The effect of paternal age per year on mutation rates is approximately 1.5 times greater in dogs than humans, suggesting that the elevated yearly mutation rate in dogs is only partially attributed to earlier reproduction. While there is no significant effect of breeds on the overall mutation rate, larger breeds accumulate proportionally more mutations earlier in development than small breeds. Interestingly, we find a 2.6 times greater mutation rate in CG Islands (CGIs) compared to the remaining genome in dogs, unlike humans, where there is no difference. Our estimated rate of mutation by recombination in dogs is more than 10 times larger than estimates in humans. We ascribe these to the fact that canids have lost PRDM9-directed recombination and draw away recombination from CGIs. In conclusion, our study sheds light on stability of mutation processes and disparities in mutation accumulation rates reflecting the influence of differences in growth patterns among breeds, and the impact of PRDM9 gene loss on the de novo mutations of canids.

evolutionary biology↗

bioRxiv2024

IP3 receptor depletion in a spontaneous canine model of Charcot-Marie-Tooth disease 1J with amelogenesis imperfecta

Inositol 1,4,5-trisphosphate receptors (IP3R) mediate Ca2+ release from intracellular stores, contributing to complex regulation of numerous physiological responses. The involvement of the three IP3R genes (ITPR1, ITPR2 and ITPR3) in inherited human diseases has started to shed light on the essential roles of each receptor in different human tissues and cell types. Variants in the ITPR3 gene, which encodes IP3R3, have recently been found to cause demyelinating sensorimotor Charcot-Marie-Tooth neuropathy type 1J (CMT1J). In addition to peripheral neuropathy, immunodeficiency and tooth abnormalities are occasionally present. Here, we report the identification of a homozygous nonsense variant in the ITPR3 gene in Lancashire Heeler dogs, presenting with a severe developmental enamel defect and reduced nerve conduction velocity. We studied the primary skin fibroblasts of the affected dogs and observed that the nonsense variant in ITPR3 led to a complete absence of full-length IP3R3 protein. Unexpectedly, the protein levels of IP3R1 and IP3R2 were also markedly decreased, suggesting co-regulation. Functional Ca2+ measurements revealed reduced IP3R-mediated Ca2+ flux upon stimulation of G-protein-coupled-receptors in the affected dog fibroblasts. We were able to rescue the IP3R1 and IP3R2 depletion by proteasome inhibition but not the IP3R3 loss, which was facilitated by nonsense-mediated mRNA decay. These findings highlight the first spontaneous mammalian phenotype caused by a nonsense variant in ITPR3, leading to the loss of IP3R3. The human and canine IP3R3 proteins are highly similar, and our study suggests that the tissue involvement resulting from the receptors dysfunction is also conserved. In summary, IP3R3 is critical for enamel formation and peripheral nerve maintenance. Author summaryWe investigated pet dogs, Lancashire Heelers, with impairments in tooth development and in the nerves that regulate limb muscles. Through genetic studies of the dog pedigree, we found that the phenotypes were caused by a recessively inherited mutation in the ITPR3 gene, which encodes one of three IP3 receptors (IP3R) isoforms (IP3R3 isoform) that are needed for intracellular Ca2+ signaling. Mutated IP3R3 has been recently linked to a human inherited neuropathy called Charcot-Marie-Tooth disease type 1J, which impairs peripheral nerve function and is accompanied by immunodeficiency and abnormal teeth in some individuals. We showed that in the skin cells of the affected dogs, the full-length IP3R3 protein was completely absent, and also the protein levels of the other two IP3R isoforms (IP3R1 and IP3R2) were severely lowered. This led to impaired agonist-induced Ca2+ release and signaling. Our results demonstrate the high conservation between human and canine IP3 receptors and their significance for different tissue systems. The genetic studies now highlight that IP3R3 is vital for peripheral nerve function and enamel development.

genetics↗

bioRxiv2021

Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats

In the largest DNA-based study of domestic cat to date, 11,036 individuals (10,419 pedigreed cats from 91 breeds and breed types and 617 non-pedigreed cats) were genotyped via commercial panel testing, elucidating the distribution and frequency of known genetic variants associated with blood type, disease and physical traits across cat breeds. Blood group determining variants, which are relevant clinically and in cat breeding, were genotyped to assess the across breed distribution of blood types A, B and AB. Extensive panel testing identified 13 disease-associated variants in 48 breeds or breed types for which the variant had not previously been observed, strengthening the argument for panel testing across populations. The study also indicates that multiple breed clubs have effectively used DNA testing to reduce disease-associated genetic variants within certain pedigreed cat populations. Appearance-associated genetic variation in all cats is also discussed. Additionally, we combined genotypic data with phenotype information and clinical documentation, actively conducted owner and veterinarian interviews, and recruited cats for clinical examination to investigate the causality of a number of tested variants across different breed backgrounds. Lastly, genome-wide informative SNP heterozygosity levels were calculated to obtain a comparable measure of the genetic diversity in different cat breeds. This study represents the first comprehensive exploration of informative Mendelian variants in felines by screening over 10,000 domestic cats. The results qualitatively contribute to the understanding of feline variant heritage and genetic diversity and demonstrate the clinical utility and importance of such information in supporting breeding programs and the research community. The work also highlights the crucial commitment of pedigreed cat breeders and registries in supporting the establishment of large genomic databases that when combined with phenotype information can advance scientific understanding and provide insights that can be applied to improve the health and welfare of cats.

genetics↗

bioRxiv2021

Risk and protective factors of feline tooth resorption in 8115 Finnish cats

Tooth resorption (TR) is one of cats most common dental diseases. It is a painful condition characterized by progressive dental destruction, which eventually results in loss of teeth. The aetiology of the TR remains unclear, but associations with old age, breed, other oral and dental diseases, and certain environmental factors have been suspected. In our study, we used part of the data from the extensive feline health and environmental survey of 8115 Finnish cats collected through an online survey targeted at cat owners. We aimed to investigate the characteristics of cats having TR and to study risk factors for TR. Because TR is difficult to detect and, in addition, the feline health survey was very comprehensive and included diagnoses defined by both veterinarians and owners themselves, we limited our study to a subpopulation of cats diagnosed with oral or dental disease by a veterinarian and undergone dental examination or surgery under sedation (n=944). The frequency of veterinary-diagnosed TR was 3.9% in the entire health survey data (316/8115) and increased to 21% in the subpopulation of veterinarian-diagnosed and sedated cats (202/944). We utilized case-control multivariable logistic regression in this subpopulation to determine the risk factors and breed variation of feline TR. The 202 cats diagnosed with TR were defined as TR cases and the 742 cats without TR diagnoses served as controls. Results indicate that the risk of TR increases with age. Dental calculus, gingivitis, and periodontitis were associated with TR. These findings and the interaction of dental calculus with gingivitis and periodontitis might suggest that inflammatory changes caused by dental calculus increase the risk of TR. We found Cornish Rex, European, and Ragdoll at higher risk for TR. Exotic-Persians had lower risk, and Turkish van and Devon Rex had no TR. The observed differences between breeds highlight a genetic contribution. In addition, female cats that had food available constantly had significantly less TR than female cats that had feeding times. The underlying influential reasons for this result remain unexplained in our study.

pathology↗

bioRxiv2020

Dog color patterns explained by modular promoters of ancient canid origin

Distinctive color patterns in dogs are an integral component of canine diversity. Color pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves 1,2 but important gaps remain in understanding how these patterns evolved and are genetically controlled 3,4. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments 3,5-7. Here we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog color patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with arctic white wolves and that its hair cycle-specific module likely originated from an extinct canid that diverged from grey wolves more than 2 million years before present. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread color variation in dogs and wolves.

genetics↗

bioRxiv2020

Elevated blood creatinine -a biomarker of renal function- associates with multiple metabolic perturbations in dogs

BACKGROUNDRenal diseases, such as chronic kidney disease (CKD) are common in dogs. While the kidneys have multiple important metabolic functions, the occurrence of metabolic disturbances in canine renal diseases has not been extensively studied. OBJECTIVESTo identify metabolic changes in blood samples exhibiting elevated blood creatinine, indicating reduced renal filtration. ANIMALSSamples consisted of clinical samples analysed by a 1H NMR-based metabolomics platform. The case group included 23 samples with creatinine > 125 mol/l, and the control group 873 samples with creatinine within the reference interval. METHODSBiomarker association with elevated creatinine was evaluated utilizing three statistical approaches: Wilcoxon rank-sum test and logistic regression analysis (FDR-corrected p-values), and classification using random forest. Means of the biomarkers were compared to reference intervals. A heatmap and histograms visualized the differences. RESULTSThe levels of citrate, tyrosine, branched-chain amino acids, valine, leucine, albumin, linoleic acid % and the ratio of phenylalanine to tyrosine differed significantly both in the Wilcoxon test and logistic regression, acetate levels only in Wilcoxon test and docosapentaenoic acid % only in logistic regression (p <. 05). The ten most significant markers in random forest corresponded to the Wilcoxon test, supplemented with alanine. CONCLUSIONS AND CLINICAL IMPORTANCEThis study identified multiple metabolic changes associated with elevated blood creatinine, including prospective diagnostic markers and therapeutic targets. The NMR metabolomics test is a promising tool for improving diagnostics and management of canine renal diseases. Further research is needed to verify the association of these changes to the canine patients clinical state.

molecular biology↗

bioRxiv2019

Characteristics of a novel NMR-based metabolomics platform for dogs

Metabolomics has proven itself an invaluable research tool, providing comprehensive insight to systemic metabolism. However, the lack of scalable and quantitative methods with known reference intervals and documented reproducibility has prevented the use of metabolomics in the clinical setting. This study describes the development and validation of a quantitative nuclear magnetic resonance (NMR) -based metabolomics platform for canine serum and plasma samples. Altogether 8247 canine samples were analyzed using a Brukers 500 MHz NMR spectrometer. Using statistical approaches derived from international guidelines, we defined reference intervals for 123 biomarkers, studied method precision, analyte storage stability, the effect of prolonged contact to red blood cells, differences of blood collection tubes, interference of lipemia, hemolysis and bilirubinemia, method comparison, and demonstrated the methods practical relevance in a hyperglycemic cohort. Owing to the advantages of quantitative results, high reproducibility, and scalability, this canine metabolomics platform holds great potential for numerous clinical and research applications to improve canine health and well-being.

molecular biology↗