The genetic background of five canine models of rare human disease

This thesis addresses the genetic background of five spontaneous canine models of rare human disease. By utilizing genome-wide mapping methods, next-generation sequencing analyses and variant validation combined with detailed clinical and post-mortem examinations, we characterized new canine models, identified novel disease-associated variants and dissected their effects on health and morphology. In Study I, next-generation sequencing analysis in a Central Asian Shepherd dog affected by epidermolysis bullosa revealed a nonsense variant in COL7A1. Validation of the variant in 190 dogs confirmed the disease type as recessive dystrophic epidermolysis bullosa. Immunohistochemical stainings in skin samples illustrated the lack of full-length type VII collagen protein in the affected dog. In Study II, genome-wide association analysis combined with next-generation sequence analysis identified a locus and candidate variant associated with recessive pituitary dwarfism in Karelian Bear Dogs. A splice site variant in POU1F1 was confirmed with validation in over 8000 dogs. Computational predictions indicated weakening of the splice acceptor site at the affected intron-exon junction. In Study III, homozygosity mapping combined with next-generation sequence analysis identified candidate regions and variants associated with recessive congenital hearing loss in Rottweilers. A missense variant in LOXHD1 was confirmed with validation in over 800 000 dogs, revealing a link between the variant and Rottweiler breed background. In Study IV, variant screening combined with clinical examinations and statistical analyses revealed novel morphological consequences of a previously described variant in DVL2. The findings showed that the variant is involved in variable caudal vertebral anomalies and contributes to a brachycephalic phenotype. Varying allele frequencies were identified across populations, indicating the differential impact of the variant on the genetic health of dog breeds. In Study V, clinical and post-mortem examinations revealed malignant polymorphic ventricular arrhythmia and sudden cardiac death in young Leonberger dogs. The high prevalence of the disorder in litters and families strongly indicated a genetic aetiology. However, genome-wide association analyses failed to reveal associated loci, likely due to genetic or phenotypic heterogeneity. Future studies aim to overcome these obstacles with expanded cohorts and improved clinical and molecular phenotypes. Our findings have multiple scientific and practical implications. The discoveries facilitate diagnostics and treatment by revealing the molecular and pathophysiological mechanisms of the disorders. Affected dogs also provide novel large animal models for preclinical studies, benefitting both human and veterinary medicine. Finally, the development of gene tests support dog owners and breeders in revising breeding programmes to improve the health of dog breeds.Tässä väitöskirjatyössä selvitettiin viiden koirilla esiintyvän perinnöllisen sairauden taustaa. Tutkimuksissa käytettiin genominlaajuista assosiaatioanalyysiä, seuraavan sukupolven sekvensointianalyysiä ja geneettisten varianttien validaatiota yhdessä yksityiskohtaisten kliinisten ja patologisten tutkimusten kanssa. Työn tuloksena kuvattiin uusia koirilla esiintyviä sairauksia ja tunnistettiin sairauksia aiheuttavia geenimuunnoksia ja niiden vaikutuksia koirien terveyteen ja ruumiinrakenteeseen. Osatyössä I tunnistettiin seuraavan sukupolven sekvensointianalyysillä keskiaasiankoirien epidermolysis bullosa -ihosairauteen liittyvä ehdokasgeenivirhe COL7A1-geenissä. Geenivirheen yhteys sairauteen varmennettiin 190 koiran perimässä, ja sairauden alatyypiksi tarkennettiin resessiivinen dystrofinen epidermolysis bullosa. Immunohistokemialliset värjäykset ihonäytteissä paljastivat täyspitkän kollageeni VII -proteiinin puutoksen sairastuneen koiran ihossa. Osatyössä II tunnistettiin genominlaajuista assosiaatioanalyysiä ja seuraavan sukupolven sekvensointianalyysiä käyttäen karjalankarhukoirien aivolisäkeperäiseen lyhytkasvuisuuteen liittyvä perimän alue ja ehdokasgeenivirhe. POU1F1-geenin silmukointialueella sijaitsevan geenivirheen yhteys sairauteen varmennettiin yli 8000 koiran perimässä. Laskennallinen ennuste viittasi geenivirheen sisältävän introni-eksoni -liitoksen silmukointialueen heikentymiseen. Osatyössä III tunnistettiin homotsygotiakartoitusta ja seuraavan sukupolven sekvensointianalyysiä käyttäen rottweilerien synnynnäiseen kuurouteen liittyviä perimän ehdokasalueita ja -geenivirheitä. LOXHD1-geenissä sijaitsevan geenivirheen yhteys sairauteen varmennettiin yli 800 000 koiran perimässä. Varmennus paljasti myös geenivirheen esiintyvän lähes yksinomaan rottweiler-taustaisissa koirissa. Osatyössä IV tarkennettiin varianttiseulontaa, kliinisiä tutkimuksia ja tilastoanalyysejä käyttäen aiemmin kuvatun DVL2-geenivirheen vaikutuksia koirien ruumiinrakenteeseen. Tulokset osoittivat geenivirheen yhteyden erilaisiin kaudaalinikamien epämuodostumiin ja kuonon pituuden lyhenemiseen. Vaihteleva frekvenssi osoitti geenivirheeseen liittyvien terveysongelmien kuorman eroavan rotujen välillä. Osatyössä V tunnistettiin kliinisiä ja patologisia tutkimuksia käyttäen pahanlaatuisia kammiorytmihäiriöitä ja äkillisiä sydänperäisiä kuolemia nuorissa leonberginkoirissa. Sairauden korkea esiintyvyys pentueittain ja suvuittain viittasi perinnölliseen taustaan, mutta genominlaajuista analyysiä käyttäen ei tunnistettu ehdokasalueita perimästä. Tämä johtui todennäköisesti geneettisestä tai fenotyyppisestä heterogeniasta, mikä pyritään tulevissa analyyseissä huomioimaan suuremmalla otoskoolla ja tarkemmilla kliinisillä ja molekyylitason tutkimuksilla. Väitöstyön tuloksilla on useita tieteellisiä ja käytännön vaikutuksia. Löydökset edistävät diagnostiikkaa ja hoidon kehittämistä paljastamalla sairauksien taustalla olevat molekyylitason patofysiologiset mekanismit. Sairastuneet koirat voivat toimia mallieläiminä prekliinisissä tutkimuksissa, mikä hyödyttää sekä ihmis- että eläinlääketiedettä. Löydöksiin perustuvat geenitestit tukevat lisäksi koiranomistajia ja -kasvattajia jalostussuunnitelmien kehittämisessä terveempään suuntaan

Kökkähenkeä vai ei? Paikkaimagon hyödyntäminen suomalaisen maaseutukunnan paikkabrändin johtamisessa - Tapaus Isonkyrön kunta

Paikkojen välisessä kilpailussa brändit ovat yhä merkittävämpiä kilpailutekijöitä. Persoonalliset kulttuurit, nähtävyydet tai yritykset toimivat yhä useammin paikkojen imagojen muodostajina ja vetovoimatekijöinä, kun ihmisten riippumattomuus paikasta on lisääntynyt. Paikkamarkkinointia tulisi hyödyntää erityisesti suomalaisissa maaseutukunnissa, jotka uhkaavat tyhjentyä väestön karatessa kaupunkeihin. Tämä tapaustutkimus tuo esiin suomalaisen maaseutukunnan Isonkyrön potentiaalia kiihtyvässä paikkakilpailussa. Koska mielikuvat ohjaavat vahvasti ihmisten toimintaa, tutkimus kartoittaa Isonkyrön paikkaimagon sekä hyödyntää tästä saatua tietoa kunnan paikkabrändin strategisessa johtamisessa. Paikkaimago kartoitetaan teemahaastatteluilla, jossa 30 isokyröläistä kertovat avoimesti kokemuksistaan. Haastattelujen tueksi analysoidaan kunnan luovuttamia sekundäärilähteitä sekä havainnoidaan haastattelutilanteita ja kunnan ympäristöä. Tutkimus muodostaa teoreettisen viitekehyksen paikkabrändin johtamiseen yhdistelemällä tutkimuksia, jotka ammentavat muun muassa markkinoinnin, johtamisen sekä maantieteen teorioista. Viitekehystä hyödynnetään deduktiivisesti paikkaimagon analysoinnissa, josta johdetaan tavoitteet Isonkyrön paikkabrändin johtamiseen kolmenlaisen paikkaidentiteetin, laatu-, kilpailukyky- sekä merkityksellisyys-identiteetin kautta. Merkittäviksi tavoitteiksi tapauskunnassa nousevat tunnettuuden kasvattaminen, vapaa-ajan palveluiden viestinnän kehittäminen sekä yhteisöllisten tilojen hyödyntäminen ympäristössä. Yllättäväksi havainnoksi muodostui pohjalaisuuden tuottamien mielikuvien negatiivinen vaikutus paikkaimagoon erityisesti vastamuuttajien keskuudessa. Tämä on ristiriidassa paikallisten kokeman yhteisöllisen ”kökkähengen” kanssa, joka myös koetaan osaksi pohjalaisuutta positiivisemmassa mielessä.fi=Opinnäytetyö kokotekstinä PDF-muodossa.|en=Thesis fulltext in PDF format.|sv=Lärdomsprov tillgängligt som fulltext i PDF-format

Age, breed, sex and diet influence serum metabolite profiles of 2000 pet dogs

As an individual's metabolism reflects health and disease states well, metabolomics holds a vast potential in biomedical applications. However, normal physiological factors, such as age, can also influence metabolism, challenging the establishment of disease-specific metabolic aberrations. Here, we examined how physiological and diet-related factors drive variance in the metabolism of healthy pet dogs. We analysed 2068 serum samples using a canine nuclear magnetic resonance (NMR) spectroscopy-based metabolomics platform. With generalized linear models, we discovered that age, breed, sex, sterilization, diet type and fasting time significantly affected the canine metabolite profiles. Especially, breed and age caused considerable variation in the metabolite concentrations, and breeds with very different body conformations systematically differed in several lipid measurands. Our results enhance the understanding how normal physiological factors influence canine metabolism, aid accurate interpretation of the NMR results, and suggest the NMR platform might be applied in identifying aberrations in nutrient absorption and metabolism.Peer reviewe

Nonsense variant in COL7A1 causes recessive dystrophic epidermolysis bullosa in Central Asian Shepherd dogs

A rare hereditary mechanobullous disorder called epidermolysis bullosa (EB) causes blistering in the skin and the mucosal membranes. To date, nineteen EB-related genes have been discovered in human and other species. We describe here a novel EB variant in dogs. Two newborn littermates of Central Asian Shepherd dogs with severe signs of skin blistering were brought to a veterinary clinic and euthanized due to poor prognosis. In post-mortem examination, the puppies were shown to have findings in the skin and the mucosal membranes characteristic of EB. A whole-genome sequencing of one of the affected puppies was performed to identify the genetic cause. The resequencing data were filtered under a recessive model against variants from 31 other dog genomes, revealing a homozygous case-specific nonsense variant in one of the known EB-causing genes, COL7A1 (c.4579C> T, p.R1527*). The variant results in a premature stop codon and likely absence of the functional protein in the basement membrane of the skin in the affected dogs. This was confirmed by immunohistochemistry using a COL7A1 antibody. Additional screening of the variant indicated full penetrance and breed specificity at similar to 28% carrier frequency. In summary, this study reveals a novel COL7A1 variant causing recessive dystrophic EB and provides a genetic test for the eradication of the disease from the breed.Peer reviewe

Recessive missense LAMP3 variant associated with defect in lamellar body biogenesis and fatal neonatal interstitial lung disease in dogs

Neonatal interstitial lung diseases due to abnormal surfactant biogenesis are rare in humans and have never been reported as a spontaneous disorder in animals. We describe here a novel lung disorder in Airedale Terrier (AT) dogs with clinical symptoms and pathology similar to the most severe neonatal forms of human surfactant deficiency. Lethal hypoxic respiratory distress and failure occurred within the first days or weeks of life in the affected puppies. Transmission electron microscopy of the affected lungs revealed maturation arrest in the formation of lamellar bodies (LBs) in the alveolar epithelial type II (AECII) cells. The secretory organelles were small and contained fewer lamellae, often in combination with small vesicles surrounded by an occasionally disrupted common limiting membrane. A combined approach of genome-wide association study and whole exome sequencing identified a recessive variant, c.1159G>A, p.(E387K), in LAMP3, a limiting membrane protein of the cytoplasmic surfactant organelles in AECII cells. The substitution resides in the LAMP domain adjacent to a conserved disulfide bond. In summary, this study describes a novel interstitial lung disease in dogs, identifies a new candidate gene for human surfactant dysfunction and brings important insights into the essential role of LAMP3 in the process of the LB formation. Author summary We have characterized a lethal lung disease in neonatal Airedale Terrier dogs. The pathological features of the disease resemble those of the surfactant dysfunction in newborn babies. Surfactant is essential for lung function and we observed a maturation defect in the surfactant producing organelles of the lung epithelial type II cells. Genetic analyses revealed a recessive variant in the lysosome associated membrane LAMP3 gene. LAMP3 is a structural, limiting membrane protein of the surfactant organelles. This study provides an excellent candidate gene for human surfactant disorders as well as new insights into LAMP3 biology and pathophysiology while the affected breed will benefit from genetic testing to eradicate this severe disease.Peer reviewe

New scientific discoveries : plants and fungi

Scientific discovery, including naming new taxa, is important because without a scientific name, a species is invisible to science and the possibilities of researching its ecology, applications and threats, and conserving it, are greatly reduced. We review new scientific discoveries in the plant and fungal kingdoms, based largely on new names of taxa published in 2019 and indexed in the International Plant Names Index and Index Fungorum. Numbers of new species in both kingdoms were similar with 1942 new species of plant published and 1882 species of fungi. However, while >50% of plant species have likely been discovered, >90% of fungi remain unknown. This gulf likely explains the greater number of higher order taxa for fungi published in 2019: three classes, 18 orders, 48 families and 214 genera versus one new family and 87 new genera for plants. We compare the kingdoms in terms of rates of scientific discovery, globally and in different taxonomic groups and geographic areas, and with regard to the use of DNA in discovery. We review species new to science, especially those of interest to humanity as new products, and also by life‐form. We consider where future such discoveries can be expected. We recommend an urgent increase in investment in scientific discovery of plant and fungal species, while they still survive. Priorities include more investment in training taxonomists, in building and equipping collections‐based research centers for them, especially in species‐rich, income‐poor countries where the bulk of species as yet unknown to science are thought to occur

Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human

BackgroundDilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiology; however, as a complex disease, the exact genetic risk factors are largely unknown, and many patients remain without a molecular diagnosis.MethodsWe performed GWAS followed by whole-genome, transcriptome, and immunohistochemical analyses in a spontaneously occurring canine model of DCM. Canine gene discovery was followed up in three human DCM cohorts.ResultsOur results revealed two independent additive loci associated with the typical DCM phenotype comprising left ventricular systolic dysfunction and dilatation. We highlight two novel candidate genes, RNF207 and PRKAA2, known for their involvement in cardiac action potentials, energy homeostasis, and morphology. We further illustrate the distinct genetic etiologies underlying the typical DCM phenotype and ventricular premature contractions. Finally, we followed up on the canine discoveries in human DCM patients and discovered candidate variants in our two novel genes.ConclusionsCollectively, our study yields insight into the molecular pathophysiology of DCM and provides a large animal model for preclinical studies

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes : sequences, taxa and classifications reconsidered

Acknowledgements We acknowledge Marie Zirk for her work in designing the UNITE logotype and creating the visual abstract for this article. Funding UNITE database development is financed by the Estonian Research Council [PRG1170]; European Union's Horizon 2020 project BGE [101059492]. The PlutoF digital infrastructure is supported by the European Union's Horizon 2020 project BiCIKL [101007492]; Estonian Research Infrastructure roadmap project DiSSCo Estonia. Funding for open access charge: UNITE Community. Conflict of interest statement. None declared.Peer reviewedPublisher PD

Fungal diversity notes 253–366: taxonomic and phylogenetic contributions to fungal taxa

Notes on 113 fungal taxa are compiled in this paper, including 11 new genera, 89 new species, one new subspecies, three new combinations and seven reference specimens. A wide geographic and taxonomic range of fungal taxa are detailed. In the Ascomycota the new genera Angustospora (Testudinaceae), Camporesia (Xylariaceae), Clematidis, Crassiparies (Pleosporales genera incertae sedis), Farasanispora, Longiostiolum (Pleosporales genera incertae sedis), Multilocularia (Parabambusicolaceae), Neophaeocryptopus (Dothideaceae), Parameliola (Pleosporales genera incertae sedis), and Towyspora (Lentitheciaceae) are introduced. Newly introduced species are Angustospora nilensis, Aniptodera aquibella, Annulohypoxylon albidiscum, Astrocystis thailandica, Camporesia sambuci, Clematidis italica, Colletotrichum menispermi, C. quinquefoliae, Comoclathris pimpinellae, Crassiparies quadrisporus, Cytospora salicicola, Diatrype thailandica, Dothiorella rhamni, Durotheca macrostroma, Farasanispora avicenniae, Halorosellinia rhizophorae, Humicola koreana, Hypoxylon lilloi, Kirschsteiniothelia tectonae, Lindgomyces okinawaensis, Longiostiolum tectonae, Lophiostoma pseudoarmatisporum, Moelleriella phukhiaoensis, M. pongdueatensis, Mucoharknessia anthoxanthi, Multilocularia bambusae, Multiseptospora thysanolaenae, Neophaeocryptopus cytisi, Ocellularia arachchigei, O. ratnapurensis, Ochronectria thailandica, Ophiocordyceps karstii, Parameliola acaciae, P. dimocarpi, Parastagonospora cumpignensis, Pseudodidymosphaeria phlei, Polyplosphaeria thailandica, Pseudolachnella brevifusiformis, Psiloglonium macrosporum, Rhabdodiscus albodenticulatus, Rosellinia chiangmaiensis, Saccothecium rubi, Seimatosporium pseudocornii, S. pseudorosae, Sigarispora ononidis and Towyspora aestuari. New combinations are provided for Eutiarosporella dactylidis (sexual morph described and illustrated) and Pseudocamarosporium pini. Descriptions, illustrations and / or reference specimens are designated for Aposphaeria corallinolutea, Cryptovalsa ampelina, Dothiorella vidmadera, Ophiocordyceps formosana, Petrakia echinata, Phragmoporthe conformis and Pseudocamarosporium pini. The new species of Basidiomycota are Agaricus coccyginus, A. luteofibrillosus, Amanita atrobrunnea, A. digitosa, A. gleocystidiosa, A. pyriformis, A. strobilipes, Bondarzewia tibetica, Cortinarius albosericeus, C. badioflavidus, C. dentigratus, C. duboisensis, C. fragrantissimus, C. roseobasilis, C. vinaceobrunneus, C. vinaceogrisescens, C. wahkiacus, Cyanoboletus hymenoglutinosus, Fomitiporia atlantica, F. subtilissima, Ganoderma wuzhishanensis, Inonotus shoreicola, Lactifluus armeniacus, L. ramipilosus, Leccinum indoaurantiacum, Musumecia alpina, M. sardoa, Russula amethystina subp. tengii and R. wangii are introduced. Descriptions, illustrations, notes and / or reference specimens are designated for Clarkeinda trachodes, Dentocorticium ussuricum, Galzinia longibasidia, Lentinus stuppeus and Leptocorticium tenellum. The other new genera, species new combinations are Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis from Neocallimastigomycota, Phytophthora estuarina, P. rhizophorae, Salispina, S. intermedia, S. lobata and S. spinosa from Oomycota, and Absidia stercoraria, Gongronella orasabula, Mortierella calciphila, Mucor caatinguensis, M. koreanus, M. merdicola and Rhizopus koreanus in Zygomycota