Mapping genetic susceptibility to hypertrophic cardiomyopathy in cats and assessing their utility as a disease study model
Lead Research Organisation:
Royal Veterinary College
Department Name: Clinical Sciences and Services
Abstract
Sarcomeric genes (e.g. MYBPC3) are commonly associated with hypertrophic cardiomyopathy (HCM) in humans and Maine coon and Ragdoll cats, but no such variants are identified in 40-60% of people with HCM. Clinical and histopathological similarities between the two species render cats a useful study model. Genome-wide genotyping technologies offer the opportunity for novel studies that could provide new insights in the genetic architecture of the disease in cats, potentially leading to previously unidentified causes in humans. Alternatively, if feline and human HCM mutations are similar, this would further support the notion of using cats as a model for the human disease.
In the proposed study we will conduct genome-wide association (GWA) analyses to detect loci affecting HCM susceptibility using 150 meticulously phenotyped domestic cats (HCM cases and breed-matched controls) from Birman, Norwegian Forest, British shorthair, Bengal and Ragdoll cats. Different GWA models will be investigated to assess the genetic architecture of HCM susceptibility within and across breeds. Analysis according to disease severity will help identify putative genetic modifiers. Using available pedigree and genomic relationships in a mixed model analysis we will estimate the heritability and the genetic effects associated with the identified significant SNP markers. In order to identify causative genes and mutations underlying HCM, whole-genome sequencing (WGS 30X coverage) will be performed in an affected family (heterozygous parents, and homozygous affected and non-affected offspring) and compared with published data in humans. Human WGS data from HCM patients and controls will be analysed focusing on human orthologue genes identified as good candidates in the cat analysis.
Blood and DNA samples are already available for this project. Phenotyping will be based on echocardiography and histopathology records at QMHA. Genotyping will be performed using a genome-wide 70K DNA array. The high-performance computer cluster at RVC will be utilised for all computational analyses.
In the proposed study we will conduct genome-wide association (GWA) analyses to detect loci affecting HCM susceptibility using 150 meticulously phenotyped domestic cats (HCM cases and breed-matched controls) from Birman, Norwegian Forest, British shorthair, Bengal and Ragdoll cats. Different GWA models will be investigated to assess the genetic architecture of HCM susceptibility within and across breeds. Analysis according to disease severity will help identify putative genetic modifiers. Using available pedigree and genomic relationships in a mixed model analysis we will estimate the heritability and the genetic effects associated with the identified significant SNP markers. In order to identify causative genes and mutations underlying HCM, whole-genome sequencing (WGS 30X coverage) will be performed in an affected family (heterozygous parents, and homozygous affected and non-affected offspring) and compared with published data in humans. Human WGS data from HCM patients and controls will be analysed focusing on human orthologue genes identified as good candidates in the cat analysis.
Blood and DNA samples are already available for this project. Phenotyping will be based on echocardiography and histopathology records at QMHA. Genotyping will be performed using a genome-wide 70K DNA array. The high-performance computer cluster at RVC will be utilised for all computational analyses.
Publications
Raffle J
(2021)
156 Identification of novel variants associated with feline hypertrophic cardiomyopathy (HCM) using targeted next-generation sequencing
in Animal - science proceedings
Raffle J
(2021)
172 A genome wide association study of hypertrophic cardiomyopathy in cats
in Animal - science proceedings
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M009513/1 | 01/10/2015 | 31/03/2024 | |||
| 1903448 | Studentship | BB/M009513/1 | 01/10/2017 | 30/06/2022 | Jade Raffle |
| Description | - HCM is the main cause of cardiac death in cats. The disease is very prevalent (1 in 7 cats) and has a genetic background. Nevertheless, so far only a handful of causative mutations have been identified for specific cat breeds. The work funded through this award aims to discover novel causative mutations and SNP markers associated with feline HCM using targeting next generation sequencing and genome-wide association studies. So far we have performed a number of experiments - some of them completed and some on going. Specifically: - Discovery of genetic variants associated with HCM predisposition in Birman cats using NGS (manuscript in progress). - Discovery of genetic variants associated with HCM predisposition across cat breeds using NGS (manuscript in progress). - Discovery of genetic variants associated with HCM predisposition across cat breeds through a genome-wide association study of 200 cats (work in progress). - Pilot study modelling risk factors of HCM in cats, across pedigree and non-pedigree breeds (this aspect of the study is ongoing as the database builds) - Development and implementation of an owner-based questionnaire collecting data on cat environment, lifestyle and personality, to be analysed for the discovery of non-genetic factors affecting HCM susceptibility (currently collecting questionnaires, awaiting analysis). - Improved research methods through the optimisation of DNA extractions from cat residual blood samples. - Discovery of genetic variants associated with HCM predisposition in DSH cats through a Whole Genome Sequencing Study of 12 cats (work in progress). |
| Exploitation Route | Our overall findings will be discussed with our UCL collaborators to compare with data from human HCM studies. Outcomes of these genetic studies, after validation, could lead to novel HCM therapeutics both gene therapies as well as novel drug target discovery, which are of interest for the pharmaceutical and healthcare technology industries. A greater understanding of the feline HCM genetics will facilitate development of targeted DNA tests, which could be useful tools for selective breeding programmes. Moreover, these tests could help identify genetically susceptible individuals prior to the onset of clinical signs, and suggest preventive management measures. Future work based on findings from this study could lead to novel treatment interventions for both cats and humans. The project will have social and economic impacts on both veterinarian and human medicine since cats could be used as a good study model for the human disease. In addition to the genetic studies of the project, non-genetic risk factors of HCM will be analysed through a cat owner-based questionnaire. Outcomes from this aspect of the study could lead to improvements in animal welfare and aid in the prevention of HCM developing in cats, but also could provide insights on potential environmental, lifestyle and behavioural factors that affect human HCM. |
| Sectors | Agriculture, Food and Drink,Education,Healthcare,Pharmaceuticals and Medical Biotechnology |
| Description | As a STEM ambassador I have drawn on my research background to educate and inspire children into the science field, including presenting my research poster as an example of the project at school open days. Moreover, several cat foundations and breeder associations have become aware of our research. Recently (on the 25/02/2021) we provided an invited webinar on feline HCM sponsored by the EveryCat Health Foundation to increase the cat breeders, vet practitioners and pet owners awareness regarding the disease phenotype and HCM genetics background. We have had numerous pet owners/vets and breeders reaching out to inquire how they can participate in this study as an outcome from this webinar. |
| First Year Of Impact | 2019 |
| Sector | Education,Healthcare |
| Impact Types | Societal |
| Description | "Genetic control of hypertrophic cardiomyopathy (HCM) in cats: genomic and transcriptomic characterisation"; funder Petplan Charitable Trust ; Principal Investigator A. Psifidi; Co-investigators V. Luis-Fuentes, D. Connolly, P. Syrris, G. Banos, |
| Amount | £147,389 (GBP) |
| Organisation | Royal Veterinary College (RVC) |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 10/2021 |
| End | 09/2024 |
| Description | Dissecting the genetic architecture of hypertrophy cardiomyopathy in cats |
| Amount | £10,000 (GBP) |
| Organisation | Petplan Charitable Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 12/2018 |
| End | 12/2019 |
| Title | Database of HCM affected and healthy control cats for the genomic analysis of HCM across cat breeds |
| Description | Initially I merged data from four feline databases comprising clinical and echocardiogram measurement data for pedigree and non-pedigree cats during both internal (RVC) and external (outreach e.g. CatScan and breeders) examinations, to create a master database comprising of >1000 cats. This database was used for the pilot epidemiological study to model non-genetic risk factors of feline HCM. I formulated this databased in 2018 however this is being continually updated to include clinical data of cats visiting the Cardiology Clinic at the Royal Veterinary College (RVC) (available through various clinical softwares at the Queen Mother Animal Hospital at the RVC), including echocardiogram reports. Based on the information in this database I have identified the best samples (residual blood where available) to send for genotyping to investigate the genetic architecture of feline HCM. This will continue for recruitment of samples for the Whole Genome Sequencing aspect of the project later on. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | The creation of this database is ongoing as it expands with cases that are seen within the QMHA clinic. Notable impacts: - Pilot study was completed modelling epidemiological risk factors of HCM in cats (2018) - Identification and recruitment of cat samples into the GWAS aspect of the project in order to perform genomic analysis investigating HCM in cats (ongoing) |
| Title | Genome wide association study of HCM in cats across breeds |
| Description | Initially cats were chosen for the GWAS project as HCM cases or Controls (normal heart) through extensive phenotyping using echocardiography and medical records. Blood was collected, DNA was extracted from the blood samples within the laboratory at the RVC. DNA extracts were assessed for quality and quantity before being genotyped using the feline 60k SNP illumine Infinium iSelect DNA array. A genome wide association analysis was performed for 198 cats across three cat breeds; Bengal, NFC, Sphynx and domestic short hair cats using the GEMMA algorithm with a standard univariate linear mixed model in which breed, age and sex were fitted as fixed effects and the genomic relatedness matrix among individuals fitted as a polygenic random effect. The GWAS revealed the presence of numerous markers associated with HCM at the suggestive significance level. Regional Heritability Mapping (RHM) was performed to look for markers of interest not detected by the GWAS. Finally a pathway and network analysis was performed to identify underlying pathways and highlight good candidate genes for feline HCM. detected in the GWAS, RHM and Fst analyses - this is ongoing. |
| Type Of Material | Data analysis technique |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | This data analysis will be published and has already been presented at an international conference. |
| Title | Identification of novel genetic variants associated with feline hypertrophic cardiomyopathy (HCM) using targeted next-generation sequencing |
| Description | Two targeted sequencing experiments were performed in two cohorts of cats to identify variants associated with feline HCM using a gene panel of 18 genes associated with human HCM. One cohort comprised of 31 Birman cats and included additional cardiomyopathies (RCM, DCM, ARVC) in the analysis alongside HCM. The second cohort was comprised of a HCM case control study of 44 cats across several pedigree breeds and DSH. Phenotyping of cats was performed using echocardiography and collection of medical records at the RVC. GATK was used for variant discovery. Chi squared analyses were initially run to investigate allelic and genotypic frequencies of variants between cases and controls. A genomic association analysis was next run to identify further variants associated with HCM using as covariates breed, age and sex as fixed effects. Multiple variants of interest were detected through our analysis suggesting feline HCM is a complex polygenic disease. |
| Type Of Material | Data analysis technique |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | This data will be published in the future. Preliminary results have already been presented at an international conference. |
| Title | Identifying environmental and lifestyle risk factors associated with the development of hypertrophic cardiomyopathy in cats database - from owner based questionnaire |
| Description | Collection of environment, lifestyle and personality data of cats is being implemented within the Queen Mother Animal Hospital through the use of an owner based questionnaire developed for the project. Data collection from these questionnaire responses are inputted into a database which will be used to assess the impact of non-genetic risk factors associated with HCM susceptibility. The development of this questionnaire database is ongoing as collection of questionnaire forms is continuing as the project is still active. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | The collection of data for this database is still active. Once enough responses are collected, analysis will be performed with the aim to publish findings. Aim: - Identify non-genetic risk factors of HCM susceptibility impacting feline HCM disease progression to better understand the underlying genetic architecture of feline HCM. Potential Outcomes: - Scientific publications - Preventative management of feline HCM |
| Title | Whole Genome Sequencing (WGS) data creation and analysis in cats with HCM and healthy controls. |
| Description | Initially cats were chosen for the WGS project as HCM cases or Controls (normal heart) through extensive phenotyping using echocardiography and medical records. Blood or myocardial tissue was collected, DNA was extracted from the blood samples/myocardial tissue within the laboratory at the RVC. DNA extracts were assessed for quality and quantity before WGS being performed. A total of 12 domestic shorthair (DSH) cats were chosen for this cohort comprised of 6 HCM cases and 6 controls. WGS data was then inputted through the bioinformatic pipeline in order to identify variants associated with disease. This analysis is ongoing. |
| Type Of Material | Data analysis technique |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | This dataset will be published in the future. |
| Description | University College London |
| Organisation | University of London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The aim of the collaboration between the Royal Veterinary College and University College London is to assess whether cats can be used as a good study model for the human equivalent disease. Our contribution includes phenotyping and genotyping of a large number of cats (both HCM cases and controls) in order to perform genomic analysis to identify genomic regions associated with HCM in cats. Then in collaboration with our UCL colleagues we will assess how useful are these findings. |
| Collaborator Contribution | We have collaborated with our UCL colleagues to produce target gene panels associated with HCM based on human studies which have been implemented in the targeted next generation sequencing experiments we have performed in cats. |
| Impact | - Use of the UCL targeted gene panel has led to the discovery of genetic variants associated with HCM in Birman cats. - Use of the UCL targeted gene panel has led to the discovery of genetic variants associated with HCM across cat breeds. |
| Start Year | 2017 |
| Description | An invited webinar at the EveryCAT Health Foundation (previous Winn foundation) entitled : "Veterinary Cardiologists, Geneticists & Pedigree Cat Enthusiasts Converge Resources to Progress Understanding of HCM Genetics" |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | over 200 people, cat breeders, cat owners, vet, students attended this webinar . An initial presentation was followed by a very long Q&A session. Lots of questions and enthusiasm related to the seminar and our work aiming to develop genetic tools to control HCM. |
| Year(s) Of Engagement Activity | 2021 |
| URL | http://everycat.org/webinar |
| Description | Invited seminar at The Roslin Institute, University of Edinburgh entitled: : "Integrating genetics and omics data to dissect host resistance to disease". |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented in this scientific seminar the different research projects I am currently involved in with an emphasis on the work we are doing in the "One Health Poultry Hub" and the "Aetiopathogenesis and genomic architecture of resistance to claw horn disruption lesions in dairy cattle" project. This was a well attended seminar, with lots of questions and discussion afterwards. Interest expressed for future collaborative work. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Postgraduate Research Day |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Oral presentation of a project overall (aims, methods, outcomes, impact) at the Royal Veterinary College postgraduate research day. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Postgraduate Research Day |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Presentation of a graphical abstract and an impact statement for the project at the Royal Veterinary College postgraduate research day. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Press Release detailing the project on the Royal Veterinary College website |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | This was a press release put through the RVC website detailing the project and who is involved alongside the project aims and potential impact. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.rvc.ac.uk/research/news/general/dissecting-the-genetic-architecture-of-hypertrophic-card... |
| Description | STEM Day - School Visit Careers Day (London) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | School Careers Fair - Helping students make informed decision around GCSE Options - Workshops to inspire students around STEM. The workshop involved engaging with students in Year 9 at a school in North London where they gained information on my education, career path and current research. For this workshop I took a number of props from the Royal Veterinary College alongside my conference research poster for my PhD project to inspire attendees with the aim to engage them in STEM. |
| Year(s) Of Engagement Activity | 2019 |
| Description | University College London Poster Competition |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Presentation of the project poster at the University College London poster competition day. Title of poster: Identification of clinical and genetic factors associated with hypertrophic cardiomyopathy in cats. |
| Year(s) Of Engagement Activity | 2019 |