Functional Characterization of Lipid Regulatory Effects of Three Genes Using Knockout Mouse Models

Integrative analysis that combines genome-wide association data with expression quantitative trait analysis and network representation may illuminate causal relationships between genes and diseases. To identify causal lipid genes, we utilized genotype, gene expression, protein-protein interaction networks, and phenotype data from 5,257 Framingham Heart Study participants and performed Mendelian randomization to investigate possible mechanistic explanations for observed associations. We selected three putatively causal candidate genes ( ABCA6, ALDH2 , and SIDT2 ) for lipid traits (LDL cholesterol, HDL cholesterol and triglycerides) in humans and conducted mouse knockout studies for each gene to confirm its causal effect on the corresponding lipid trait. We conducted the RNA-seq from mouse livers to explore transcriptome-wide alterations after knocking out the target genes. Our work builds upon a lipid-related gene network and expands upon it by including protein-protein interactions. These resources, along with the innovative combination of emerging analytical techniques, provide a groundwork upon which future studies can be designed to more fully understand genetic contributions to cardiovascular diseases. ### Competing Interest Statement The authors have declared no competing interest. ### Clinical Trial No clinical trial in this study. ### Funding Statement This project was supported by an American Heart Association Cardiovascular Genome Phenome Study (CVGPS) Grant 15CVGPS23430000. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Protocol ID: H-27984, Boston University Medical Center IRB (BUMC IRB) Title: FRAMINGHAM HEART STUDY BIOMARKER PROJECT All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The genotype data, gene expression, phenotype data that support the findings from the FHS of this 403 study have been deposited in dbGaP (dbGaP Study Accession: phs000363.v16.p10).