Research concerning genetics of hypertension Flashcards
What is Hypertension?
– SBP ≥ 140mmHg and DBP ≥
90mmHg
- 1 billion hypertensives worldwide
Causes 4.5% of global disease burden - Risk factor for CVD
What are types of hypertension?
- Primary hypertension (90%):
- 30 - 50% - genes
– Twins and family studies
- 50 -70% lifestyle factors: Dietary salt intake, alcohol consumption, weight, inactivity etc - Secondary hypertension (~10%)
Causes include - primary aldosteronism (Conns syndrome), phaeochromacytoma, thyroid disease, side effects of medications - Rare monogenic syndromes (~1%)
What do monogenic forms of hypertension include?
- Glucocorticoid Remediable Aldosteronism
- Apparent Mineralocorticoid Excess
- Gordon’s syndrome
- Liddle’s syndrome
- Hypertension with bracydactyly
If know mode of inheritance allows linkage studies to be considered
Now WES and WGS can be used
These monogenic forms are typically syndromic thus have number of different symptoms
Individuals with these monogenic disorders experience much higher blood pressure
Genes that give rise to monogenic forms of hypertension primarily affect salt and water handling in kidney
What did the first GWAS for Hypertension conclude?
No genes with large odds ratio found to be related to hypertension, thus must be an accumulation of small genetic changes as we know HT is genetic.
Field thus moved to conducting a GWAS of diastolic and systolic blood pressure, as this would mean more patients with HT
What did the first breakthrough by the International Consortium forBlood Pressure(ICBP)conclude?
8/29 SNPs are in high LD (r2 > 0.8) with a non-synonymous coding SNP.
Some evidence that the 29 SNPs are enriched for eSNPs.
Effect sizes are small (~1/0.5 mmHg for SBP/DBP)
The phenotypic variance
explained by the 29 variants is
~1%.
Genes with prior knowledge from cellular and animal work to show that these are proteins and pathways which do affect blood pressure, Genes whereby working hypothesis can be devised that gene is involved in bp control but not yet studied
and potential candidate genes in bp control that are completely novel found.
What was the design of the 2018 – the 1M GWAS (Evangelou et al, Nature Genetics 2018)?
UK Biobank + ICBP GWAS Discovery meta-analysis
Two stage design and a one stage design used
Two stage design- All genetic variants at blood pressure loci that were known excluded.
Next one genetic variation in each base pair region taken forward into replication, in new samples
Stage 1 design- Consider any novel sentinel lookup SNPs which do not replicate from the 2- stage analysis
- What did the 2018 – the 1M GWAS find?
2. What was used to measure heritability and explain variance?
- 535 novel Loci
Overlap between SBP and DBP genes
66 of the 535 novel loci 97 non-synonymous SNPs were identified, including 8 predicted to be damaging- Mostly common variants (as per study design)
Support for all 274 previously published loci (P < 0.01) - at least 95% of the exact SNPs covered in the GWAS reaching genome-wide significance
Total 901 BP loci tripling the number of previously known loci
- SNP-wide heritability
Once a GWAS is performed, what was the next step (Evangelou et al, Nature Genetics 2018)?
Integrative bioinformatics
Expand number of snps that may be casual
Functional enrichment: list of genetic variants associated, compare to list of variants not associated to bp and may identify properties of bp variants that give clues to key mechanisms and pathways.
How did Evangelou et al. analyse gene Expression & Enrichment?
- Lookups of all novel sentinel SNPs & proxies (r2 ≥ 0.8) for eQTLs (expression quantitative trait loci) across 44 tissues using the Genotype- Tissue Expression (GTEx) database
- 60 novel loci with co-localised eQTLs in arterial tissue
- 20 in adrenal tissue
Thus now building information of the properties of these variants
- DEPICT analysis of expression across 50 tissues and cells:
- strongest enrichment in vasculature (supporting prior work)
- increased enrichment in adrenal tissue
- new enrichment in adipose tissues
What is Hi-C analysis used for?
Snps can be noncoding in promotor and enhancer region, thus if have highly significant genetic variant, potentially gene that is closest to where that genetic variation, might not be gene that the promotor is working on
Hi-c data can be used to ask if there is experimental data that the promotor or enhancer region where your snp is located might acutally have physical interaction with another gene which might be up or downstream and thus that might indicate candidate gene
To identify long-range target genes of non-coding SNPs
Using chromatin interaction Hi-C data from: HUVECs; neural progenitor cells; mesenchymal stem cells; aorta tissue; adrenal gland tissue
What did Evangelou et al. 2018 find when using HI-C analysis?
498 novel loci that contained a potential regulatory SNP
- in 484 of these we identified long-range interactions in at least one of the tissues or cell types
- We found several potential long-range target genes that do not overlap with the sentinel SNPs in the LD block
e. g. for genes in the TGFβ pathway
Pathway Analysis & Druggability when used in Evangelou et al. 2018 found what?
Ingenuity pathway analysis (IPA) for genes within BP loci-
IPA showed enrichment of pathways implicated in CVD
Including pathways targeted by antihypertensive drugs
Upstream analysis identified several known therapeutic targets
SLC5A1: potential repurposing (targeted by T2D drug canagliflozin)
Druggability analysis: overlap between genes associated with BP and those associated with antihypertensive drug targets
→ new genetic support for known drug mechanisms
What therapeutic targets were identified by Evangelou et al. 2018?
Identified new GWAS signals at loci which are targeted by established anti-hypertensive drugs:
PKD2L1: potassium-sparing diuretics (amiloride)
SLC12A2: loop diuretics (bumetanide and furosemide)
CACNA1C: calcium channel blockers (dihydropyridine)
CACNB4: non-dihydropyridines
CA7: thiazide-like diuretics (chlortalidone)
What lab work comprises follow up of GWAS loci?
Identify candidate genes:
‘In vitro’ assays to determine effect of BP associated SNP in CV tissues
Luciferase assays, mini-gene splicing assays, Overexpression/siRNA etc
Develop models of disease:
International mouse phenotyping consortium and Jackson Laboratories, Zebrafish
How can rare variants be discovered in BP?
Exome chip - designed to facilitate analyses of rare coding variants with potential functional consequences.
Can identify:
Rare (MAF<=1%)
Low frequency (1%5%)
