PIK3R3 is a candidate regulator of platelet count in people of Bangladeshi ancestry

Abstract

Background: Blood platelets are mediators of atherothrombotic disease and are regulated by complex sets of genes. Association studies in European ancestry populations have already detected informative platelet regulatory loci. Studies in other ancestries can potentially reveal new associations because of different allele frequencies, linkage structures, and variant effects.

Objectives: To reveal new regulatory genes for platelet count (PLT).

Methods: Genome-wide association studies (GWAS) were performed in 20,218 Bangladeshi and 9198 Pakistani individuals from the Genes & Health study. Loci significantly associated with PLT underwent fine-mapping to identify candidate genes.

Results: Of 1588 significantly associated variants (P < 5 × 10^-8) at 20 loci in the Bangladeshi analysis, most replicated findings in prior transancestry GWAS and in the Pakistani analysis. However, the Bangladeshi locus defined by rs946528 (chr1:46019890) did not associate with PLT in the Pakistani analysis but was in the same linkage disequilibrium block (r² ≥ 0.5) as PLT-associated variants in prior East Asian GWAS. The single independent association signal was refined to a 95% credible set of 343 variants spanning 8 coding genes. Functional annotation, mapping to megakaryocyte regulatory regions, and colocalization with blood expression quantitative trait loci identified the likely mediator of the PLT phenotype to be PIK3R3 encoding a regulator of phosphoinositol 3-kinase (PI3K).

Conclusion: Abnormal PI3K activity in the vessel wall is already implicated in the pathogenesis of atherothrombosis. Our identification of a new association between PIK3R3 and PLT provides further mechanistic insights into the contribution of the PI3K pathway to platelet biology.

Keywords: Bangladesh; blood platelets; cardiovascular diseases; genome-wide association study; phosphatidylinositol 3-kinases.

Figure 1

Genomic associations with platelet count in the Bangladeshi population (n = 20,292). (A) Manhattan plot showing 20 loci in which the index variant has a probability of association above the genome-wide significance threshold of P < 5 × 10⁻⁸ (red line). Selected loci are annotated with gene names identified using variant effect predictor most severe consequence option. The inset figure is the quantile-quantile plot of genome-wide association study P values. (B) Minor allele frequency (MAF), effect size (beta), and phenotypic variation explained (PVE) for each of the 1588 platelet count–associated variants identified in the Bangladeshi population compared to the same variants in the Pakistani population. For the Bangladeshi locus on chromosome 1, variants in the association interval (r² > 0.5) of the index variant rs964528 are indicated by the red dots.

Figure 2

Detailed view of the Bangladeshi rs946528 association interval. LocusZoom plot of associations in the 562 kB association interval for the chromosome 1 index variant rs946528, defined as variants within r² ≥ 0.5 calculated using linkage disequilibrium (LD) reference data from the Bengali from Bangladesh 1000 Genomes dataset. Variants with P > .05 are excluded to enable visualization of the recombination peaks. Indicated variants are the index rs946528 and the 3 variants associated with platelet count in prior East Asian ancestry–specific genome-wide association studies. Beneath and aligned with this are the 8 UCSC Genome Browser–annotated genes within the interval; positions of the 95% credible set of 343 variants and annotated regions of epigenetic activity from CD34⁻, CD41⁺, and CD42⁺ megakaryocytes, the progenitor cell for circulating platelets, which were provided by the BLUEPRINT Epigenomics Project [25]. Megakaryocyte chromatin immunoprecipitation sequencing (ChIP-seq) data are also shown indicating relevant transcription factor binding sites [16]. The expanded view shows the relationship between the significantly associated variant rs1707303 and a putative regulatory region surrounding the first exon of the candidate gene PIK3R3.

Figure 3

Interaction network for PIK3R3. The nodes represent PIK3R3 and interacting genes designated within Platelet Web [25] as present in the platelet proteome (blue) and in both the proteome and transcriptome (yellow). The edges indicate physical interactions between the encoded proteins. Only STRING database v11.5 first order interactions with confidence scores of >0.7 are shown [19].