Longitudinal RNA-Seq Analysis of the Repeatability of Gene Expression and Splicing in Human Platelets Identifies a Platelet SELP Splice QTL

Abstract

Rationale: Longitudinal studies are required to distinguish within versus between-individual variation and repeatability of gene expression. They are uniquely positioned to decipher genetic signal from environmental noise, with potential application to gene variant and expression studies. However, longitudinal analyses of gene expression in healthy individuals—especially with regards to alternative splicing—are lacking for most primary cell types, including platelets. Objective: To assess repeatability of gene expression and splicing in platelets and use repeatability to identify novel platelet expression quantitative trait loci (QTLs) and splice QTLs. Methods and Results: We sequenced the transcriptome of platelets isolated repeatedly up to 4 years from healthy individuals. We examined within and between individual variation and repeatability of platelet RNA expression and exon skipping, a readily measured alternative splicing event. We find that platelet gene expression is generally stable between and within-individuals over time—with the exception of a subset of genes enriched for the inflammation gene ontology. We show an enrichment among repeatable genes for associations with heritable traits, including known and novel platelet expression QTLs. Several exon skipping events were also highly repeatable, suggesting heritable patterns of splicing in platelets. One of the most repeatable was exon 14 skipping of SELP . Accordingly, we identify rs6128 as a platelet splice QTL and define an rs6128-dependent association between SELP exon 14 skipping and race. In vitro experiments demonstrate that this single nucleotide variant directly affects exon 14 skipping and changes the ratio of transmembrane versus soluble P-selectin protein production. Conclusions: We conclude that the platelet transcriptome is generally stable over 4 years. We demonstrate the use of repeatability of gene expression and splicing to identify novel platelet expression QTLs and splice QTLs. rs6128 is a platelet splice QTL that alters SELP exon 14 skipping and soluble versus transmembrane P-selectin protein production.

Platelet gene expression and function in patients with COVID-19

“…Leukocyte-depleted platelets were isolated as previously described from whole blood drawn from SARS-CoV-2–infected patients and healthy donors. 12 , 21 - 24 …”

“…RNA-seq and analysis were performed on total RNA extracted from platelets isolated from SARS-CoV-2–infected patients and age- and sex-matched healthy donors, as before. 12 , 21 - 24 RNA-seq files were deposited in NCBI short-read archives under PRJNA634489.…”

Aspirin effects on platelet gene expression are associated with a paradoxical, increase in platelet function.

“…We have previously shown that platelet gene expression levels are highly correlated within an individual between Visits 1 and Visit 4. [23] Therefore in all subsequent analyses, these two visits were treated equivalently as no-drug treatment visits and no adjustment for leukocyte contamination was performed.…”

Circulating platelets as liquid biopsy sources for cancer detection

“…While the platelet transcriptome is dynamically altered in disease states (Best et al, 2018;Wurdinger et al, 2020), in the absence of disease platelet gene expression remains remarkably stable (Rondina et al, 2020). One of the challenges in using TEPs as liquid biopsy for cancer diagnostics is to understand which transcriptomic profiles are specifically associated with, for example, inflammation, other non-cancerous processes, and therapeutics (anti-coagulants and other pharmacological treatments).…”