Transcriptomic landscape of blood platelets in healthy donors

Abstract

Blood platelet RNA-sequencing is increasingly used among the scientific community. Aberrant platelet transcriptome is common in cancer or cardiovascular disease, but reference data on platelet RNA content in healthy individuals are scarce and merit complex investigation. We sought to explore the dynamics of platelet transcriptome. Datasets from 204 healthy donors were used for the analysis of splice variants, particularly with regard to age, sex, blood storage time, unit of collection or library size. Genes B2M, PPBP, TMSB4X, ACTB, FTL, CLU, PF4, F13A1, GNAS, SPARC, PTMA, TAGLN2, OAZ1 and OST4 demonstrated the highest expression in the analysed cohort, remaining substantial transcription consistency. CSF3R gene was found upregulated in males (fold change 2.10, FDR q < 0.05). Cohort dichotomisation according to the median age, showed upregulated KSR1 in the older donors (fold change 2.11, FDR q < 0.05). Unsupervised hierarchical clustering revealed two clusters which were irrespective of age, sex, storage time, collecting unit or library size. However, when donors are analysed globally (as vectors), sex, storage time, library size, the unit of blood collection as well as age impose a certain degree of between- and/or within-group variability. Healthy donor platelet transcriptome retains general consistency, with very few splice variants deviating from the landscape. Although multidimensional analysis reveals statistically significant variability between and within the analysed groups, biologically, these changes are minor and irrelevant while considering disease classification. Our work provides a reference for studies working both on healthy platelets and pathological conditions affecting platelet transcriptome.

Figure 1

Age and sex distribution of healthy donors.

Figure 2

Functional annotation analysis of top expressed spliced genes among the analysed sex and age groups. For each group, 1000 spliced genes with the highest expression level were subjected to over-representation analysis and top20 Reactome pathways were identified based on − log10(q-value).

Figure 3

Plot representing the relation between log2 median spliced platelet RNA profile of donors younger (X axis) and older than 42 years (Y axis).

Figure 4

Top 1000 splice variants notably overlap between the studied five age groups.

Figure 5

Heatmap depicts the expression of 224 spliced genes with the greatest, at least fourfold mean changes between the two clusters revealed by unsupervised hierarchical clustering. Colour legend indicates the sex, age group, blood collection unit, storage time and library size of each sample. The clusters presented substantial similarity in terms of the expression of spliced junction reads. 62% of spliced platelet RNAs demonstrated less than a twofold expression difference. Only 16% of spliced genes in the dataset (649/3954) demonstrated at least a threefold expression difference, while at least fourfold difference was observed in only 6% of the spliced reads (224/3954). Due to prior clustering, all these observations were statistically significant (FDR corrected q value < 0.05).