Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Dębinki 1, 80-211, Gdańsk, Poland.
Department of Algorithms and Systems Modelling, Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Gdańsk, Poland.
Sci Rep. 2021 Aug 3;11(1):15679. doi: 10.1038/s41598-021-94003-z.
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.
血小板 RNA 测序在科学界中的应用越来越广泛。异常的血小板转录组在癌症或心血管疾病中很常见，但健康个体血小板 RNA 含量的参考数据稀缺，值得进行复杂的研究。我们试图探索血小板转录组的动态变化。对 204 名健康供体的数据集进行了剪接变体分析，特别是考虑了年龄、性别、血液储存时间、采集单位或文库大小。在分析的队列中，B2M、PPBP、TMSB4X、ACTB、FTL、CLU、PF4、F13A1、GNAS、SPARC、PTMA、TAGLN2、OAZ1 和 OST4 等基因的表达最高，转录一致性较强。CSF3R 基因在男性中表达上调（倍数变化 2.10，FDR q < 0.05）。根据中位年龄对队列进行二分法分析，发现较年长的供体中 KSR1 上调（倍数变化 2.11，FDR q < 0.05）。无监督层次聚类显示，两个聚类与年龄、性别、储存时间、采集单位或文库大小无关。然而，当以供体为整体（作为向量）进行分析时，性别、储存时间、文库大小、采血单位以及年龄会导致组间和/或组内存在一定程度的变异性。健康供体血小板转录组保持一般一致性，只有极少数剪接变体偏离了整体情况。尽管多维分析显示分析组之间和组内存在统计学上显著的变异性，但从生物学角度来看，这些变化在考虑疾病分类时是微小的且无关紧要的。我们的工作为研究健康血小板和影响血小板转录组的病理状况的研究提供了参考。
