The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome.

Authors

Eric R Londin, Computational Medicine Center, Thomas Jefferson University Jefferson Medical CollegeFollow
Eleftheria Hatzimichael, Computational Medicine Center, Thomas Jefferson University
Phillipe Loher, Computational Medicine Center, Thomas Jefferson UniversityFollow
Leonard Edelstein, Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Thomas Jefferson UniversityFollow
Chad Shaw, Department of Molecular and Human Genetics, Baylor College of MedicineFollow
Kathleen Delgrosso, Cancer Genomics Laboratory, Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson UniversityFollow
Paolo Fortina, Cancer Genomics Laboratory, Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University; Department of Molecular Medicine, Universita' La SapienzaFollow
Paul Bray, Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Thomas Jefferson UniversityFollow
Steven E. McKenzie, Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Thomas Jefferson UniversityFollow
Isidore Rigoutsos, Computational Medicine Center, Thomas Jefferson UniversityFollow

Document Type

Article

Publication Date

2-14-2014

Comments

This article has been peer reviewed and is published in Biology Direct.

Volume 9, Issue 1, 14 February 2014, Article number 3.

The published version is available at DOI: 10.1186/1745-6150-9-3

Copyright © 2014 Londin et al.; licensee BioMed Central Ltd.

Abstract

BACKGROUND: For the anucleate platelet it has been unclear how well platelet transcriptomes correlate among different donors or across different RNA profiling platforms, and what the transcriptomes' relationship is with the platelet proteome. We profiled the platelet transcriptome of 10 healthy young males (5 white and 5 black) with no notable clinical history using RNA sequencing and by Affymetrix microarray.

RESULTS: We found that the abundance of platelet mRNA transcripts was highly correlated across the 10 individuals, independently of race and of the employed technology. Our RNA-seq data showed that these high inter-individual correlations extend beyond mRNAs to several categories of non-coding RNAs. Pseudogenes represented a notable exception by exhibiting a difference in expression by race. Comparison of our mRNA signatures to a publicly available quantitative platelet proteome showed that most (87.5%) identified platelet proteins had a detectable corresponding mRNA. However, a high number of mRNAs that were present in the transcriptomes of all 10 individuals had no representation in the proteome. Spearman correlations of the relative abundances for those genes represented by both an mRNA and a protein showed a weak (~0.3) connection. Further analysis of the overlapping and non-overlapping platelet mRNAs and proteins identified gene groups corresponding to distinct cellular processes.

CONCLUSIONS: The results of our analyses provide novel insights for platelet biology, show only a weak connection between the platelet transcriptome and proteome, and indicate that it is feasible to assemble a platelet mRNA-ome that can serve as a reference for future platelet transcriptomic studies of human health and disease.

REVIEWED BY: This article was reviewed by Dr Mikhail Dozmorov (nominated by Dr Yuri Gusev), Dr Neil Smalheiser and Dr Eugene Koonin.

Recommended Citation

Londin, Eric R; Hatzimichael, Eleftheria; Loher, Phillipe; Edelstein, Leonard; Shaw, Chad; Delgrosso, Kathleen; Fortina, Paolo; Bray, Paul; McKenzie, Steven E.; and Rigoutsos, Isidore, "The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome." (2014). Computational Medicine Center Faculty Papers. Paper 3.
https://jdc.jefferson.edu/tjucompmedctrfp/3

PubMed ID

24524654