Revealing single cell transcriptomes in red blood cells
Erja Kerkelä1, Jenni Lahtela2, Antti Larjo1, and Pirkko Mattila1,2,*
1Finnish Red Cross Blood Service, 2Institute of Molecular Medicine Finland (FIMM)
Human red blood cells (RBCs) consist of mature RBCs, erythrocytes, as well as immature RBCs, reticulocytes (~ 1.0 % of all RBCs). As being anucleated cells, RBCs have been considered to totally lack nucleic acids. This hypothesis has been lately re-evaluated by us and others. Currently, RBCs are known to contain low amounts of long transcripts as well as microRNAs (ref). Isolation of pure reticulocyte fraction for bulk RNAseq analysis is difficult due to gradual or constant expression of relevant cell surface markers (CD71, CD235a). We performed a single cell analysis on RBCs to reveal their transcriptional profiles and comparative RNA contents at single cell resolution. Two thousand cells from leukocyte free red cell product (FRCBS) and Ficoll –purified fresh RBCs were analyzed using the Chromium Single Cell 3’RNAseq-platform (10x Genomics). The libraries were sequenced until saturation. Cell Ranger Count –software v.1.3 (10x Genomics) was used to analyse single cell data. When the transcriptomes in 2 000 cells of red cell product and fresh RBCs were analyzed, 234 and 108 cells contained transcripts, respectively. The amount of cells containing transcriptome matched well to the expected amount of reticulocytes in RBC population. The transcriptomes of single cells in the red cell product and in the freshly isolated RBC sample were very similar, median of expressed genes per cell being 10 and 17, respectively, and the amount of total genes detected was >600 in both samples. The transcriptomes of single cells matched well to our previous unpublished data from the bulk transcriptomes of red cell products. Single cell transcriptomics enables us to reveal the role of RNA in RBCs. Possible role of transcripts in RBC maturation and communication will be discussed.
Reference: Doss et al. A comprehensive joint analysis of the long and short RNA transcriptomes of human erythrocytes. BMC Genomics 2015, 16:952 DOI: 10.1186/s12864-015-2156-2