Characterization of all small RNAs in and comparisons across cultured megakaryocytes and platelets of healthy individuals and COVID-19 patients

Background: The small non-coding RNAs (sncRNAs) in megakaryocytes (MKs) and platelets are not well characterized. Neither is the impact of SARS-CoV-2 infection on the sncRNAs of platelets. Methods: We profiled sncRNAs from MKs cultured from cord blood-derived CD34+ cells; platelets from healthy donors; and platelets from patients with moderate and severe SARS-CoV-2 infection. We also profiled AGO-bound sncRNAs from the cultured MKs. Results: We exhaustively characterized the sncRNAs in MKs and platelets and can account for ~95% of all sequenced reads. We found that MKs primarily comprise microRNA isoforms (isomiRs), tRNA-derived fragments (tRFs), rRNA-derived fragments (rRFs), and Y RNA-derived fragments (yRFs) in comparable abundances. The platelets of healthy donors showed a skewed distribution by comparison: 56.7% of all sncRNAs are yRFs, 34.4% are isomiRs, and less than 2.0% are tRFs and rRFs. Most isomiRs in MKs and platelets are either non-canonical, non-templated, or both. When comparing MKs and platelets from healthy donors, we found numerous isomiRs, tRFs, rRFs, and yRFs showing opposite enrichments or depletions, including molecules from the same parental miRNA arm, tRNA, rRNA, or Y RNA. The sncRNAome of platelets from COVID-19 patients is skewed compared to healthy donors: only 19.8% of all sncRNAs are yRFs, with isomiRs increasing to 63.6%, and tRFs, rRFs more than tripling their presence to 6.1%. Conclusions: The findings show that the sncRNAomes for MKs and platelets are very rich. The findings also suggest complex mechanisms that sort MK sncRNAs into platelets. SARS-CoV-2 infection acutely changes the relative proportions of sncRNAs in platelets.