Comparative transcriptomic analysis of human and Drosophila extracellular vesicles

Abstract

Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of genetic material. In mammals, EVs can mediate the horizontal transfer of various cargos and signaling molecules, notably miRNA and mRNA species. Whether this form of intercellular communication prevails in other metazoans remains unclear. Here, we report the first parallel comparative morphologic and transcriptomic characterization of EVs from Drosophila and human cellular models. Electronic microscopy revealed that human and Drosophila cells release similar EVs with diameters ranging from 30 to 200 nm, which contain complex populations of transcripts. RNA-seq identified abundant ribosomal RNAs, related pseudogenes and retrotransposons in human and Drosophila EVs. Vault RNAs and Y RNAs abounded in human samples, whereas small nucleolar RNAs involved in pseudouridylation were most prevalent in Drosophila EVs. Numerous mRNAs were identified, largely consisting of exonic sequences displaying full-length read coverage and enriched for translation and electronic transport chain functions. By analogy with human systems, these sizeable similarities suggest that EVs could potentially enable RNA-mediated intercellular communication in Drosophila.

CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells

“…Biochemical purification and highthroughput RNA expression analysis, either using microarray or RNA-seq as a read out, has been used in several studies to identify specific populations of RNAs associated with structures such as the nucleus (Bhatt et al 2012;Tilgner et al 2012;Bahar Halpern et al 2015;Lefebvre et al 2016), cytoplasm (Bhatt et al 2012;Bahar Halpern et al 2015;Carlevaro-Fita et al 2016), cytosol (Chen et al 2011;Tilgner et al 2012;Wang et al 2012;van Heesch et al 2014), the ER (Kopczynski et al 1998;Diehn et al 2000Diehn et al , 2006Lerner et al 2003;de Jong et al 2006), mitochondria (Marc et al 2002), microtubules (Blower et al 2007;Sharp et al 2011), pseudopodia (Mili et al 2008), and neuronal projections (Eberwine et al 2001;Job and Eberwine 2001;Moccia et al 2003;Poon et al 2006;Zivraj et al 2010;Gumy et al 2011;Khaladkar et al 2013;Sasaki et al 2014;Taliaferro et al 2016). However, these efforts generally focused on defining enriched transcript populations associated with single structures, without simultaneously probing RNA expression signatures across other compartments derived from the same starting cellular specimens, thus limiting the capacity to evaluate global RNA localization prevalence.…”

“…Likewise, subcellular targeting strongly influences the function of various noncoding RNA species, such as long noncoding RNAs (lncRNAs) and small nucleolar RNAs (snoRNAs), and it has been proposed that such RNAs may act as key components of subcellular addressing systems (Batista and Chang 2013). Over the years, several transcriptome profiling surveys of purified organelles and subcellular compartments have revealed cofractionation of functionally coherent collections of mRNAs (Kopczynski et al 1998;Diehn et al 2000Diehn et al , 2006Eberwine et al 2001;Marc et al 2002;Lerner et al 2003;Blower et al 2007;Garcia et al 2007;Mili et al 2008;Pyhtila et al 2008;Zivraj et al 2010;Cajigas et al 2012;Wang et al 2012;Jan et al 2014;Williams et al 2014;Lefebvre et al 2016). Similarly, global RNA imaging-based screens in Drosophila oocytes and embryos have demonstrated that as much as 70% of coding transcripts are localized in patterns that broadly correlate with the distribution and function of their encoded proteins (Lécuyer et al 2007;Jambor et al 2015;Wilk et al 2016).…”

Extracellular Vesicles Could Carry an Evolutionary Footprint in Interkingdom Communication

“…A series of molecules derived from EVs have been involved in cell signaling and intra-regulation (Mutai and Waitumbi, 2010;Proto et al, 2013), including a variety of proteins and genetic material, and, potentially, transposons (Lefebvre et al, 2016;Preusser et al, 2018), all of which are known to mediate communication between host and pathogens (Schorey et al, 2015). For instance, recent studies on P. falciparum show that EVs carry proteins and nucleic acids potentially involved in the horizontal transfer of information parasite←→parasite and/or parasite−→host (Mantel et al, 2013(Mantel et al, , 2016Regev-Rudzki et al, 2013).…”

Small Luggage for a Long Journey: Transfer of Vesicle-Enclosed Small RNA in Interspecies Communication

“…Microarray and deep-sequencing approaches have revealed that repertoires of secreted sRNA don't mirror cellular populations, suggesting the involvement of selective sorting mechanisms (Valadi et al, 2007; Hunter et al, 2008; Lasser et al, 2011; Lefebvre et al, 2016). Various proteins of the RNAi machinery have been found in mammalian EVs and can perform cell-independent sRNA maturation (Melo et al, 2014).…”