Endogenous RNAs modulate microRNA sorting to exosomes and transfer to acceptor cells.

MicroRNA (miRNA) transfer via exosomes may mediate cell-to-cell communication. Interestingly, specific miRNAs are enriched in exosomes in a cell-type-dependent fashion. However, the mechanisms whereby miRNAs are sorted to exosomes and the significance of miRNA transfer to acceptor cells are unclear. We used macrophages and endothelial cells (ECs) as a model of heterotypic cell communication in order to investigate both processes. RNA profiling of macrophages and their exosomes shows that miRNA sorting to exosomes is modulated by cell-activation-dependent changes of miRNA target levels in the producer cells. Genetically perturbing the expression of individual miRNAs or their targeted transcripts promotes bidirectional miRNA relocation from the cell cytoplasm/P bodies (sites of miRNA activity) to multivesicular bodies (sites of exosome biogenesis) and controls miRNA sorting to exosomes. Furthermore, the use of Dicer-deficient cells and reporter lentiviral vectors (LVs) for miRNA activity shows that exosomal miRNAs are transferred from macrophages to ECs to detectably repress targeted sequences.

[1]  Sebastian D. Mackowiak,et al.  Circular RNAs are a large class of animal RNAs with regulatory potency , 2013, Nature.

[2]  Florian Buettner,et al.  The sufficient minimal set of miRNA seed types , 2011, Bioinform..

[3]  Martin Hintersteiner,et al.  The rough endoplasmatic reticulum is a central nucleation site of siRNA-mediated RNA silencing , 2013, The EMBO journal.

[4]  S. Gordon,et al.  Alternative activation of macrophages: an immunologic functional perspective. , 2009, Annual review of immunology.

[5]  Stefan L Ameres,et al.  Molecular Basis for Target RNA Recognition and Cleavage by Human RISC , 2007, Cell.

[6]  J. Lötvall,et al.  Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells , 2007, Nature Cell Biology.

[7]  D. Bartel.  MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[8]  Simon C Watkins,et al.  Endocytosis, intracellular sorting, and processing of exosomes by dendritic cells. , 2004, Blood.

[9]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[10]  Vikram Agarwal,et al.  Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. , 2014, Molecular cell.

[11]  Hamid Cheshmi.  Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers , 2011 .

[12]  Ravi Sachidanandam,et al.  Kinetic Analysis Reveals the Fate of a MicroRNA following Target Regulation in Mammalian Cells , 2011, Current Biology.

[13]  M. Pittet,et al.  MicroRNA-mediated control of macrophages and its implications for cancer. , 2013, Trends in immunology.

[14]  P. Pandolfi,et al.  A coding-independent function of gene and pseudogene mRNAs regulates tumour biology , 2010, Nature.

[15]  E. Chan,et al.  Disruption of GW bodies impairs mammalian RNA interference , 2005, Nature Cell Biology.

[16]  R. Sachidanandam,et al.  High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries , 2012, Nature Methods.

[17]  W. Reith,et al.  Conditional gene targeting in macrophages and granulocytes using LysMcre mice , 1999, Transgenic Research.

[18]  Achilleas S. Frangakis,et al.  Atheroprotective communication between endothelial cells and smooth muscle cells through miRNAs , 2012, Nature Cell Biology.

[19]  David W. Taylor,et al.  A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity , 2010, Science.

[20]  Zhiping Weng,et al.  Target RNA–Directed Trimming and Tailing of Small Silencing RNAs , 2010, Science.

[21]  C. Norbury,et al.  The Long and Short of MicroRNA , 2013, Cell.

[22]  Anders Krogh,et al.  MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. , 2011, RNA.

[23]  Amaia Agirre,et al.  A small noncoding RNA signature found in exosomes of GBM patient serum as a diagnostic tool. , 2014, Neuro-oncology.

[24]  E. Lai.  Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation , 2002, Nature Genetics.

[25]  D. Tollervey,et al.  Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding , 2013, Cell.

[26]  Luigi Naldini,et al.  Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state , 2007, Nature Biotechnology.

[27]  D. Cacchiarelli,et al.  A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA , 2011, Cell.

[28]  Jasenka Guduric-Fuchs,et al.  Selective extracellular vesicle-mediated export of an overlapping set of microRNAs from multiple cell types , 2012, BMC Genomics.

[29]  Barbara Burwinkel,et al.  Extracellular miRNAs: the mystery of their origin and function. , 2012, Trends in biochemical sciences.

[30]  Y. Matsuki,et al.  Secretory Mechanisms and Intercellular Transfer of MicroRNAs in Living Cells*♦ , 2010, The Journal of Biological Chemistry.

[31]  R. Lyle,et al.  miR-511-3p modulates genetic programs of tumor-associated macrophages. , 2012, Cell reports.

[32]  Gregory J. Hannon,et al.  MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies , 2005, Nature Cell Biology.

[33]  L. Naldini,et al.  Coordinate dual-gene transgenesis by lentiviral vectors carrying synthetic bidirectional promoters , 2005, Nature Biotechnology.

[34]  R. Pillai.  MicroRNA function: multiple mechanisms for a tiny RNA? , 2005, RNA.

[35]  Luigi Naldini,et al.  Stable knockdown of microRNA in vivo by lentiviral vectors , 2009, Nature Methods.

[36]  Fátima Sánchez-Cabo,et al.  Unidirectional transfer of microRNA-loaded exosomes from T cells to antigen-presenting cells , 2011, Nature communications.

[37]  Luigi Naldini,et al.  Exploiting and antagonizing microRNA regulation for therapeutic and experimental applications , 2009, Nature Reviews Genetics.

[38]  Graça Raposo,et al.  Exosomes--vesicular carriers for intercellular communication. , 2009, Current opinion in cell biology.

[39]  Qinxi Li,et al.  Axin determines cell fate by controlling the p53 activation threshold after DNA damage , 2009, Nature Cell Biology.

[40]  H. Buermans,et al.  Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions , 2012, Nucleic acids research.

[41]  L. Lim,et al.  MicroRNA targeting specificity in mammals: determinants beyond seed pairing. , 2007, Molecular cell.

[42]  M. Iruela-Arispe,et al.  Reciprocal interactions between endothelial cells and macrophages in angiogenic vascular niches. , 2013, Experimental cell research.

[43]  Ferdinando Di Cunto,et al.  Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs , 2011, Cell.

[44]  D. Bartel,et al.  The impact of microRNAs on protein output , 2008, Nature.

[45]  V. Palanisamy,et al.  Horizontal transfer of RNAs: exosomes as mediators of intercellular communication , 2012, Wiley interdisciplinary reviews. RNA.

[46]  F. Sánchez‐Madrid,et al.  Sumoylated hnRNPA2B1 controls the sorting of miRNAs into exosomes through binding to specific motifs , 2013, Nature Communications.

[47]  P. Pandolfi,et al.  The multilayered complexity of ceRNA crosstalk and competition , 2014, Nature.

[48]  M. L. Hastings,et al.  Selective Release of MicroRNA Species from Normal and Malignant Mammary Epithelial Cells , 2010, PloS one.