<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.1d3 20150301//EN"  "JATS-archivearticle1.dtd"><article article-type="research-article" dtd-version="1.1d3" xmlns:xlink="http://www.w3.org/1999/xlink"><front><journal-meta><journal-id journal-id-type="nlm-ta">elife</journal-id><journal-id journal-id-type="hwp">eLife</journal-id><journal-id journal-id-type="publisher-id">eLife</journal-id><journal-title-group><journal-title>eLife</journal-title></journal-title-group><issn publication-format="electronic">2050-084X</issn><publisher><publisher-name>eLife Sciences Publications, Ltd</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">07197</article-id><article-id pub-id-type="doi">10.7554/eLife.07197</article-id><article-categories><subj-group subj-group-type="display-channel"><subject>Research Article</subject></subj-group><subj-group subj-group-type="heading"><subject>Cancer Biology</subject></subj-group></article-categories><title-group><article-title><italic>KRAS</italic>-dependent sorting of miRNA to exosomes</article-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes" id="author-2212"><name><surname>Cha</surname><given-names>Diana J</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="fn" rid="equal-contrib">†</xref><xref ref-type="fn" rid="con1"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" equal-contrib="yes" id="author-30113"><name><surname>Franklin</surname><given-names>Jeffrey L</given-names></name><xref ref-type="aff" rid="aff3">3</xref><xref ref-type="aff" rid="aff4">4</xref><xref ref-type="aff" rid="aff5">5</xref><xref ref-type="fn" rid="equal-contrib">†</xref><xref ref-type="other" rid="par-4"/><xref ref-type="fn" rid="con2"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-30114"><name><surname>Dou</surname><given-names>Yongchao</given-names></name><xref ref-type="aff" rid="aff6">6</xref><xref ref-type="fn" rid="con3"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-30115"><name><surname>Liu</surname><given-names>Qi</given-names></name><xref ref-type="aff" rid="aff6">6</xref><xref ref-type="fn" rid="con4"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-30116"><name><surname>Higginbotham</surname><given-names>James N</given-names></name><xref ref-type="aff" rid="aff3">3</xref><xref ref-type="aff" rid="aff4">4</xref><xref ref-type="fn" rid="con5"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-30117"><name><surname>Demory Beckler</surname><given-names>Michelle</given-names></name><xref ref-type="aff" rid="aff4">4</xref><xref ref-type="fn" rid="con6"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-29098"><name><surname>Weaver</surname><given-names>Alissa M</given-names></name><xref ref-type="aff" rid="aff3">3</xref><xref ref-type="aff" rid="aff7">7</xref><xref ref-type="aff" rid="aff8">8</xref><xref ref-type="fn" rid="con9"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-30118"><name><surname>Vickers</surname><given-names>Kasey</given-names></name><xref ref-type="aff" rid="aff9">9</xref><xref ref-type="fn" rid="con10"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-30119"><name><surname>Prasad</surname><given-names>Nirpesh</given-names></name><xref ref-type="aff" rid="aff10">10</xref><xref ref-type="fn" rid="con7"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-30120"><name><surname>Levy</surname><given-names>Shawn</given-names></name><xref ref-type="aff" rid="aff10">10</xref><xref ref-type="fn" rid="con8"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-30121"><name><surname>Zhang</surname><given-names>Bing</given-names></name><xref ref-type="aff" rid="aff6">6</xref><xref ref-type="fn" rid="con13"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" corresp="yes" id="author-30122"><name><surname>Coffey</surname><given-names>Robert J</given-names></name><xref ref-type="aff" rid="aff3">3</xref><xref ref-type="aff" rid="aff4">4</xref><xref ref-type="aff" rid="aff5">5</xref><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="other" rid="par-1"/><xref ref-type="other" rid="par-2"/><xref ref-type="other" rid="par-3"/><xref ref-type="fn" rid="con11"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" corresp="yes" id="author-2183"><name><surname>Patton</surname><given-names>James G</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="corresp" rid="cor2">*</xref><xref ref-type="other" rid="par-1"/><xref ref-type="fn" rid="con12"/><xref ref-type="fn" rid="conf1"/></contrib><aff id="aff1"><label>1</label><institution content-type="dept">Department of Biological Sciences</institution>, <institution>Vanderbilt University Medical Center</institution>, <addr-line><named-content content-type="city">Nashville</named-content></addr-line>, <country>United States</country></aff><aff id="aff2"><label>2</label><institution>Vanderbilt University</institution>, <addr-line><named-content content-type="city">Nashville</named-content></addr-line>, <country>United States</country></aff><aff id="aff3"><label>3</label><institution content-type="dept">Department of Cell and Developmental Biology</institution>, <institution>Vanderbilt University Medical Center</institution>, <addr-line><named-content content-type="city">Nashville</named-content></addr-line>, <country>United States</country></aff><aff id="aff4"><label>4</label><institution content-type="dept">Department of Medicine</institution>, <institution>Vanderbilt University Medical Center</institution>, <addr-line><named-content content-type="city">Nashville</named-content></addr-line>, <country>United States</country></aff><aff id="aff5"><label>5</label><institution>Affairs Medical Center</institution>, <addr-line><named-content content-type="city">Nashville</named-content></addr-line>, <country>United States</country></aff><aff id="aff6"><label>6</label><institution content-type="dept">Department of Biomedical Informatics</institution>, <institution>Vanderbilt University Medical Center</institution>, <addr-line><named-content content-type="city">Nashville</named-content></addr-line>, <country>United States</country></aff><aff id="aff7"><label>7</label><institution content-type="dept">Department of Cancer Biology</institution>, <institution>Vanderbilt University Medical Center</institution>, <addr-line><named-content content-type="city">Nashville</named-content></addr-line>, <country>United States</country></aff><aff id="aff8"><label>8</label><institution content-type="dept">Department of Pathology, Microbiology and Immunology</institution>, <institution>Vanderbilt University Medical Center</institution>, <addr-line><named-content content-type="city">Nashville</named-content></addr-line>, <country>United States</country></aff><aff id="aff9"><label>9</label><institution content-type="dept">Department of Cardiology</institution>, <institution>Vanderbilt University Medical Center</institution>, <addr-line><named-content content-type="city">Nashville</named-content></addr-line>, <country>United States</country></aff><aff id="aff10"><label>10</label><institution>HudsonAlpha Institute for Biotechnology</institution>, <addr-line><named-content content-type="city">Huntsville</named-content></addr-line>, <country>United States</country></aff></contrib-group><contrib-group content-type="section"><contrib contrib-type="editor" id="author-1206"><name><surname>Zamore</surname><given-names>Phillip D</given-names></name><role>Reviewing editor</role><aff><institution>Howard Hughes Medical Institute, University of Massachusetts Medical School</institution>, <country>United States</country></aff></contrib></contrib-group><author-notes><corresp id="cor1"><label>*</label>For correspondence: <email>robert.coffey@vanderbilt.edu</email> (RJC);</corresp><corresp id="cor2"><email>james.g.patton@vanderbilt.edu</email> (JGP)</corresp><fn fn-type="con" id="equal-contrib"><label>†</label><p>These authors contributed equally to this work</p></fn></author-notes><pub-date date-type="pub" publication-format="electronic"><day>01</day><month>07</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>4</volume><elocation-id>e07197</elocation-id><history><date date-type="received"><day>26</day><month>02</month><year>2015</year></date><date date-type="accepted"><day>29</day><month>06</month><year>2015</year></date></history><permissions><copyright-statement>© 2015, Cha et al</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Cha et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This article is distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="elife-07197-v2.pdf"/><abstract><object-id pub-id-type="doi">10.7554/eLife.07197.001</object-id><p>Mutant <italic>KRAS</italic> colorectal cancer (CRC) cells release protein-laden exosomes that can alter the tumor microenvironment. To test whether exosomal RNAs also contribute to changes in gene expression in recipient cells, and whether mutant <italic>KRAS</italic> might regulate the composition of secreted microRNAs (miRNAs), we compared small RNAs of cells and matched exosomes from isogenic CRC cell lines differing only in <italic>KRAS</italic> status. We show that exosomal profiles are distinct from cellular profiles, and mutant exosomes cluster separately from wild-type <italic>KRAS</italic> exosomes. <italic>miR-10b</italic> was selectively increased in wild-type exosomes, while <italic>miR-100</italic> was increased in mutant exosomes. Neutral sphingomyelinase inhibition caused accumulation of <italic>miR-100</italic> only in mutant cells, suggesting <italic>KRAS</italic>-dependent miRNA export. In Transwell co-culture experiments, mutant donor cells conferred <italic>miR-100</italic>-mediated target repression in wild-type-recipient cells. These findings suggest that extracellular miRNAs can function in target cells and uncover a potential new mode of action for mutant <italic>KRAS</italic> in CRC.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.001">http://dx.doi.org/10.7554/eLife.07197.001</ext-link></p></abstract><abstract abstract-type="executive-summary"><object-id pub-id-type="doi">10.7554/eLife.07197.002</object-id><title>eLife digest</title><p>Cells use several different methods to control which genes are expressed to produce the proteins and RNA molecules that they need to work efficiently. The first step of gene expression is to transcribe a gene to form an RNA molecule. Protein-coding mRNA molecules can then be translated to make proteins. However, many RNA transcripts do not encode proteins. One example of these non-coding RNAs is a class of small RNAs called microRNAs (miRNAs), which are predicted to target more than 60% of protein-coding genes and can control which proteins are made.</p><p>It was once thought that miRNAs exist only within the cell where they are synthesized. Recently, however, miRNAs have been found outside the cell bound to lipids and proteins, or encased in extracellular vesicles, such as exosomes. Exosomes are small bubble-like structures used by cells to export material into the space outside of cells. Exosomes containing miRNAs can circulate throughout the body, potentially transferring information between cells to alter gene expression in recipient cells.</p><p>Many colorectal cancer cells have mutations in a gene that encodes a protein called KRAS. In 2011 and 2013, researchers found that the contents of the exosomes released from these mutant <italic>KRAS</italic> colorectal cancer cells can influence normal cells in ways that would help a cancer to spread. Furthermore, the exosomes released from the <italic>KRAS</italic> mutant cells contain different proteins than non-mutant cells.</p><p>Now, Cha, Franklin et al.—including several researchers who worked on the 2011 and 2013 studies—show that exosomes released by mutant <italic>KRAS</italic> cells also contain miRNAs, and that these miRNAs are different from the ones exported in exosomes by cells with a normal copy of the <italic>KRAS</italic> gene. In particular, several miRNAs that suppress cancer growth in a healthy cell are found at lower levels in mutant KRAS cells. Instead, these miRNAs are highly represented in the exosomes that are released by the <italic>KRAS</italic> mutant cells.</p><p>When cells with a normal copy of the <italic>KRAS</italic> gene were exposed to the contents of the exosomes released from <italic>KRAS</italic> mutant cells, an important gene involved in cell growth was suppressed. This indicates that the miRNAs exported from cancerous cells can influence gene expression in neighboring cells. Getting rid of such cancer-suppressing miRNAs could give cancer cells a growth advantage over normal cells to promote tumor growth. Cha, Franklin et al. also suggest that it might be possible to create a non-invasive test to detect colorectal cancer by monitoring the levels of circulating miRNAs in patients. Potential treatments for the disease could also target these miRNAs.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.002">http://dx.doi.org/10.7554/eLife.07197.002</ext-link></p></abstract><kwd-group kwd-group-type="author-keywords"><title>Author keywords</title><kwd>cancer</kwd><kwd>miRNA</kwd><kwd>KRAS</kwd><kwd>colorectal cancer</kwd><kwd>extracellular RNA</kwd></kwd-group><kwd-group kwd-group-type="research-organism"><title>Research organism</title><kwd>Human</kwd></kwd-group><funding-group><award-group id="par-1"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000002</institution-id><institution>National Institutes of Health (NIH)</institution></institution-wrap></funding-source><award-id>U19CA179514</award-id><principal-award-recipient><name><surname>Coffey</surname><given-names>Robert J</given-names></name><name><surname>Patton</surname><given-names>James G</given-names></name></principal-award-recipient></award-group><award-group id="par-2"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000054</institution-id><institution>National Cancer Institute (NCI)</institution></institution-wrap></funding-source><award-id>P50 95103</award-id><principal-award-recipient><name><surname>Coffey</surname><given-names>Robert J</given-names></name></principal-award-recipient></award-group><award-group id="par-3"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000002</institution-id><institution>National Institutes of Health (NIH)</institution></institution-wrap></funding-source><award-id>RO1 CA163563</award-id><principal-award-recipient><name><surname>Coffey</surname><given-names>Robert J</given-names></name></principal-award-recipient></award-group><award-group id="par-4"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000002</institution-id><institution>National Institutes of Health (NIH)</institution></institution-wrap></funding-source><award-id>P30 DK058404</award-id><principal-award-recipient><name><surname>Franklin</surname><given-names>Jeffrey L</given-names></name></principal-award-recipient></award-group><funding-statement>The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</funding-statement></funding-group><custom-meta-group><custom-meta><meta-name>elife-xml-version</meta-name><meta-value>2.3</meta-value></custom-meta><custom-meta specific-use="meta-only"><meta-name>Author impact statement</meta-name><meta-value>In isogenically matched colorectal cancer (CRC) cell lines, mutant <italic>KRAS</italic> alters the composition of secreted miRNAs in extracellular vesicles that can then transfer repressive activity to wild type cells.</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="s1" sec-type="intro"><title>Introduction</title><p>An emerging paradigm in the study of cell signaling is the potential role for post-transcriptional gene regulation by extracellular RNAs. microRNAs (miRNAs) are perhaps the best characterized class of small noncoding RNAs (ncRNAs) that have been detected in extracellular fluids (<xref ref-type="bibr" rid="bib60">Valadi et al., 2007</xref>). Mature miRNAs are 21–23 nucleotides in length and bind to target mRNAs to inhibit their expression (<xref ref-type="bibr" rid="bib37">Krol et al., 2010</xref>). Because miRNAs imperfectly pair with their mRNA targets, they can potentially regulate hundreds of transcripts within a genome (<xref ref-type="bibr" rid="bib5">Bartel and Chen, 2004</xref>). However, individual miRNAs exhibit exquisite tissue-specific patterns of expression (<xref ref-type="bibr" rid="bib66">Wienholds et al., 2005</xref>), control cell fate decisions (<xref ref-type="bibr" rid="bib1">Alvarez-Garcia and Miska, 2005</xref>), and are often aberrantly expressed in human cancers (<xref ref-type="bibr" rid="bib59">Thomson et al., 2006</xref>), affording possible disease-specific signatures with diagnostic, prognostic, and therapeutic potential (<xref ref-type="bibr" rid="bib40">Lu et al., 2005</xref>; <xref ref-type="bibr" rid="bib63">Volinia et al., 2006</xref>).</p><p>In addition to their intracellular roles, recent experiments have identified miRNAs outside the cell in extracellular vesicles (EVs) including exosomes or larger vesicles (<xref ref-type="bibr" rid="bib60">Valadi et al., 2007</xref>; <xref ref-type="bibr" rid="bib17">Crescitelli et al., 2013</xref>), in high-density lipoprotein particles (<xref ref-type="bibr" rid="bib61">Vickers et al., 2011</xref>), or in smaller complexes with Argonaute 2 protein (<xref ref-type="bibr" rid="bib3">Arroyo et al., 2011</xref>). Exosomes are small 40–130 nm vesicles of endosomal origin that are secreted by all cells and can fuse and be internalized by recipient cells (<xref ref-type="bibr" rid="bib60">Valadi et al., 2007</xref>; <xref ref-type="bibr" rid="bib36">Kosaka et al., 2010</xref>; <xref ref-type="bibr" rid="bib30">Higginbotham et al., 2011</xref>; <xref ref-type="bibr" rid="bib45">Mittelbrunn et al., 2011</xref>; <xref ref-type="bibr" rid="bib46">Montecalvo et al., 2012</xref>). It has been suggested that protein cargo transfer by exosomes between cells is associated with tumor aggressiveness and metastasis (<xref ref-type="bibr" rid="bib55">Skog et al., 2008</xref>; <xref ref-type="bibr" rid="bib30">Higginbotham et al., 2011</xref>; <xref ref-type="bibr" rid="bib41">Luga et al., 2012</xref>; <xref ref-type="bibr" rid="bib31">Hoshino et al., 2013</xref>; <xref ref-type="bibr" rid="bib16">Costa-Silva et al., 2015</xref>). With the discovery that miRNAs and other RNAs can also be packaged into EVs, or exported by other extracellular mechanisms, it remains unclear the extent to which RNA cargo is sorted for export and how it is dysregulated in disease conditions, such as cancer.</p><p>Despite accumulating evidence that exosomes are biologically active, little is known regarding how oncogenic signaling affects the repertoire of miRNAs or proteins that are selected for secretion. Given the potential of cancer-derived secreted RNAs to modulate the tumor microenvironment, elucidation of the potential mechanisms for selective sorting of cargo into exosomes is critical to understanding extracellular signaling by RNA. <italic>KRAS</italic> mutations occur in approximately 34–45% of colon cancers (<xref ref-type="bibr" rid="bib67">Wong and Cunningham, 2008</xref>). We have previously shown that exosomes from mutant <italic>KRAS</italic> colorectal cancer (CRC) cells can be transferred to wild-type cells to induce cell growth and migration (<xref ref-type="bibr" rid="bib30">Higginbotham et al., 2011</xref>; <xref ref-type="bibr" rid="bib18">Demory Beckler et al., 2013</xref>). Compared to exosomes derived from isogenically matched wild-type cells, exosomes derived from mutant <italic>KRAS</italic> cells contain dramatically different protein cargo (<xref ref-type="bibr" rid="bib18">Demory Beckler et al., 2013</xref>). Here, we show that <italic>KRAS</italic> status also prominently affects the miRNA profile in cells and their corresponding exosomes. Exosomal miRNA profiles are distinct from cellular miRNA patterns, and exosomal miRNA profiles are better predictors of <italic>KRAS</italic> status than cellular miRNA profiles. Furthermore, we show that cellular trafficking of miRNAs is sensitive to neutral sphingomyelinase (nSMase) inhibition in mutant, but not wild type, <italic>KRAS</italic> cells and that transfer of miRNAs between cells can functionally alter gene expression in recipient cells.</p></sec><sec id="s2" sec-type="results"><title>Results</title><sec id="s2-1"><title>Small ncRNAs are differentially distributed in exosomes</title><p>Because small RNAs are thought to be sorted at endosomal membranes and since <italic>KRAS</italic> signaling can also occur on late endosomes (<xref ref-type="bibr" rid="bib40">Lu et al., 2005</xref>), we hypothesized that oncogenic KRAS signaling could alter RNA export into exosomes. We prepared small RNA libraries from both exosomes and whole cells using isogenically matched CRC cell lines that differ only in <italic>KRAS</italic> status (<xref ref-type="supplementary-material" rid="SD1-data">Figure 1—source data 1</xref>) (<xref ref-type="bibr" rid="bib54">Shirasawa et al., 1993</xref>). Exosomes were purified using differential centrifugation and consisted of vesicles ranging in size from 40 to 130 nm (<xref ref-type="bibr" rid="bib30">Higginbotham et al., 2011</xref>; <xref ref-type="bibr" rid="bib18">Demory Beckler et al., 2013</xref>). These preparations exclude larger microvesicles but contain smaller lipoproteins and probably other small RNA–protein complexes (unpublished observation). Comprehensive sequencing analyses of both cellular and exosomal small RNAs from all three cell lines revealed that more than 85% of the reads from the cellular RNA libraries mapped to the genome, compared to only 50–71% from the exosomal libraries (<xref ref-type="fig" rid="fig1">Figure 1A</xref>). The non-mappable reads consisted largely of sequences that contain mismatches to genomic sequences.<fig-group><fig id="fig1" position="float"><object-id pub-id-type="doi">10.7554/eLife.07197.003</object-id><label>Figure 1.</label><caption><title>Small RNA sequencing analysis of cellular and exosomal RNAs from CRC cell lines.</title><p>Shown are (<bold>A</bold>) total read numbers (y-axis) and the total percentage of mappable reads (red), percentage of unique mappable reads (green), reads that map to multiple genomic locations (dark blue), and those that could not be mapped (cyan). (<bold>B</bold>) The majority of mappable small RNA reads were derived from noncoding RNAs in cells and exosomes. In cells, the majority of small RNA reads mapped to microRNAs (miRNAs) (miRbase 19), whereas in exosomes, the majority of small RNA reads mapped to repetitive elements. (<bold>C</bold>) The origin of repetitive reads from exosomal small RNA sequencing is shown. Repeat reads were annotated based on RepeatMasker and Rfam classified into tRNAs, rRNAs, snRNAs, and others. (<bold>D</bold>) The length distribution of reads mapping to miRNA hairpins was determined for small RNA reads from the three CRC cell lines and their purified exosomes. Colors represent the nucleotides identified for the 5′ base, T (cyan), A (red), G (green), and C (blue). <xref ref-type="fig" rid="fig1s1">Figure 1—figure supplement 1</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.003">http://dx.doi.org/10.7554/eLife.07197.003</ext-link></p><p><supplementary-material id="SD1-data"><object-id pub-id-type="doi">10.7554/eLife.07197.004</object-id><label>Figure 1—source data 1.</label><caption><title>Colorectal cancer (CRC) cell lines.</title><p>Small RNA sequencing libraries were prepared from three isogenic CRC cell lines with the indicated alleles of KRAS. Table is based on work done in <xref ref-type="bibr" rid="bib18">Demory Beckler et al. (2013)</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.004">http://dx.doi.org/10.7554/eLife.07197.004</ext-link></p></caption><media mime-subtype="docx" mimetype="application" xlink:href="elife-07197-fig1-data1-v2.docx"/></supplementary-material></p></caption><graphic xlink:href="elife-07197-fig1-v2.tif"/></fig><fig id="fig1s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.07197.005</object-id><label>Figure 1—figure supplement 1.</label><caption><title>Length distribution of small RNA reads to genome.</title><p>The small RNA read length distribution from serum-starved cells and from purified exosomes was determined, as well as the 5′ nucleotide from each read. The pattern from total cellular small RNA is consistent with primarily miRNA reads, the distribution from exosomes is much broader, encompassing a number of small reads derived from many sources (see <xref ref-type="fig" rid="fig1">Figure 1C,D</xref>). Colors represent the nucleotides identified for the 5′ base, T (cyan), A (red), G (green), and C (blue).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.005">http://dx.doi.org/10.7554/eLife.07197.005</ext-link></p></caption><graphic xlink:href="elife-07197-fig1-figsupp1-v2.tif"/></fig></fig-group></p><p>The global small RNA profiles identified reads from various classes of RNA, including miRNAs, with differential enrichment of specific RNAs in both the cellular and exosomal fractions. Compared to cellular RNA samples, which displayed an enrichment of miRNA sequences (∼70%), miRNA reads in exosomal samples comprised a smaller percentage of the total small reads (5–18%) compared to other ncRNA classes (e.g., tRNAs, rRNAs, snRNAs) (<xref ref-type="fig" rid="fig1">Figure 1B,C</xref>, <xref ref-type="supplementary-material" rid="SD2-data">Supplementary file 1</xref>). Most of these reads appear to be the fragments of larger RNAs, both cytoplasmic and nuclear. It is not clear how these RNAs are associated with and/or deposited into exosomes.</p><p>The size distribution of cellular small RNA matched that expected from miRNA-derived reads (21–23 nucleotides). However, the small RNA read distribution from exosomes was much broader with many reads smaller than 22 nucleotides in length (<xref ref-type="fig" rid="fig1s1">Figure 1—figure supplement 1</xref>). Given that these reads map to RNAs other than known miRNAs, these data suggest that a large proportion of small exosomal RNA reads is derived from processing of other RNAs, in addition to post-transcriptionally modified miRNA reads that are apparently subject to editing, trimming, and/or tailing (<xref ref-type="bibr" rid="bib35">Koppers-Lalic et al., 2014</xref>). Consistent with this, when read identity was restricted to miRNAs by mapping back to known miRNA hairpin sequences, the length distribution of mappable reads was nearly identical between cells and exosomes (<xref ref-type="fig" rid="fig1">Figure 1D</xref>).</p></sec><sec id="s2-2"><title>miRNAs are differentially enriched in exosomes dependent on <italic>KRAS</italic> status</title><p>Focusing on mappable reads, we sought to ascertain whether miRNAs might be differentially represented when comparing cells to their secreted exosomes. For this, we quantified the relative abundance of individual miRNAs and made pairwise comparisons between normalized miRNA reads. Spearman correlation analyses demonstrated high correlation between replicates of individual cell lines (r = 0.95–0.96) and between cellular data sets differing only in <italic>KRAS</italic> status (r = 0.92–0.96) (<xref ref-type="fig" rid="fig2s1 fig2s2 fig2s3">Figure 2—figure supplements 1–3</xref>). In contrast, the miRNA profiles from exosomes compared to their parent cells were less correlated (DKO-1 r = 0.67–0.81, DKs-8 r = 0.64–0.71, DLD-1 r = 0.64–0.69) (<xref ref-type="fig" rid="fig2s1 fig2s2 fig2s4">Figure 2—figure supplements 1, 2, 4</xref>).</p><p>We next utilized principal component (PC) analysis to determine whether the overall miRNA profiles could distinguish between cells and exosomes and/or between wild-type and mutant <italic>KRAS</italic> status. The miRNA profiles from the three cell lines all clustered close to one another indicating that overall miRNA expression profiles are fairly similar among the different cell types (<xref ref-type="fig" rid="fig2">Figure 2</xref>). In marked contrast, PC analysis revealed that exosomal miRNA profiles clearly segregate according to <italic>KRAS</italic> status (<xref ref-type="fig" rid="fig2">Figure 2</xref>). Relatively, minor differences between cellular miRNA expression profiles become much more prominent when comparing exosomal miRNA patterns (<xref ref-type="fig" rid="fig2s3">Figure 2—figure supplement 3</xref>). This indicates that the presence of a mutant <italic>KRAS</italic> allele alters sorting of specific miRNAs to exosomes, a finding that has potentially important implications for biomarker development.<fig-group><fig id="fig2" position="float"><object-id pub-id-type="doi">10.7554/eLife.07197.006</object-id><label>Figure 2.</label><caption><title>Small RNA composition segregates with KRAS status.</title><p>Principal component analysis was performed comparing small RNA sequencing data sets from CRC cells and exosomes. The small RNA composition from cells differed significantly from exosomes. Nevertheless, clustering showed that mutant <italic>KRAS</italic> status could be inferred from small RNA composition. Also see <xref ref-type="fig" rid="fig2s1 fig2s2 fig2s3 fig2s4">Figure 2—figure supplements 1–4</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.006">http://dx.doi.org/10.7554/eLife.07197.006</ext-link></p></caption><graphic xlink:href="elife-07197-fig2-v2.tif"/></fig><fig id="fig2s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.07197.007</object-id><label>Figure 2—figure supplement 1.</label><caption><title>Spearman correlations between miRNA expression profiles in cells and exosomes.</title><p>Pairwise similarity between the RNA sequencing data sets derived from cells and exosomes. Spearman correlations are shown between the cell samples (R = 0.93–0.96), between exosomes and cognate cells (R = 0.64–0.83) and between exosome samples (R = 0.74–0.86). Results were generated using the DESeq ‘pooled’ method.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.007">http://dx.doi.org/10.7554/eLife.07197.007</ext-link></p></caption><graphic xlink:href="elife-07197-fig2-figsupp1-v2.tif"/></fig><fig id="fig2s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.07197.008</object-id><label>Figure 2—figure supplement 2.</label><caption><title>Spearman correlations between miRNA expression profiles in cells and exosomes.</title><p>Similar to supplemental <xref ref-type="fig" rid="fig2">Figure 2A</xref>. Differential analysis using the DESeq ‘per condition’ method.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.008">http://dx.doi.org/10.7554/eLife.07197.008</ext-link></p></caption><graphic xlink:href="elife-07197-fig2-figsupp2-v2.tif"/></fig><fig id="fig2s3" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.07197.009</object-id><label>Figure 2—figure supplement 3.</label><caption><title>Spearman correlations between miRNA expression profiles in cells (top) and exosomes (bottoms) in reads per million (RPM).</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.009">http://dx.doi.org/10.7554/eLife.07197.009</ext-link></p></caption><graphic xlink:href="elife-07197-fig2-figsupp3-v2.tif"/></fig><fig id="fig2s4" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.07197.010</object-id><label>Figure 2—figure supplement 4.</label><caption><title>Spearman correlations comparing miRNA expression profiles in exosomes to parent cell in RPM.</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.010">http://dx.doi.org/10.7554/eLife.07197.010</ext-link></p></caption><graphic xlink:href="elife-07197-fig2-figsupp4-v2.tif"/></fig></fig-group></p><p>To gain more insight into the relative abundance of miRNAs in cells vs matched exosomes, we examined the most abundant miRNA species in the various sequencing libraries (determined by mean reads of individual miRNAs). For many miRNAs, exosomal abundance correlated with cellular abundance (<xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 2</xref>). However, calculation of fold changes among the three isogenic <italic>KRAS</italic> cell lines, and exosomes released from these cells, showed that distinct subsets of miRNAs are enriched in either exosomes or cells (<xref ref-type="table" rid="tbl1 tbl2">Tables 1, 2</xref>). For all three cell lines, 25 miRNAs were consistently upregulated in cells and 29 miRNAs were consistently upregulated in exosomes (<xref ref-type="fig" rid="fig3">Figure 3A,B</xref>). Additionally, the diversity of miRNAs was substantially greater in mutant <italic>KRAS</italic> DKO-1 exosomes (94 unique miRNAs) compared to parental DLD-1 or wild-type <italic>KRAS</italic> DKs-8 exosomes (<xref ref-type="fig" rid="fig3">Figure 3B</xref>). A select subset of cell and exosomally targeted miRNAs were validated separately by quantitative reverse-transcription PCR (qRT/PCR) (<xref ref-type="fig" rid="fig3">Figure 3C</xref>). Collectively, these data indicate that the miRNA profiles observed in exosomes are distinct from their parental cells with specific miRNAs preferentially overrepresented or underrepresented in exosomes. We observed a mutant <italic>KRAS</italic>-specific pattern of secreted miRNAs, consistent with the hypothesis that dysregulation of miRNA metabolism is associated with tumorigenesis, a previously unrecognized feature of mutant <italic>KRAS</italic>.<table-wrap id="tbl1" position="float"><object-id pub-id-type="doi">10.7554/eLife.07197.011</object-id><label>Table 1.</label><caption><p>Differential expression of miRNAs in colorectal cancer cells<xref ref-type="table-fn" rid="tblfn1">*</xref></p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.011">http://dx.doi.org/10.7554/eLife.07197.011</ext-link></p></caption><table frame="hsides" rules="groups"><tbody><tr><td colspan="4">DKO-1</td></tr><tr><td> hsa-miR-548u</td><td>hsa-miR-16-1-3p</td><td>hsa-miR-33a-3p</td><td>hsa-miR-33a-5p</td></tr><tr><td> hsa-miR-31-5p</td><td>hsa-miR-181b-3p</td><td>hsa-miR-450a-5p</td><td>hsa-miR-424-5p</td></tr><tr><td> hsa-miR-9-5p</td><td>hsa-miR-219-5p</td><td>hsa-miR-190a</td><td>hsa-miR-573</td></tr><tr><td> hsa-miR-30d-3p</td><td>hsa-miR-204-5p</td><td>hsa-miR-1226-3p</td><td>hsa-miR-499a-5p</td></tr><tr><td> hsa-miR-450b-5p</td><td>hsa-miR-499b-3p</td><td>hsa-miR-3662</td><td>hsa-miR-20a-3p</td></tr><tr><td> hsa-miR-27b-5p</td><td>hsa-miR-5701</td><td>hsa-miR-4677-3p</td><td>hsa-let-7i-5p</td></tr><tr><td> hsa-miR-331-3p</td><td>hsa-miR-31-3p</td><td>hsa-miR-651</td><td>hsa-miR-1306-5p</td></tr><tr><td> hsa-miR-147b</td><td>hsa-miR-3611</td><td>hsa-miR-1305</td><td>hsa-miR-148a-3p</td></tr><tr><td> hsa-miR-27b-3p</td><td>hsa-miR-1306-3p</td><td>hsa-miR-374b-3p</td><td>hsa-miR-1260b</td></tr><tr><td> hsa-miR-3940-3p</td><td>hsa-miR-200c-5p</td><td>hsa-miR-548ar-3p</td><td/></tr><tr><td colspan="4">DKs-8</td></tr><tr><td> hsa-miR-132-5p</td><td>hsa-miR-484</td><td>hsa-miR-374a-5p</td><td>hsa-miR-1180</td></tr><tr><td> hsa-miR-1307-3p</td><td>hsa-miR-200a-5p</td><td>hsa-miR-548o-3p</td><td>hsa-miR-149-5p</td></tr><tr><td> hsa-miR-3615</td><td>hsa-miR-100-5p</td><td>hsa-miR-197-3p</td><td>hsa-miR-378a-5p</td></tr><tr><td> hsa-let-7a-3p</td><td/><td/><td/></tr><tr><td colspan="4">DLD-1</td></tr><tr><td> hsa-miR-141-3p</td><td>hsa-miR-26b-5p</td><td>hsa-miR-24-3p</td><td>hsa-miR-3074-5p</td></tr><tr><td> hsa-miR-15a-5p</td><td>hsa-miR-27a-3p</td><td>hsa-miR-3613-5p</td><td>hsa-miR-30b-5p</td></tr><tr><td> hsa-miR-29a-3p</td><td>hsa-miR-301a-5p</td><td>hsa-let-7i-3p</td><td>hsa-miR-185-5p</td></tr><tr><td> hsa-let-7g-5p</td><td>hsa-miR-23b-3p</td><td>hsa-miR-22-3p</td><td/></tr><tr><td colspan="4">DKO-1 and DKs-8</td></tr><tr><td> hsa-miR-141-5p</td><td>hsa-miR-582-5p</td><td/><td/></tr><tr><td colspan="4">DKO-1 and DLD-1</td></tr><tr><td> hsa-miR-556-3p</td><td>hsa-miR-374a-3p</td><td>hsa-miR-106b-5p</td><td>hsa-miR-17-3p</td></tr><tr><td> hsa-miR-24-1-5p</td><td>hsa-miR-340-3p</td><td/><td/></tr><tr><td colspan="4">DLD-1 and DKs-8</td></tr><tr><td> hsa-miR-24-2-5p</td><td>hsa-miR-106a-5p</td><td>hsa-miR-30e-5p</td><td>hsa-miR-107</td></tr><tr><td> hsa-miR-429</td><td>hsa-miR-98-5p</td><td>hsa-miR-425-5p</td><td>hsa-miR-140-5p</td></tr><tr><td> hsa-miR-93-5p</td><td>hsa-miR-210</td><td>hsa-miR-126-3p</td><td>hsa-miR-194-5p</td></tr><tr><td> hsa-miR-29b-3p</td><td>hsa-miR-15b-5p</td><td>hsa-miR-362-5p</td><td>hsa-miR-27a-5p</td></tr><tr><td> hsa-miR-454-3p</td><td>hsa-miR-452-5p</td><td>hsa-miR-196b-5p</td><td/></tr><tr><td colspan="4">DKO-1, DLD-1 and DKs-8</td></tr><tr><td> hsa-miR-32-5p</td><td>hsa-miR-582-3p</td><td>hsa-miR-542-3p</td><td>hsa-miR-96-5p</td></tr><tr><td> hsa-miR-101-3p</td><td>hsa-miR-18a-5p</td><td>hsa-miR-3529-3p</td><td>hsa-miR-7-5p</td></tr><tr><td> hsa-miR-19a-3p</td><td>hsa-miR-142-3p</td><td>hsa-miR-20a-5p</td><td>hsa-miR-32-3p</td></tr><tr><td> hsa-miR-130b-5p</td><td>hsa-miR-1278</td><td>hsa-miR-7-1-3p</td><td>hsa-miR-590-3p</td></tr><tr><td> hsa-miR-4473</td><td>hsa-miR-17-5p</td><td>hsa-miR-103a-3p</td><td>hsa-miR-103b</td></tr><tr><td> hsa-miR-19b-3p</td><td>hsa-miR-340-5p</td><td>hsa-miR-200a-3p</td><td>hsa-miR-34a-5p</td></tr><tr><td> hsa-miR-372</td><td/><td/><td/></tr></tbody></table><table-wrap-foot><fn id="tblfn1"><label>*</label><p>miRNAs differentially enriched in cells when comparing mean reads in exosomes vs cell.</p></fn><fn><p>miRNAs expression patterns were compared between DKs-8, DKO-1, and DLD-1 cells. miRNAs were identified that were enriched in just one of the three cell types or that overlapped between combinations of cells. For miRNAs, 25 were identified that are expressed in all three cell types, 13 were enriched in DKs-8 cells, 15 in DLD-1 cells, and 39 were unique to DKO-1 cells.</p></fn></table-wrap-foot></table-wrap><table-wrap id="tbl2" position="float"><object-id pub-id-type="doi">10.7554/eLife.07197.012</object-id><label>Table 2.</label><caption><p>Differential distribution of miRNAs in exosomes<xref ref-type="table-fn" rid="tblfn2">*</xref></p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.012">http://dx.doi.org/10.7554/eLife.07197.012</ext-link></p></caption><table frame="hsides" rules="groups"><tbody><tr><td colspan="4">DKO-1</td></tr><tr><td> hsa-miR-139-5p</td><td>hsa-miR-3178</td><td>hsa-miR-151b</td><td>hsa-miR-125b-1-3p</td></tr><tr><td> hsa-miR-193b-3p</td><td>hsa-miR-935</td><td>hsa-miR-130b-3p</td><td>hsa-miR-628-3p</td></tr><tr><td> hsa-miR-139-3p</td><td>hsa-let-7d-3p</td><td>hsa-miR-589-3p</td><td>hsa-miR-4532</td></tr><tr><td> hsa-miR-451a</td><td>hsa-miR-6087</td><td>hsa-miR-151a-5p</td><td>hsa-miR-940</td></tr><tr><td> hsa-miR-222-3p</td><td>hsa-miR-766-5p</td><td>hsa-miR-505-5p</td><td>hsa-miR-3187-3p</td></tr><tr><td> hsa-miR-125a-3p</td><td>hsa-miR-3679-5p</td><td>hsa-miR-4436b-3p</td><td>hsa-miR-4787-3p</td></tr><tr><td> hsa-miR-2277-3p</td><td>hsa-miR-361-5p</td><td>hsa-miR-1293</td><td>hsa-miR-3183</td></tr><tr><td> hsa-miR-3162-5p</td><td>hsa-miR-642a-3p</td><td>hsa-miR-642b-5p</td><td>hsa-miR-197-5p</td></tr><tr><td> hsa-miR-324-3p</td><td>hsa-miR-145-3p</td><td>hsa-miR-3182</td><td>hsa-miR-3127-3p</td></tr><tr><td> hsa-miR-3127-5p</td><td>hsa-miR-4728-3p</td><td>hsa-miR-3184-5p</td><td>hsa-miR-125b-5p</td></tr><tr><td> hsa-miR-186-5p</td><td>hsa-miR-1</td><td>hsa-miR-100-5p</td><td>hsa-miR-423-3p</td></tr><tr><td> hsa-miR-766-3p</td><td>hsa-miR-4753-5p</td><td>hsa-miR-145-5p</td><td>hsa-miR-4724-5p</td></tr><tr><td> hsa-miR-373-3p</td><td>hsa-miR-223-5p</td><td>hsa-miR-1307-5p</td><td>hsa-miR-1914-3p</td></tr><tr><td> hsa-miR-3121-3p</td><td>hsa-miR-3613-3p</td><td>hsa-miR-205-5p</td><td>hsa-miR-98-3p</td></tr><tr><td> hsa-miR-23a-3p</td><td>hsa-miR-3124-5p</td><td>hsa-miR-3656</td><td>hsa-miR-3918</td></tr><tr><td> hsa-miR-4449</td><td>hsa-miR-378c</td><td>hsa-miR-3138</td><td>hsa-miR-1910</td></tr><tr><td> hsa-miR-3174</td><td>hsa-miR-4466</td><td>hsa-miR-3679-3p</td><td>hsa-miR-3200-5p</td></tr><tr><td> hsa-miR-6511b-5p</td><td>hsa-miR-1247-5p</td><td>hsa-miR-22-3p</td><td>hsa-miR-877-5p</td></tr><tr><td> hsa-miR-4687-3p</td><td>hsa-miR-1292-5p</td><td>hsa-miR-181c-5p</td><td>hsa-miR-6131</td></tr><tr><td> hsa-miR-6513-5p</td><td>hsa-miR-3661</td><td>hsa-miR-132-3p</td><td>hsa-miR-214-3p</td></tr><tr><td> hsa-miR-574-3p</td><td>hsa-miR-3190-3p</td><td>hsa-miR-326</td><td>hsa-miR-3191-5p</td></tr><tr><td> hsa-miR-3198</td><td>hsa-miR-3928</td><td>hsa-miR-629-3p</td><td>hsa-miR-4489</td></tr><tr><td> hsa-miR-4700-5p</td><td>hsa-miR-5006-5p</td><td>hsa-miR-5088</td><td>hsa-miR-2110</td></tr><tr><td> hsa-miR-3911</td><td>hsa-miR-3146</td><td/><td/></tr><tr><td colspan="4">DKs-8</td></tr><tr><td> hsa-miR-1224-5p</td><td>hsa-let-7b-5p</td><td>hsa-miR-155-5p</td><td>hsa-let-7c</td></tr><tr><td> hsa-let-7a-5p</td><td>hsa-miR-146b-5p</td><td>hsa-miR-4647</td><td>hsa-miR-4494</td></tr><tr><td> hsa-miR-711</td><td>hsa-miR-1263</td><td/><td/></tr><tr><td colspan="4">DLD-1</td></tr><tr><td> hsa-miR-1226-5p</td><td>hsa-miR-4745-5p</td><td>hsa-miR-4435</td><td>hsa-miR-939-5p</td></tr><tr><td> hsa-miR-409-3p</td><td>hsa-miR-1304-3p</td><td/><td/></tr><tr><td colspan="4">DKO-1 and DKs-8</td></tr><tr><td> hsa-miR-146a-5p</td><td>hsa-miR-4508</td><td>hsa-miR-224-5p</td><td>hsa-miR-4429</td></tr><tr><td> hsa-miR-222-5p</td><td>hsa-miR-629-5p</td><td>hsa-miR-4492</td><td>hsa-miR-3653</td></tr><tr><td> hsa-miR-320a</td><td>hsa-miR-1290</td><td>hsa-miR-1262</td><td>hsa-miR-5010-5p</td></tr><tr><td> hsa-miR-204-3p</td><td>hsa-miR-4461</td><td>hsa-miR-5187-5p</td><td/></tr><tr><td colspan="4">DKO-1 and DLD-1</td></tr><tr><td> hsa-miR-483-5p</td><td>hsa-miR-4658</td><td>hsa-miR-4758-5p</td><td>hsa-miR-492</td></tr><tr><td> hsa-miR-5001-5p</td><td>hsa-miR-371a-5p</td><td>hsa-miR-1323</td><td>hsa-miR-371b-3p</td></tr><tr><td> hsa-miR-501-3p</td><td>hsa-miR-4446-3p</td><td>hsa-miR-6511a-5p</td><td>hsa-miR-30a-3p</td></tr><tr><td> hsa-miR-4727-3p</td><td/><td/><td/></tr><tr><td colspan="4">DLD-1 and DKs-8</td></tr><tr><td> hsa-miR-28-3p</td><td>hsa-miR-3934-5p</td><td/><td/></tr><tr><td colspan="4">DKO-1, DLD-1 and DKs-8</td></tr><tr><td> hsa-miR-658</td><td>hsa-miR-320d</td><td>hsa-miR-4792</td><td>hsa-miR-1246</td></tr><tr><td> hsa-miR-320e</td><td>hsa-miR-4516</td><td>hsa-miR-320b</td><td>hsa-miR-4488</td></tr><tr><td> hsa-miR-1291</td><td>hsa-miR-320c</td><td>hsa-miR-4634</td><td>hsa-miR-3605-5p</td></tr><tr><td> hsa-miR-4741</td><td>hsa-miR-3591-3p</td><td>hsa-miR-122-5p</td><td>hsa-miR-486-3p</td></tr><tr><td> hsa-miR-184</td><td>hsa-miR-223-3p</td><td>hsa-miR-3651</td><td>hsa-miR-486-5p</td></tr><tr><td> hsa-miR-3180</td><td>hsa-miR-3180-3p</td><td>hsa-miR-3168</td><td>hsa-miR-4497</td></tr><tr><td> hsa-miR-423-5p</td><td>hsa-miR-3184-3p</td><td>hsa-miR-150-5p</td><td>hsa-miR-664a-5p</td></tr><tr><td> hsa-miR-182-5p</td><td/><td/><td/></tr></tbody></table><table-wrap-foot><fn id="tblfn2"><label>*</label><p>miRNAs differentially enriched in exosomes when comparing mean reads in exosomes vs cell.</p></fn><fn><p>miRNAs expression patterns were compared between exosomes purified from DKs-8, DKO-1, and DLD-1 cells. miRNAs were identified that were enriched in exosomes from just one of the three cell lines or that overlapped between combinations of cell lines. 29 miRNAs were common between exosomes from all three cell lines. 94 were enriched in exosomes from DKO-1 cells, 10 in exosomes from DKs-8 cells, and only 6 in exosomes from DLD-1 cells.</p></fn></table-wrap-foot></table-wrap><fig id="fig3" position="float"><object-id pub-id-type="doi">10.7554/eLife.07197.013</object-id><label>Figure 3.</label><caption><title><italic>KRAS</italic>-dependent regulation of miRNAs in exosomes and cells.</title><p>Differentially distributed miRNAs in (<bold>A</bold>) cells and (<bold>B</bold>) exosomes from the three CRC cell lines differing in <italic>KRAS</italic> status. (<bold>C</bold>) qRT-PCR validation of selected miRs from DKs-8 and DKO-1 cellular and exosomal RNA samples normalized to U6 snRNA. Fold changes were calculated using the ΔΔC(t) method comparing exosomes to cells. Negative fold changes indicate greater enrichment in cells, and positive fold changes indicate greater enrichment in exosomes. Also see <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 2</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.013">http://dx.doi.org/10.7554/eLife.07197.013</ext-link></p></caption><graphic xlink:href="elife-07197-fig3-v2.tif"/></fig></p></sec><sec id="s2-3"><title><italic>KRAS-</italic>dependent sorting of miRNAs</title><sec id="s2-3-1"><title>miR-100</title><p>Down regulation of <italic>miR-100-5p</italic> was observed in mutant <italic>KRAS</italic> DKO-1 and parental DLD-1 cells compared to wild-type <italic>KRAS</italic> DKs-8 cells (<xref ref-type="table" rid="tbl1">Table 1</xref>). This is consistent with reports that have shown decreased <italic>miR-100</italic> expression in metastatic cancers (<xref ref-type="bibr" rid="bib51">Petrelli et al., 2012</xref>; <xref ref-type="bibr" rid="bib25">Gebeshuber and Martinez, 2013</xref>). <italic>miR-100</italic> has also been shown to negatively regulate migration, invasion, and the epithelial–mesenchymal transition (EMT) (<xref ref-type="bibr" rid="bib13">Chen et al., 2014</xref>; <xref ref-type="bibr" rid="bib64">Wang et al., 2014</xref>; <xref ref-type="bibr" rid="bib69">Zhou et al., 2015</xref>). Interestingly, <italic>miR-100</italic> was enriched in exosomes derived from mutant <italic>KRAS</italic> cells (&gt;eightfold and &gt;threefold enriched in DKO-1 and DLD-1 exosomes, respectively; <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 2</xref>), suggesting that decrease of <italic>miR-100</italic> in cells is due to secretion in exosomes. This is in line with findings that circulating levels of <italic>miR-100</italic> are upregulated in the plasma of mutant <italic>KRAS</italic>-expressing mouse pancreatic cancer models and in patients with pancreatic cancer (<xref ref-type="bibr" rid="bib38">LaConti et al., 2011</xref>). More broadly, the observation that <italic>miR-100-5p</italic> specifically accumulates in exosomes suggests that there may be sequence-specific requirements for the sorting of certain miRNAs into exosomes.</p></sec><sec id="s2-3-2"><title>miR-10b</title><p>Our RNA sequencing data identified <italic>miR-10b</italic> as preferentially secreted in exosomes isolated from cells harboring a wild-type <italic>KRAS</italic> allele (&gt;threefold-change and &gt;twofold-change enrichment in DKs-8 and DLD-1 exosomes, respectively) but retained in mutant <italic>KRAS</italic> DKO-1 cells (∼threefold-change cell enrichment). <italic>miR-10b</italic> is referred to as an oncomiR because it is frequently upregulated during progression of various cancers, including CRC (<xref ref-type="bibr" rid="bib42">Ma, 2010</xref>).</p></sec><sec id="s2-3-3"><title>miR-320</title><p><italic>miR-320</italic> is aberrantly expressed in several types of cancer, including colon cancer. It is expressed in the proliferative compartment of normal colonic crypts (<xref ref-type="bibr" rid="bib53">Schepeler et al., 2008</xref>; <xref ref-type="bibr" rid="bib32">Hsieh et al., 2013</xref>). <italic>miR-320</italic> members (<italic>miR-320b, -c, d, and -e</italic>) were abundant in both mutant <italic>KRAS</italic> (DKO-1) and wild-type <italic>KRAS</italic> (DKs-8) exosomes, but underrepresented in the matched cells, indicating that some miRNAs are transcribed and predominantly exported into exosomes, independent of <italic>KRAS</italic> status (<xref ref-type="table" rid="tbl2">Table 2</xref>, <xref ref-type="supplementary-material" rid="SD2-data">Supplementary file 1A</xref>). Of these family members, <italic>miR-320a</italic> and <italic>miR</italic>-<italic>320b</italic> were the most abundant species represented in exosomes by our RNA sequencing analyses (<italic>miR-320a</italic> in DKO-1 exosomes, and <italic>miR-320b</italic> in DKs-8 and DKO-1 exosomes). Interestingly, however, we observed the largest enrichment for <italic>miR-320d</italic> (fold changes &gt;241 in DKs-8 and &gt;229 in DKO-1) in exosomes relative to cells, despite being ∼fourfold less abundant than <italic>miR-320b</italic> levels. Because the 3′-terminus may be important in regulating miRNA stability and turnover, coupled to the fact that the sequences of <italic>miR-320a-d</italic> members differ only at their 3′-termini, enrichment of certain miRNAs in exosomes could be due to higher turnover/decay rates in cells.</p></sec></sec><sec id="s2-4"><title>Exosomal secretion and strand selection</title><p>Because we observed differential export of specific miRNAs, we investigated whether there might be miRNA sequence-specific sorting signals. Previous reports have shown differential accumulation of 5p or 3p strands in exosomes compared to parental cells (<xref ref-type="bibr" rid="bib33">Ji et al., 2014</xref>). Thus, we analyzed our data sets to test whether exosomes might be preferentially enriched for one strand over the other. We were able to identify individual miRNAs where the two strands differentially sorted between cells and exosomes. For example, the -5p strands of <italic>miR-423</italic> were overrepresented in DKO-1 exosomes but in exosomes from DKs-8 cells, both strands were overrepresented compared to cells (data not shown). This indicates that <italic>KRAS</italic> status may differentially affect selection of passenger or guide strands for sorting into exosomes for select individual miRNAs.</p><p>Individual miRNAs often exist as populations of variants (isomiRs) that differ in length and/or nucleotide composition generated by template- or non-template-directed variation (<xref ref-type="bibr" rid="bib10">Burroughs et al., 2010</xref>; <xref ref-type="bibr" rid="bib49">Newman et al., 2011</xref>; <xref ref-type="bibr" rid="bib48">Neilsen et al., 2012</xref>). When we analyzed our sequencing data sets, we did not detect differential accumulation of isomers with variable 5′ termini (data not shown). For cellular miRNAs, most reads were full length with a slight enrichment in 3′ non-templated addition of A-tailed miRNAs, regardless of <italic>KRAS</italic> status (<xref ref-type="fig" rid="fig4">Figure 4</xref>; <xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1</xref>). For exosomes, we observed a slight enrichment for C residues added to the 3′ ends of miRNAs from wild-type <italic>KRAS</italic> cells (<xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1</xref>). We did not observe this in mutant <italic>KRAS</italic> exosomes, where instead, we noticed an increase in 3′ trimming of miRNAs (<xref ref-type="fig" rid="fig4">Figure 4</xref>, <xref ref-type="fig" rid="fig4s2">Figure 4—figure supplement 2</xref>). Overall, it remains to be determined whether such modifications constitute a global exosomal sorting signal in these cells.<fig-group><fig id="fig4" position="float"><object-id pub-id-type="doi">10.7554/eLife.07197.014</object-id><label>Figure 4.</label><caption><title>Comparison of miRNA 3′ trimming and tailing between cells and exosomes.</title><p>Data from the heat maps shown in <xref ref-type="fig" rid="fig4s2">Figure 4—figure supplement 2</xref> were pooled to illustrate overall changes in either 3′ nucleotide additions (tailing) or 3′ resection (trimming) compared to full length miRNA sequences (intact). Overall, the patterns between cells and between exosomes are very similar. A comparison of cells to exosomes shows that exosomes display a slight increase in trimmed miRNAs. Also see <xref ref-type="fig" rid="fig4s2">Figure 4—figure supplement 2</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.014">http://dx.doi.org/10.7554/eLife.07197.014</ext-link></p></caption><graphic xlink:href="elife-07197-fig4-v2.tif"/></fig><fig id="fig4s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.07197.015</object-id><label>Figure 4—figure supplement 1.</label><caption><title>Non-templated addition (NTA) of nucleotides to 3′ ends of miRNAs.</title><p>3′ NTA of A-tailed miRNAs is enriched in cells independent of <italic>KRAS</italic> status, whereas NTA of C residues are more abundant in wild-type <italic>KRAS</italic> DKs-8 exosomes. miRNAs with read counts ≥500 reads in both cells and exosomes were used in the analysis. Reads mapping to hairpin sequences were considered as templated miRNAs (untrimmed). Reads ≥18 nucleotides that did not map to hairpin or genome sequences were trimmed one nucleotide at the 3′-termini and mapped again to hairpin sequences. This was repeated three times to account for NTA's extending up to three nucleotides from the 3′-terminus. miRNAs significantly enriched in exosomes or cells are represented by red and blue circles, respectively.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.015">http://dx.doi.org/10.7554/eLife.07197.015</ext-link></p></caption><graphic xlink:href="elife-07197-fig4-figsupp1-v2.tif"/></fig><fig id="fig4s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.07197.016</object-id><label>Figure 4—figure supplement 2.</label><caption><title>Comparison of miRNA 3′ trimming and tailing between cells and exosomes.</title><p>Heat maps show the extent of either 3′ nucleotide additions (tailing) or 3′ resection (trimming) compared to full-length miRNA sequences (intact).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.016">http://dx.doi.org/10.7554/eLife.07197.016</ext-link></p></caption><graphic xlink:href="elife-07197-fig4-figsupp2-v2.tif"/></fig><fig id="fig4s3" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.07197.017</object-id><label>Figure 4—figure supplement 3.</label><caption><title>MEME analysis of miRNA sequence in exosomes.</title><p>MEME analysis was performed to attempt to identify sequence motifs that might target miRNAs for export into exosomes. The top most abundant motifs found in miRNAs in <xref ref-type="table" rid="tbl1 tbl2">Tables 1, 2</xref> are shown for both cells and exosomes from DKO-1, DKs-8, or DLD-1 cell lines. (Upregulated in DKO-1 exo: 51, 1.5e-009; Upregulated in DKO-1 cell: 28,1.5e-007; Upregulated in DKs-8 exo, 22, 1.7e-010; Upregulated in DKs-8 cell, 19, 7.6e-007; Upregulated in DLD-1 exo, 8, 2.3e-003; Upregulated in DLD-1 cell 23, 3.3e-012).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.017">http://dx.doi.org/10.7554/eLife.07197.017</ext-link></p></caption><graphic xlink:href="elife-07197-fig4-figsupp3-v2.tif"/></fig></fig-group></p><p>Consistent with published data, we have shown that miRNA expression patterns vary between parental cells and their cognate exosomes (<xref ref-type="table" rid="tbl1 tbl2">Tables 1, 2</xref>, <xref ref-type="fig" rid="fig3">Figure 3A,B</xref>) (<xref ref-type="bibr" rid="bib60">Valadi et al., 2007</xref>; <xref ref-type="bibr" rid="bib45">Mittelbrunn et al., 2011</xref>; <xref ref-type="bibr" rid="bib19">Ekstrom et al., 2012</xref>; <xref ref-type="bibr" rid="bib46">Montecalvo et al., 2012</xref>; <xref ref-type="bibr" rid="bib56">Squadrito et al., 2014</xref>). Differential export suggests that specific signals must exist to sort distinct miRNAs (<xref ref-type="bibr" rid="bib6">Batagov et al., 2011</xref>; <xref ref-type="bibr" rid="bib62">Villarroya-Beltri et al., 2013</xref>). We therefore conducted MEME analysis to attempt to identify sequence motifs that might serve as targeting signals. When we examined all miRNA reads detected in exosomes, we did not find any global enrichment for specific sequences or motifs, including those reported to be bound by hnRNP A2B1 (GGAG or U/CC) (<xref ref-type="bibr" rid="bib8">Bolukbasi et al., 2012</xref>; <xref ref-type="bibr" rid="bib62">Villarroya-Beltri et al., 2013</xref>) (<xref ref-type="fig" rid="fig4s3">Figure 4—figure supplement 3</xref>). However, when we analyzed <italic>miR-320</italic> because it is preferentially exported to exosomes independent of <italic>KRAS</italic> status, we were able to identify the GGAG sequence contained within the 3′ end of the mature sequence. Additionally, upon restricting our analysis to reads from the most differentially expressed miRNAs when comparing exosomes to cells, we found a slight enrichment for C residues, possibly alternating C residues in exosomal miRNAs (<xref ref-type="fig" rid="fig4s3">Figure 4—figure supplement 3</xref>).</p></sec><sec id="s2-5"><title>Sphingomyelinase-dependent sorting of miRNAs to exosomes</title><p>Although little is understood regarding the molecular mechanisms for packaging exosomal miRNAs, recent evidence suggests that the secretion of miRNAs in exosomes is dependent on ceramide via its production by neutral sphingomyelinase 2 (nSMase 2) (<xref ref-type="bibr" rid="bib36">Kosaka et al., 2010</xref>; <xref ref-type="bibr" rid="bib45">Mittelbrunn et al., 2011</xref>). Inhibition of de novo ceramide synthesis by treatment with a nSMase inhibitor impaired exosomal miRNA release, apparently due to decreased formation of miRNA-containing exosomes (<xref ref-type="bibr" rid="bib36">Kosaka et al., 2010</xref>; <xref ref-type="bibr" rid="bib45">Mittelbrunn et al., 2011</xref>). To test the role of nSMase in miRNA secretion in our system, we treated CRC cells with the nSMase inhibitor, GW4869. We determined the effect of this inhibitor on <italic>miR-10b</italic> since it is preferentially found in wild-type <italic>KRAS</italic> DKs-8 exosomes, <italic>miR-100</italic> since it is preferentially found in mutant <italic>KRAS</italic> DKO-1 and DLD-1 exosomes, and <italic>miR-320</italic> which sorts into exosomes regardless of <italic>KRAS</italic> status. For <italic>miR-10b</italic>, we did not observe significant changes in its cellular levels after treatment with GW4869 in either wild-type <italic>KRAS</italic> DKs-8 or mutant <italic>KRAS</italic> DKO-1 cells (<xref ref-type="fig" rid="fig5">Figure 5C</xref>). In contrast, inhibition of nSMase caused a ∼threefold increase in intracellular levels of <italic>miR-100</italic> in mutant <italic>KRAS</italic> DKO-1 cells but remained unchanged in wild-type DKs-8 <italic>KRAS</italic> cells (<xref ref-type="fig" rid="fig5">Figure 5A,B,C</xref>). Similarly, <italic>miR-320</italic> levels were found to increase (∼2.5 fold) only in GW4869-treated mutant <italic>KRAS</italic> DKO-1 cells (<xref ref-type="fig" rid="fig5">Figure 5C</xref>). These data are most consistent with the hypothesis that impaired ceramide synthesis alters cellular accumulation of miRNAs dependent on mutant <italic>KRAS</italic> and suggest that multiple biogenic routes exist for miRNA secretion.<fig id="fig5" position="float"><object-id pub-id-type="doi">10.7554/eLife.07197.018</object-id><label>Figure 5.</label><caption><title>Ceramide-dependent miRNA export into exosomes.</title><p>DKO-1 or DKs-8 cells were treated with an inhibitor of neutral sphingomyelinase 2 (nSMase 2), GW4869. After treatment, in situ hybridization experiments were performed with probes against <italic>miR-100</italic> (<bold>A</bold>, <bold>B</bold>). (<bold>C</bold>) qRT-PCR for <italic>miR-10b, miR-100</italic>, and <italic>miR-320a</italic> was performed on cells treated with GW4869 or DMSO, and fold change in expression was determined in treated vs untreated cells. In wild-type <italic>KRAS</italic> cells (DKs-8), inhibition of nSMase 2 had little or no effect on the cellular levels of these miRNAs. In contrast, mutant <italic>KRAS</italic> cells (DKO-1) showed an increase in cellular miRNA levels after inhibition of nSMAse 2. Data were derived from three biological replicates and performed in technical triplicates for qRT-PCR. Significance was determined by two-tailed, paired t-tests where * are p values ≤ 0.05 and ** ≤0.01.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.018">http://dx.doi.org/10.7554/eLife.07197.018</ext-link></p></caption><graphic xlink:href="elife-07197-fig5-v2.tif"/></fig></p></sec><sec id="s2-6"><title>Extracellular transfer of <italic>miR-100</italic></title><p>Several reports have found that extracellular miRNAs can be taken up by recipient cells to mediate heterotypic cell–cell interactions and facilitate target repression in neighboring cells (<xref ref-type="bibr" rid="bib45">Mittelbrunn et al., 2011</xref>; <xref ref-type="bibr" rid="bib7">Boelens et al., 2014</xref>; <xref ref-type="bibr" rid="bib56">Squadrito et al., 2014</xref>). To determine whether secreted miRNAs function in recipient cells, we designed luciferase (Luc) constructs containing either 3 perfect <italic>miR-100</italic> recognition elements (MREs) in the 3′ untranslated region (UTR) (Luc-100-PT) or scrambled 3′UTR sequences that do not match any known miRNAs (Luc-CTL). These constructs were expressed in wild-type <italic>KRAS</italic> DKs-8 cells (recipient cells) in the presence or absence of donor cells. Baseline repression of Luc in the absence of donor cells was first analyzed to determine the levels of repression from endogenous <italic>miR-100</italic> in DKs-8 cells. Compared to the scrambled control (Luc-CTL), strong Luc repression in the absence of donor cells was observed with perfect MREs (<italic>miR-100</italic>-PT) (<xref ref-type="fig" rid="fig6">Figure 6A</xref>). This supports our finding that <italic>miR-100</italic> is expressed and retained in DKs-8 cells.<fig-group><fig id="fig6" position="float"><object-id pub-id-type="doi">10.7554/eLife.07197.019</object-id><label>Figure 6.</label><caption><title>Transfer of extracellular miRNAs by mutant DKO-1 cells promotes target repression in wild-type DKs-8 cells.</title><p>Transwell co-culture of DKs-8 recipient cells with or without DKs-8 or DKO-1 donor cells. Luciferase (Luc) expression was measured in DKs-8 recipient cells transiently expressing (<bold>A</bold>) Luc fused to three perfectly complementary synthetic <italic>miR-100</italic> target sites (<italic>miR-100</italic>-PT) or (<bold>B</bold>) Luc fused to the 3′UTR of mTOR, which harbors 3 endogenous target sites for <italic>miR-100</italic>. (<bold>C</bold>) Luc expression increased upon mutation of two (MS2) sites with full expression upon mutation of all three sites (MS3). Luc-CTL contains three random scrambled target sites that do not match any known miRNA sequence. (<bold>D</bold>) Luc expression was restored in recipient cells expressing <italic>miR-100-</italic>PT upon pretreatment of donor DKO-1 cells with 100 nM <italic>miR-100</italic> antagomirs (AI-100) compared to pre-treatment of donor DKO-1 cells with 100 nm control antagomirs (AI-CTL) targeting <italic>cel-miR-67</italic>. (<bold>E</bold>) Taqman qRT-PCR for <italic>miR-100</italic>. Compared to DKs-8 recipient cells grown without donor cells, <italic>mir-100</italic> levels increased by approximately 34% in the presence of mutant DKO-1 donor cells pre-treated with AI-CTL compared to an 8% increase in AI-100 pre-treated donor cells. Y axis is % increase in <italic>miR-100</italic> = (CP<sub>AI-CTL</sub> or CP<sub>AI-100</sub> − CP<sub>no donor</sub>/CP<sub>no donor</sub>)<sup>*</sup>100, where CP = absolute copy number. All Luc values were normalized to co-transfected vectors expressing β-galactosidase; n = 3 independent experiments in <bold>A</bold>–<bold>C</bold> and n = 4 in <bold>D</bold>, <bold>E</bold>. All Luc assays were performed in technical triplicate. Significance was determined by two-tailed, paired t-tests where * are p values ≤ 0.05 and ** ≤0.01. Also see <xref ref-type="fig" rid="fig6s1 fig6s2 fig6s3">Figure 6—figure supplements 1–3</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.019">http://dx.doi.org/10.7554/eLife.07197.019</ext-link></p></caption><graphic xlink:href="elife-07197-fig6-v2.tif"/></fig><fig id="fig6s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.07197.020</object-id><label>Figure 6—figure supplement 1.</label><caption><title><italic>miR-100</italic> binding sites in the mTOR 3′UTR.</title><p><italic>miR-100</italic> binding sites within the mTOR 3′UTR. Mutated nucleotides indicated in red (oligonucleotide sequences in <xref ref-type="supplementary-material" rid="SD4-data">Supplementary file 3</xref>).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.020">http://dx.doi.org/10.7554/eLife.07197.020</ext-link></p></caption><graphic xlink:href="elife-07197-fig6-figsupp1-v2.tif"/></fig><fig id="fig6s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.07197.021</object-id><label>Figure 6—figure supplement 2.</label><caption><title>Presence of mutant DKO-1 donor cells augments <italic>miR-100</italic> levels in DKs-8 recipient cells.</title><p>Taqman qRT-PCR for <italic>miR-100</italic>. <italic>miR-100</italic> levels increased by approximately 114 copies in recipient cells cultured with DKO-1 donor cells pre-treated with AI-CTL compared to recipient cells cultured without donor cells. Pre-treatment of mutant DKO-1 donor cells with <italic>miR-100</italic> antagomir inhibitor (AI-100) attenuated this effect. Absolute levels of <italic>miR-100</italic> determined by standard curve generation of synthetically derived <italic>miR-100</italic> (see ‘Materials and methods’). Approximately, 357.23 ± 16.65, 442.58 ± 12.59, and 329.48 ± 13.62 copies of <italic>miR-100</italic> per input RNA were found in DKs-8 recipient cells cultured with DKO-1 donor AI-100, DKO-1 donor AI-CTL and without donor cells, respectively.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.021">http://dx.doi.org/10.7554/eLife.07197.021</ext-link></p></caption><graphic xlink:href="elife-07197-fig6-figsupp2-v2.tif"/></fig><fig id="fig6s3" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.07197.022</object-id><label>Figure 6—figure supplement 3.</label><caption><title>Transfer of extracellular miRNAs by mutant DKO-1 cells promotes target repression in wild-type DKs-8 cells.</title><p>Transwell co-culture of DKs-8-recipient cells with or without DKs-8 or DKO-1 donor cells. Luc expression was measured in DKs-8-recipient cells expressing Luc fused to three perfectly complementary synthetic <italic>miR-222</italic> target sites (miR-222-PT).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.022">http://dx.doi.org/10.7554/eLife.07197.022</ext-link></p></caption><graphic xlink:href="elife-07197-fig6-figsupp3-v2.tif"/></fig></fig-group></p><p>To determine whether secretion of <italic>miR-100</italic> by mutant <italic>KRAS</italic> DKO-1 donor cells could further augment <italic>miR-100</italic> function in recipient wild-type cells, Transwell co-culture experiments were performed with DKs-8 recipient cells expressing the Luc reporters in the presence of DKO-1 donor cells (<xref ref-type="fig" rid="fig6">Figure 6</xref>). Significantly increased repression of Luc was observed when the reporter construct containing three perfect <italic>miR-100</italic> sites was used (<italic>miR-100</italic>-PT) (<xref ref-type="fig" rid="fig6">Figure 6A</xref>). Because exosomes released from DKO-1 cells contain abundant levels of <italic>miR-100,</italic> increased Luc repression is consistent with transfer of additional copies of <italic>miR-100.</italic> Two control experiments were performed to test the hypothesis that additional copies of <italic>miR-100</italic> are transferred between donor and recipient cells. First, we treated donor cells with antagomirs that block production of <italic>miR-100</italic>. Luc repression was almost completely reversed upon pre-treatment of DKO-1 donor cells with a <italic>miR-100</italic> hairpin antagomir inhibitor (AI-100) (<xref ref-type="fig" rid="fig6">Figure 6D</xref>). Second, we performed qRT/PCR to calculate the increase in <italic>miR-100</italic> levels in recipient cells. Cells grown in the presence or absence of donor cells showed an approximate 34% increase in the levels of <italic>miR-100</italic> (<xref ref-type="fig" rid="fig6">Figure 6E</xref> and <xref ref-type="fig" rid="fig6s2">Figure 6—figure supplement 2</xref>).</p><p>To further probe the repressive activity of <italic>miR-100</italic>, we performed co-culture experiments in which the recipient Dks-8 cells express Luc fused to the 3′UTR of mTOR, an endogenous <italic>miR-100</italic> target (<xref ref-type="bibr" rid="bib47">Nagaraja et al., 2010</xref>; <xref ref-type="bibr" rid="bib29">Grundmann et al., 2011</xref>; <xref ref-type="bibr" rid="bib24">Ge et al., 2014</xref>). As observed with <italic>miR-100</italic>-PT repression, Luc-mTOR was significantly repressed in the presence of mutant <italic>KRAS</italic> DKO-1 but not in the presence of wild-type <italic>KRAS</italic> DKs-8 donor cells (<xref ref-type="fig" rid="fig6">Figure 6B</xref>). This suggests that <italic>miR-100</italic>-repressive activity is specific to the presence of mutant <italic>KRAS</italic> DKO-1 donor cells. To confirm these results, we mutated the MREs within the mTOR 3′UTR and assayed for <italic>miR-100</italic> activity (<xref ref-type="fig" rid="fig6s1">Figure 6—figure supplement 1</xref>). Mutation of individual sites did not show significantly different Luc repression (data not shown). However, upon mutation of two MREs (MS2), we observed a partial rescue of Luc expression (<xref ref-type="fig" rid="fig6">Figure 6C</xref>). This was further augmented upon mutation of all three sites (MS3), with a complete rescue of <italic>miR-100-</italic>mediated repressive activity (<xref ref-type="fig" rid="fig6">Figure 6C</xref>).</p><p>As a final test of miRNA transfer in the Transwell co-culture experiments, we created vectors expressing Luc fused to a 3′UTR containing perfect sites for <italic>miR-222</italic> because <italic>miR-222</italic> is not detectable in DKs-8-recipient cells, unlike <italic>miR-100</italic>. In this case, silencing of Luc should be due to transfer of <italic>miR-222</italic> and not due to unforeseen changes in endogenous miRNA activity. We observed a greater than twofold repression of the <italic>miR-222</italic> Luc reporter in recipient cells (<xref ref-type="fig" rid="fig6s3">Figure 6—figure supplement 3</xref>). These results support the hypothesis that miRNAs secreted by mutant <italic>KRAS</italic> cells can be transferred to recipient cells.</p></sec></sec><sec id="s3" sec-type="discussion"><title>Discussion</title><p>In this study, we comprehensively examined the composition of small ncRNAs from exosomes and cells of isogenic CRC cell lines that differ only in <italic>KRAS</italic> status. By employing small RNA transcriptome analyses, we found that oncogenic <italic>KRAS</italic> selectively alters the miRNA profile in exosomes, and that ceramide depletion selectively promotes miRNA accumulation in mutant <italic>KRAS</italic> CRC cells. Distinct miRNA profiles between cells and their exosomes may be functionally coupled to mitogenic signaling.</p><p><italic>KRAS</italic> status-specific patterns of secreted miRNAs support the idea of using exosomes as potential biomarkers in CRC. Our finding that <italic>miR-10b</italic> is preferentially enriched in wild-type <italic>KRAS</italic>-derived exosomes, while <italic>miR-100</italic> is enriched in mutant <italic>KRAS</italic>-derived exosomes raises interesting questions regarding how they are selected for secretion. <italic>miR-10b</italic> and <italic>miR-100</italic> are both part of the <italic>miR-10/100</italic> family and differ by only one base in the seed region, allowing regulation of distinct sets of target mRNAs (<xref ref-type="bibr" rid="bib58">Tehler et al., 2011</xref>). Whether the accumulation or export of these miRNAs is a result or a consequence of oncogenic signaling remains unknown. Preventing the export or retention of certain miRNAs, such as <italic>miR-100 and miR-10b,</italic> may serve a therapeutic role in reversing the tumorigenic effects seen with aberrant miRNA expression.</p><p><italic>KRAS</italic>-dependent differential miRNA expression more prominently affected miRNA expression patterns observed in exosomes than in the parent cells. This could reflect a mechanism by cells to selectively export miRNAs so as to maintain specific growth or gene expression states. This is consistent with a recent report that found that the cellular levels of <italic>miR-218-5p</italic> could be maintained, despite changes in the abundance of its target, likely through a ‘miRNA relocation effect’ where unbound miRNAs that are in excess have the potential to be sorted to exosomes (<xref ref-type="bibr" rid="bib56">Squadrito et al., 2014</xref>). Another mechanism may be through sequence-specific motifs that direct miRNA trafficking by interaction with specific chaperone proteins (<xref ref-type="bibr" rid="bib8">Bolukbasi et al., 2012</xref>; <xref ref-type="bibr" rid="bib62">Villarroya-Beltri et al., 2013</xref>). Although we did not find any globally significant motif overrepresented in exosomal miRNAs, we cannot rule out that individual miRNAs might undergo sequence-specific export. <italic>miR-320</italic> family members all contain the GGAG motif that has been proposed to serve as an exosomal targeting signal (<xref ref-type="bibr" rid="bib62">Villarroya-Beltri et al., 2013</xref>). We found that members of the <italic>miR-320</italic> family are preferentially enriched in exosomes independent of <italic>KRAS</italic> status; however, the GGAG sequence was not found in other miRNAs that are targeted to exosomes. It has been reported that the biogenesis of <italic>miR-320</italic> family members occurs by a non-canonical pathway that requires neither Drosha (<xref ref-type="bibr" rid="bib15">Chong et al., 2010</xref>) nor XPO5 (<xref ref-type="bibr" rid="bib68">Xie et al., 2013</xref>). Instead, the 5′ ends contain a 7-methyl guanosine cap that facilitates nuclear–cytoplasmic transport through XPO1 (<xref ref-type="bibr" rid="bib68">Xie et al., 2013</xref>). XPO1 is present in DKO-1, DKs-8, and DLD-1 exosomes as detected by mass spectrometry (<xref ref-type="bibr" rid="bib18">Demory Beckler et al., 2013</xref>). It will be interesting to investigate whether alternate processing pathways and associated biogenic machinery contribute to the heterogeneity of EV cargo and affect miRNA secretion.</p><p>It was recently demonstrated that miRNAs in B-cell exosomes display enriched levels of non-template-directed 3′-uridylated miRNAs, while 3′-adenylated miRNA species are preferentially cell enriched (<xref ref-type="bibr" rid="bib35">Koppers-Lalic et al., 2014</xref>). In certain contexts, the addition of non-templated uridine residues to cognate miRNAs accelerates miRNA turnover (<xref ref-type="bibr" rid="bib4">Baccarini et al., 2011</xref>; <xref ref-type="bibr" rid="bib65">Wei et al., 2012</xref>). Thus, it is possible that the stability/half-life of a miRNA affects whether it is retained or secreted. While the exact functional significance of 3′-end modifications of miRNAs detected in both cells and exosomes remains to be determined, it could be that differential export of ‘tagged’ miRNAs could allow cells to export specific miRNAs. However, the lack of any apparent motif upon global analysis of miRNAs enriched in exosomes, coupled to the finding that even untagged miRNAs are differentially exported, suggests multiple strategies for loading of miRNAs into EVs, and that not all EVs and exosomes contain identical cargo. This further implies that different cell types secrete a heterogeneous population of vesicles. Although the biological relevance of these findings remains to be determined, the specific sorting of miRNAs into exosomes may enable cancer cells to discard tumor-suppressive miRNAs so as to increase their oncogenic potential or perhaps modulate gene expression in neighboring and distant cells to promote tumorigenesis. In support of this hypothesis, <italic>miR-100</italic>, which we found to be enriched in mutant <italic>KRAS</italic> exosomes, was found to down-regulate LGR5 in CRC cells and thereby inhibit migration and invasion of such cells (<xref ref-type="bibr" rid="bib69">Zhou et al., 2015</xref>). In this context, removal of <italic>miR-100</italic> from the cell would be a tumor-promoting event.</p><p>In other contexts, <italic>miR-100</italic> can have contradictory activities, both inducing EMT by down-regulating E-cadherin through targeting SMARCA5 and inhibiting tumorigenicity by targeting HOXA1 (<xref ref-type="bibr" rid="bib13">Chen et al., 2014</xref>). Thus, although <italic>miR-100</italic> can function as a tumor suppressor under normal conditions, augmenting its levels, for example, by EV uptake, could potentially promote EMT. In this regard, the role of <italic>miR-100</italic> in tumorigenesis would be twofold, where its secretion in exosomes could function to maintain low-intracellular levels within mutant cells, while inducing EMT in wild-type-recipient cells. Along these lines, <italic>miR-100</italic> is part of the <italic>miR-125b/let-7a-2/miR-100</italic> cluster that is transcribed and expressed coordinately (<xref ref-type="bibr" rid="bib20">Emmrich et al., 2014</xref>). Interestingly, in malignant colonic tissues from individuals with CRC, <italic>miR-100</italic> levels were significantly decreased while <italic>let-7a</italic> levels were strongly upregulated (<xref ref-type="bibr" rid="bib57">Tarasov et al., 2014</xref>). Based on our finding that there is differential accumulation of individual miRNAs within this cluster between mutant <italic>KRAS</italic> cells and exosomes, it will be interesting to determine whether cancer cells down-regulate specific miRNAs by active secretion, while simultaneously maintaining the levels of other miRNAs transcribed within the same cluster.</p><p>miRNAs are secreted from malignant breast epithelial cells after packaging into vesicles larger than conventional exosomes that are enriched in CD44, whose expression is linked to breast cancer metastasis (<xref ref-type="bibr" rid="bib50">Palma et al., 2012</xref>). Normal cells tend to release miRNAs in more homogenous types of exosomes, suggesting that malignant transformation may alter the formation of secreted vesicles that could alter miRNA export and lead to differences in exosome content and morphology (<xref ref-type="bibr" rid="bib50">Palma et al., 2012</xref>; <xref ref-type="bibr" rid="bib44">Melo et al., 2014</xref>). In support of this, it was recently shown that in exosomes from breast cancer cells, CD43 mediates the accumulation of Dicer (<xref ref-type="bibr" rid="bib44">Melo et al., 2014</xref>). These exosomes also contain other RNA-induced silencing complex (RISC) proteins and pre-miRNAs, indicating that miRNA processing can occur in exosomes (<xref ref-type="bibr" rid="bib44">Melo et al., 2014</xref>). These components were absent in exosomes derived from normal cells. It remains to be determined whether components of the RISC-loading complex assemble within endosomes before their secretion as exosomes or by the fusion of exosomes containing heterogeneous cargo after they are secreted. The observation that cells can selectively release miRNAs and also release a heterogeneous population of vesicles raises the possibility that differential release of miRNAs is associated with different classes of exosomes and microvesicles.</p><p>Recently, quantitative analysis of secreted miRNAs suggested that the levels of extracellular miRNAs are limited and raise the question as to how such levels can alter gene expression in recipient cells (<xref ref-type="bibr" rid="bib14">Chevillet et al., 2014</xref>). The results of our Transwell co-culture experiments are most consistent with extracellular transfer of specific miRNAs to alter expression of reporter constructs. Nevertheless, the level of exosomal transfer that is needed to alter recipient cell gene expression in vivo remains an open question. Our finding that mutant <italic>KRAS</italic> protein can be functionally transferred in exosomes indicates that the full effect of exosomes on recipient cells can be due to a combination of both RNA delivery and protein-based signaling (<xref ref-type="bibr" rid="bib30">Higginbotham et al., 2011</xref>). This could include activation of Toll-like receptors with possible downstream effects following nuclear factor kappa-light-chain-enhancer of activated B cells or mitogen-activated protein kinase cascades (<xref ref-type="bibr" rid="bib21">Fabbri et al., 2012</xref>; <xref ref-type="bibr" rid="bib12">Chen et al., 2013</xref>). The complexity of <italic>miR-100</italic> function in the tumor microenvironment underscores this argument by its potential for inhibiting mTOR expression which is required for proliferation of <italic>Apc</italic>-deficient tumors in mouse models (<xref ref-type="bibr" rid="bib22">Faller et al., 2015</xref>). In tumors where some cells have incurred activating mutations in <italic>KRAS</italic>, while others have not, <italic>miR-100</italic> could accumulate in wild-type <italic>KRAS</italic> tumor cells through exosomal transfer, inhibiting mTOR and cell growth. Conversely, <italic>miR-100</italic> could be secreted from mutant <italic>KRAS</italic> cells giving them a growth advantage. In this way, exosomal transfer of miRNAs might act to select for cells carrying specific tumor driver mutations. Our studies have direct implications for CRC and, together with other studies, indicate that delivery of exosomes to recipient cells can induce cell migration, inflammation, immune responses, angiogenesis, invasion, pre-metastatic niche formation, and metastasis (<xref ref-type="bibr" rid="bib34">Kahlert and Kalluri, 2013</xref>; <xref ref-type="bibr" rid="bib7">Boelens et al., 2014</xref>; <xref ref-type="bibr" rid="bib44">Melo et al., 2014</xref>; <xref ref-type="bibr" rid="bib16">Costa-Silva et al., 2015</xref>).</p></sec><sec id="s4" sec-type="materials|methods"><title>Materials and methods</title><sec id="s4-1"><title>Exosome isolation</title><p>Exosomes were isolated from conditioned medium of DKO-1, Dks-8, and DLD-1 cells as previously described, with slight modification (<xref ref-type="bibr" rid="bib30">Higginbotham et al., 2011</xref>). Briefly, cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% bovine growth serum until 80% confluent. The cells were then washed three times with Phosphate buffered saline (PBS) and cultured for 24 hr in serum-free medium. The medium was collected and replaced with ionomycin-containing medium for 1 hr, after which ionomycin-containing medium was collected and pooled with the previously collected serum-free medium. Pooled media was centrifuged for 10 min at 300×<italic>g</italic> to remove cellular debris, and the resulting supernatant was then filtered through a 0.22-mm polyethersulfone filter (Nalgene, Rochester, NY, USA) to reduce microparticle contamination. The filtrate was concentrated ∼300-fold with a 100,000 molecular weight cut-off centrifugal concentrator (Millipore, Darmstadt, Germany). The concentrate was then subjected to high-speed centrifugation at 150,000×<italic>g</italic> for 2 hr. The resulting exosome-enriched pellet was resuspended in PBS containing 25 mM hydroxyethyl-piperazineethanesulfonic acid (HEPES) (pH 7.2) and washed by centrifuging again at 150,000×<italic>g</italic> for 3 hr. The wash steps were repeated a minimum of three times until no trace of phenol red was detected. The resulting pellet was resuspended in PBS containing 25 mM HEPES (pH 7.2), and protein concentrations were determined with a MicroBCA kit (Pierce/Thermo, Rockford, IL, USA). The number of exosomes per μg of protein was determined by means of nanoparticle tracking analysis (NanoSight, Wiltshire, UK). Analysis was performed on three independent preparations of exosomes.</p></sec><sec id="s4-2"><title>RNA purification</title><p>Total RNA from exosomes and cells was isolated using TRIzol (Life Technologies/Thermo, Grand Island, NY). In the case of exosomal RNA isolation, TRIzol was incubated with 100 μl or less of concentrated exosomes for an extended 15 min incubation prior to chloroform extraction. RNA pellets were resuspended in 60 μl of RNase-free water and were then re-purified using the miRNeasy kit (Qiagen Inc., Valencia, CA, USA). Final RNAs were eluted with two rounds of 30 μl water extraction.</p></sec><sec id="s4-3"><title>miRNA library preparation and sequencing</title><p>Total RNA from each sample was used for small RNA library preparation using NEBNext Small RNA Library Prep Set from Illumina (New England BioLabs Inc., Ipswich, MA, USA). Briefly, 3′ adapters were ligated to total input RNA followed by hybridization of multiplex single read (SR) reverse transcription (RT) primers and ligation of multiplex 5′ SR adapters. RT was performed using ProtoScript II RT for 1 hr at 50°C. Immediately after RT reactions, PCR amplification was performed for 15 cycles using LongAmp Taq 2× master mix. Illumina-indexed primers were added to uniquely barcode each sample. Post-PCR material was purified using QIAquick PCR purification kits (Qiagen Inc.). Post-PCR yield and concentration of the prepared libraries were assessed using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, California, CA, USA) and DNA 1000 chip on Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA, USA), respectively. Size selection of small RNA with a target size range of approximately 146–148 bp was performed using 3% dye free agarose gel cassettes on a Pippin Prep instrument (Sage Science Inc., Beverly, MA, USA). Post-size selection yield and concentration of libraries were assessed using Qubit 2.0 Fluorometer and DNA high-sensitivity chip on an Agilent 2100 Bioanalyzer, respectively. Accurate quantification for sequencing applications was performed using qPCR-based KAPA Biosystems Library Quantification kits (Kapa Biosystems, Inc., Woburn, MA, USA). Each library was diluted to a final concentration of 1.25 nM and pooled in equimolar ratios prior to clustering. Cluster generation was carried out on a cBot v8.0 using Illumina's Truseq Single Read Cluster Kit v3.0. Single-end sequencing was performed to generate at least 15 million reads per sample on an Illumina HiSeq2000 using a 50-cycleTruSeq SBSHSv3 reagent kit. Clustered flow cells were sequenced for 56 cycles, consisting of a 50-cycle read, followed by a 6-cycle index read. Image analysis and base calling were performed using the standard Illumina pipeline consisting of Real Time Analysis version v1.17 and demultiplexed using bcl2fastq converter with default settings.</p></sec><sec id="s4-4"><title>Mapping of RNA reads</title><p>Read sequence quality checks were performed by FastQC (Babraham Bioinformatics [<ext-link ext-link-type="uri" xlink:href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</ext-link>]). Adapters from the 3′ ends of reads were trimmed using Cutadpt with a maximum allowed error rate of 0.1 (<xref ref-type="bibr" rid="bib43">Martin, 2011</xref>). Reads shorter than 15 nucleotides in length were excluded from further analysis. Reads were mapped to the human genome hg19 using Bowtie version 1.1.1 (<xref ref-type="bibr" rid="bib39">Langmead and Salzberg, 2012</xref>). Mapped reads were annotated using ncPRO-seq (<xref ref-type="bibr" rid="bib11">Chen et al., 2012</xref>) based on miRbase (<xref ref-type="bibr" rid="bib27">Griffiths-Jones et al., 2008</xref>), Rfam (<xref ref-type="bibr" rid="bib23">Gardner et al., 2011</xref>; <xref ref-type="bibr" rid="bib9">Burge et al., 2013</xref>), and RepeatMasker (<ext-link ext-link-type="uri" xlink:href="http://www.repeatmasker.org/">http://www.repeatmasker.org/</ext-link>), and expression levels were quantified based on read counts. Mature miRNA annotation was extended 2 bp in both upstream and downstream regions to accommodate inaccurate processing of precursor miRNAs. Reads with multiple mapping locations were weighted by the number of mapping locations.</p></sec><sec id="s4-5"><title>PC analysis</title><p>DESeq Version 1.16.0 was used to perform PC analyses (<xref ref-type="bibr" rid="bib2">Anders and Huber, 2010</xref>).</p></sec><sec id="s4-6"><title>Enrichment analysis</title><p>Differential expression was analyzed using DESeq Version 1.16.0 (<xref ref-type="bibr" rid="bib2">Anders and Huber, 2010</xref>). Negative binomial distribution was used to compare miRNA abundance between cells vs exosomes and wild-type vs mutant <italic>KRAS</italic> status. The trimmed mean of M values method was used for normalization (<xref ref-type="bibr" rid="bib52">Robinson and Oshlack, 2010</xref>). Differential expression was determined based on log2 fold change (log2 fold change) and false discovery rate (FDR) with |log2 fold change| ≥ 1 and FDR ≤ 0.001.</p></sec><sec id="s4-7"><title>Trimming and tailing</title><p>Trimming and tailing analysis was based on miRBase annotation (<xref ref-type="bibr" rid="bib26">Griffiths-Jones et al., 2006</xref>, <xref ref-type="bibr" rid="bib27">2008</xref>; <xref ref-type="bibr" rid="bib28">Griffiths-Jones, 2010</xref>). Only high-confidence miRNAs (544) and corresponding hairpin sequences were used. Bowtie version 1.1.1 with 0 mismatch was used for mapping. miRNA reads were first mapped to hairpin sequences with unmapped reads, then mapped to the human genome hg19. Remaining reads were trimmed 1 bp from the 3′ end and remapped to hairpin sequences. The remapping process was repeated 10 times. Finally, all mapped reads were collected for further analysis.</p></sec><sec id="s4-8"><title>qRT/PCR</title><p>Taqman small RNA assays (Life Technologies) (individual assay numbers are listed below) were performed for indicated miRNAs on cellular and exosomal RNA samples. Briefly, 10 ng of total RNA was used per individual RT reactions; 0.67 μl of the resultant cDNA was used in 10 μl qPCR reactions. qPCR reactions were conducted in 96-well plates on a Bio-Rad CFX96 instrument. All C(t) values were ≤30. Triplicate C(t) values were averaged and normalized to U6 snRNA. Fold changes were calculated using the ∆∆C(t) method, where ∆ = C(t)<sub>miRNA</sub> − C(t)<sub>U6 snRNA</sub>, and ∆∆C(t) = ∆C(t)<sub>exo</sub> − ∆C(t)<sub>cell</sub>, and FC = 2<sup>−∆∆C(t)</sup>. Analysis was performed on three independent cell and exosomal RNA samples. Taqman probe #: U6 snRNA: 001973; <italic>hsa-let-7a-5p</italic>: 000377; <italic>hsa-miR-100-5p</italic>: 000437; <italic>hsa-miR-320b</italic>: 002844; hsa-miR-320a: 002277.</p></sec><sec id="s4-9"><title>Generation of miRNA standard curves</title><p>RNase-free, HPLC-purified 5′-phosphorylated miRNA oligoribonucleotides were synthesized (Integrated DNA Technologies) for human <italic>miR-100-5p</italic> (5′-phospho-AACCCGUAGAUCCGAACUUGUG-OH-3′) and <italic>cel-miR-39-3p</italic> (5′-phospho-UCACCGGGUGUAAAUCAGCUUG-OH-3′). Stock solutions of 10 μM synthetic oligonucleotide in RNase-free and DNase-free water were prepared according to the concentrations and sample purity quoted by the manufacturer (based on spectrophotometry analysis). Nine twofold dilution series beginning with 50 pM synthetic oligonucleotide were used in 10 µl RT reactions (Taqman small RNA assays), and qPCR was performed. Each dilution was performed in triplicate from three independent experiments. Linear regression was used to determine mean C(t) values plotted against log(miRNA copies/µl).</p></sec><sec id="s4-10"><title>miRNA in situ hybridizations and ceramide dependence</title><p>Cells were plated in 6-well plates containing coverslips at a density of ∼2.5 × 10<sup>5</sup> cells and cultured in DMEM supplemented with 10% bovine growth serum for 24 hr. The cells were then washed three times with PBS and cultured for 24 hr in serum-free medium containing either 5 μM GW4869 (Cayman Chemicals # 13127, Ann Arbor, MI, USA) or DMSO. Medium was removed and cells were washed three times with PBS and fixed with 4% Paraformaldehyde (PFA) for ∼15 min at room temperature. After, cells were washed three times in DEPC-treated PBS and permeabilized in 70% ethanol for ∼4 hr at 4°C, and rehydrated in DEPC-treated PBS for 5 min. Pre-hybridization was performed in hybridization buffer (25% formamide, 0.05 M EDTA, 4× saline-sodium citrate (SSC), 10% dextran sulfate, 1X Denhardt’s solution 1 mg/ml <italic>Escherichia coli</italic> tRNA) in a humidified chamber at 60°C for 60 min. Hybridization buffer was removed and replaced with 10 nM of probe (probe numbers are listed below) diluted in hybridization buffer and incubated at either 55°C (<italic>miR-100</italic> and <italic>miR-10b</italic>) or 57°C for scrambled and U6 probes for 2 hr. Coverslips were then washed in series with pre-heated SSC at 37°C as follows: 4× SSC briefly, 2× SSC for 30 min, 1× SSC for 30 min, and 0.1× SSC for 20 min. miRNA detection was conducted using Tyramide Signal Amplification (Perkin Elmer, # NEL741001KT, Waltham, MA, USA). Briefly, coverslips were blocked in blocking buffer (0.1 M TRIS-HCl, pH 7.5, 0.15 M NaCl, 0.5% Blocking Reagent [Roche, #11096176001, Basel, Switzerland]) at 4°C overnight. Blocking buffer was replaced with anti-DIG-POD (Roche, # 11207733910) diluted 1:100 in blocking buffer and incubated for 60 min. Coverslips were washed three times, 5 min per wash, in wash buffer (0.1 M Tris-HCl, pH 7.5, 0.15 M NaCl, 0.5% Saponin) followed by incubation with 1× Fluorescein diluted in 1× amplification reagent for 5 min. Fluorescent coverslips were then washed two times, 5 min per wash, in wash buffer. To preserve fluorescent signals, coverslips were fixed with 2% PFA containing 2% Bovine serum albumin in 1× PBS for 15 min. After fixation, coverslips were washed 2 times, 5 min per wash, in wash buffer, followed by a final wash in 1× PBS for 5 min. Coverslips were then mounted in Prolong Gold (Life Technologies) and visualized on a Zeiss LSM510 at 63× objective. 3′-DIG labeled probes for in situ hybridizations-U6 snRNA: 99002-05; Scramble: 99004-05; <italic>miR-10b-5p</italic>: 38486-05; <italic>miR-100-5p</italic>: 18009-05 (Exiqon, Woburn, MA, USA).</p></sec><sec id="s4-11"><title>Co-culture and Luc reporter assays</title><p>Recipient cells were plated in six-well plates at a density of ∼2.5 × 10<sup>5</sup> cells and cultured in DMEM supplemented with 10% bovine growth serum for 24 hr. Media was replaced and cells were co-transfected (Promega, E2311, Madison, WI, USA) with 1.5 μg of Luc-reporter plasmid and 1.5 μg β-gal plasmid DNA/well. Donor cells were plated in 0.4-μm polyester membrane Transwell filters (Corning, 3450, Corning, NY, USA) at ∼2.5 × 10<sup>5</sup> cells/well for 24 hr. Media from donor Transwells and recipient 6-well plates were removed and replaced with DMEM without FBS. Co-culture of donor and recipient cells was conducted for either 24 or 48 hr before recipient cells were harvested. Lysates were prepared in 1× Reporter lysis buffer (Promega, E2510), and Luc assays were performed according to the manufacturer's protocol (Promega, E2510). β-gal expression was simultaneously determined from the lysates according to the manufacturer's protocol (Promega, E2000). Differences in transfection efficiency were accounted for by normalizing Luc expression to β-Gal expression (Luc/β-Gal). All assays were performed on three biological replicates, each with three technical replicates.</p></sec><sec id="s4-12"><title>Antagomir treatment</title><p>Donor cells were plated in 0.4-μm polyester membrane Transwell filters (Corning, 3450, Corning, NY, USA) at ∼1.4 × 10<sup>4</sup> cells/well for 24 hr. Medium was replaced and donor cells were transfected with either <italic>miR-100</italic> hairpin antagomirs (# IH-300517-05, GE Life Sciences) or negative control hairpin antagomirs corresponding to <italic>cel-miR-67</italic> (# IN-001005-01, GE Life Sciences) to produce a final concentration of 100 nM of antagomir for 24 hr. Medium from donor Transwells and recipient 6-well plates was removed and replaced with DMEM without FBS. Co-culture of donor and recipient cells was conducted for 24 hr before recipient cells were harvested for RNA isolation.</p></sec><sec id="s4-13"><title>Plasmid construction</title><p>For the pLuc-mTOR construct, the 3′UTR of <italic>mTOR</italic> was PCR amplified (primer sequences in <xref ref-type="supplementary-material" rid="SD4-data">Supplementary file 3</xref>) from genomic DNA isolated from DKs-8 cells. The amplicon was cloned into pMiR-Report (Life Technologies) via SpeI/HinDIII restriction sites. Mutation of <italic>miR-100</italic> binding sites in mTOR 3′UTR (MS) was performed on pLuc-mTOR using forward or reverse primers targeting either all three MRE's, or MRE 2 and 3 with QuikChange Lightning Multi-Site Directed Mutagenesis (Agilent, Santa Clara, CA, USA) according to manufacturer's protocol. To create the reporter construct containing three <italic>miR-100</italic> perfect sites (miR-100-PT), oligonucleotides (<xref ref-type="supplementary-material" rid="SD4-data">Supplementary file 3</xref>) were annealed to produce a synthetic fragment containing the perfect sites with CTAGT and AGCTT overhangs. The fragment was cloned into pMiR-report via SpeI/HinDIII restriction sites. All plasmids were sequence verified (GeneWiz, South Plainfield, NJ, USA).</p></sec></sec></body><back><ack id="ack"><title>Acknowledgements</title><p>This work was supported by grants from the National Institutes of Health, U19CA179514, RO1 CA163563 and a GI Special Program of Research Excellence (SPORE) P50 95103 to RJC, and a pilot in P30 DK058404 to JLF. Vanderbilt Digestive Disease Research Center (P30 DK058404) and associated Cores.</p></ack><sec id="s5" sec-type="additional-information"><title>Additional information</title><fn-group content-type="competing-interest"><title>Competing interests</title><fn fn-type="conflict" id="conf1"><p>The authors declare that no competing interests exist.</p></fn></fn-group><fn-group content-type="author-contribution"><title>Author contributions</title><fn fn-type="con" id="con1"><p>DJC, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article</p></fn><fn fn-type="con" id="con2"><p>JLF, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article</p></fn><fn fn-type="con" id="con3"><p>YD, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con4"><p>QL, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con5"><p>JNH, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con6"><p>MDB, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con7"><p>NP, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con8"><p>SL, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con9"><p>AMW, Conception and design, Drafting or revising the article</p></fn><fn fn-type="con" id="con10"><p>KV, Conception and design, Drafting or revising the article</p></fn><fn fn-type="con" id="con11"><p>RJC, Conception and design, Drafting or revising the article</p></fn><fn fn-type="con" id="con12"><p>JGP, Conception and design, Drafting or revising the article</p></fn><fn fn-type="con" id="con13"><p>BZ, Conception and design, Analysis and interpretation of data, Drafting or revising the article</p></fn></fn-group></sec><sec id="s6" sec-type="supplementary-material"><title>Additional files</title><supplementary-material id="SD2-data"><object-id pub-id-type="doi">10.7554/eLife.07197.023</object-id><label>Supplementary file 1.</label><caption><p>Read counts for (<bold>A</bold>) individual miRNA species and (<bold>B</bold>) repeat families.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.023">http://dx.doi.org/10.7554/eLife.07197.023</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-07197-supp1-v2.xlsx"/></supplementary-material><supplementary-material id="SD3-data"><object-id pub-id-type="doi">10.7554/eLife.07197.024</object-id><label>Supplementary file 2.</label><caption><p>Abundant miRNAs. Normalized read counts (see ‘Materials and methods’) were used to determine the miRNAs with the highest number of reads (top 50) from cell and exosomal data sets. The top 50 most abundant miRNAs were compared between exosomes and cells for each cell line. Most abundant miRNAs in exosomes (blue), cells (orange), or both.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.024">http://dx.doi.org/10.7554/eLife.07197.024</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-07197-supp2-v2.xlsx"/></supplementary-material><supplementary-material id="SD4-data"><object-id pub-id-type="doi">10.7554/eLife.07197.025</object-id><label>Supplementary file 3.</label><caption><p>Related to experimental procedures. 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D</given-names></name><role>Reviewing editor</role><aff><institution>Howard Hughes Medical Institute, University of Massachusetts Medical School</institution>, <country>United States</country></aff></contrib></contrib-group></front-stub><body><boxed-text><p>eLife posts the editorial decision letter and author response on a selection of the published articles (subject to the approval of the authors). An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see <ext-link ext-link-type="uri" xlink:href="http://elifesciences.org/review-process">review process</ext-link>). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.</p></boxed-text><p>Thank you for sending your work entitled “<italic>KRAS</italic>-Dependent Sorting of miRNA to Exosomes” for consideration at <italic>eLife</italic>. Your article has been favorably evaluated by Sean Morrison (Senior editor) and two reviewers, one of whom is a member of our Board of Reviewing Editors.</p><p>The Reviewing editor and the other reviewer discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission.</p><p>The function of exosomal miRNAs is a highly controversial area of research, with some studies, such as this manuscript, claiming that miRNAs are not only exported from cells in exosomes, but also taken up by other cells as biologically functional signaling molecules, and others arguing they have no biological function. This manuscript, likely for the first time in the field establishes a well-defined experimental system: three isogenic cells lines that differ solely in <italic>KRAS</italic> status.</p><p>The manuscript makes some progress toward testing the idea that miRNAs can be transferred from cell-to-cell, but given the controversies in the field, a higher standard of proof is required to merit publication in <italic>eLife</italic>. We recommend the authors be given the opportunity to revise their manuscript, providing the requested new experiments and analyses. Most importantly, I urge the authors to spend less time selling their story and more effort rigorously testing-not proving-their hypotheses.</p><p>1) The major paper deficiency is lack of a clear biological model or mechanism explaining the data. While this is also true for most published exosome papers, one expects an <italic>eLife</italic> paper to propose some explanation for why specific miRNAs are transferred from cell-to-cell according to the exporting cell's <italic>KRAS</italic> status.</p><p>2) Correlation analysis plays a central role in testing the authors' hypothesis. Given the low correlation of the independent biological replicates (deep sequencing replicates typically correlate with R &gt; 0.90 in one of our labs), the authors should apply an appropriate statistical test to determine that R-values of 0.92-0.96 between cells are unlikely to differ from R-values of 0.67-0.89 comparing exosomes to the exporting cells? If the bottom quartile of miRNAs by abundance (i.e., the ones least well measured by convention, rather than digital, sequencing methods) are excluded, do the Pearson correlation values change? Can all the biological replicates be used to make the comparisons, not simply pairwise combinations of individual data sets?</p><p>3) Is the degree of reporter repression small because the abundance of exosome-delivered miRNAs is low? The miRNA literature overwhelmingly supports the view that low abundance miRNAs have no biological effects, because the cellular concentration of miRNA-binding sites is much, much greater than the concentration of miRNA. That is, the stoichiometric mechanism of miRNA-mediated repression in mammals requires that miRNAs be highly abundant. When DKs-8 cells obtain a miRNA, such as <italic>miR-222</italic>, from exosomes, does that new miRNA rank in the top 25% or 50% of miRNAs by abundance? If not, it is difficult to imagine how it could be functional, given the aggregate intracellular concentration of seed-matched target sites. The authors need to report an estimate of how many molecules of a given miRNA sequence are present per exosome and how many are delivered to an individual recipient cell.</p><p>4) Why were three perfect sites used? Were controls performed validating the reporter using anti-miRs and miRNA mimics?</p><p>5) In the ceramide experiments, the authors interpret the change in exosomal and cellular abundance for <italic>miR-100</italic> and <italic>miR-320</italic> as evidence that a subset of miRNA sorting is altered by ceramide while a separate, ceramide-independent pathway delivers other miRNAs to exosomes. The data are interesting, but don't seem to contribute to our understanding of the mechanism of putative sorting of miRNAs into exosomes. Perhaps <italic>miR-10b</italic> is simply less abundant than <italic>miR-100</italic> or <italic>miR-320</italic>, making it harder to reliably detect changes in its abundance?</p><p>6A) High-Throughput Sequencing Data. How were the data normalized? How was the normalization procedure validated? Best practice is to select the normalization method that produces the greatest congruence among otherwise identical biologically independent replicates.</p><p>6B) Extending miRNA sequences {plus minus} 2 nt “to accommodate inaccurate processing of precursor miRNAs” would be a great idea if miRBase were always right; but miRBase is often wrong. It would be better to use the sequence of the most abundant isoform of the miRNA as the “accurately” processed form and to pool reads for all isoforms with the same 5′ end (i.e., the same seed sequence).</p><p>6C) Whenever read data is presented, species data should be presented in parallel. For example, the data in <xref ref-type="fig" rid="fig1">Figure 1</xref> would have a very different meaning if most of the “repeat” sequences were from just a few species, rather than a diverse set of RNAs.</p></body></sub-article><sub-article article-type="reply" id="SA2"><front-stub><article-id pub-id-type="doi">10.7554/eLife.07197.027</article-id><title-group><article-title>Author response</article-title></title-group></front-stub><body><p><italic>1) The major paper deficiency is lack of a clear biological model or mechanism explaining the data. While this is also true for most published exosome papers, one expects an</italic> eLife <italic>paper to propose some explanation for why specific miRNAs are transferred from cell-to-cell according to the exporting cell's</italic> KRAS <italic>status</italic>.</p><p>It remains a key question as to how specific miRNAs are selected for export. We conducted a series of experiments as detailed in the Results to determine whether any previously proposed mechanistic models can explain why we detect enrichment for some miRNAs within exosomes. We rigorously evaluated our data sets and described in the Results and the Discussion that we could not find support for:</p><p>A) “Zip-code” sequences (Bolukbasi et al. Mol Therapy-Nucleic Acids, 1 e10, Batagov et al. BMC Genomics 12: S18). These papers proposed that specific nucleotide patterns within secreted RNAs targeted them for export. We tested for the presence of those signals, as well as common motifs using MEME analysis, in our data sets and could not find evidence for a universal zip code sequence. However, when we restricted our analysis to the most differentially represented miRNAs in exosomes compared to cells, we detected a possible enrichment for C residues or alternating C residues. This is shown in <xref ref-type="fig" rid="fig4s3">Figure 4–figure supplement 3</xref>. We have added sentences to address these findings but we were careful to ensure that readers understand that the overall conclusion is that we were unable to identify a short sequence that could serve as a zip code targeting element.</p><p>B) 3’ and 5’ modifications (Koppers-Lalic et al. Cell Reports 8:1-10, Katoh et al. Genes Dev 23: 433, Burns et al. Nature 473: 105, Fernandez-Valverde et al. RNA 16: 1881, Wei et al. RNA 18: 915, Thornton et al. NAR 42: 11777). Numerous reports have proposed that 5’ and 3’ modifications can alter miRNA metabolism. Most commonly, addition of U residues to 3’ ends is thought to promote turnover whereas the addition of A residues promotes stabilization. G and C additions are generally rare. We tested whether exosomal export might be linked to 3’ or 5’ modifications. We did not observe significant 5’ modifications from reads derived from miRNAs in either cells or exosomes. For 3’ modifications, we found that cellular miRNAs tended to have increased numbers of modified 3’ ends with added A residues. We did not observe an enrichment of 3’-NTA of A residues in reads derived from exosomal miRNAs. Further analysis showed that there was enrichment of reads containing extra C residues at the 3’ ends in exosomes from wild-type KRAS cells. These data are now included in <xref ref-type="fig" rid="fig4s1">Figure 4–figure supplement 1</xref>. It remains unclear whether these changes are key to providing mechanistic insight into miRNA export. We have added sentences to carefully address this point.</p><p>C) Sumoylated hnRNPA2 B1 (Villarroya-Bletri et al. Nature Comm 4:2980). This paper proposed that miRNAs destined for exosomal export contain GGAG motifs that are bound by hnRNP A2B1. We found this motif in some exosomal miRNAs but clearly not all, indicating that this motif is not a universal targeting signal.</p><p>D) ESCRTs vs. Sphingomyelinase. As shown in the Results and discussed in the Discussion (with references), we tested whether different biogenesis pathways might explain miRNA export selectivity. We indeed observed changes in miRNA signals in cells when treated with a sphingomyelinase inhibitor suggesting that there may be a distinct pathway for export. This only affected miRNA trafficking in mutant KRAS cells but not wild-type KRAS cells. While the data are intriguing, we were careful to qualify our results with the caveat that sorting in this situation might be cell-type or context-specific.</p><p>We agree that we have not solved the overall problem to understand or mechanistically explain miRNA export but we believe that our paper makes a significant contribution to the field by using our well controlled model system to test whether earlier proposed models hold up. Even though the data are negative, they provide a valuable tool for the field. We also include discussion of possible mechanisms that could explain selective export (see Discussion).</p><p><italic>2) Correlation analysis plays a central role in testing the authors' hypothesis. Given the low correlation of the independent biological replicates (deep sequencing replicates typically correlate with R &gt; 0.90 in one of our labs), the authors should apply an appropriate statistical test to determine that R-values of 0.92-0.96 between cells are unlikely to differ from R-values of 0.67-0.89 comparing exosomes to the exporting cells</italic>?</p><p>We thank the reviewers for this important comment. Variation between exosomes was obviously much larger than those between cells. In DESeq, the “per-condition” method is designed to handle this situation by calculating an empirical dispersion value for each condition separately. The “per-condition” method was the default option in an earlier version of DESeq. We were not aware of the change of the default to the “pooled” method in a more recent version, which was used to generate the results presented in the previous version of the manuscript. In the revision, we re-did differential analysis using the “per-condition” method and updated all related results accordingly (<xref ref-type="table" rid="tbl1 tbl2">Tables 1, 2</xref>, <xref ref-type="fig" rid="fig2s1 fig2s2 fig2s3 fig2s4">Figure 2–figure supplement 1-4</xref>, <xref ref-type="fig" rid="fig3">Figures 3A, B</xref>, and motif analysis, <xref ref-type="fig" rid="fig4s3">Figure 4–figure supplement 3</xref>). The new results do not alter the conclusions of the manuscript.</p><p><italic>If the bottom quartile of miRNAs by abundance (i.e., the ones least well measured by convention, rather than digital, sequencing methods) are excluded, do the Pearson correlation values change</italic>?</p><p><xref ref-type="fig" rid="fig2s2">Figure 2–figure supplement 2</xref> shows new correlation values after removing the bottom quartile of miRNAs by abundance. These values are very similar to those calculated based on all miRNAs.</p><p><italic>Can all the biological replicates be used to make the comparisons, not simply pairwise combinations of individual data sets</italic>?</p><p>Data from all biological replicates were used together in the differential expression analysis. The pair-wise analysis is just an exploratory analysis to gain a high-level overview of the pair-wise correlations of samples within or between different experimental groups.</p><p><italic>3) Is the degree of reporter repression small because the abundance of exosome-delivered miRNAs is low? The miRNA literature overwhelmingly supports the view that low abundance miRNAs have no biological effects, because the cellular concentration of miRNA-binding sites is much, much greater than the concentration of miRNA. That is, the stoichiometric mechanism of miRNA-mediated repression in mammals requires that miRNAs be highly abundant. When DKs-8 cells obtain a miRNA, such as</italic> miR-222<italic>, from exosomes, does that new miRNA rank in the top 25% or 50% of miRNAs by abundance? If not, it is difficult to imagine how it could be functional, given the aggregate intracellular concentration of seed-matched target sites. The authors need to report an estimate of how many molecules of a given miRNA sequence are present per exosome and how many are delivered to an individual recipient cell</italic>.</p><p>The reviewers are indeed correct that the degree of reporter repression is small because the abundance of exosomal-delivered miRNA is low. This is not unexpected and is central to controversies in the field as to the stoichiometry and function of secreted RNA. Indeed, we think this is the key question moving forward because experimental proof of transfer can be difficult. Many studies successfully showing RNA transfer utilized experiments where nonphysiological concentrations of purified exosomes were added to recipient cells (see manuscript references). Evidence of transfer has also been demonstrated between immune cells that can remain opposed to one another for hours facilitating exRNA transfer but making it very difficult to precisely quantify the level of transfer (Mittelbrunn et al., Nature Communications 2:282, Ekstrom et al. JEV 1:18389, Montecalvo et al. Blood 119: 756). In our experiments, we chose to use Transwell co-culture experiments to resemble a more physiological system and also to test functional miRNA transfer with reporter constructs. We observed a ∼60-65% decrease with perfect sites and a ∼40% decrease with a wild-type mTOR 3’ UTR. Analysis of <italic>miR-100</italic> levels in recipient cells showed an approximate 34 % increase in <italic>miR-100</italic> levels compared to cells cultured in the absence of donor cells (<xref ref-type="fig" rid="fig6">Figure 6E</xref>). The increase in <italic>miR-100</italic> levels is supported by precise copy number calculations that show that there are 329 molecules of <italic>miR-100</italic> per ng of total input RNA in cells grown in the absence of donor cells and those numbers increase to 443 molecules of <italic>miR-100</italic> in the presence of donor cells (<xref ref-type="fig" rid="fig6s2">Figure 6–figure supplement 2</xref>).</p><p>The statement that “overwhelming evidence supports the view that low abundance miRNAs have no biological effects” might be true on a global genomic scale but becomes a bit too generalized when applied to specific cells or developmental time points. There are two issues. First, one has to account for the concentration of a specific miRNA and second, the concentration of all target mRNAs in specific cells and/or at specific developmental time points. The fact that there have been about 11 different published target prediction algorithms speaks to the fact that we do not yet know precisely how to identify mRNA targets, nor do we know the exact set of rules that govern pairing and repression. Seed pairing is clearly important (Lewis et al. Cell 115: 787; Brennecke et al. PLos Biol 3: e85; Grimson, Mol Cell 27: 91; Lewis et al. Cell 120: 15; Krek et al. Nat Gen 37: 495) but there are lots of examples where imperfect seed sequences are robustly silenced (Li et al. NAR 36: 4277; Didiano and Hobert, NSMB 13: 849). Identifying bona fide targets requires experimental validation; in silico prediction is just a starting point with many false positive and negatives. Thus, knowing the exact concentration of target mRNAs and extending that to determine whether a miRNA is low abundance or not is not trivial. An historical example is <italic>lsy6</italic> in <italic>C. elegans</italic> which cannot be detected in sequencing approaches because it is so low abundance in worms, yet it controls the formation of left/right asymmetry between two neurons and regulates <italic>cog-1</italic> through a non-canonical binding sequence (Johnston and Hobert, Nature 426: 845). The effects of <italic>lsy6</italic> manifest themselves as part of a downstream network that is put in play by initial miRNA regulation, nicely illustrating the point that time and place matters. Our work on the role of miRNAs during vertebrate development has also identified numerous miRNAs that are not highly abundant but whose disruption leads to specific developmental defects (Flynt et al. Nat Gen 39: 259; Li et al. Dev 138: 1817; Thatcher et al. PNAS 105: 18384). Interestingly, we often find that non-canonical targets are the key targets even though we always begin our search using seed-based algorithms. Beyond our own work, perhaps the best example arguing against abundance and functional activity is <italic>miR-33</italic> which is expressed at approximately 30-40 copies per liver cell compared to <italic>miR-122</italic> which has about 3 million copies per liver cell. Despite the numbers, modest antagonism of <italic>miR-33</italic> down to about 15-20 copies per cell is enough to disrupt cholesterol metabolism and rescue atherosclerosis in mice (Najafi-Shoushtari et al. Science 328: 1566, Rayner et al. Science 328: 1570, Rayner et al. JCI 121: 2921, Rayner Nature 478: 404). Another good example is <italic>miR-802</italic> which is not even in the top 100 miRNAs as far as abundance in liver, yet it controls glucose homeostasis and type II diabetes (Kornfeld et al. Nature 494: 111). The Mendel lab had a nice paper using overexpression of <italic>miR-26</italic> in transgenic mice to try to resolve why <italic>miR-26</italic> can act as both a tumor suppressor and an oncogene in intestinal tumors. After overexpression, global analysis (GSEA) of likely mRNA targets identified numerous targets that were repressed by greater than 1.5. However, a known target of <italic>miR-26</italic> (EZH2) did not show up in their analysis yet they, and others, showed that <italic>miR-26</italic> regulates EZH2 (Zeitels et al. Genes and Dev 28: 2585). Lastly, <italic>miR-206</italic> was identified as one of several low abundance miRNAs that play key roles in colon cancer (Parasramka et al. Clin Epigenetics 4:16).</p><p>Nevertheless, we agree completely that stoichiometry is a key issue. The Tewari lab has published quantitative analysis of the amounts of miRNA per exosome and the numbers are startling low – 0.008 molecules of miRNA per exosome (Chevillet et al. PNAS 111: 14888). This illustrates the importance of the issue raised by the reviewers, something we completely agree with. Nevertheless, we observe silencing by <italic>miR-100</italic> and <italic>miR-222</italic> so despite stoichiometry issues aside, miRNAs are being functionally transferred.</p><p><italic>4) Why were three perfect sites used? Were controls performed validating the reporter using anti-miRs and miRNA mimics</italic>?</p><p>Perfect sites were used in half of our reporter constructs to optimize detection of silencing. By creating perfect sites, we are inducing an RNAi-based Ago2 cleavage of mRNA targets which helps detect silencing through a catalytic mechanism. This provided the necessary proof of principle to try targeting an endogenous gene which was observed using the mTOR 3’ UTR. The binding sites in the mTOR 3’ UTR are typical miRNA binding sites with imperfect pairing so that repression is via miRNA-based mechanisms. Even with imperfect pairing, we were still able to observe silencing albeit less than when perfect sites were used. Further, mutation of the sites derepressed silencing. Three perfect sites were used (as opposed to one perfect site) because the endogenous mTOR 3’UTR also contains three <italic>miR-100</italic> sites. Having three perfect sites rather than one would actually underestimate the strength of Luc repression due to <italic>miR-100</italic> transfer.</p><p>The reviewers are entirely correct that we need to run extensive controls to ensure that the silencing we observe in our Transwell culture experiments is via <italic>miR-100</italic>. As requested, we performed antagomir experiments to decrease the expression of <italic>miR-100</italic> in donor cells (new <xref ref-type="fig" rid="fig6">Figure 6D</xref>). We also included new data analyzing the absolute levels of <italic>miR-100</italic> in recipient cells grown in the presence or absence of donor cells (new <xref ref-type="fig" rid="fig6">Figure 6E</xref>, <xref ref-type="fig" rid="fig6s2">Figure 6–figure supplement 2</xref>).</p><p><italic>5) In the ceramide experiments, the authors interpret the change in exosomal and cellular abundance for</italic> miR-100 <italic>and</italic> miR-320 <italic>as evidence that a subset of miRNA sorting is altered by ceramide while a separate, ceramide-independent pathway delivers other miRNAs to exosomes. The data are interesting, but don't seem to contribute to our understanding of the mechanism of putative sorting of miRNAs into exosomes. Perhaps</italic> miR-10b <italic>is simply less abundant than</italic> miR-100 <italic>or</italic> miR-320<italic>, making it harder to reliably detect changes in its abundance</italic>?</p><p>The sphingomyelinase inhibition experiments begin to address mechanisms underlying the biogenesis of miRNA export into exosomes. In contrast to the statement by the reviewers, <italic>miR-10b</italic> is actually more abundant than <italic>miR-100</italic> or <italic>miR-320</italic> so levels do not appear to determine whether a miRNA is sphingomyelinase dependent or not. Overall, our findings are less about abundance and more about biogenesis and export of miRNA from cells. Controversy remains as to the varying roles of ESCRTs versus ceramide so it was important for us to demonstrate what we observe with our cells. As summarized in the Discussion, it seems that cell context is important and unifying conclusions are not yet possible for ceramide dependence.</p><p><italic>6A) High-Throughput Sequencing Data. How were the data normalized? How was the normalization procedure validated? Best practice is to select the normalization method that produces the greatest congruence among otherwise identical biologically independent replicates</italic>.</p><p>The data were normalized using the DESeq package, in which the effective library size (i.e. size factor) for each sample is estimated using the function “estimateSizeFactors”. Dillies et al. (2013) evaluated several normalization methods based on real and simulated data sets (Dillies et al. Briefings in Bioinformatics 14.6 (2013): 671-683). Similar performance was observed for the DESeq normalization method and the TMM method, and both of them outperformed other methods.</p><p><italic>6B) Extending miRNA sequences {plus minus} 2 nt</italic> “<italic>to accommodate inaccurate processing of precursor miRNAs</italic>” <italic>would be a great idea if miRBase were always right; but miRBase is often wrong. It would be better to use the sequence of the most abundant isoform of the miRNA as the</italic> “<italic>accurately</italic>” <italic>processed form and to pool reads for all isoforms with the same 5′ end (i.e., the same seed sequence)</italic>.</p><p>For each miRNA with a read count greater than 100, we compared the position of the most abundant isoform to the annotated position in miRBase. As shown in <xref ref-type="table" rid="tbl3">Author response table 1</xref>, consistency was found for around 75% of the miRNAs in all samples. Moreover, we compared miRNA counts based on miRBase annotations and positions of the most abundant reads, both with the +/- 2 strategy. As shown in <xref ref-type="table" rid="tbl4">Author response table 2</xref>, about 80% of the miRNAs had exactly the same counts and only about 5% of the miRNAs showed a difference of more than 10%. Based on these results, we decided to keep the miRBase-based counting results.<table-wrap id="tbl3" position="float"><object-id pub-id-type="doi">10.7554/eLife.07197.028</object-id><label>Author response table 1.</label><caption><p>Comparison of miRNA positions based on the most abundant reads and annotations from miRBase.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.028">http://dx.doi.org/10.7554/eLife.07197.028</ext-link></p></caption><table frame="hsides" rules="groups"><thead><tr><th>Sample</th><th>Same</th><th>Different</th><th>Same percentage</th></tr></thead><tbody><tr><td>DKO1.cell.1</td><td>279</td><td>96</td><td>74.4%</td></tr><tr><td>DKO1.cell.2</td><td>274</td><td>86</td><td>76.1%</td></tr><tr><td>DKO1.cell.3</td><td>255</td><td>90</td><td>73.9%</td></tr><tr><td>DKO1.exo.1</td><td>129</td><td>52</td><td>71.3%</td></tr><tr><td>DKO1.exo.2</td><td>134</td><td>43</td><td>75.7%</td></tr><tr><td>DKO1.exo.3</td><td>84</td><td>28</td><td>75.0%</td></tr><tr><td>DKS8.cell.1</td><td>330</td><td>125</td><td>72.5%</td></tr><tr><td>DKS8.cell.2</td><td>293</td><td>108</td><td>73.1%</td></tr><tr><td>DKS8.cell.3</td><td>272</td><td>90</td><td>75.1%</td></tr><tr><td>DKS8.exo.1</td><td>60</td><td>21</td><td>74.1%</td></tr><tr><td>DKS8.exo.2</td><td>48</td><td>16</td><td>75.0%</td></tr><tr><td>DKS8.exo.3</td><td>76</td><td>24</td><td>76.0%</td></tr><tr><td>DLD1.cell.1</td><td>277</td><td>92</td><td>75.1%</td></tr><tr><td>DLD1.cell.2</td><td>308</td><td>115</td><td>72.8%</td></tr><tr><td>DLD1.cell.3</td><td>290</td><td>97</td><td>74.9%</td></tr><tr><td>DLD1.exo.1</td><td>62</td><td>17</td><td>78.5%</td></tr><tr><td>DLD1.exo.2</td><td>53</td><td>16</td><td>76.8%</td></tr><tr><td>DLD1.exo.3</td><td>70</td><td>21</td><td>76.9%</td></tr></tbody></table></table-wrap><table-wrap id="tbl4" position="float"><object-id pub-id-type="doi">10.7554/eLife.07197.029</object-id><label>Author response table 2.</label><caption><p>Comparison of miRNA counts based on miRBase annotations and positions of the most abundant reads.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.07197.029">http://dx.doi.org/10.7554/eLife.07197.029</ext-link></p></caption><table frame="hsides" rules="groups"><thead><tr><th>Sample</th><th>Same</th><th>Difference more than 10%</th></tr></thead><tbody><tr><td>DKO1.cell.1</td><td>77.00%</td><td>6.90%</td></tr><tr><td>DKO1.cell.2</td><td>78.80%</td><td>7.20%</td></tr><tr><td>DKO1.cell.3</td><td>79.10%</td><td>6.70%</td></tr><tr><td>DKO1.exo.1</td><td>78.90%</td><td>6.50%</td></tr><tr><td>DKO1.exo.2</td><td>80.00%</td><td>5.80%</td></tr><tr><td>DKO1.exo.3</td><td>86.80%</td><td>2.30%</td></tr><tr><td>DKS8.cell.1</td><td>77.30%</td><td>7.80%</td></tr><tr><td>DKS8.cell.2</td><td>79.70%</td><td>6.70%</td></tr><tr><td>DKS8.cell.3</td><td>79.70%</td><td>6.30%</td></tr><tr><td>DKS8.exo.1</td><td>82.50%</td><td>6.20%</td></tr><tr><td>DKS8.exo.2</td><td>85.10%</td><td>4.50%</td></tr><tr><td>DKS8.exo.3</td><td>79.80%</td><td>4.00%</td></tr><tr><td>DLD1.cell.1</td><td>79.70%</td><td>6.00%</td></tr><tr><td>DLD1.cell.2</td><td>77.10%</td><td>7.60%</td></tr><tr><td>DLD1.cell.3</td><td>78.30%</td><td>6.10%</td></tr><tr><td>DLD1.exo.1</td><td>79.80%</td><td>3.60%</td></tr><tr><td>DLD1.exo.2</td><td>87.70%</td><td>2.70%</td></tr><tr><td>DLD1.exo.3</td><td>85.10%</td><td>2.10%</td></tr></tbody></table></table-wrap></p><p><italic>6C) Whenever read data is presented, species data should be presented in parallel. For example, the data in</italic> <xref ref-type="fig" rid="fig1"><italic>Figure 1</italic></xref> <italic>would have a very different meaning if most of the</italic> “<italic>repeat</italic>” <italic>sequences were from just a few species, rather than a diverse set of RNAs</italic>.</p><p>A count table for miRNAs is included in . Portions of reads from different repeat families are shown in <xref ref-type="fig" rid="fig1">Figure 1C</xref>. A count table of the repeat families is also included in <xref ref-type="supplementary-material" rid="SD2-data">Supplementary file 1B</xref>.</p></body></sub-article></article>