Selected publications of exosomal mRNA

1. Del Re M, Biasco E, Crucitta S, Derosa L, Rofi E, Orlandini C, Miccoli M, Galli L, Falcone A, Jenster GW, van Schaik RH, Danesi R. The Detection of Androgen Receptor Splice Variant 7 in Plasma-derived Exosomal RNA Strongly Predicts Resistance to Hormonal Therapy in Metastatic Prostate Cancer Patients. Eur Urol. 2017 Apr;71(4):680-687. PMID: 27733296

This study showed that androgen receptor splice variant 7 (AR-V7) is detectable in plasma-derived exosomal RNA of patients with castration-resistant prostate cancer (CRPC) by ddPCR, and suggested that blood exosomal AR-V7 RNA is a predictive biomarker of resistance to hormonal therapy in CRPC.

2. Goldvaser H, Gutkin A, Beery E, Edel Y, Nordenberg J, Wolach O, Rabizadeh E, Uziel O, Lahav M. Characterisation of blood-derived exosomal hTERT mRNA secretion in cancer patients: a potential pan-cancer marker. Br J Cancer. 2017 Jul 25;117(3):353-357.

This study found that human telomerase reverse transcriptase (TERT) mRNA level was found to be absent in serum-derived exosomes from normal persons, but was variably detected in patients with different cancer types.

3. Wang Z, Deng Z, Dahmane N, Tsai K, Wang P, Williams DR, Kossenkov AV, Showe LC, Zhang R, Huang Q, Conejo-Garcia JR, Lieberman PM. Telomeric repeat-containing RNA (TERRA) constitutes a nucleoprotein component of extracellular inflammatory exosomes. Proc Natl Acad Sci U S A. 2015 Nov 17;112(46):E6293-300. PMID: 26578789

This study reported that elomeric repeat-containing RNA (TERRA) can also be found in extracellular fractions that stimulate innate immune signaling. RNA-seq analyses revealed TERRA to be among the most highly represented transcripts in extracellular fractions derived from both normal and cancer patient blood plasma. cfTERRA is a shorter form (∼200 nt) of cellular TERRA and copurifies with CD63- and CD83-positive exosome vesicles

4. Enderle D, Spiel A, Coticchia CM, Berghoff E, Mueller R, Schlumpberger M, Sprenger-Haussels M, Shaffer JM, Lader E, Skog J, Noerholm M. Characterization of RNA from Exosomes and Other Extracellular Vesicles Isolated by a Novel Spin Column-Based Method. PLoS One. 2015 Aug 28;10(8):e0136133. PMID: 26317354

This study reported the development and characterization of a spin column-based method for the isolation of total RNA from EVs in serum and plasma. The spin columns have a capacity to handle up to 4 mL sample volume, enabling detection of low-abundance transcripts in serum and plasma. This new procedure captures nearly 100% of mRNA from plasma samples and is equal to or better than ultracentrifugation in mRNA yield.

5. Shao H, Chung J, Lee K, Balaj L, Min C, Carter BS, Hochberg FH, Breakefield XO, Lee H, Weissleder R. Chip-based analysis of exosomal mRNA mediating drug resistance in glioblastoma. Nat Commun. 2015 May 11;6:6999. PMID: 25959588

This study presented a microfluidic chip to analyse mRNA levels of MGMT (O(6)-methylguanine DNA methyltransferase) and APNG (alkylpurine-DNA-N-glycosylase) in enriched tumour exosomes obtained from patient blood with glioblastoma multiforme (GBM). They show that exosomal mRNA levels of these enzymes correlate well with levels found in parental cells and that levels change considerably during treatment of seven patients.

6. Li M, Zeringer E, Barta T, Schageman J, Cheng A, Vlassov AV. Analysis of the RNA content of the exosomes derived from blood serum and urine and its potential as biomarkers. Philos Trans R Soc Lond B Biol Sci. 2014 Sep 26;369(1652). pii: 20130502. PMID: 25135963

This study described the strategies for isolation of exosomes from human blood serum and urine, characterization of their RNA cargo by sequencing.

• Blood exosomal RNA extraction
• Exosomal RNA sequencing library preparation
• RNAseq data analysis

Selected publications of blood exosomal lncRNA

1. Nabet BY, Qiu Y, Shabason JE, Wu TJ, Yoon T, Kim BC, Benci JL, DeMichele AM, Tchou J, Marcotrigiano J, Minn AJ. Exosome RNA Unshielding Couples Stromal Activation to Pattern Recognition Receptor Signaling in Cancer. Cell. 2017 Jul 13;170(2):352-366.e13. PMID: 28709002

This study showed that triggering of stromal NOTCH-MYC by breast cancer cells results in a POL3-driven increase in RN7SL1, an endogenous RNA normally shielded by RNA binding proteins SRP9/14. This increase in RN7SL1 alters its stoichiometry with SRP9/14 and generates unshielded RN7SL1 in stromal exosomes. After exosome transfer to immune cells, unshielded RN7SL1 drives an inflammatory response. Upon transfer to breast cancer cells, unshielded RN7SL1 activates the PRR RIG-I to enhance tumor growth, metastasis, and therapy resistance. Corroborated by evidence from patient tumors and blood, these results demonstrate that regulation of RNA unshielding couples stromal activation with deployment of RNA DAMPs that promote aggressive features of cancer.

2. Savelyeva AV, Kuligina EV, Bariakin DN, Kozlov VV2, Ryabchikova EI, Richter VA, Semenov DV. Variety of RNAs in Peripheral Blood Cells, Plasma, and Plasma Fractions. Biomed Res Int. 2017;2017:7404912. PMID: 28127559

This study performed identification, classification, and quantification of RNAs from blood fractions: cells, plasma, plasma vesicles pelleted at 16,000g and 160,000g, and vesicle-depleted plasma supernatant of healthy donors and non-small cell lung cancer (NSCLC) patients. Their findings suggest that not only extracellular microRNAs but also circulating fragments of messenger and small nuclear/nucleolar RNAs represent prominent classes of circulating regulatory ncRNAs as well as promising circulating biomarkers for the development of disease diagnostic approaches.

3. Qu L, Ding J, Chen C, Wu ZJ, Liu B, Gao Y, Chen W, Liu F, Sun W, Li XF, Wang X, Wang Y, Xu ZY, Gao L, Yang Q, Xu B, Li YM, Fang ZY, Xu ZP, Bao Y, Wu DS, Miao X, Sun HY, Sun YH, Wang HY, Wang LH. Exosome-Transmitted lncARSR Promotes Sunitinib Resistance in Renal Cancer by Acting as a Competing Endogenous RNA. Cancer Cell. 2016 May 9;29(5):653-68. PMID: 27117758

This study identified an lncRNA, named lncARSR (lncRNA Activated in RCC with Sunitinib Resistance), which correlated with clinically poor sunitinib response. lncARSR promoted sunitinib resistance via competitively binding miR-34/miR-449 to facilitate AXL and c-MET expression in RCC cells. Furthermore, bioactive lncARSR could be incorporated into exosomes and transmitted to sensitive cells, thus disseminating sunitinib resistance.

4. Dong L, Lin W, Qi P, Xu MD, Wu X, Ni S, Huang D, Weng WW, Tan C, Sheng W, Zhou X, Du X. Circulating Long RNAs in Serum Extracellular Vesicles: Their Characterization and Potential Application as Biomarkers for Diagnosis of Colorectal Cancer. Cancer Epidemiol Biomarkers Prev. 2016 Jul;25(7):1158-66. PMID: 27197301

This study showed that exosomal mRNAs and lncRNAs in serum (especially in exosomes) could be used as biomarkers to detect colorectal cancer.

5. Qin Y, Yao J, Wu DC, Nottingham RM, Mohr S, Hunicke-Smith S, Lambowitz AM. High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases. RNA. 2016 Jan;22(1):111-28. PMID: 26554030

This study developed a new RNA-seq method that exploits thermostable group II intron reverse transcriptases (TGIRTs) and used it to profile human plasma RNAs. TGIRT-seq of RNA in 1-mL plasma samples from a healthy individual revealed RNA fragments mapping to a diverse population of protein-coding gene and long ncRNAs.

6. Li Q, Shao Y, Zhang X, Zheng T, Miao M, Qin L, Wang B, Ye G, Xiao B, Guo J. Plasma long noncoding RNA protected by exosomes as a potential stable biomarker for gastric cancer. Tumour Biol. 2015 Mar;36(3):2007-12. PMID: 25391424

This study showed that the levels of plasma long intergenic non-protein-coding RNA 152 (LINC00152) were significantly elevated in gastric cancer patients compared with healthy controls. The sensitivity and specificity of plasma LINC00152 in the diagnosis of gastric cancer were 48.1 and 85.2%, respectively. There were also no differences between LINC00152 levels in plasma and in exosomes. The results suggested that LINC00152 can be detected in plasma, and one of the possible mechanisms of its stable existence in blood was protected by exosomes.

7. Song J, Kim D, Han J, Kim Y, Lee M, Jin EJ. PBMC and exosome-derived Hotair is a critical regulator and potent marker for rheumatoid arthritis. Clin Exp Med. 2015 Feb;15(1):121-6. PMID: 24722995

This study aimed to identify lncRNA signatures that have prognostic values in rheumatoid arthritis (RA). There was a notably high expression level of Hotair in blood mononuclear cells and serum exosome of RA patients, leading the migration of active macrophage. In contrast, markedly lower level of Hotair was detected in differentiated osteoclasts and rheumatoid synoviocytes and enforced expression of Hotair led to significantly decreased levels of MMP-2 and MMP-13. This exploratory study provides novel empirical evidence that Hotair could be one of potential biomarkers for diagnosing RA.

8. Wang J, Zhou Y, Lu J, Sun Y, Xiao H, Liu M, Tian L. Combined detection of serum exosomal miR-21 and HOTAIR as diagnostic and prognostic biomarkers for laryngeal squamous cell carcinoma. Med Oncol. 2014 Sep;31(9):148. PMID: 25099764

This study investigated the prognostic and diagnostic values of exosomal ncRNA by comparing the amounts of exosomal miR-21 and HOTAIR in serum of laryngeal squamous cell carcinoma (LSCC) patients with those of polyps of vocal cords, and by determinating whether combined detection of the two molecules could provide useful information in the diagnosis of LSCC. Serum exosomal miR-21 and HOTAIR were significantly correlated with clinical parameters of LSCC, and combined evaluation of their serum expressions may be a valuable biomarker to screen LSCC and might be a promising predicting tool for LSCC patient.

Selected publications of circRNA

1. Lasda E, Parker R. Circular RNAs Co-Precipitate with Extracellular Vesicles: A Possible Mechanism for circRNA Clearance. PLoS One. 2016 Feb 5;11(2):e0148407. PMID: 26848835

This study investigated the possibility that cells can eliminate circRNAs into extracellular space, possibly within released vesicles such as exosomes and microvesicles. From three different cell lines and examining multiple circRNAs, they show that extracellular vesicle (EVs) preparations recovered from cell culture conditioned media contain established circRNAs. Moreover, these circRNAs are enriched over their linear counterparts within EV preparations when compared to the producing cells. This supports the idea that expulsion from cells into extracellular space, as by EVs release, can be a mechanism by which cells clear circRNAs. Moreover, since EVs can be taken up by other cells, excreted circRNAs could contribute to cell to cell communication.

2. Dou Y, Cha DJ, Franklin JL, Higginbotham JN, Jeppesen DK, Weaver AM, Prasad N, Levy S, Coffey RJ, Patton JG, Zhang B. Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes. Sci Rep. 2016 Nov 28;6:37982. PMID: 27892494

This study found that circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes, suggesting that circRNAs may serve as promising cancer biomarkers.

3. Li Y, Zheng Q, Bao C, Li S, Guo W, Zhao J, Chen D, Gu J, He X, Huang S. Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis. Cell Res. 2015 Aug;25(8):981-4. PMID: 26138677

This study showed for the first time the presence of abundant circular RNAs (circRNAs) in exosomes. RNA-seq analyses revealed that circRNAs were enriched in exosomes compared to the producer cells. circRNAs originated from human cancer xenografts could enter the circulation and be readily measured in the serum. Serum exosomal circRNAs were able to distinguish patients with colon cancer from healthy controls. This study lay the foundation for development of circRNAs as a new class of exosome-based cancer biomarkers.