The landscape of MicroRNA, piwi-interacting RNA, and circular RNA in human saliva

Clinical Chemistry

Volumn 61, Issue 1, 2015, Pages 221-230

  Bahn, Jae Hoon ^a   Zhang, Qing ^a   Li, Feng ^a   Chan, Tak Ming ^a   Lin, Xianzhi ^a   Kim, Yong ^a,b   Wong, David T W ^a,b,c   Xiao, Xinshu ^a,b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c University of California   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR RNA; MICRORNA; PIWI INTERACTING RNA; RNA; UNCLASSIFIED DRUG; BIOLOGICAL MARKER; RNA, CIRCULAR; SMALL INTERFERING RNA;

ARTICLE; BIOINFORMATICS; BODY FLUID; CEREBROSPINAL FLUID; CONTROLLED STUDY; EMBRYONIC STEM CELL; ENVIRONMENTAL IMPACT; HIGH THROUGHPUT SEQUENCING; HUMAN; RNA SEQUENCE; SALIVA; SKIN CELL; BLOOD; CHEMISTRY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS;

BASE SEQUENCE; BIOMARKERS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICRORNAS; MOLECULAR SEQUENCE DATA; REPRODUCIBILITY OF RESULTS; RNA; RNA, SMALL INTERFERING; SALIVA; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, RNA;

EID: 84920511291     PISSN: 00099147     EISSN: 15308561     Source Type: Journal    
DOI: 10.1373/clinchem.2014.230433     Document Type: Article

References (44)

1. Wong DT. Salivaomics. J Am Dent Assoc 2012;143: 19S-24S.
2. Li Y, St John MA, Zhou X, Kim Y, Sinha U, Jordan RC, et al. Salivary transcriptome diagnostics for oral cancer detection. Clin Cancer Res 2004;10:8442-50.
3. Hu S, Wang J, Meijer J, Ieong S, Xie Y, Yu T, et al. Salivary proteomic and genomic biomarkers for primary Sjogren's syndrome. Arthritis Rheum 2007;56:3588-600.
4. Park NJ, Zhou X, Yu T, Brinkman BM, Zimmermann BG, Palanisamy V, Wong DT. Characterization of salivary RNA by cDNA library analysis. Arch Oral Biol 2007;52:30-5.
5. Park NJ, Li Y, Yu T, Brinkman BM, Wong DT. Characterization of RNA in saliva. Clin Chem 2006;52:988-94.
6. Walz A, Stuhler K, Wattenberg A, Hawranke E, Meyer HE, Schmalz G, et al. Proteome analysis of glandular parotid and submandibular-sublingual saliva in comparison to whole human saliva by two-dimensional gel electrophoresis. Proteomics 2006;6:1631-9.
7. Zhang L, Farrell JJ, Zhou H, Elashoff D, Akin D, Park NH, et al. Salivary transcriptomic biomarkers for detection of resectable pancreatic cancer. Gastroenterology 2010; 138:949-57;e1-7.
8. Spielmann N, Ilsley D, Gu J, Lea K, Brockman J, Heater S, et al. The human salivary RNA transcriptome revealed by massively parallel sequencing. Clin Chem 2012;58: 1314-21.
9. St John MA, Li Y, Zhou X, Denny P, Ho CM, Montemagno C, et al. Interleukin 6 and interleukin 8 as potential biomarkers for oral cavity and oropharyngeal squamous cell carcinoma. Arch Otolaryngol Head Neck Surg 2004; 130:929-35.
10. Zhang L, Xiao H, Zhou H, Santiago S, Lee JM, Garon EB, et al. Development of transcriptomic biomarker signature in human saliva to detect lung cancer. Cell Mol Life Sci 2012;69:3341-50.
11. Lee YH, Kim JH, Zhou H, Kim BW, Wong DT. Salivary transcriptomic biomarkers for detection of ovarian cancer: for serous papillary adenocarcinoma. J Mol Med (Berl) 2012;90:427-34.
12. Zhang L, Xiao H, Karlan S, Zhou H, Gross J, Elashoff D, et al. Discovery and preclinical validation of salivary transcriptomic and proteomic biomarkers for the noninvasive detection of breast cancer. PLoS One 2010;5: e15573.
13. Tandon M, Gallo A, Jang SI, Illei GG, Alevizos I. Deep sequencing of short RNAs reveals novel micrornas in minor salivary glands of patients with Sjogren's syndrome. Oral Dis 2012;18:127-31.
14. Ogawa Y, Taketomi Y, Murakami M, Tsujimoto M, Yanoshita R. Small RNA transcriptomes of two types of exosomes in human whole saliva determined by next generation sequencing. Biol Pharm Bull 2013;36:66-75.
15. Burgos KL, Javaherian A, Bomprezzi R, Ghaffari L, Rhodes S, Courtright A, et al. Identification of extracellular miRNA in human cerebrospinal fluid by nextgeneration sequencing. RNA 2013;19:712-22.
16. Hu L, Wu C, Guo C, Li H, Xiong C. Identification of microRNAs predominately derived from testis and epididymis in human seminal plasma. Clin Biochem 2014; 47:967-72.
17. Williams Z, Ben-Dov IZ, Elias R, Mihailovic A, Brown M, Rosenwaks Z, Tuschl T. Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. Proc Natl Acad Sci U S A 2013;110:4255-60.
18. Huang X, Yuan T, Tschannen M, Sun Z, Jacob H, Du M, et al. Characterization of human plasma-derived exosomal rnas by deep sequencing. BMC Genomics 2013; 14:319.
19. Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs. Nat Biotechnol 2014;32:453-61.
20. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J. Natural RNA circles function as efficient microRNA sponges. Nature 2013;495: 384-8.
21. Lee YH, Zhou H, Reiss JK, Yan X, Zhang L, Chia D, Wong DT. Direct saliva transcriptome analysis. Clin Chem 2011;57:1295-302.
22. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10:R25.
23. Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE. Human oral microbiome database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford) 2010;2010:baq013. http://www.homd.org (accessed October 2014).
24. Gallo A, Tandon M, Alevizos I, Illei GG. The majority of microRNAs detectable in serum and saliva is concentrated in exosomes. PLoS One 2012;7:e30679.
25. Li BS, Zhao YL, Guo G, Li W, Zhu ED, Luo X, et al. Plasma microRNAs, miR-223, miR-21 and miR-218, as novel potential biomarkers for gastric cancer detection. PLoS One 2012;7:e41629.
26. Xu J, Wu C, Che X, Wang L, Yu D, Zhang T, et al. Circulating micrornas, miR-21, miR-122, and miR-223, in patients with hepatocellular carcinoma or chronic hepatitis. Mol Carcinog 2011;50:136-42.
27. Wang JF, Yu ML, Yu G, Bian JJ, Deng XM, Wan XJ, Zhu KM. Serum miR-146a and miR-223 as potential new biomarkers for sepsis. Biochem Biophys Res Commun 2010;394:184-8.
28. Chen X, Ba Y, Ma L, Cai X, Yin Y, Wang K, et al. Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 2008;18:997-1006.
29. Zhou X, Zhao F, Wang ZN, Song YX, Chang H, Chiang Y, XuHM.Altered expression of miR-152 and miR-148a in ovarian cancer is related to cell proliferation. Oncol Rep 2012;27:447-54.
30. Farid WR, Pan Q, van der Meer AJ, de Ruiter PE, Ramakrishnaiah V, de Jonge J, et al. Hepatocyte-derived microRNAs as serum biomarkers of hepatic injury and rejection after liver transplantation. Liver Transpl 2012; 18:290-7.
31. Kim SY, Jeon TY, Choi CI, Kim DH, Kim GH, Ryu DY, et al. Validation of circulating miRNA biomarkers for predicting lymph node metastasis in gastric cancer. J Mol Diagn 2013;15:661-9.
32. Thery C, Amigorena S, Raposo G, Clayton A. Isolation and characterization of exosomes from cell culture supernatants and biological fluids. Curr Protoc Cell Biol 2006;Chapter 3:Unit 3.22.
33. Sharma S, Rasool HI, Palanisamy V, Mathisen C, Schmidt M, Wong DT, Gimzewski JK. Structuralmechanical characterization of nanoparticle exosomes in human saliva, using correlative AFM, FESEM, and force spectroscopy. ACS Nano 2010;4:1921-6.
34. Lau C, Kim Y, Chia D, Spielmann N, Eibl G, Elashoff D, et al. Role of pancreatic cancer-derived exosomes in salivary biomarker development. J Biol Chem 2013;288: 26888-97.
35. Somel M, Guo S, Fu N, Yan Z, Hu HY, Xu Y, et al. MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. Genome Res 2010;20:1207-18.
36. Joyce CE, Zhou X, Xia J, Ryan C, Thrash B, Menter A, et al. Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome. Hum Mol Genet 2011;20:4025-40.
37. Kuchen S, Resch W, Yamane A, Kuo N, Li Z, Chakraborty T, et al. Regulation of microRNA expression and abundance during lymphopoiesis. Immunity 2010;32: 828-39.
38. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010;11:R106.
39. Sai Lakshmi S, Agrawal S. PiRNAbank: A web resource on classified and clustered piwi-interacting RNAs. Nucleic Acids Res 2008;36:D173-7.
40. Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 2012;7:e30733.
41. Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 2013;495: 333-8.
42. Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, Liu J, et al. Circular RNAs are abundant, conserved, and associated with Alu repeats. RNA 2013;19:141-57.
43. Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Cell-type specific features of circular RNA expression. PLoS Genet 2013;9:e1003777.
44. Zhang Y, Zhang XO, Chen T, Xiang JF, Yin QF, Xing YH, et al. Circular intronic long noncoding RNAs. Mol Cell 2013;51:792-806.