title: In-depth characterization of microRNA transcriptome in melanoma.
abstract: The full repertoire of human microRNAs (miRNAs) that could distinguish common (benign) nevi from cutaneous (malignant) melanomas remains to be established. In an effort to gain further insight into the role of miRNAs in melanoma, we applied Illumina next-generation sequencing (NGS) platform to carry out an in-depth analysis of miRNA transcriptome in biopsies of nevi, thick primary (>4.0 mm) and metastatic melanomas with matched normal skin in parallel to melanocytes and melanoma cell lines (both primary and metastatic) (n=28). From this data representing 698 known miRNAs, we defined a set of top-40 list, which properly classified normal from cancer; also confirming 23 (58%) previously discovered miRNAs while introducing an additional 17 (42%) known and top-15 putative novel candidate miRNAs deregulated during melanoma progression. Surprisingly, the miRNA signature distinguishing specimens of melanoma from nevus was significantly different than that of melanoma cell lines from melanocytes. Among the top list, miR-203, miR-204-5p, miR-205-5p, miR-211-5p, miR-23b-3p, miR-26a-5p and miR-26b-5p were decreased in melanomas vs. nevi. In a validation cohort (n=101), we verified the NGS results by qRT-PCR and showed that receiver-operating characteristic curves for miR-211-5p expression accurately discriminated invasive melanoma (AUC=0.933), melanoma in situ (AUC=0.933) and dysplastic (atypical) nevi (AUC=0.951) from common nevi. Target prediction analysis of co-transcribed miRNAs showed a cooperative regulation of key elements in the MAPK signaling pathway. Furthermore, we found extensive sequence variations (isomiRs) and other non-coding small RNAs revealing a complex melanoma transcriptome. Deep-sequencing small RNAs directly from clinically defined specimens provides a robust strategy to improve melanoma diagnostics.
authors.affiliation: Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut, United States of America ; Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, United States of America.
authors.forename: James
authors.initials: J
authors.lastname: Kozubek
authors.forename: Zhihai
authors.initials: Z
authors.lastname: Ma
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Fleming
authors.forename: Tatiana
authors.initials: T
authors.lastname: Duggan
authors.forename: Rong
authors.initials: R
authors.lastname: Wu
authors.forename: Dong-Guk
authors.initials: DG
authors.lastname: Shin
authors.forename: Soheil S
authors.initials: SS
authors.lastname: Dadras
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D005260:Female; D006801:Humans; D066298:In Vitro Techniques; D008297:Male; D008544:Melanocytes / Q000378:metabolism; D008545:Melanoma / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D008875:Middle Aged; D012878:Skin Neoplasms / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D035683:MicroRNAs
references.citation: Expert Rev Mol Med. 2011 Nov 01;13:e33
references.pmid: 22044938
references.citation: Cell. 2005 Mar 11;120(5):635-47
references.pmid: 15766527
references.citation: Cell. 2010 Jun 25;141(7):1195-207
references.pmid: 20603000
references.citation: Leukemia. 2005 Nov;19(11):2013-6
references.pmid: 16167061
references.citation: Cell Cycle. 2011 Jun 1;10(11):1845-52
references.pmid: 21543894
references.citation: Nat Genet. 2011 Oct 09;43(11):1114-8
references.pmid: 21983785
references.citation: PLoS One. 2013 May 16;8(5):e64393
references.pmid: 23696889
references.citation: J Transl Med. 2010 Mar 19;8:27
references.pmid: 20302635
references.citation: Int J Cancer. 2011 Sep 1;129(5):1064-74
references.pmid: 21077158
references.citation: Mol Cells. 2012 Sep;34(3):329-34
references.pmid: 22949171
references.citation: Clin Cancer Res. 2010 Mar 1;16(5):1577-86
references.pmid: 20179230
references.citation: J Biol Chem. 2011 May 13;286(19):16606-14
references.pmid: 21454583
references.citation: Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2999-3004
references.pmid: 14973191
references.citation: PLoS One. 2010 Oct 04;5(10):
references.pmid: 20957176
references.citation: Nucleic Acids Res. 2012 Jul;40(Web Server issue):W498-504
references.pmid: 22649059
references.citation: Am J Pathol. 2012 Nov;181(5):1823-35
references.pmid: 22982443
references.citation: Mol Cell. 2010 Dec 10;40(5):841-9
references.pmid: 21109473
references.citation: Methods Mol Biol. 2006;342:129-38
references.pmid: 16957372
references.citation: Nat Biotechnol. 2008 Apr;26(4):407-15
references.pmid: 18392026
references.citation: Acta Histochem. 2012 Oct;114(6):582-8
references.pmid: 22130252
references.citation: Genome Res. 2008 Apr;18(4):610-21
references.pmid: 18285502
references.citation: J Cutan Pathol. 2009 Jul;36(7):772-80
references.pmid: 19032379
references.citation: J Invest Dermatol. 2012 Jul;132(7):1860-8
references.pmid: 22551973
references.citation: Cancer Res. 2008 Apr 15;68(8):2745-54
references.pmid: 18417445
references.citation: Proc Natl Acad Sci U S A. 2002 May 14;99(10):6567-72
references.pmid: 12011421
references.citation: EMBO J. 2011 May 18;30(10):1990-2007
references.pmid: 21468029
references.citation: Science. 2001 Oct 26;294(5543):858-62
references.pmid: 11679671
references.citation: PLoS One. 2011 Apr 25;6(4):e18936
references.pmid: 21541354
references.citation: Arch Dermatol. 2002 May;138(5):617-21
references.pmid: 12020222
references.citation: J Mol Diagn. 2009 Sep;11(5):420-9
references.pmid: 19710399
references.citation: Br J Cancer. 2011 Sep 27;105(7):1023-9
references.pmid: 21863027
references.citation: PLoS One. 2010 Nov 01;5(11):e13779
references.pmid: 21072171
references.citation: Oncologist. 2010;15(7):673-82
references.pmid: 20576643
references.citation: Cancer Res. 2005 Nov 1;65(21):9628-32
references.pmid: 16266980
references.citation: J Invest Dermatol. 2009 Jul;129(7):1740-51
references.pmid: 19212343
references.citation: PLoS One. 2011;6(6):e20494
references.pmid: 21698147
references.citation: Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15524-9
references.pmid: 12434020
references.citation: Genome Res. 2004 Jan;14(1):160-9
references.pmid: 14707178
references.citation: J Invest Dermatol. 2010 Aug;130(8):2062-70
references.pmid: 20357817
references.citation: Pigment Cell Melanoma Res. 2011 Oct;24(5):953-65
references.pmid: 21711453
references.citation: Cancer Res. 2010 May 15;70(10):4163-73
references.pmid: 20442294
references.citation: N Engl J Med. 2005 Nov 17;353(20):2135-47
references.pmid: 16291983
references.citation: Nature. 2011 Mar 24;471(7339):513-7
references.pmid: 21430779
references.citation: Lab Invest. 2012 Oct;92(10):1390-7
references.pmid: 22890556
references.citation: Am J Surg Pathol. 2010 Mar;34(3):314-26
references.pmid: 20118771
references.citation: Int J Cancer. 2010 Jun 1;126(11):2553-62
references.pmid: 19830692
references.citation: Cancer Res. 1998 Apr 1;58(7):1515-20
references.pmid: 9537257
references.citation: Stat Methods Med Res. 2013 Oct;22(5):519-36
references.pmid: 22127579
references.citation: J Invest Dermatol. 2013 May;133(5):1286-93
references.pmid: 23190898
references.citation: Br J Cancer. 2012 Jan 31;106(3):553-61
references.pmid: 22223089
references.citation: Nucleic Acids Res. 2007;35(19):e130
references.pmid: 17932070
references.citation: J Clin Oncol. 2009 Dec 20;27(36):6199-206
references.pmid: 19917835
references.citation: Genomics. 2013 Jul;102(1):8-14
references.pmid: 23562991
references.citation: Cell. 2004 Jan 23;116(2):281-97
references.pmid: 14744438
references.citation: BMC Biol. 2010 May 11;8:58
references.pmid: 20459774
references.citation: Genome Res. 2008 Nov;18(11):1787-97
references.pmid: 18849523
references.citation: Lab Invest. 2012 Jul;92(7):1084-96
references.pmid: 22525428
references.citation: J Biol Chem. 2012 Apr 6;287(15):11769-77
references.pmid: 22354972
references.citation: Melanoma Res. 2010 Dec;20(6):479-84
references.pmid: 20827223
references.citation: PLoS One. 2010 Mar 12;5(3):e9685
references.pmid: 20300190