title: Long intergenic non-coding RNAs (LincRNAs) identified by RNA-seq in breast cancer.
abstract: In an attempt to find the correlation of aberrant expression of long intergenic noncoding RNAs (lincRNAs) with cancer, twenty-five samples of breast cancer tissue and respective adjacent normal tissue were studied for the expression of lincRNAs by RNA-seq. Among the 538 lincRNAs studied, 124 lincRNAs were exclusively expressed in cancer adjacent tissues and 62 lincRNAs were exclusively expressed in the cancer tissues. Furthermore, the expression of 134 lincRNAs was higher while 272 lower in breast cancer tissue compared with adjacent tissue. The expression of four selected lincRNAs (BC2, BC4, BC5, and BC8) was validated by semi-quantitative and real-time PCR. It was revealed that expression of lincRNA-BC5 was positively correlated with patients' age, pathological stage, and progesterone receptor concentration, while lincRNA-BC8 was negatively correlated with progesterone receptor expression. Higher expression of lincRNA-BC4 was seen in advanced breast cancer grade. LincRNA-BC2 showed no specific changes in the pathological features studied. Interactions between selected lincRNAs and breast cancer associated proteins were highly suggested by RPIseq based on the specific secondary structure. The results demonstrated that this group of lincRNAs was aberrantly expressed in breast cancer. They might play important roles in the function of oncogenes or tumor suppressors affecting the development and progression of breast cancer.
authors.affiliation: Institute of Bioengineering, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, P.R. China.
authors.forename: Xianfeng
authors.initials: X
authors.lastname: Ding
authors.affiliation: Institute of Bioengineering, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, P.R. China.
authors.forename: Limin
authors.initials: L
authors.lastname: Zhu
authors.affiliation: Institute of Bioengineering, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, P.R. China.
authors.forename: Ting
authors.initials: T
authors.lastname: Ji
authors.affiliation: Zhejiang Cancer Research Institute, Department of Breast Tumor Surgery, Zhejiang Cancer Hospital, Banshan Bridge, Hangzhou, Zhejiang, P.R. China.
authors.forename: Xiping
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China.
authors.forename: Fengmei
authors.initials: F
authors.lastname: Wang
authors.affiliation: Institute of Bioengineering, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, P.R. China.
authors.forename: Shaoju
authors.initials: S
authors.lastname: Gan
authors.affiliation: Institute of Bioengineering, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, P.R. China.
authors.forename: Ming
authors.initials: M
authors.lastname: Zhao
authors.affiliation: Zhejiang Cancer Research Institute, Department of Breast Tumor Surgery, Zhejiang Cancer Hospital, Banshan Bridge, Hangzhou, Zhejiang, P.R. China.
authors.forename: Hongjian
authors.initials: H
authors.lastname: Yang
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D002874:Chromosome Mapping; D019295:Computational Biology; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D062085:RNA, Long Noncoding / Q000235:genetics*; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA
chemical_list: D062085:RNA, Long Noncoding
references.citation: Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11667-72
references.pmid: 19571010
references.citation: Nature. 2007 Jun 14;447(7146):799-816
references.pmid: 17571346
references.citation: Biomed Rep. 2014 Jan;2(1):19-23
references.pmid: 24649062
references.citation: Nature. 1996 Jan 11;379(6561):131-7
references.pmid: 8538762
references.citation: Annu Rev Genomics Hum Genet. 2008;9:387-402
references.pmid: 18576944
references.citation: J Clin Endocrinol Metab. 2000 Sep;85(9):3183-90
references.pmid: 10999806
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: Ann Surg Oncol. 2010 Jun;17(6):1471-4
references.pmid: 20180029
references.citation: Science. 1994 Oct 7;266(5182):66-71
references.pmid: 7545954
references.citation: CA Cancer J Clin. 2013 Jan;63(1):11-30
references.pmid: 23335087
references.citation: Trends Cell Biol. 2011 Jun;21(6):354-61
references.pmid: 21550244
references.citation: Science. 1987 Jan 9;235(4785):177-82
references.pmid: 3798106
references.citation: Science. 1997 Mar 28;275(5308):1943-7
references.pmid: 9072974
references.citation: Hum Genet. 2006 Apr;119(3):295-304
references.pmid: 16446976
references.citation: Genomics. 2000 Feb 1;63(3):299-306
references.pmid: 10704277
references.citation: Nat Rev Genet. 2010 Jan;11(1):31-46
references.pmid: 19997069
references.citation: Breast Cancer Res. 2009;11(6):R86
references.pmid: 19995430
references.citation: Nat Protoc. 2008;3(6):1101-8
references.pmid: 18546601
references.citation: Nature. 2010 Apr 15;464(7291):1071-6
references.pmid: 20393566
references.citation: Genes Chromosomes Cancer. 2000 Jun;28(2):145-52
references.pmid: 10824999
references.citation: Methods Mol Biol. 2010;609:285-306
references.pmid: 20221926
references.citation: Biotechniques. 2000 Aug;29(2):332-7
references.pmid: 10948434
references.citation: Cancer Metastasis Rev. 2006 Sep;25(3):409-16
references.pmid: 16951987
references.citation: Science. 2010 Aug 6;329(5992):689-93
references.pmid: 20616235
references.citation: Hum Mol Genet. 2010 Oct 15;19(R2):R152-61
references.pmid: 20729297
references.citation: Teratog Carcinog Mutagen. 2003;Suppl 1:35-45
references.pmid: 12616595
references.citation: Breast Cancer Res Treat. 1998;51(3):227-38
references.pmid: 10068081
references.citation: BMC Bioinformatics. 2011 Dec 22;12:489
references.pmid: 22192482
references.citation: J Pediatr Hematol Oncol. 2002 Mar-Apr;24(3):205-10
references.pmid: 11990307
references.citation: Hepatology. 2002 Jun;35(6):1476-84
references.pmid: 12029633
references.citation: Nat Genet. 2010 Feb;42(2):132-6
references.pmid: 20062064
references.citation: Cancer Res. 1989 Sep 1;49(17):4682-9
references.pmid: 2547513
references.citation: Oncologist. 2004;9(4):361-77
references.pmid: 15266090
references.citation: Science. 1994 Sep 30;265(5181):2088-90
references.pmid: 8091231
references.citation: Nat Rev Genet. 2010 Jul;11(7):476-86
references.pmid: 20531367
references.citation: Nat Rev Cancer. 2006 Nov;6(11):857-66
references.pmid: 17060945
references.citation: Oncogene. 2003 Sep 11;22(39):8031-41
references.pmid: 12970751
references.citation: Mol Cell. 2012 Aug 24;47(4):648-55
references.pmid: 22841487
references.citation: Genes Chromosomes Cancer. 1999 Apr;24(4):337-44
references.pmid: 10092132
references.citation: Int J Cancer. 2000 May 20;89(3):305-10
references.pmid: 10861509