Characterization of microRNAs expression profiling in one group of Chinese urothelial cell carcinoma identified by Solexa sequencing

Chen, Yuhua; Wang, Siqi; Wu, Ximei; Shen, Mo; Chen, Zhanguo; Chen, Xiaogang; Liu, Yong-Xia; Zhu, Xiaoli; Guo, Fei; Duan, Xiuzhi; Han, Xiucui; Tao, Zhihua

doi:10.1016/j.urolonc.2010.11.007

Cited by 34 publications

(31 citation statements)

References 35 publications

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“…Overall, these observations indicate that the performance of the RNAqueous ® Micro kit is much superior to the PicoPure ® kit, especially as it pertains to small/microRNA isolation. Consistent with this is the observation by Goossens et al [18] that microRNAs were not retained using the PicoPure ® kit, but is in contrast to the report by Chen et al [20] who used the PicoPure ® kit to purify their small RNAs. The RNAqueous ® Micro kit was thus used for all subsequent analyses.…”

Section: Resultssupporting

confidence: 79%

“…A PubMed search for LCM and microRNAs in the National Center of Biotechnology Information (NCBI) database retrieved 12 reports [16–27] (Supplemental Table 1), all but one [20], describing the use of fixed tissue samples; in contrast to our protocol, this report [20] identified differentially expressed miRNAs from normal and epithelial tumor cells of urothelial cell carcinoma after LCM and deep-sequencing of small RNA libraries (see also below). For gDNA isolation, a search for LCM and DNA Methylation/CpG Methylation/Pyrosequencing retrieved 21 reports [17, 21, 28–46], 5 of which determined gene-specific CpG methylation levels by bisulfite sequencing analysis (Supplemental Table 1).…”

Section: Resultsmentioning

confidence: 99%

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Epigenetic analysis of laser capture microdissected fetal epithelia

Seelan

Warner

Mukhopadhyay

et al. 2013

Analytical Biochemistry

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Laser capture microdissection (LCM) is a superior method for non-destructive collection of specific cell populations from tissue sections. While DNA, RNA and protein have been analyzed from LCM-procured samples, epigenetic analyses, particularly of fetal, highly hydrated tissue, have not been attempted. A standardized protocol with quality assurance measures was established to procure cells by LCM of the medial edge epithelia (MEE) of the fetal palatal processes for isolation of intact microRNA for expression analyses and genomic DNA for CpG methylation analyses. MicroRNA preparations, obtained using the RNAqueous® Micro kit (Life Technologies), exhibited better yields and higher quality than those obtained using the Arcturus® PicoPure® RNA Isolation kit (Life Technologies). The approach was validated using real-time PCR to determine expression of selected microRNAs (miR-99a and miR-200b) and pyrosequencing to determine CpG methylation status of selected genes (Aph1a and Dkk4) in the MEE. These studies describe an optimized approach for employing LCM of epithelial cells from fresh frozen fetal tissue that enables quantitative analyses of miRNA expression levels and CpG methylation.

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Section: Resultssupporting

confidence: 79%

Section: Resultsmentioning

confidence: 99%

Epigenetic analysis of laser capture microdissected fetal epithelia

Seelan

Warner

Mukhopadhyay

et al. 2013

Analytical Biochemistry

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“…In general, the numbers of the novel microRNAs were significantly lower than those of conserved microRNAs (33). We identified just 61 novel microRNAs that exhibited significant differences in expression.…”

Section: Discussionmentioning

confidence: 87%

Analysis of microRNAs in patients with systemic lupus erythematosus, using Solexa deep sequencing

Chen¹,

Tan

Huang³

et al. 2014

Connective Tissue Research

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“…To date, only several studies were reported concerning the research of miR-183-5p in BC. It was validated that miR-183-5p expression in samples from patients with BC, including tissues (26,(40)(41)(42), urine (27,43) and serum (29), were all prominently higher than that those in normal counterparts. In the present study, we revealed the consistent results in tissue samples.…”

Section: Discussionmentioning

confidence: 93%

Clinical value and potential pathways of miR-183-5p in bladder cancer: A study based on miRNA-seq data and bioinformatics analysis

Gao

Huang

et al. 2018

Oncol Lett

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Abstract. The clinicopathological value and exploration of the potential molecular mechanism of microRNA-183-5p (miR-183-5p) have been investigated in various cancers; however, to the best of the author's knowledge, no similar research has been reported for bladder cancer. In the present study, it was revealed that the expression level of miR-183-5p was notably increased in bladder cancer tissues compared with adjacent non-cancerous tissues (P=0.001) and was markedly increased in the tissue samples of papillary, pathological T stage (T0-T2) and pathological stage (I-II) compared with tissue samples of their counterparts (P=0.05), according to data from The Cancer Genome Atlas. Receiver operating characteristic analysis revealed the robust diagnostic value of miR-183-5p for distinguishing bladder cancer from non-cancerous bladder tissues (area under curve=0.948; 95% confidence interval: 0.919-0.977). Amplification and deep deletion of miR-183-5p were indicated by cBioPortal, accounting for 1% (4/412) of bladder cancer cases. Data from YM500v3 demonstrated that compared with other cancers, bladder cancer exhibited high expression levels of miR-183-5p, and miR-183-5p expression in primary solid tumors was much higher compared with solid normal tissues. A meta-analysis indicated that miR-183-5p was more highly expressed in bladder cancer samples compared with normal counterparts. A total of 88 potential target genes of miR-183-5p were identified, 13 of which were discerned as hub genes by protein-protein interaction. The epithelial-to-mesenchymal transition pathway was the most significantly enriched pathway by FunRich (P= 0.0001). In summary, miR-183-5p may participate in the tumorigenesis and development of bladder cancer via certain signaling pathways, particularly the epithelial-to-mesenchymal transition pathway. However, the exact molecular mechanism of miR-183-5p in bladder cancer must be validated by in vitro and in vivo experiments.

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Characterization of microRNAs expression profiling in one group of Chinese urothelial cell carcinoma identified by Solexa sequencing

Cited by 34 publications

References 35 publications

Epigenetic analysis of laser capture microdissected fetal epithelia

Epigenetic analysis of laser capture microdissected fetal epithelia

Analysis of microRNAs in patients with systemic lupus erythematosus, using Solexa deep sequencing

Clinical value and potential pathways of miR-183-5p in bladder cancer: A study based on miRNA-seq data and bioinformatics analysis

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