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MicroRNA Expression Profile in Penile Cancer Revealed by Next-Generation Small RNA Sequencing.

Zhang L, Wei P, Shen X, Zhang Y, Xu B, Zhou J, Fan S, Hao Z, Shi H, Zhang X, Kong R, Xu L, Gao J, Zou D, Liang C - PLoS ONE (2015)

Bottom Line: As a result, a total of 751 and 806 annotated miRNAs were identified in normal and cancerous penile tissues, respectively.Among which, 56 miRNAs with significantly different expression levels between paired tissues were identified.Our work presents a global view of the differentially expressed miRNAs and potentially regulatory networks of their target genes for clarifying the pathogenic transformation of normal penis to PeCa, which research resource also provides new insights into future investigations aimed to explore the in-depth mechanisms of miRNAs and other small RNAs including piRNAs in penile carcinogenesis regulation and effective target-specific theragnosis.

View Article: PubMed Central - PubMed

Affiliation: Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; Institute of Urology, Anhui Medical University, Hefei, Anhui, China.

ABSTRACT
Penile cancer (PeCa) is a relatively rare tumor entity but possesses higher morbidity and mortality rates especially in developing countries. To date, the concrete pathogenic signaling pathways and core machineries involved in tumorigenesis and progression of PeCa remain to be elucidated. Several studies suggested miRNAs, which modulate gene expression at posttranscriptional level, were frequently mis-regulated and aberrantly expressed in human cancers. However, the miRNA profile in human PeCa has not been reported before. In this present study, the miRNA profile was obtained from 10 fresh penile cancerous tissues and matched adjacent non-cancerous tissues via next-generation sequencing. As a result, a total of 751 and 806 annotated miRNAs were identified in normal and cancerous penile tissues, respectively. Among which, 56 miRNAs with significantly different expression levels between paired tissues were identified. Subsequently, several annotated miRNAs were selected randomly and validated using quantitative real-time PCR. Compared with the previous publications regarding to the altered miRNAs expression in various cancers and especially genitourinary (prostate, bladder, kidney, testis) cancers, the most majority of deregulated miRNAs showed the similar expression pattern in penile cancer. Moreover, the bioinformatics analyses suggested that the putative target genes of differentially expressed miRNAs between cancerous and matched normal penile tissues were tightly associated with cell junction, proliferation, growth as well as genomic instability and so on, by modulating Wnt, MAPK, p53, PI3K-Akt, Notch and TGF-β signaling pathways, which were all well-established to participate in cancer initiation and progression. Our work presents a global view of the differentially expressed miRNAs and potentially regulatory networks of their target genes for clarifying the pathogenic transformation of normal penis to PeCa, which research resource also provides new insights into future investigations aimed to explore the in-depth mechanisms of miRNAs and other small RNAs including piRNAs in penile carcinogenesis regulation and effective target-specific theragnosis.

No MeSH data available.


Related in: MedlinePlus

Results of geneome mapping and distribution of RNAs among different categories.The unique tags and total reads aligned to the human genome sequence dataset were obtained. The mapped unique tags and clean reads were annotated and classified as miRNA, piRNA, rRNA, sRNA, snRNA, snoRNA, tRNA, repeats, etc. based on comparison with analytical databases, partial tags and reads were not annotated.
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pone.0131336.g002: Results of geneome mapping and distribution of RNAs among different categories.The unique tags and total reads aligned to the human genome sequence dataset were obtained. The mapped unique tags and clean reads were annotated and classified as miRNA, piRNA, rRNA, sRNA, snRNA, snoRNA, tRNA, repeats, etc. based on comparison with analytical databases, partial tags and reads were not annotated.

Mentions: For each sample, 13,796,889 (out of 15,702,009 reads) and 14,051,355 sequence reads (out of 15,698,197 reads) aligned to the human genome sequence dataset were obtained, representing 704,514 (out of 966,914) and 787,447 (out of 1,090,353) unique tags, respectively (S2 Table). Among which, 6,898 unique tags corresponding to 4,795,955 reads and 7,173 unique tags corresponding to 3,815,482 reads were matched to known miRNAs for normal and cancerous tissues, respectively. Meanwhile, 5,877 corresponding to 172,216 reads and 6,272 corresponding to 119,724 reads were matched to known piRNAs for normal and cancerous tissues, respectively. The rest of the sequences were matched into other types of RNAs, including mRNAs, rRNAs, sRNAs, snRNAs, snoRNAs, tRNAs, repeats and so on (Fig 2 and S2 Table). Among which, the repeats mainly consisted of rRNA either based on total reads or unique tags (S3 Table).


MicroRNA Expression Profile in Penile Cancer Revealed by Next-Generation Small RNA Sequencing.

Zhang L, Wei P, Shen X, Zhang Y, Xu B, Zhou J, Fan S, Hao Z, Shi H, Zhang X, Kong R, Xu L, Gao J, Zou D, Liang C - PLoS ONE (2015)

Results of geneome mapping and distribution of RNAs among different categories.The unique tags and total reads aligned to the human genome sequence dataset were obtained. The mapped unique tags and clean reads were annotated and classified as miRNA, piRNA, rRNA, sRNA, snRNA, snoRNA, tRNA, repeats, etc. based on comparison with analytical databases, partial tags and reads were not annotated.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4497725&req=5

pone.0131336.g002: Results of geneome mapping and distribution of RNAs among different categories.The unique tags and total reads aligned to the human genome sequence dataset were obtained. The mapped unique tags and clean reads were annotated and classified as miRNA, piRNA, rRNA, sRNA, snRNA, snoRNA, tRNA, repeats, etc. based on comparison with analytical databases, partial tags and reads were not annotated.
Mentions: For each sample, 13,796,889 (out of 15,702,009 reads) and 14,051,355 sequence reads (out of 15,698,197 reads) aligned to the human genome sequence dataset were obtained, representing 704,514 (out of 966,914) and 787,447 (out of 1,090,353) unique tags, respectively (S2 Table). Among which, 6,898 unique tags corresponding to 4,795,955 reads and 7,173 unique tags corresponding to 3,815,482 reads were matched to known miRNAs for normal and cancerous tissues, respectively. Meanwhile, 5,877 corresponding to 172,216 reads and 6,272 corresponding to 119,724 reads were matched to known piRNAs for normal and cancerous tissues, respectively. The rest of the sequences were matched into other types of RNAs, including mRNAs, rRNAs, sRNAs, snRNAs, snoRNAs, tRNAs, repeats and so on (Fig 2 and S2 Table). Among which, the repeats mainly consisted of rRNA either based on total reads or unique tags (S3 Table).

Bottom Line: As a result, a total of 751 and 806 annotated miRNAs were identified in normal and cancerous penile tissues, respectively.Among which, 56 miRNAs with significantly different expression levels between paired tissues were identified.Our work presents a global view of the differentially expressed miRNAs and potentially regulatory networks of their target genes for clarifying the pathogenic transformation of normal penis to PeCa, which research resource also provides new insights into future investigations aimed to explore the in-depth mechanisms of miRNAs and other small RNAs including piRNAs in penile carcinogenesis regulation and effective target-specific theragnosis.

View Article: PubMed Central - PubMed

Affiliation: Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; Institute of Urology, Anhui Medical University, Hefei, Anhui, China.

ABSTRACT
Penile cancer (PeCa) is a relatively rare tumor entity but possesses higher morbidity and mortality rates especially in developing countries. To date, the concrete pathogenic signaling pathways and core machineries involved in tumorigenesis and progression of PeCa remain to be elucidated. Several studies suggested miRNAs, which modulate gene expression at posttranscriptional level, were frequently mis-regulated and aberrantly expressed in human cancers. However, the miRNA profile in human PeCa has not been reported before. In this present study, the miRNA profile was obtained from 10 fresh penile cancerous tissues and matched adjacent non-cancerous tissues via next-generation sequencing. As a result, a total of 751 and 806 annotated miRNAs were identified in normal and cancerous penile tissues, respectively. Among which, 56 miRNAs with significantly different expression levels between paired tissues were identified. Subsequently, several annotated miRNAs were selected randomly and validated using quantitative real-time PCR. Compared with the previous publications regarding to the altered miRNAs expression in various cancers and especially genitourinary (prostate, bladder, kidney, testis) cancers, the most majority of deregulated miRNAs showed the similar expression pattern in penile cancer. Moreover, the bioinformatics analyses suggested that the putative target genes of differentially expressed miRNAs between cancerous and matched normal penile tissues were tightly associated with cell junction, proliferation, growth as well as genomic instability and so on, by modulating Wnt, MAPK, p53, PI3K-Akt, Notch and TGF-β signaling pathways, which were all well-established to participate in cancer initiation and progression. Our work presents a global view of the differentially expressed miRNAs and potentially regulatory networks of their target genes for clarifying the pathogenic transformation of normal penis to PeCa, which research resource also provides new insights into future investigations aimed to explore the in-depth mechanisms of miRNAs and other small RNAs including piRNAs in penile carcinogenesis regulation and effective target-specific theragnosis.

No MeSH data available.


Related in: MedlinePlus