Screening Biomarkers of Prostate Cancer by Integrating microRNA and mRNA Microarrays

Feng, Jiexiong; Chi-bing, Huang; Diao, Xinping; Mao, Fan; Wang, Pingxian; Xiao, Yue; Zhong, Xiao; Wu, Ronghua

doi:10.1089/gtmb.2013.0226

Cited by 21 publications

(17 citation statements)

References 36 publications

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“…more aggressive nature of AA PCa), which could be assessed by systematically disrupting reciprocal pairs with mimic/antagomir treatment of population-specific PCa cell lines and testing for a loss (or gain) of oncogenic function. To date, the integrated analysis of miRNA-mRNA pairs has been limited to a handful of PCa studies (32, 33) and none have been related to PCa disparities.…”

Section: Discussionmentioning

confidence: 99%

Identification and Functional Validation of Reciprocal microRNA–mRNA Pairings in African American Prostate Cancer Disparities

Wang

Ceniccola

Yang

et al. 2015

Clinical Cancer Research

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Purpose African Americans (AA) exhibit higher rates of prostate cancer (PCa) incidence and mortality compared to European American (EA) men. In addition to socioeconomic influences, biological factors are believed to play a critical role in PCa disparities. We investigated whether population-specific and -enriched miRNA-mRNA interactions might contribute to PCa disparities. Experimental Design Integrative genomics was employed, combining miRNA and mRNA profiling, miRNA target prediction, pathway analysis and functional validation, to map miRNA-mRNA interactions associated with PCa disparities. Results We identified 22 AA-specific and 18 EA-specific miRNAs in PCa versus patient-matched normal prostate, and 10 ‘AA-enriched/-depleted’ miRNAs in AA PCa versus EA PCa comparisons. Many of these population-specific/-enriched miRNAs could be paired with target mRNAs that exhibited an inverse pattern of differential expression. Pathway analysis revealed epidermal growth factor receptor (EGFR or ERBB) signaling as a critical pathway significantly regulated by AA-specific/-enriched mRNAs and miRNA-mRNA pairings. Novel miRNA-mRNA pairings were validated by qRT-PCR, western blot and/or IHC analyses in PCa specimens. Loss/gain of function assays performed in population-specific PCa cell lines confirmed miR-133a/MCL1, miR-513c/STAT1, miR-96/FOXO3A, miR-145/ITPR2 and miR-34a/PPP2R2A as critical miRNA-mRNA pairings driving oncogenesis. Manipulating the balance of these pairings resulted in decreased proliferation and invasion, and enhanced sensitization to docetaxel-induced cytotoxicity in AA PCa cells. Conclusion Our data suggest that AA-specific/-enriched miRNA-mRNA pairings may play a critical role in the activation of oncogenic pathways in AA PCa. Our findings also suggest that miR-133a/MCL1, miR-513c/STAT1 and miR-96/FOXO3A may have clinical significance in the development of novel strategies for treating aggressive PCa.

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Section: Discussionmentioning

confidence: 99%

Identification and Functional Validation of Reciprocal microRNA–mRNA Pairings in African American Prostate Cancer Disparities

Wang

Ceniccola

Yang

et al. 2015

Clinical Cancer Research

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“…The authors underlined the implication of miRNA-648 in PCa progression, predicting 10 target genes, including eight that have not been previously described in PCa. Using a similar procedure, Feng et al [82] found the overexpression of miR-31, proposing this biomarker to distinguish PCa tissues from benign tissues.…”

Section: Functional Enrichment Resources For Mirna Analysismentioning

confidence: 99%

miRNAs as novel biomarkers in the management of prostate cancer

Filella

Foj

2017

Clinical Chemistry and Laboratory Medicine (CCLM)

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microRNAs (miRNAs) are small non-coding RNAs that control gene expression posttranscriptionally and are part of the giant non codifying genoma. Cumulating data suggest that miRNAs are promising potential biomarkers for many diseases, including cancer. Prostate cancer (PCa) detection is currently based in the serum prostate-specific antigen biomarker and digital rectal examination. However, these methods are limited by a low predictive value and the adverse consequences associated with overdiagnosis and overtreatment. New biomarkers that could be used for PCa detection and prognosis are still needed. Recent studies have demonstrated that aberrant expressions of microRNAs are associated with the underlying mechanisms of PCa. This review attempts to extensively summarize the current knowledge of miRNA expression patterns, as well as their targets and involvement in PCa pathogenesis. We focused our review in the value of circulating and urine miRNAs as biomarkers in PCa patients, highlighting the existing discrepancies between different studies, probably associated with the important methodological issues related to their quantitation and normalization. The majority of studies have been performed in serum or plasma, but urine obtained after prostate massage appears as a new way to explore the usefulness of miRNAs. Large screening studies to select a miRNA profile have been completed, but bioinformatics tools appear as a new approach to select miRNAs that are relevant in PCa development.Promising preliminary results were published concerning miR-141, miR-375 and miR-21, but larger and prospective studies using standardized methodology are necessary to define the value of miRNAs in the detection and prognosis of PCa.

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“…Upregulation of "hsa-miR199a" and "hsa-miR-943" [7,19] and downregulation of "hsa-miR-127-3p" [36] are found responsible for melanoma. The investigations by Feng et al [6] and He et al [9] reported that upregulation of "hsa-miR-505" and "hsa-mir181b," respectively, causes prostate cancer by promoting cell proliferation in prostate gland, and our miRNA selection methodology also identified them as the relevant ones. FMIMS also predicted some miRNAs which target cancer-related genes.…”

Section: Discussionmentioning

confidence: 77%

Identifying relevant group of miRNAs in cancer using fuzzy mutual information

Pal

Ray

Pal

2015

Med Biol Eng Comput

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MicroRNAs (miRNAs) act as a major biomarker of cancer. All miRNAs in human body are not equally important for cancer identification. We propose a methodology, called FMIMS, which automatically selects the most relevant miRNAs for a particular type of cancer. In FMIMS, miRNAs are initially grouped by using a SVM-based algorithm; then the group with highest relevance is determined and the miRNAs in that group are finally ranked for selection according to their redundancy. Fuzzy mutual information is used in computing the relevance of a group and the redundancy of miRNAs within it. Superiority of the most relevant group to all others, in deciding normal or cancer, is demonstrated on breast, renal, colorectal, lung, melanoma and prostate data. The merit of FMIMS as compared to several existing methods is established. While 12 out of 15 selected miRNAs by FMIMS corroborate with those of biological investigations, three of them viz., "hsa-miR-519," "hsa-miR-431" and "hsa-miR-320c" are possible novel predictions for renal cancer, lung cancer and melanoma, respectively. The selected miRNAs are found to be involved in disease-specific pathways by targeting various genes. The method is also able to detect the responsible miRNAs even at the primary stage of cancer. The related code is available at http://www.jayanta.droppages.com/FMIMS.html .

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Screening Biomarkers of Prostate Cancer by Integrating microRNA and mRNA Microarrays

Cited by 21 publications

References 36 publications

Identification and Functional Validation of Reciprocal microRNA–mRNA Pairings in African American Prostate Cancer Disparities

Identification and Functional Validation of Reciprocal microRNA–mRNA Pairings in African American Prostate Cancer Disparities

miRNAs as novel biomarkers in the management of prostate cancer

Identifying relevant group of miRNAs in cancer using fuzzy mutual information

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