publication . Article . Other literature type . 2018

Genome-wide analysis of NGS data to compile cancer-specific panels of miRNA biomarkers.

Bhowmick, Shib Sankar; Saha, Indrajit; Bhattacharjee, Debotosh; Genovese, Loredana M.; Geraci, Filippo;
Open Access English
  • Published: 26 Jul 2018 Journal: PLoS ONE, volume 13, issue 7 (eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science
Abstract
MicroRNAs are small non-coding RNAs that influence gene expression by binding to the 3' UTR of target mRNAs in order to repress protein synthesis. Soon after discovery, microRNA dysregulation has been associated to several pathologies. In particular, they have often been reported as differentially expressed in healthy and tumor samples. This fact suggested that microRNAs are likely to be good candidate biomarkers for cancer diagnosis and personalized medicine. With the advent of Next-Generation Sequencing (NGS), measuring the expression level of the whole miRNAome at once is now routine. Yet, the collaborative effort of sharing data opens to the possibility of p...
Subjects
free text keywords: Research Article, Biology and life sciences, Genetics, Gene expression, Gene regulation, MicroRNAs, Biochemistry, Nucleic acids, RNA, Non-coding RNA, Biomarkers, Physical Sciences, Mathematics, Applied Mathematics, Algorithms, Research and Analysis Methods, Simulation and Modeling, Computational Biology, Genome Analysis, Gene Ontologies, Genomics, Developmental Biology, Morphogenesis, Evolutionary Algorithms, Computational Techniques, Evolutionary Computation, Mathematical and Statistical Techniques, Statistical Methods, Multivariate Analysis, Principal Component Analysis, Statistics (Mathematics), Medicine and Health Sciences, Oncology, Cancer Risk Factors, Genetic Causes of Cancer, Medicine, R, Science, Q, Genome wide analysis, Computer science, Cancer, medicine.disease, Biomarker (medicine), microRNA
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55 references, page 1 of 4

1 Wu L, Qu X. Cancer biomarker detection: recent achievements and challenges. Chemical Society Reviews. 2015;44(10):2963–2997. 10.1039/c4cs00370e 25739971 [OpenAIRE] [PubMed] [DOI]

2 Bartel DP. MicroRNAs-Genomics, Biogenesis, Mechanism, and Function. Cell. 2004;2(116):281–297. 10.1016/S0092-8674(04)00045-5 [DOI]

3 Perkins D, Jeffries C, Jarskog L, Thomson J, Woods K, Newman M, et al microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder. Genome Biology. 2007;8(2):R27 10.1186/gb-2007-8-2-r27 17326821 [OpenAIRE] [PubMed] [DOI]

4 Shalgi R, Lieber D, Oren M, Pilpel Y. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Computational Biology. 2007;3(7):e131 10.1371/journal.pcbi.0030131 17630826 [OpenAIRE] [PubMed] [DOI]

5 Lu J, Getz G, Miska E, Saavedra E, Lamb J, Peck D, et al MicroRNA expression profiles classify human cancers. Nature. 2005;435(7043):834–838. 10.1038/nature03702 15944708 [OpenAIRE] [PubMed] [DOI]

6 Sourvinou IS, Markou A, Lianidou ES. Quantification of circulating miRNAs in plasma: effect of preanalytical and analytical parameters on their isolation and stability. The Journal of Molecular Diagnostics. 2013;15(6):827–834. 10.1016/j.jmoldx.2013.07.005 23988620 [OpenAIRE] [PubMed] [DOI]

7 Kok MG, Halliani A, Moerland PD, Meijers JC, Creemers EE, Pinto-Sietsma SJ. Normalization panels for the reliable quantification of circulating microRNAs by RT-qPCR. The FASEB Journal. 2015;29(9):3853–3862. 10.1096/fj.15-271312 26023181 [OpenAIRE] [PubMed] [DOI]

8 Duttagupta R, Jiang R, Gollub J, Getts RC, Jones KW. Impact of cellular miRNAs on circulating miRNA biomarker signatures. PloS One. 2011;6(6):e20769 10.1371/journal.pone.0020769 21698099 [OpenAIRE] [PubMed] [DOI]

9 Gilad S, Meiri E, Yogev Y, Benjamin S, Lebanony D, Yerushalmi N, et al Serum microRNAs are promising novel biomarkers. PloS One. 2008;3(9):e3148 10.1371/journal.pone.0003148 18773077 [OpenAIRE] [PubMed] [DOI]

10 Hayes J, Peruzzi PP, Lawler S. MicroRNAs in cancer: biomarkers, functions and therapy. Trends in Molecular Medicine. 2014;20(8):460–469. 10.1016/j.molmed.2014.06.005 25027972 [OpenAIRE] [PubMed] [DOI]

11 Rosenfeld N, Aharonov R, Meiri E, Rosenwald S, Spector Y, Zepeniuk M, et al MicroRNAs accurately identify cancer tissue origin. Nature Biotechnology. 2008;26(4):462–469. 10.1038/nbt1392 18362881 [OpenAIRE] [PubMed] [DOI]

12 Church RJ, McDuffie JE, Sonee M, Otieno M, Ma JY, Liu X, et al MicroRNA-34c-3p is an early predictive biomarker for doxorubicin-induced glomerular injury progression in male Sprague-Dawley rats. Toxicology Research. 2014;3(5):384–394. 10.1039/C4TX00051J [OpenAIRE] [DOI]

13 Taylor DD, Gercel-Taylor C. MicroRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer. Gynecologic Oncology. 2008;110(1):13–21. 10.1016/j.ygyno.2008.04.033 18589210 [OpenAIRE] [PubMed] [DOI]

14 Mattie MD, Benz CC, Bowers J, Sensinger K, Wong L, Scott GK, et al Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Molecular Cancer. 2006;5(1):24 10.1186/1476-4598-5-24 16784538 [OpenAIRE] [PubMed] [DOI]

15 Fabbri M. MicroRNAs and cancer: towards a personalized medicine. Current Molecular Medicine. 2013;13(5):751–756. 10.2174/1566524011313050006 23642056 [OpenAIRE] [PubMed] [DOI]

55 references, page 1 of 4
Abstract
MicroRNAs are small non-coding RNAs that influence gene expression by binding to the 3' UTR of target mRNAs in order to repress protein synthesis. Soon after discovery, microRNA dysregulation has been associated to several pathologies. In particular, they have often been reported as differentially expressed in healthy and tumor samples. This fact suggested that microRNAs are likely to be good candidate biomarkers for cancer diagnosis and personalized medicine. With the advent of Next-Generation Sequencing (NGS), measuring the expression level of the whole miRNAome at once is now routine. Yet, the collaborative effort of sharing data opens to the possibility of p...
Subjects
free text keywords: Research Article, Biology and life sciences, Genetics, Gene expression, Gene regulation, MicroRNAs, Biochemistry, Nucleic acids, RNA, Non-coding RNA, Biomarkers, Physical Sciences, Mathematics, Applied Mathematics, Algorithms, Research and Analysis Methods, Simulation and Modeling, Computational Biology, Genome Analysis, Gene Ontologies, Genomics, Developmental Biology, Morphogenesis, Evolutionary Algorithms, Computational Techniques, Evolutionary Computation, Mathematical and Statistical Techniques, Statistical Methods, Multivariate Analysis, Principal Component Analysis, Statistics (Mathematics), Medicine and Health Sciences, Oncology, Cancer Risk Factors, Genetic Causes of Cancer, Medicine, R, Science, Q, Genome wide analysis, Computer science, Cancer, medicine.disease, Biomarker (medicine), microRNA
Download fromView all 4 versions
PLoS ONE
Article . 2018
PLoS ONE
Article . 2018
Provider: Crossref
PLoS ONE
Article
Provider: UnpayWall
55 references, page 1 of 4

1 Wu L, Qu X. Cancer biomarker detection: recent achievements and challenges. Chemical Society Reviews. 2015;44(10):2963–2997. 10.1039/c4cs00370e 25739971 [OpenAIRE] [PubMed] [DOI]

2 Bartel DP. MicroRNAs-Genomics, Biogenesis, Mechanism, and Function. Cell. 2004;2(116):281–297. 10.1016/S0092-8674(04)00045-5 [DOI]

3 Perkins D, Jeffries C, Jarskog L, Thomson J, Woods K, Newman M, et al microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder. Genome Biology. 2007;8(2):R27 10.1186/gb-2007-8-2-r27 17326821 [OpenAIRE] [PubMed] [DOI]

4 Shalgi R, Lieber D, Oren M, Pilpel Y. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Computational Biology. 2007;3(7):e131 10.1371/journal.pcbi.0030131 17630826 [OpenAIRE] [PubMed] [DOI]

5 Lu J, Getz G, Miska E, Saavedra E, Lamb J, Peck D, et al MicroRNA expression profiles classify human cancers. Nature. 2005;435(7043):834–838. 10.1038/nature03702 15944708 [OpenAIRE] [PubMed] [DOI]

6 Sourvinou IS, Markou A, Lianidou ES. Quantification of circulating miRNAs in plasma: effect of preanalytical and analytical parameters on their isolation and stability. The Journal of Molecular Diagnostics. 2013;15(6):827–834. 10.1016/j.jmoldx.2013.07.005 23988620 [OpenAIRE] [PubMed] [DOI]

7 Kok MG, Halliani A, Moerland PD, Meijers JC, Creemers EE, Pinto-Sietsma SJ. Normalization panels for the reliable quantification of circulating microRNAs by RT-qPCR. The FASEB Journal. 2015;29(9):3853–3862. 10.1096/fj.15-271312 26023181 [OpenAIRE] [PubMed] [DOI]

8 Duttagupta R, Jiang R, Gollub J, Getts RC, Jones KW. Impact of cellular miRNAs on circulating miRNA biomarker signatures. PloS One. 2011;6(6):e20769 10.1371/journal.pone.0020769 21698099 [OpenAIRE] [PubMed] [DOI]

9 Gilad S, Meiri E, Yogev Y, Benjamin S, Lebanony D, Yerushalmi N, et al Serum microRNAs are promising novel biomarkers. PloS One. 2008;3(9):e3148 10.1371/journal.pone.0003148 18773077 [OpenAIRE] [PubMed] [DOI]

10 Hayes J, Peruzzi PP, Lawler S. MicroRNAs in cancer: biomarkers, functions and therapy. Trends in Molecular Medicine. 2014;20(8):460–469. 10.1016/j.molmed.2014.06.005 25027972 [OpenAIRE] [PubMed] [DOI]

11 Rosenfeld N, Aharonov R, Meiri E, Rosenwald S, Spector Y, Zepeniuk M, et al MicroRNAs accurately identify cancer tissue origin. Nature Biotechnology. 2008;26(4):462–469. 10.1038/nbt1392 18362881 [OpenAIRE] [PubMed] [DOI]

12 Church RJ, McDuffie JE, Sonee M, Otieno M, Ma JY, Liu X, et al MicroRNA-34c-3p is an early predictive biomarker for doxorubicin-induced glomerular injury progression in male Sprague-Dawley rats. Toxicology Research. 2014;3(5):384–394. 10.1039/C4TX00051J [OpenAIRE] [DOI]

13 Taylor DD, Gercel-Taylor C. MicroRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer. Gynecologic Oncology. 2008;110(1):13–21. 10.1016/j.ygyno.2008.04.033 18589210 [OpenAIRE] [PubMed] [DOI]

14 Mattie MD, Benz CC, Bowers J, Sensinger K, Wong L, Scott GK, et al Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Molecular Cancer. 2006;5(1):24 10.1186/1476-4598-5-24 16784538 [OpenAIRE] [PubMed] [DOI]

15 Fabbri M. MicroRNAs and cancer: towards a personalized medicine. Current Molecular Medicine. 2013;13(5):751–756. 10.2174/1566524011313050006 23642056 [OpenAIRE] [PubMed] [DOI]

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publication . Article . Other literature type . 2018

Genome-wide analysis of NGS data to compile cancer-specific panels of miRNA biomarkers.

Bhowmick, Shib Sankar; Saha, Indrajit; Bhattacharjee, Debotosh; Genovese, Loredana M.; Geraci, Filippo;