401
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Affiliation(s)
- Julie Anne Saugstad
- Department of Anesthesiology and Perioperative Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239-3098, USA.
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402
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Fullston T, Ohlsson Teague EMC, Palmer NO, DeBlasio MJ, Mitchell M, Corbett M, Print CG, Owens JA, Lane M. Paternal obesity initiates metabolic disturbances in two generations of mice with incomplete penetrance to the F2 generation and alters the transcriptional profile of testis and sperm microRNA content. FASEB J 2013; 27:4226-43. [PMID: 23845863 DOI: 10.1096/fj.12-224048] [Citation(s) in RCA: 373] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Obesity is highly prevalent, and its incidence is increasing. The previous study showing a major effect of paternal obesity on metabolic health of offspring is confounded by comorbidity with diabetes. Therefore, we investigated the effect of diet-induced paternal obesity, in the absence of diabetes, on the metabolic health of two resultant generations and the molecular profiles of the testes and sperm. Founder (F0) male C57BL6 mice were fed either a high-fat diet (HFD) or a control diet (CD); n = 10/diet for a period of 10 wk. Testis expression of mRNA/microRNAs was analyzed by microarray and qPCR and sperm microRNA abundance by qPCR. Two subsequent generations were generated by mating F0 and then F1 mice to CD mice, and their metabolic health was investigated. All mice, other than F0 males, were maintained on a CD. HFD feeding induced paternal obesity with a 21% increase in adiposity, but not overt diabetes, and initiated intergenerational transmission of obesity and insulin resistance in two generations of offspring. This distinct phenotypic constellation is either partially or fully transmitted to both female and male F1 offspring and further transmitted through both parental lineages to the F2 generation, with a heightened effect on female F1 offspring (+67% in adiposity) and their F2 sons (+24% in adiposity). Founder male obesity altered the testes expression of 414 mRNAs by microarray and 11 microRNAs by qPCR, concomitant with alterations in sperm microRNA content and a 25% reduction in global methylation of germ cell DNA. Diet-induced paternal obesity modulates sperm microRNA content and germ cell methylation status, which are potential signals that program offspring health and initiate the transmission of obesity and impaired metabolic health to future generations. This study implicates paternal obesity in the transgenerational amplification of obesity and type 2 diabetes in humans.
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Affiliation(s)
- Tod Fullston
- 1Level 3 Medical School South, University of Adelaide, Adelaide, SA, Australia 5005.
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403
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Torres A, Torres K, Wdowiak P, Paszkowski T, Maciejewski R. Selection and validation of endogenous controls for microRNA expression studies in endometrioid endometrial cancer tissues. Gynecol Oncol 2013; 130:588-94. [PMID: 23811003 DOI: 10.1016/j.ygyno.2013.06.026] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 06/18/2013] [Accepted: 06/19/2013] [Indexed: 10/26/2022]
Abstract
OBJECTIVES microRNAs comprise a family of small, non-coding RNAs, which regulate gene expression at the posttranscriptional level. Multiple studies implicated important roles of microRNAs in various malignancies including endometrioid endometrial carcinoma (EEC). qPCR is widely used in the studies investigating microRNA expression. Relative quantification of microRNA expression requires proper normalization methods and endogenous controls are widely used for this purpose. The aim of this study was experimental identification of stable endogenous controls for normalization of microRNA qPCR expression studies in EEC. METHODS Expression of twelve candidate endogenous controls (miR-16, miR-26b, miR-92a, RNU44, RNU48, U75, U54, U6, U49, RNU6B, RNU38B, U18A) was investigated in tissue samples obtained from 45 patients (30 EEC, 15 normal endometrium) using qPCR. Stability of candidate endogenous controls was evaluated using NormFinder, geNorm, BestKeeper and equivalency test. The results were then validated using larger group of samples. RESULTS RNU48, U75 and RNU44 were identified as stably and equivalently expressed between malignant and normal tissues. Both NormFinder and geNorm indicated that those three snRNAs were optimal for qPCR data normalization in EEC tissues. CONCLUSIONS In conclusion, we suggest that average expression of those snoRNAs could be used as a reliable endogenous control in microRNA qPCR studies in endometrioid endometrial cancer. In addition to identifying suitable endogenous controls in EEC, our study presents an appropriate strategy for validation of candidate reference genes for any microRNA qPCR study.
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Affiliation(s)
- Anna Torres
- Laboratory of Biostructure, Department of Human Anatomy, Medical University of Lublin, Jaczewskiego 4, 20-090, Lublin, Poland.
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404
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Abstract
MicroRNAs (miRNAs) in human saliva have recently become an emerging field in saliva research for -diagnostics applications and its potential role in biological implications. miRNAs are short noncoding RNA molecules that play important roles in regulating a variety of cellular processes. Dysregulation of miRNAs are known to be associated with many diseases. miRNAs were found present in the saliva of OSCC patients and could serve as potential biomarkers for oral cancer detection. Understanding the biological function of miRNAs in association with diseases is important towards utilizing miRNAs as diagnostic markers. There are currently a variety of profiling methods available for detecting miRNA expression levels. In this chapter, we overview the Applied Biosystem Stem-loop RT based Taqman MicroRNA Assay for salivary miRNA profiling. Using this highly sensitive and specific assay, miRNAs in saliva are profiled with only a few nanograms of starting RNA. This method is also applicable for studying biomarkers in other body fluids or clinical samples that contain small amounts of RNA.
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405
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Duskova K, Nagilla P, Le HS, Iyer P, Thalamuthu A, Martinson J, Bar-Joseph Z, Buchanan W, Rinaldo C, Ayyavoo V. MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts. BMC Infect Dis 2013; 13:250. [PMID: 23721325 PMCID: PMC3680326 DOI: 10.1186/1471-2334-13-250] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 05/16/2013] [Indexed: 12/13/2022] Open
Abstract
Background Disease progression in the absence of therapy varies significantly in HIV-1 infected individuals. Both viral and host cellular molecules are implicated; however, the exact role of these factors and/or the mechanism involved remains elusive. To understand how microRNAs (miRNAs), which are regulators of transcription and translation, influence host cellular gene expression (mRNA) during HIV-1 infection, we performed a comparative miRNA and mRNA microarray analysis using PBMCs obtained from infected individuals with distinct viral load and CD4 counts. Methods RNA isolated from PBMCs obtained from HIV-1 seronegative and HIV-1 positive individuals with distinct viral load and CD4 counts were assessed for miRNA and mRNA profile. Selected miRNA and mRNA transcripts were validated using in vivo and in vitro infection model. Results Our results indicate that HIV-1 positive individuals with high viral load (HVL) showed a dysregulation of 191 miRNAs and 309 mRNA transcripts compared to the uninfected age and sex matched controls. The miRNAs miR-19b, 146a, 615-3p, 382, 34a, 144 and 155, that are known to target innate and inflammatory factors, were significantly upregulated in PBMCs with high viral load, as were the inflammatory molecules CXCL5, CCL2, IL6 and IL8, whereas defensin, CD4, ALDH1, and Neurogranin (NRGN) were significantly downregulated. Using the transcriptome profile and predicted target genes, we constructed the regulatory networks of miRNA-mRNA pairs that were differentially expressed between control, LVL and HVL subjects. The regulatory network revealed an inverse correlation of several miRNA-mRNA pair expression patterns, suggesting HIV-1 mediated transcriptional regulation is in part likely through miRNA regulation. Conclusions Results from our studies indicate that gene expression is significantly altered in PBMCs in response to virus replication. It is interesting to note that the infected individuals with low or undetectable viral load exhibit a gene expression profile very similar to control or uninfected subjects. Importantly, we identified several new mRNA targets (Defensin, Neurogranin, AIF) as well as the miRNAs that could be involved in regulating their expression through the miRNA-mRNA interaction.
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Affiliation(s)
- Karolina Duskova
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 425 Parran Hall, 130 Desoto Street, Pittsburgh, PA 15261, USA
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406
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Hermansen SK, Kristensen BW. MicroRNA biomarkers in glioblastoma. J Neurooncol 2013; 114:13-23. [PMID: 23700324 DOI: 10.1007/s11060-013-1155-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 05/12/2013] [Indexed: 12/27/2022]
Abstract
Recent research suggests that deregulation of microRNAs (miRNAs) is involved in initiation and progression of many cancers, including gliomas and that miRNAs hold great potential as future diagnostic and therapeutic tools in cancer. MiRNAs are a class of short non-coding RNA sequences (18-24 nucleotides), which base-pair to target messenger RNA (mRNA) and thereby cause translational repression or mRNA degradation based on the level of complementarity between strands. Profiling miRNAs in clinical glioblastoma samples has shown aberrant expression of numerous miRNAs when compared to normal brain tissues. Understanding these alterations is key to developing new biomarkers and intelligent treatment strategies. This review presents an overview of current knowledge about miRNA alterations in glioblastoma while focusing on the clinical future of miRNAs as biomarkers and discussing the strengths and weaknesses of various methods used in evaluating their expression.
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Affiliation(s)
- Simon Kjær Hermansen
- Department of Pathology, Odense University Hospital, Winsløwparken 15, 3. Floor, 5000, Odense C, Denmark.
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407
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Dong H, Lei J, Ding L, Wen Y, Ju H, Zhang X. MicroRNA: Function, Detection, and Bioanalysis. Chem Rev 2013; 113:6207-33. [PMID: 23697835 DOI: 10.1021/cr300362f] [Citation(s) in RCA: 836] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Haifeng Dong
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
| | - Jianping Lei
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Lin Ding
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Yongqiang Wen
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
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408
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Tompsett AR, Wiseman S, Higley E, Giesy JP, Hecker M. Effects of exposure to 17α-ethynylestradiol during sexual differentiation on the transcriptome of the African clawed frog (Xenopus laevis). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:4822-4828. [PMID: 23550701 DOI: 10.1021/es400436y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Exposure to estrogens during the period of sexual differentiation is known to adversely affect the development of testes in African clawed frogs (Xenopus laevis), but little is known about molecular changes that coincide with the development of altered phenotypes. Therefore, the transcriptome-level effects of exposure to 17α-ethynylestradiol (EE2) during sexual differentiation of X. laevis were evaluated by use of Illumina sequencing coupled with RNA-Seq expression analysis. Overall, a number of processes were affected by 17α-ethynylestradiol, including steroid biosynthesis, thyroid hormone signaling and metabolism, testicular development, and spermatogenesis. Some of the altered pathways, such as thyroid hormone signaling and testicular development, could be linked with biological effects on metamorphosis and gonadal phenotypes, respectively, that were observed in frogs that were exposed to 17α-ethynylestradiol throughout metamorphosis and the early postmetamorphic period. Thus, early changes at the transcriptome-level were predictive of pathologies that did not manifest until later in development. To validate the quantitative capacity of RNA-Seq, a subset of transcripts identified to have altered abundances in individuals exposed to 17α-ethynylestradiol was also evaluated by use of quantitative polymerase chain reaction (qPCR). While small sample sizes (n = 3) limited the ability to draw conclusions pertaining to differences in qPCR-derived abundances of transcripts between control and exposed tadpoles, there was a significant relationship (r(2) = 0.78) between fold-changes for RNA-Seq and qPCR.
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Affiliation(s)
- Amber R Tompsett
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
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409
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Zhang X, Lii Y, Wu Z, Polishko A, Zhang H, Chinnusamy V, Lonardi S, Zhu JK, Liu R, Jin H. Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues. MOLECULAR PLANT 2013; 6:704-15. [PMID: 23505223 PMCID: PMC3660955 DOI: 10.1093/mp/sst051] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 02/28/2013] [Indexed: 05/18/2023]
Abstract
A large proportion of eukaryotic genomes is transcribed from both positive and negative strands of DNA and thus may generate overlapping sense and antisense transcripts. Some of these so-called natural antisense transcripts (NATs) are possibly co-regulated. When the overlapping sense and antisense transcripts are expressed at the same time in the same cell in response to various developmental and environmental cues; they may form double-stranded RNAs, which could be recognized by the small RNA biogenesis machinery and processed into small interfering RNAs (siRNAs). cis-NAT-derived siRNAs (nat-siRNAs) are present in plants, animals, and fungi. In plants, the presence of nat-siRNAs is supported not only by Northern blot and genetic analyses, but also by the fact that there is an overall sixfold enrichment of siRNAs in the overlapping regions of cis-NATs and 19%-29% of the siRNA-generating cis-NATs in plants give rise to siRNAs only in their overlapping regions. Silencing mediated by nat-siRNAs is one of the mechanisms for regulating the expression of the cis-NATs. This review focuses on challenging issues related to the biogenesis mechanisms as well as regulation and detection of nat-siRNAs. The advantages and limitations of new technologies for detecting cis-NATs, including direct RNA sequencing and strand-specific RNA sequencing, are also discussed.
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Affiliation(s)
- Xiaoming Zhang
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Yifan Lii
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Zhigang Wu
- Department of Botany and Plant Sciences and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Anton Polishko
- Computer Science and Engineering, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Huiming Zhang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Stefano Lonardi
- Computer Science and Engineering, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- To whom correspondence should be addressed. H.J. E-mail , tel. +1-951-827-7995. R.L. E-mail . J.-k.Z. E-mail
| | - Renyi Liu
- Department of Botany and Plant Sciences and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- To whom correspondence should be addressed. H.J. E-mail , tel. +1-951-827-7995. R.L. E-mail . J.-k.Z. E-mail
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- To whom correspondence should be addressed. H.J. E-mail , tel. +1-951-827-7995. R.L. E-mail . J.-k.Z. E-mail
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410
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Taylor SK, Wang J, Kostic N, Stojanovic MN. Monovalent Streptavidin that Senses Oligonucleotides. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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411
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Taylor SK, Wang J, Kostic N, Stojanovic MN. Monovalent streptavidin that senses oligonucleotides. Angew Chem Int Ed Engl 2013; 52:5509-12. [PMID: 23606329 DOI: 10.1002/anie.201209948] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/06/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Steven K Taylor
- Department of Medicine, Division of Experimental Therapeutics, Columbia University, 630 W. 168th St., Box 84, New York, NY 10032, USA.
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412
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De Guire V, Robitaille R, Tétreault N, Guérin R, Ménard C, Bambace N, Sapieha P. Circulating miRNAs as sensitive and specific biomarkers for the diagnosis and monitoring of human diseases: promises and challenges. Clin Biochem 2013; 46:846-60. [PMID: 23562576 DOI: 10.1016/j.clinbiochem.2013.03.015] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 02/22/2013] [Accepted: 03/25/2013] [Indexed: 01/04/2023]
Abstract
The regulation and modulation of gene expression has been a central focus of modern biomedical research ever since the first molecular elucidation of DNA. The cellular mechanisms by which genes are expressed and repressed hold valuable insight for maintaining tissue homeostasis or conversely provide mechanistic understanding of disease progression. Hence, the discovery of the first miRNA in humans roughly a decade ago profoundly shook the previously established dogmas of gene regulation. Since, these small RNAs of around 20 nucleotides have unquestionably influenced almost every area of medical research. This momentum has now spread to the clinical arena. Hundreds of papers have already been published shedding light on the mechanisms of action of miRNAs, their profound stability in almost every bodily fluid and relating their presence to disease state and severity of disease progression. In this review, we explore the diagnostic potential of miRNAs in the clinical laboratory with a focus on studies reporting the detection of miRNAs in blood and urine for investigation of human disease. Sensitivities, specificities, areas under the curve, group descriptions and miRNAs of interest for 69 studies covering a broad range of diseases are provided. We discuss the practicality of miRNAs in the screening, diagnosis and prognosis of a range of pathologies. Characteristics and pitfalls of miRNA detection in blood are also discussed. The topics covered here are pertinent in the design of future miRNA-based detection strategies for use in clinical biochemistry laboratory settings.
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Affiliation(s)
- V De Guire
- Department of Biochemistry, Maisonneuve-Rosemont Hospital, 5415, boulevard de l'Assomption, Montréal, Québec, H1T 2M4, Canada.
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413
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Leshkowitz D, Horn-Saban S, Parmet Y, Feldmesser E. Differences in microRNA detection levels are technology and sequence dependent. RNA (NEW YORK, N.Y.) 2013; 19:527-38. [PMID: 23431331 PMCID: PMC3677263 DOI: 10.1261/rna.036475.112] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Identification and quantification of small RNAs are challenging because of their short length, high sequence similarities within microRNA (miRNA) families, and the existence of miRNA isoforms and O-methyl 3' modifications. In this study, the detection performance of three high-throughput commercial platforms, Agilent and Affymetrix microarrays and Illumina next-generation sequencing, was systematically and comprehensively compared. The ability to detect miRNAs was shown to depend strongly on the platform and on miRNA modifications and sequence. Using synthetic transcripts, including mature, precursor, and O-methyl-modified miRNAs spiked into human RNA, a large intensity variation in all spiked-in miRNAs and a reduced capacity in detecting O-methyl-modified miRNAs were observed between the tested platforms. In addition, endogenous human miRNA expression levels were assessed across the platforms. Detected miRNA expression levels were not consistent between platforms. Although biases in miRNA detection were previously described, here the end-point result, i.e., detection intensity, of these biases was investigated on multiple platforms in a controlled fashion. A detailed exploration of a large number of attributes, including base composition, sequence structure, and isoform miRNA attributes, suggests their impact on miRNA expression detection level. This study provides a basis for understanding the attributes that should be considered to adjust platform-dependent detection biases.
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Affiliation(s)
- Dena Leshkowitz
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
- Corresponding authorsE-mail E-mail E-mail
| | - Shirley Horn-Saban
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
- Corresponding authorsE-mail E-mail E-mail
| | - Yisrael Parmet
- Industrial Engineering and Management Department, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Ester Feldmesser
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
- Corresponding authorsE-mail E-mail E-mail
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414
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Donati C, Rappuoli R. Reverse vaccinology in the 21st century: improvements over the original design. Ann N Y Acad Sci 2013; 1285:115-32. [PMID: 23527566 DOI: 10.1111/nyas.12046] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Reverse vaccinology (RV), the first application of genomic technologies in vaccine research, represented a major revolution in the process of discovering novel vaccines. By determining their entire antigenic repertoire, researchers could identify protective targets and design efficacious vaccines for pathogens where conventional approaches had failed. Bexsero, the first vaccine developed using RV, has recently received positive opinion from the European Medicines Agency. The use of RV initiated a cascade of changes that affected the entire vaccine development process, shifting the focus from the identification of a list of vaccine candidates to the definition of a set of high throughput screens to reduce the need for costly and labor intensive tests in animal models. It is now clear that a deep understanding of the epidemiology of vaccine candidates, and their regulation and role in host-pathogen interactions, must become an integral component of the screening workflow. Far from being outdated by technological advancements, RV still represents a paradigm of how high-throughput technologies and scientific insight can be integrated into biotechnology research.
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415
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Derrick T, Roberts CH, Rajasekhar M, Burr SE, Joof H, Makalo P, Bailey RL, Mabey DCW, Burton MJ, Holland MJ. Conjunctival MicroRNA expression in inflammatory trachomatous scarring. PLoS Negl Trop Dis 2013; 7:e2117. [PMID: 23516655 PMCID: PMC3597489 DOI: 10.1371/journal.pntd.0002117] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 01/31/2013] [Indexed: 12/16/2022] Open
Abstract
Purpose Trachoma is a fibrotic disease of the conjunctiva initiated by Chlamydia trachomatis infection. This blinding disease affects over 40 million people worldwide yet the mechanisms underlying its pathogenesis remain poorly understood. We have investigated host microRNA (miR) expression in health (N) and disease (conjunctival scarring with (TSI) and without (TS) inflammation) to determine if these epigenetic differences are associated with pathology. Methods We collected two independent samples of human conjunctival swab specimens from individuals living in The Gambia (n = 63 & 194). miR was extracted, and we investigated the expression of 754 miR in the first sample of 63 specimens (23 N, 17 TS, 23 TSI) using Taqman qPCR array human miRNA genecards. Network and pathway analysis was performed on this dataset. Seven miR that were significantly differentially expressed between different phenotypic groups were then selected for validation by qPCR in the second sample of 194 specimens (93 N, 74 TS, 22 TSI). Results Array screening revealed differential expression of 82 miR between N, TS and TSI phenotypes (fold change >3, p<0.05). Predicted mRNA targets of these miR were enriched in pathways involved in fibrosis and epithelial cell differentiation. Two miR were confirmed as being differentially expressed upon validation by qPCR. miR-147b is significantly up-regulated in TSI versus N (fold change = 2.3, p = 0.03) and miR-1285 is up-regulated in TSI versus TS (fold change = 4.6, p = 0.005), which was consistent with the results of the qPCR array. Conclusions miR-147b and miR-1285 are up-regulated in inflammatory trachomatous scarring. Further investigation of the function of these miR will aid our understanding of the pathogenesis of trachoma. Trachoma is a debilitating disease that affects 40 million people worldwide. It can cause progressive fibrosis of the upper eyelid and blindness, yet the mechanism is poorly understood. We have investigated the expression of short sequences of genetic material (microRNA) that regulate gene expression. We screened for the expression of 754 microRNA sequences (miR) in genetic material isolated from conjunctival swab samples from individuals in trachoma-endemic communities in The Gambia. This sample included healthy controls, individuals with trachomatous scarring and individuals with trachomatous scarring in the presence of clinically significant inflammation. We found 82 miR that were differentially expressed. Computer simulations predict that these miR regulate genes in epithelial cell differentiation, inflammation and fibrosis pathways, all of which are involved in the scarring process. We then validated the expression of seven of these differentially expressed miR in a second larger biological sample set from The Gambia. We confirmed that miR-147b and miR-1285 have increased expression in individuals with trachomatous scarring in the presence of clinically significant inflammation. Further investigation into the functions of these miR will aid our understanding of this disease and present opportunities to develop treatments for ocular fibrotic diseases.
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Affiliation(s)
- Tamsyn Derrick
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
| | - Chrissy h. Roberts
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Megha Rajasekhar
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sarah E. Burr
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia, West Africa
| | - Hassan Joof
- Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia, West Africa
| | - Pateh Makalo
- Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia, West Africa
| | - Robin L. Bailey
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David C. W. Mabey
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew J. Burton
- International Centre for Eye Health, Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Martin J. Holland
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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416
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Feasibility of circulating miRNA microarray analysis from archival plasma samples. Anal Biochem 2013; 437:123-5. [PMID: 23499963 DOI: 10.1016/j.ab.2013.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 03/01/2013] [Accepted: 03/02/2013] [Indexed: 11/24/2022]
Abstract
MicroRNAs have been found to be deregulated in several diseases and, due to their high stability in body fluids, represent promising noninvasively detectable biomarkers. However, numerous technical variables can affect accurate measurement of circulating miRNAs. Using a microarray-based method we assessed the: (i) adequate intra- and inter-array reproducibility of miRNA profiling; (ii) feasibility of using archival plasma samples stored for an extended period of time and available in limited amounts; (iii) good correlation between different batches; and (iv) time-dependent increase of background signals close to the chip expiration date.
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417
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Normalization of miRNA qPCR high-throughput data: a comparison of methods. Biotechnol Lett 2013; 35:843-51. [DOI: 10.1007/s10529-013-1150-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
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418
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Liu N, Yang J, Guo S, Xu Y, Zhang M. Genome-wide identification and comparative analysis of conserved and novel microRNAs in grafted watermelon by high-throughput sequencing. PLoS One 2013; 8:e57359. [PMID: 23468976 PMCID: PMC3582568 DOI: 10.1371/journal.pone.0057359] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stresses response. However less is known about miRNAs involvement in grafting behaviors, especially with the watermelon (Citrullus lanatus L.) crop, which is one of the most important agricultural crops worldwide. Grafting method is commonly used in watermelon production in attempts to improve its adaptation to abiotic and biotic stresses, in particular to the soil-borne fusarium wilt disease. In this study, Solexa sequencing has been used to discover small RNA populations and compare miRNAs on genome-wide scale in watermelon grafting system. A total of 11,458,476, 11,614,094 and 9,339,089 raw reads representing 2,957,751, 2,880,328 and 2,964,990 unique sequences were obtained from the scions of self-grafted watermelon and watermelon grafted on-to bottle gourd and squash at two true-leaf stage, respectively. 39 known miRNAs belonging to 30 miRNA families and 80 novel miRNAs were identified in our small RNA dataset. Compared with self-grafted watermelon, 20 (5 known miRNA families and 15 novel miRNAs) and 47 (17 known miRNA families and 30 novel miRNAs) miRNAs were expressed significantly different in watermelon grafted on to bottle gourd and squash, respectively. MiRNAs expressed differentially when watermelon was grafted onto different rootstocks, suggesting that miRNAs might play an important role in diverse biological and metabolic processes in watermelon and grafting may possibly by changing miRNAs expressions to regulate plant growth and development as well as adaptation to stresses. The small RNA transcriptomes obtained in this study provided insights into molecular aspects of miRNA-mediated regulation in grafted watermelon. Obviously, this result would provide a basis for further unravelling the mechanism on how miRNAs information is exchanged between scion and rootstock in grafted watermelon, and its relevance to diverse biological processes and environmental adaptation.
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Affiliation(s)
- Na Liu
- Laboratory of Genetics Resources & Functional Improvement for Horticultural Plant, Department of Horticulture, Zhejiang University, Hangzhou, People’s Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Jinghua Yang
- Laboratory of Genetics Resources & Functional Improvement for Horticultural Plant, Department of Horticulture, Zhejiang University, Hangzhou, People’s Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, People’s Republic of China
| | - Shaogui Guo
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, People’s Republic of China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, People’s Republic of China
- * E-mail: (YX); (MZ)
| | - Mingfang Zhang
- Laboratory of Genetics Resources & Functional Improvement for Horticultural Plant, Department of Horticulture, Zhejiang University, Hangzhou, People’s Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, People’s Republic of China
- * E-mail: (YX); (MZ)
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419
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Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues. PLoS One 2013; 8:e52517. [PMID: 23382819 PMCID: PMC3561362 DOI: 10.1371/journal.pone.0052517] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 11/15/2012] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs play a role in regulating diverse biological processes and have considerable utility as molecular markers for diagnosis and monitoring of human disease. Several technologies are available commercially for measuring microRNA expression. However, cross-platform comparisons do not necessarily correlate well, making it difficult to determine which platform most closely represents the true microRNA expression level in a tissue. To address this issue, we have analyzed RNA derived from cell lines, as well as fresh frozen and formalin-fixed paraffin embedded tissues, using Affymetrix, Agilent, and Illumina microRNA arrays, NanoString counting, and Illumina Next Generation Sequencing. We compared the performance within- and between the different platforms, and then verified these results with those of quantitative PCR data. Our results demonstrate that the within-platform reproducibility for each method is consistently high and although the gene expression profiles from each platform show unique traits, comparison of genes that were commonly detectable showed that detection of microRNA transcripts was similar across multiple platforms.
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420
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Tang YW, Stratton CW. Diagnosis and Assessment of Microbial Infections with Host and Microbial microRNA Profiles. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2013. [PMCID: PMC7120657 DOI: 10.1007/978-1-4614-3970-7_46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Biomarkers are continuously being sought in the field of diagnostic microbiology for the laboratory diagnosis and assessment of microbial infections. A set of clinical and laboratory criteria necessary for an ideal diagnostic marker of infection have previously been proposed by Ng and his colleagues [1]. According these criteria, an ideal biomarker should possess at a minimum the following characteristics: (a) biochemically, a biomarker should be stable and remain significantly deregulated in the body fluid compartment for at least 12–24 h even after commencement of appropriate treatment that may allow an adequate time window for specimen collection or storage without significant decomposition of the active compound until laboratory processing; (b) its concentration should be determined quantitatively and the method of measurement should be automatic, rapid, easy, and inexpensive; (c) the collection of a specimen should be minimally invasive and require a small volume (e.g., <0.5 mL blood). Numerous biomarkers have been found and tested in clinical practice. Currently, microRNA (miRNA) molecules are without a doubt the biomarkers with the greatest potential capacities in the diagnostic microbiology field.
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Affiliation(s)
- Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, 10065 New York USA
| | - Charles W. Stratton
- Vanderbilt Clinic, Clinical Microbiology Laboratory, Vanderbilt University Medical Center, 22nd Avenue 1301, Nashville, 37232-5310 Tennessee USA
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421
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Abstract
Mature microRNAs (miRNAs) are single-stranded RNA molecules of 20-23-nucleotide (nt) length that control gene expression in many cellular processes. These molecules typically reduce the translation and stability of mRNAs, including those of genes that mediate processes in tumorigenesis, such as inflammation, cell cycle regulation, stress response, differentiation, apoptosis, and invasion. miRNA targeting is initiated through specific base-pairing interactions between the 5' end ("seed" region) of the miRNA and sites within coding and untranslated regions (UTRs) of mRNAs; target sites in the 3' UTR lead to more effective mRNA destabilization. Since miRNAs frequently target hundreds of mRNAs, miRNA regulatory pathways are complex. To provide a critical overview of miRNA dysregulation in cancer, we first discuss the methods currently available for studying the role of miRNAs in cancer and then review miRNA genomic organization, biogenesis, and mechanism of target recognition, examining how these processes are altered in tumorigenesis. Given the critical role miRNAs play in tumorigenesis processes and their disease specific expression, they hold potential as therapeutic targets and novel biomarkers.
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422
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Elucidating the Role of microRNAs in Cancer Through Data Mining Techniques. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 774:291-315. [DOI: 10.1007/978-94-007-5590-1_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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423
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Nam S, Long X, Kwon C, Kim S, Nephew KP. An integrative analysis of cellular contexts, miRNAs and mRNAs reveals network clusters associated with antiestrogen-resistant breast cancer cells. BMC Genomics 2012; 13:732. [PMID: 23270413 PMCID: PMC3560207 DOI: 10.1186/1471-2164-13-732] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/20/2012] [Indexed: 12/28/2022] Open
Abstract
Background A major goal of the field of systems biology is to translate genome-wide profiling data (e.g., mRNAs, miRNAs) into interpretable functional networks. However, employing a systems biology approach to better understand the complexities underlying drug resistance phenotypes in cancer continues to represent a significant challenge to the field. Previously, we derived two drug-resistant breast cancer sublines (tamoxifen- and fulvestrant-resistant cell lines) from the MCF7 breast cancer cell line and performed genome-wide mRNA and microRNA profiling to identify differential molecular pathways underlying acquired resistance to these important antiestrogens. In the current study, to further define molecular characteristics of acquired antiestrogen resistance we constructed an “integrative network”. We combined joint miRNA-mRNA expression profiles, cancer contexts, miRNA-target mRNA relationships, and miRNA upstream regulators. In particular, to reduce the probability of false positive connections in the network, experimentally validated, rather than prediction-oriented, databases were utilized to obtain connectivity. Also, to improve biological interpretation, cancer contexts were incorporated into the network connectivity. Results Based on the integrative network, we extracted “substructures” (network clusters) representing the drug resistant states (tamoxifen- or fulvestrant-resistance cells) compared to drug sensitive state (parental MCF7 cells). We identified un-described network clusters that contribute to antiestrogen resistance consisting of miR-146a, -27a, -145, -21, -155, -15a, -125b, and let-7s, in addition to the previously described miR-221/222. Conclusions By integrating miRNA-related network, gene/miRNA expression and text-mining, the current study provides a computational-based systems biology approach for further investigating the molecular mechanism underlying antiestrogen resistance in breast cancer cells. In addition, new miRNA clusters that contribute to antiestrogen resistance were identified, and they warrant further investigation.
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Affiliation(s)
- Seungyoon Nam
- Cancer Genomics Branch, National Cancer Center, Goyang-si, Gyeonggi-do, 410-769, Korea.
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424
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Eldem V, Çelikkol Akçay U, Ozhuner E, Bakır Y, Uranbey S, Unver T. Genome-wide identification of miRNAs responsive to drought in peach (Prunus persica) by high-throughput deep sequencing. PLoS One 2012; 7:e50298. [PMID: 23227166 PMCID: PMC3515591 DOI: 10.1371/journal.pone.0050298] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/18/2012] [Indexed: 12/13/2022] Open
Abstract
Peach (Prunus persica L.) is one of the most important worldwide fresh fruits. Since fruit growth largely depends on adequate water supply, drought stress is considered as the most important abiotic stress limiting fleshy fruit production and quality in peach. Plant responses to drought stress are regulated both at transcriptional and post-transcriptional level. As post-transcriptional gene regulators, miRNAs (miRNAs) are small (19–25 nucleotides in length), endogenous, non-coding RNAs. Recent studies indicate that miRNAs are involved in plant responses to drought. Therefore, Illumina deep sequencing technology was used for genome-wide identification of miRNAs and their expression profile in response to drought in peach. In this study, four sRNA libraries were constructed from leaf control (LC), leaf stress (LS), root control (RC) and root stress (RS) samples. We identified a total of 531, 471, 535 and 487 known mature miRNAs in LC, LS, RC and RS libraries, respectively. The expression level of 262 (104 up-regulated, 158 down-regulated) of the 453 miRNAs changed significantly in leaf tissue, whereas 368 (221 up-regulated, 147 down-regulated) of the 465 miRNAs had expression levels that changed significantly in root tissue upon drought stress. Additionally, a total of 197, 221, 238 and 265 novel miRNA precursor candidates were identified from LC, LS, RC and RS libraries, respectively. Target transcripts (137 for LC, 133 for LS, 148 for RC and 153 for RS) generated significant Gene Ontology (GO) terms related to DNA binding and catalytic activites. Genome-wide miRNA expression analysis of peach by deep sequencing approach helped to expand our understanding of miRNA function in response to drought stress in peach and Rosaceae. A set of differentially expressed miRNAs could pave the way for developing new strategies to alleviate the adverse effects of drought stress on plant growth and development.
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Affiliation(s)
- Vahap Eldem
- Cankırı Karatekin University, Faculty of Science, Department of Biology, Cankiri, Turkey
- Istanbul University, Faculty of Science, Department of Biology, Istanbul, Turkey
| | - Ufuk Çelikkol Akçay
- Suleyman Demirel University, Faculty of Agriculture, Department of Agricultural Biotechnology, Isparta, Turkey
| | - Esma Ozhuner
- Cankırı Karatekin University, Faculty of Science, Department of Biology, Cankiri, Turkey
| | - Yakup Bakır
- Marmara University, Faculty of Arts and Science, Department of Biology, Istanbul, Turkey
| | - Serkan Uranbey
- Cankırı Karatekin University, Faculty of Science, Department of Biology, Cankiri, Turkey
| | - Turgay Unver
- Cankırı Karatekin University, Faculty of Science, Department of Biology, Cankiri, Turkey
- * E-mail:
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425
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Berard A, Kroeker AL, Coombs KM. Transcriptomics and quantitative proteomics in virology. Future Virol 2012. [DOI: 10.2217/fvl.12.112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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426
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Seumois G, Vijayanand P, Eisley CJ, Omran N, Kalinke L, North M, Ganesan AP, Simpson LJ, Hunkapiller N, Moltzahn F, Woodruff PG, Fahy JV, Erle DJ, Djukanovic R, Blelloch R, Ansel KM. An integrated nano-scale approach to profile miRNAs in limited clinical samples. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL IMMUNOLOGY 2012; 1:70-89. [PMID: 23304658 PMCID: PMC3538381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 09/26/2012] [Indexed: 06/01/2023]
Abstract
Profiling miRNA expression in cells that directly contribute to human disease pathogenesis is likely to aid the discovery of novel drug targets and biomarkers. However, tissue heterogeneity and the limited amount of human diseased tissue available for research purposes present fundamental difficulties that often constrain the scope and potential of such studies. We established a flow cytometry-based method for isolating pure populations of pathogenic T cells from bronchial biopsy samples of asthma patients, and optimized a high-throughput nano-scale qRT-PCR method capable of accurately measuring 96 miRNAs in as little as 100 cells. Comparison of circulating and airway T cells from healthy and asthmatic subjects revealed asthma-associated and tissue-specific miRNA expression patterns. These results establish the feasibility and utility of investigating miRNA expression in small populations of cells involved in asthma pathogenesis, and set a precedent for application of our nano-scale approach in other human diseases. The microarray data from this study (Figure 7) has been submitted to the NCBI Gene Expression Omnibus (GEO; http://ncbi.nlm.nih.gov/geo) under accession no. GSE31030.
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Affiliation(s)
- Grégory Seumois
- Sandler Asthma Basic Research Center, University of California San FranciscoSan Francisco, CA, USA
- Division of Infection, Inflammation and Immunity, University of outhampton, School of Medicine, Southampton NIHR Respiratory Biomedical Research Unit, Sir Henry Wellcome Laboratories, Southampton General HospitalSouthampton, UK
- Pulmonary and Critical Care Division, Department of Medicine, University of California San FranciscoSan Francisco, CA, USA
- Current address: Division of Cell Signaling and Gene Expression, La Jolla Institute for Allergy and ImmunologySan Diego, USA
| | - Pandurangan Vijayanand
- Sandler Asthma Basic Research Center, University of California San FranciscoSan Francisco, CA, USA
- Division of Infection, Inflammation and Immunity, University of outhampton, School of Medicine, Southampton NIHR Respiratory Biomedical Research Unit, Sir Henry Wellcome Laboratories, Southampton General HospitalSouthampton, UK
- Pulmonary and Critical Care Division, Department of Medicine, University of California San FranciscoSan Francisco, CA, USA
- Current address: Division of Cell Signaling and Gene Expression, La Jolla Institute for Allergy and ImmunologySan Diego, USA
| | - Christopher J Eisley
- Lung Biology Center, University of California San FranciscoSan Francisco, CA, USA
| | - Nada Omran
- Division of Infection, Inflammation and Immunity, University of outhampton, School of Medicine, Southampton NIHR Respiratory Biomedical Research Unit, Sir Henry Wellcome Laboratories, Southampton General HospitalSouthampton, UK
| | - Lukas Kalinke
- Division of Infection, Inflammation and Immunity, University of outhampton, School of Medicine, Southampton NIHR Respiratory Biomedical Research Unit, Sir Henry Wellcome Laboratories, Southampton General HospitalSouthampton, UK
| | - Mal North
- Division of Infection, Inflammation and Immunity, University of outhampton, School of Medicine, Southampton NIHR Respiratory Biomedical Research Unit, Sir Henry Wellcome Laboratories, Southampton General HospitalSouthampton, UK
| | - Asha P Ganesan
- Division of Infection, Inflammation and Immunity, University of outhampton, School of Medicine, Southampton NIHR Respiratory Biomedical Research Unit, Sir Henry Wellcome Laboratories, Southampton General HospitalSouthampton, UK
| | - Laura J Simpson
- Sandler Asthma Basic Research Center, University of California San FranciscoSan Francisco, CA, USA
- Department of Microbiology & Immunology, University of California San FranciscoSan Francisco, CA, USA
| | - Nathan Hunkapiller
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San FranciscoSan Francisco, CA, USA
| | - Felix Moltzahn
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, and Department of Urology, University of California San FranciscoSan Francisco, CA, USA
| | - Prescott G Woodruff
- Pulmonary and Critical Care Division, Department of Medicine, University of California San FranciscoSan Francisco, CA, USA
| | - John V Fahy
- Pulmonary and Critical Care Division, Department of Medicine, University of California San FranciscoSan Francisco, CA, USA
| | - David J Erle
- Pulmonary and Critical Care Division, Department of Medicine, University of California San FranciscoSan Francisco, CA, USA
- Lung Biology Center, University of California San FranciscoSan Francisco, CA, USA
| | - Ratko Djukanovic
- Division of Infection, Inflammation and Immunity, University of outhampton, School of Medicine, Southampton NIHR Respiratory Biomedical Research Unit, Sir Henry Wellcome Laboratories, Southampton General HospitalSouthampton, UK
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, and Department of Urology, University of California San FranciscoSan Francisco, CA, USA
| | - K Mark Ansel
- Sandler Asthma Basic Research Center, University of California San FranciscoSan Francisco, CA, USA
- Department of Microbiology & Immunology, University of California San FranciscoSan Francisco, CA, USA
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427
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Patnaik SK, Dahlgaard J, Mazin W, Kannisto E, Jensen T, Knudsen S, Yendamuri S. Expression of microRNAs in the NCI-60 cancer cell-lines. PLoS One 2012; 7:e49918. [PMID: 23209617 PMCID: PMC3509128 DOI: 10.1371/journal.pone.0049918] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 10/15/2012] [Indexed: 12/18/2022] Open
Abstract
The NCI-60 panel of 60 human cancer cell-lines of nine different tissues of origin has been extensively characterized in biological, molecular and pharmacological studies. Analyses of data from such studies have provided valuable information for understanding cellular processes and developing strategies for the diagnosis and treatment of cancer. Here, Affymetrix® GeneChip™ miRNA version 1 oligonucleotide microarrays were used to quantify 847 microRNAs to generate an expression dataset of 495 (58.4%) microRNAs that were identified as expressed in at least one cell-line of the NCI-60 panel. Accuracy of the microRNA measurements was partly confirmed by reverse transcription and polymerase chain reaction assays. Similar to that seen among the four existing NCI-60 microRNA datasets, the concordance of the new expression dataset with the other four was modest, with mean Pearson correlation coefficients of 0.37–0.54. In spite of this, comparable results with different datasets were noted in clustering of the cell-lines by their microRNA expression, differential expression of microRNAs by the lines’ tissue of origin, and correlation of specific microRNAs with the doubling-time of cells or their radiation sensitivity. Mutation status of the cell-lines for the TP53, PTEN and BRAF but not CDKN2A or KRAS cancer-related genes was found to be associated with changes in expression of specific microRNAs. The microRNA dataset generated here should be valuable to those working in the field of microRNAs as well as in integromic studies of the NCI-60 panel.
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Affiliation(s)
- Santosh K Patnaik
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, NY, USA
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428
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Abstract
With the development of novel assay technologies, biomedical experiments and analyses have gone through substantial evolution. Today, a typical experiment can simultaneously measure hundreds to thousands of individual features (e.g. genes) in dozens of biological conditions, resulting in gigabytes of data that need to be processed and analyzed. Because of the multiple steps involved in the data generation and analysis and the lack of details provided, it can be difficult for independent researchers to try to reproduce a published study. With the recent outrage following the halt of a cancer clinical trial due to the lack of reproducibility of the published study, researchers are now facing heavy pressure to ensure that their results are reproducible. Despite the global demand, too many published studies remain non-reproducible mainly due to the lack of availability of experimental protocol, data and/or computer code. Scientific discovery is an iterative process, where a published study generates new knowledge and data, resulting in new follow-up studies or clinical trials based on these results. As such, it is important for the results of a study to be quickly confirmed or discarded to avoid wasting time and money on novel projects. The availability of high-quality, reproducible data will also lead to more powerful analyses (or meta-analyses) where multiple data sets are combined to generate new knowledge. In this article, we review some of the recent developments regarding biomedical reproducibility and comparability and discuss some of the areas where the overall field could be improved.
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Affiliation(s)
- Yunda Huang
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop M2-C200, Seattle, WA 98109-1024, USA
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429
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Abstract
microRNAs (miRNAs) are small endogenous non-coding RNAs that function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets and further inferring miRNA functions have been a critical strategy for understanding normal biological processes of miRNAs and their roles in the development of disease. In this review, we focus on computational methods of inferring miRNA functions, including miRNA functional annotation and inferring miRNA regulatory modules, by integrating heterogeneous data sources. We also briefly introduce the research in miRNA discovery and miRNA-target identification with an emphasis on the challenges to computational biology.
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Affiliation(s)
- Bing Liu
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, University Drive, Callaghan NSW 2308, Australia.
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430
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Jones CI, Zabolotskaya MV, King AJ, Stewart HJS, Horne GA, Chevassut TJ, Newbury SF. Identification of circulating microRNAs as diagnostic biomarkers for use in multiple myeloma. Br J Cancer 2012; 107:1987-96. [PMID: 23169280 PMCID: PMC3516695 DOI: 10.1038/bjc.2012.525] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Multiple myeloma is a plasma cell disorder that is characterised by clonal proliferation of malignant plasma cells in the bone marrow, monoclonal paraprotein in the blood or urine and associated organ dysfunction. It accounts for approximately 1% of cancers and 13% of haematological cancers. Myeloma arises from an asymptomatic proliferation of monoclonal plasma cells termed monoclonal gammopathy of undetermined significance (MGUS). Methods: MicroRNA expression profiling of serum samples was performed on three patient groups as well as normal controls. Validation of the nine microRNAs detected as promising biomarkers was carried out using TaqMan quantitative reverse transcription PCR. MicroRNA levels in serum were normalised using standard curves to determine the numbers of microRNAs per μl of serum. Results: Three serum microRNAs, miR-720, miR-1308 and miR-1246, were found to have potential as diagnostic biomarkers in myeloma. Use of miR-720 and miR-1308 together provides a powerful diagnostic tool for distinguishing normal healthy controls, as well as patients with unrelated illnesses, from pre-cancerous myeloma and myeloma patients. In addition, the combination of miR-1246 and miR-1308 can distinguish MGUS from myeloma patients. Conclusion: We have developed a biomarker signature using microRNAs extracted from serum, which has potential as a diagnostic and prognostic tool for multiple myeloma.
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Affiliation(s)
- C I Jones
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK
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431
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DNA Nanostructure-based Interfacial engineering for PCR-free ultrasensitive electrochemical analysis of microRNA. Sci Rep 2012; 2:867. [PMID: 23162691 PMCID: PMC3499757 DOI: 10.1038/srep00867] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/21/2012] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) have been identified as promising cancer biomarkers due to their stable presence in serum. As an alternative to PCR-based homogenous assays, surface-based electrochemical biosensors offer great opportunities for low-cost, point-of-care tests (POCTs) of disease-associated miRNAs. Nevertheless, the sensitivity of miRNA sensors is often limited by mass transport and crowding effects at the water-electrode interface. To address such challenges, we herein report a DNA nanostructure-based interfacial engineering approach to enhance binding recognition at the gold electrode surface and drastically improve the detection sensitivity. By employing this novel strategy, we can directly detect as few as attomolar (<1, 000 copies) miRNAs with high single-base discrimination ability. Given that this ultrasensitive electrochemical miRNA sensor (EMRS) is highly reproducible and essentially free of prior target labeling and PCR amplification, we also demonstrate its application by analyzing miRNA expression levels in clinical samples from esophageal squamous cell carcinoma (ESCC) patients.
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432
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Transcriptome analysis of renal ischemia/reperfusion injury and its modulation by ischemic pre-conditioning or hemin treatment. PLoS One 2012; 7:e49569. [PMID: 23166714 PMCID: PMC3498198 DOI: 10.1371/journal.pone.0049569] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/10/2012] [Indexed: 01/06/2023] Open
Abstract
Ischemia/reperfusion injury (IRI) is a leading cause of acute renal failure. The definition of the molecular mechanisms involved in renal IRI and counter protection promoted by ischemic pre-conditioning (IPC) or Hemin treatment is an important milestone that needs to be accomplished in this research area. We examined, through an oligonucleotide microarray protocol, the renal differential transcriptome profiles of mice submitted to IRI, IPC and Hemin treatment. After identifying the profiles of differentially expressed genes observed for each comparison, we carried out functional enrichment analysis to reveal transcripts putatively involved in potential relevant biological processes and signaling pathways. The most relevant processes found in these comparisons were stress, apoptosis, cell differentiation, angiogenesis, focal adhesion, ECM-receptor interaction, ion transport, angiogenesis, mitosis and cell cycle, inflammatory response, olfactory transduction and regulation of actin cytoskeleton. In addition, the most important overrepresented pathways were MAPK, ErbB, JAK/STAT, Toll and Nod like receptors, Angiotensin II, Arachidonic acid metabolism, Wnt and coagulation cascade. Also, new insights were gained about the underlying protection mechanisms against renal IRI promoted by IPC and Hemin treatment. Venn diagram analysis allowed us to uncover common and exclusively differentially expressed genes between these two protective maneuvers, underscoring potential common and exclusive biological functions regulated in each case. In summary, IPC exclusively regulated the expression of genes belonging to stress, protein modification and apoptosis, highlighting the role of IPC in controlling exacerbated stress response. Treatment with the Hmox1 inducer Hemin, in turn, exclusively regulated the expression of genes associated with cell differentiation, metabolic pathways, cell cycle, mitosis, development, regulation of actin cytoskeleton and arachidonic acid metabolism, suggesting a pleiotropic effect for Hemin. These findings improve the biological understanding of how the kidney behaves after IRI. They also illustrate some possible underlying molecular mechanisms involved in kidney protection observed with IPC or Hemin treatment maneuvers.
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433
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Leibowitz-Amit R, Sidi Y, Avni D. Aberrations in the micro-RNA biogenesis machinery and the emerging roles of micro-RNAs in the pathogenesis of cutaneous malignant melanoma. Pigment Cell Melanoma Res 2012; 25:740-57. [DOI: 10.1111/pcmr.12018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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434
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Li C, Weng S, Chen Y, Yu X, Lü L, Zhang H, He J, Xu X. Analysis of Litopenaeus vannamei transcriptome using the next-generation DNA sequencing technique. PLoS One 2012; 7:e47442. [PMID: 23071809 PMCID: PMC3469548 DOI: 10.1371/journal.pone.0047442] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 09/14/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Pacific white shrimp (Litopenaeus vannamei), the major species of farmed shrimps in the world, has been attracting extensive studies, which require more and more genome background knowledge. The now available transcriptome data of L. vannamei are insufficient for research requirements, and have not been adequately assembled and annotated. METHODOLOGY/PRINCIPAL FINDINGS This is the first study that used a next-generation high-throughput DNA sequencing technique, the Solexa/Illumina GA II method, to analyze the transcriptome from whole bodies of L. vannamei larvae. More than 2.4 Gb of raw data were generated, and 109,169 unigenes with a mean length of 396 bp were assembled using the SOAP denovo software. 73,505 unigenes (>200 bp) with good quality sequences were selected and subjected to annotation analysis, among which 37.80% can be matched in NCBI Nr database, 37.3% matched in Swissprot, and 44.1% matched in TrEMBL. Using BLAST and BLAST2Go softwares, 11,153 unigenes were classified into 25 Clusters of Orthologous Groups of proteins (COG) categories, 8171 unigenes were assigned into 51 Gene ontology (GO) functional groups, and 18,154 unigenes were divided into 220 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. To primarily verify part of the results of assembly and annotations, 12 assembled unigenes that are homologous to many embryo development-related genes were chosen and subjected to RT-PCR for electrophoresis and Sanger sequencing analyses, and to real-time PCR for expression profile analyses during embryo development. CONCLUSIONS/SIGNIFICANCE The L. vannamei transcriptome analyzed using the next-generation sequencing technique enriches the information of L. vannamei genes, which will facilitate our understanding of the genome background of crustaceans, and promote the studies on L. vannamei.
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Affiliation(s)
- Chaozheng Li
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Shaoping Weng
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yonggui Chen
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Xiaoqiang Yu
- Division of Cell Biology and Biophysics, School of Biological Science, University of Missouri-Kansas City, Kansas City, United States of America
| | - Ling Lü
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Haiqing Zhang
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jianguo He
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
- * E-mail: (XX); (JH)
| | - Xiaopeng Xu
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
- * E-mail: (XX); (JH)
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435
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Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues. PLoS One 2012; 7:e45105. [PMID: 23028787 PMCID: PMC3441572 DOI: 10.1371/journal.pone.0045105] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 08/14/2012] [Indexed: 01/06/2023] Open
Abstract
Background Microarray technology applied to microRNA (miRNA) profiling is a promising tool in many research fields; nevertheless, independent studies characterizing the same pathology have often reported poorly overlapping results. miRNA analysis methods have only recently been systematically compared but only in few cases using clinical samples. Methodology/Principal Findings We investigated the inter-platform reproducibility of four miRNA microarray platforms (Agilent, Exiqon, Illumina, and Miltenyi), comparing nine paired tumor/normal colon tissues. The most concordant and selected discordant miRNAs were further studied by quantitative RT-PCR. Globally, a poor overlap among differentially expressed miRNAs identified by each platform was found. Nevertheless, for eight miRNAs high agreement in differential expression among the four platforms and comparability to qRT-PCR was observed. Furthermore, most of the miRNA sets identified by each platform are coherently enriched in data from the other platforms and the great majority of colon cancer associated miRNA sets derived from the literature were validated in our data, independently from the platform. Computational integration of miRNA and gene expression profiles suggested that anti-correlated predicted target genes of differentially expressed miRNAs are commonly enriched in cancer-related pathways and in genes involved in glycolysis and nutrient transport. Conclusions Technical and analytical challenges in measuring miRNAs still remain and further research is required in order to increase consistency between different microarray-based methodologies. However, a better inter-platform agreement was found by looking at miRNA sets instead of single miRNAs and through a miRNAs – gene expression integration approach.
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436
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Yang TH, Ou DL, Hsu C, Huang SH, Chang PL. Comparative microRNA detection from precursor-microRNA-transfected hepatocellular carcinoma cells by capillary electrophoresis with dual-color laser-induced fluorescence. Electrophoresis 2012; 33:2769-76. [DOI: 10.1002/elps.201200246] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Tzu-Hsueh Yang
- Department of Chemistry; Tunghai University; Taichung; Taiwan
| | - Da-Liang Ou
- Graduate Institute of Oncology; College of Medicine; National Taiwan University; Taipei; Taiwan
| | - Chiun Hsu
- Department of Internal Medicine; National Taiwan University Hospital; Taipei; Taiwan
| | - Shih-Hua Huang
- Department of Chemistry; Tunghai University; Taichung; Taiwan
| | - Po-Ling Chang
- Department of Chemistry; Tunghai University; Taichung; Taiwan
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437
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Jenny MJ, Aluru N, Hahn ME. Effects of short-term exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin on microRNA expression in zebrafish embryos. Toxicol Appl Pharmacol 2012; 264:262-73. [PMID: 22921993 DOI: 10.1016/j.taap.2012.08.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 08/09/2012] [Accepted: 08/10/2012] [Indexed: 12/26/2022]
Abstract
Although many drugs and environmental chemicals are teratogenic, the mechanisms by which most toxicants disrupt embryonic development are not well understood. MicroRNAs, single-stranded RNA molecules of ~22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation, are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. Recent studies have demonstrated that exposure to xenobiotics can alter microRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. In this study we tested the hypothesis that developmental exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a well-known teratogen, alters microRNA expression during zebrafish development. We exposed zebrafish embryos to DMSO (0.1%) or TCDD (5nM) for 1h at 30hours post fertilization (hpf) and measured microRNA expression using several methods at 36 and 60hpf. TCDD caused strong induction of CYP1A at 36hpf (62-fold) and 60hpf (135-fold) as determined by real-time RT-PCR, verifying the effectiveness of the exposure. MicroRNA expression profiles were determined using microarrays (Agilent and Exiqon), next-generation sequencing (SOLiD), and real-time RT-PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR-451, 23a, 23b, 24 and 27e at 60hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 microRNAs as differentially expressed by TCDD in zebrafish embryos. However, miR-27e was the only microRNA to be identified as differentially expressed by all three methods (both microarrays, SOLiD sequencing, and real-time RT-PCR). These results suggest that TCDD exposure causes modest changes in expression of microRNAs, including some (miR-451, 23a, 23b, 24 and 27e) that are critical for hematopoiesis and cardiovascular development.
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Affiliation(s)
- Matthew J Jenny
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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438
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Lario S, Ramírez-Lázaro M, Aransay A, Lozano J, Montserrat A, Casalots Á, Junquera F, Álvarez J, Segura F, Campo R, Calvet X. microRNA profiling in duodenal ulcer disease caused by Helicobacter pylori infection in a Western population. Clin Microbiol Infect 2012; 18:E273-82. [DOI: 10.1111/j.1469-0691.2012.03849.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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439
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Jagadeeswaran G, Nimmakayala P, Zheng Y, Gowdu K, Reddy UK, Sunkar R. Characterization of the small RNA component of leaves and fruits from four different cucurbit species. BMC Genomics 2012; 13:329. [PMID: 22823569 PMCID: PMC3431224 DOI: 10.1186/1471-2164-13-329] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 06/29/2012] [Indexed: 12/31/2022] Open
Abstract
Background MicroRNAs (miRNAs) are a class of non-coding small RNAs involved in post-transcriptional regulation of gene expression critical for plant growth and development, stress responses and other diverse biological processes in plants. The Cucurbitaceae or cucurbit family represents some of economically important species, particularly those with edible and medicinal fruits. Genomic tools for the molecular analysis of members of this family are just emerging. Partial draft genome sequence became available recently for cucumber and watermelon facilitating investigation of the small RNA component of the transcriptomes in cucurbits. Results We generated four small RNA libraries from bottle gourd (Lagenaria siceraria), Cucurbita moschata, Cucurbita pepo, and, watermelon (Citrullus lanatus var. lanatus) in order to identify conserved and novel lineage specific miRNAs in these cucurbits. Deep sequencing of small RNA libraries from these species resulted in 1,597,263, 532,948, 601,388, and 493,384 unique sRNA reads from bottle gourd, moschata, pepo and watermelon, respectively. Sequence analysis of these four libraries resulted in identification of 21 miRNA families that are highly conserved and 8 miRNA families that are moderately conserved in diverse dicots. We also identified 4 putative novel miRNAs in these plant species. Furthermore, the tasiRNAs were identified and their biogenesis was determined in these cucurbits. Small RNA blot analysis or q-PCR analyses of leaf and fruit tissues of these cucurbits showed differential expression of several conserved miRNAs. Interestingly, the abundance of several miRNAs in leaves and fruits of closely related C. moschata and C. pepo was also distinctly different. Target genes for the most conserved miRNAs are also predicted. Conclusion High-throughput sequencing of small RNA libraries from four cucurbit species has provided a glimpse of small RNA component in their transcriptomes. The analysis also showed considerable variation within four cucurbit species with regards to expression of individual miRNAs.
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Affiliation(s)
- Guru Jagadeeswaran
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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440
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Abell JL, Garren JM, Driskell JD, Tripp RA, Zhao Y. Label-Free Detection of Micro-RNA Hybridization Using Surface-Enhanced Raman Spectroscopy and Least-Squares Analysis. J Am Chem Soc 2012; 134:12889-92. [DOI: 10.1021/ja3043432] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Justin L. Abell
- Department
of Biological and
Agricultural Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Jeonifer M. Garren
- Department of Biostatistics
and Epidemiology, Georgia Health Science University, Augusta, Georgia 30912, United States
| | - Jeremy D. Driskell
- Department of Chemistry, Illinois State University, Normal, Illinois 61790,
United States
| | - Ralph A. Tripp
- Department
of Infectious Diseases, University of Georgia, Athens, Georgia 30602, United
States
| | - Yiping Zhao
- Department of Physics
and Astronomy, University of Georgia, Athens,
Georgia 30602, United
States
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441
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Shen Y, Zheng KX, Duan D, Jiang L, Li J. Label-Free MicroRNA Profiling Not Biased by 3′ End 2′-O-Methylation. Anal Chem 2012; 84:6361-5. [DOI: 10.1021/ac301360z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ye Shen
- Division of Nanobiomedicine,
Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Ke-xiao Zheng
- Division of Nanobiomedicine,
Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Demin Duan
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Jiang
- Division of Nanobiomedicine,
Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Jiong Li
- Division of Nanobiomedicine,
Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou 215123, China
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442
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Abstract
Serum micro-RNAs (miRNAs) can be used for the diagnosis and prognosis of various diseases. Using genome-wide scans, we sought to identify serum miRNAs that could be used as prognostic predictors for sepsis patients. We used microarray screens to identify differentially expressed serum miRNAs by comparing samples from 12 surviving and 12 nonsurviving sepsis patients. These differentially expressed serum miRNAs were validated by quantitative reverse transcriptase-polymerase chain reaction assays for 118 sepsis patients. The validated miRNAs along with sepsis patients' clinical indictors were analyzed in a multivariate logistic regression model. Microarray analysis showed that miR-297 and miR-574-5p were differentially expressed in sepsis survivors and nonsurvivors. Upon validation with 118 sepsis patients' samples, these two miRNA expressions were significantly different, with P < 0.001. miR-297 was more closely associated with survival from sepsis, whereas miR-574-5p was associated with death from sepsis. Multivariable logistic regression analysis showed that a combination of sepsis stage, Sepsis-Related Organ Failure Assessment scores, and miR-574-5p was correlated with the death of sepsis patients. The predictive capability of these three combined variables was analyzed by a receiver operating characteristic curve; the area under the curve was 0.932 (95% confidence interval, 0.887-0.977). When the cutoff point was set at 0.288, these three combined variables provided 78.13% sensitivity and 91.84% specificity. Our results showed that serum miR-574-5p was correlated with the death of sepsis patients. The combined predictive capability of sepsis stage, Sepsis-Related Organ Failure Assessment scores, and serum miR-574-5p for the death of sepsis patients was better than any single indicator.
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443
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Serum microRNA signatures identified by Solexa sequencing predict sepsis patients' mortality: a prospective observational study. PLoS One 2012; 7:e38885. [PMID: 22719975 PMCID: PMC3376145 DOI: 10.1371/journal.pone.0038885] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 05/14/2012] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Sepsis is the leading cause of death in Intensive Care Units. Novel sepsis biomarkers and targets for treatment are needed to improve mortality from sepsis. MicroRNAs (miRNAs) have recently been used as finger prints for sepsis, and our goal in this prospective study was to investigate if serum miRNAs identified in genome-wide scans could predict sepsis mortality. METHODOLOGY/PRINCIPAL FINDINGS We enrolled 214 sepsis patients (117 survivors and 97 non-survivors based on 28-day mortality). Solexa sequencing followed by quantitative reverse transcriptase polymerase chain reaction assays was used to test for differences in the levels of miRNAs between survivors and non-survivors. miR-223, miR-15a, miR-16, miR-122, miR-193*, and miR-483-5p were significantly differentially expressed. Receiver operating characteristic curves were generated and the areas under the curve (AUC) for these six miRNAs for predicting sepsis mortality ranged from 0.610 (95%CI: 0.523-0.697) to 0.790 (95%CI: 0.719-0.861). Logistic regression analysis showed that sepsis stage, Sequential Organ Failure Assessment scores, Acute Physiology and Chronic Health Evaluation II scores, miR-15a, miR-16, miR-193b*, and miR-483-5p were associated with death from sepsis. An analysis was done using these seven variables combined. The AUC for these combined variables' predictive probability was 0.953 (95% CI: 0.923-0.983), which was much higher than the AUCs for Acute Physiology and Chronic Health Evaluation II scores (0.782; 95% CI: 0.712-0.851), Sequential Organ Failure Assessment scores (0.752; 95% CI: 0.672-0.832), and procalcitonin levels (0.689; 95% CI: 0.611-0.784). With a cut-off point of 0.550, the predictive value of the seven variables had a sensitivity of 88.5% and a specificity of 90.4%. Additionally, miR-193b* had the highest odds ratio for sepsis mortality of 9.23 (95% CI: 1.20-71.16). CONCLUSION/SIGNIFICANCE Six serum miRNA's were identified as prognostic predictors for sepsis patients. TRIAL REGISTRATION ClinicalTrials.gov NCT01207531.
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444
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Neff AT, Lee JY, Wilusz J, Tian B, Wilusz CJ. Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells. Genome Res 2012; 22:1457-67. [PMID: 22534399 PMCID: PMC3409259 DOI: 10.1101/gr.134312.111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pluripotency is a unique state in which cells can self-renew indefinitely but also retain the ability to differentiate into other cell types upon receipt of extracellular cues. Although it is clear that stem cells have a distinct transcriptional program, little is known about how alterations in post-transcriptional mechanisms, such as mRNA turnover, contribute to the achievement and maintenance of pluripotency. Here we have assessed the rates of decay for the majority of mRNAs expressed in induced pluripotent stem (iPS) cells and the fully differentiated human foreskin fibroblasts (HFFs) they were derived from. Comparison of decay rates in the two cell types led to the discovery of three independent regulatory mechanisms that allow coordinated turnover of specific groups of mRNAs. One mechanism results in increased stability of many histone mRNAs in iPS cells. A second pathway stabilizes a large set of zinc finger protein mRNAs, potentially through reduced levels of miRNAs that target them. Finally, a group of transcripts bearing 3' UTR C-rich sequence elements, many of which encode transcription factors, are significantly less stable in iPS cells. Intriguingly, two poly(C)-binding proteins that recognize this type of element are reciprocally expressed in iPS and HFF cells. Overall, our results highlight the importance of post-transcriptional control in pluripotent cells and identify miRNAs and RNA-binding proteins whose activity may coordinately control expression of a wide range of genes in iPS cells.
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Affiliation(s)
- Ashley T Neff
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
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445
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446
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Pritchard CC, Cheng HH, Tewari M. MicroRNA profiling: approaches and considerations. Nat Rev Genet 2012; 13:358-69. [PMID: 22510765 DOI: 10.1038/nrg3198] [Citation(s) in RCA: 1214] [Impact Index Per Article: 101.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are small RNAs that post-transcriptionally regulate the expression of thousands of genes in a broad range of organisms in both normal physiological contexts and in disease contexts. miRNA expression profiling is gaining popularity because miRNAs, as key regulators in gene expression networks, can influence many biological processes and also show promise as biomarkers for disease. Technological advances have spawned a multitude of platforms for miRNA profiling, and an understanding of the strengths and pitfalls of different approaches can aid in their effective use. Here, we review the major considerations for carrying out and interpreting results of miRNA-profiling studies.
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Affiliation(s)
- Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
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447
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Azzouzi I, Schmugge M, Speer O. MicroRNAs as components of regulatory networks controlling erythropoiesis. Eur J Haematol 2012; 89:1-9. [DOI: 10.1111/j.1600-0609.2012.01774.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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448
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Meng F, Hackenberg M, Li Z, Yan J, Chen T. Discovery of novel microRNAs in rat kidney using next generation sequencing and microarray validation. PLoS One 2012; 7:e34394. [PMID: 22470567 PMCID: PMC3314633 DOI: 10.1371/journal.pone.0034394] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 02/27/2012] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate a variety of biological processes. The latest version of the miRBase database (Release 18) includes 1,157 mouse and 680 rat mature miRNAs. Only one new rat mature miRNA was added to the rat miRNA database from version 16 to version 18 of miRBase, suggesting that many rat miRNAs remain to be discovered. Given the importance of rat as a model organism, discovery of the completed set of rat miRNAs is necessary for understanding rat miRNA regulation. In this study, next generation sequencing (NGS), microarray analysis and bioinformatics technologies were applied to discover novel miRNAs in rat kidneys. MiRanalyzer was utilized to analyze the sequences of the small RNAs generated from NGS analysis of rat kidney samples. Hundreds of novel miRNA candidates were examined according to the mappings of their reads to the rat genome, presence of sequences that can form a miRNA hairpin structure around the mapped locations, Dicer cleavage patterns, and the levels of their expression determined by both NGS and microarray analyses. Nine novel rat hairpin precursor miRNAs (pre-miRNA) were discovered with high confidence. Five of the novel pre-miRNAs are also reported in other species while four of them are rat specific. In summary, 9 novel pre-miRNAs (14 novel mature miRNAs) were identified via combination of NGS, microarray and bioinformatics high-throughput technologies.
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Affiliation(s)
- Fanxue Meng
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Michael Hackenberg
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Zhiguang Li
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Jian Yan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
- * E-mail:
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449
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Priestley CC, Anderton M, Doherty AT, Duffy P, Mellor HR, Powell H, Roberts R. Epigenetics – relevance to drug safety science. Toxicol Res (Camb) 2012. [DOI: 10.1039/c2tx00003b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Abstract
Epigenetics describes the study of heritable changes in gene expression that occur in the absence of a change to the DNA sequence. Specific patterns of epigenetic signatures can be stably transmitted through mitosis and cell division and form the molecular basis for developmental stage- and cell type-specific gene expression. Associations have been observed that endogenous and exogenous stimuli can change the epigenetic control of both somatic and stem cell differentiation and thus influence phenotypic behaviours and/or disease progression. In relation to drug safety, DNA methylation changes have been identified in many stages of tumour development following exposure to non-genotoxic carcinogens. However, it is not clear whether DNA methylation changes cause cancer, or arise as a consequence of the transformed state. Toxic agents could act at different levels, by directly modifying the epigenome or indirectly by altering signalling pathways. These alterations in chromatin structure may or may not be heritable but are probably reversible. That said, there is currently insufficient data to support inclusion of epigenetic profiling into pre-clinical evaluation studies. Several international collaborations aim to generate data to determine whether epigenetic modifications are causal links in disease and/or tumour progression. It will only be when an understanding of chemical mode-of-action is required that evaluation of epigenetic changes might be considered. The current toxicological testing battery is expected to identify any potential adverse effects regardless of the mechanism, epigenetic or otherwise. It is recommended that toxicologists keep a close watch of new developments in this field, in particular identification of early epigenetic markers for non-genotoxic carcinogenicity. Scientific collaborations between academia and industry will help to understand inter-individual variations in response to drug and toxin exposure to be able to distinguish between adverse and non-adverse epigenetic changes.
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Affiliation(s)
- Catherine C. Priestley
- Safety Assessment, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. Fax: +44 1625 231281; Tel: +44 1625 232435
| | - Mark Anderton
- Safety Assessment, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. Fax: +44 1625 231281; Tel: +44 1625 232435
| | - Ann T. Doherty
- Safety Assessment, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. Fax: +44 1625 231281; Tel: +44 1625 232435
| | - Paul Duffy
- Safety Assessment, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. Fax: +44 1625 231281; Tel: +44 1625 232435
| | - Howard R. Mellor
- Safety Assessment, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. Fax: +44 1625 231281; Tel: +44 1625 232435
| | - Helen Powell
- Safety Assessment, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. Fax: +44 1625 231281; Tel: +44 1625 232435
| | - Ruth Roberts
- Safety Assessment, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. Fax: +44 1625 231281; Tel: +44 1625 232435
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450
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Characterization of the uterine leiomyoma microRNAome by deep sequencing. Genomics 2012; 99:275-81. [PMID: 22446413 DOI: 10.1016/j.ygeno.2012.03.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/05/2012] [Accepted: 03/09/2012] [Indexed: 11/21/2022]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs, which are negative regulators of gene expression. Many genes in human uterine leiomyoma (ULM) are aberrantly expressed and in some cases this can be due to dysregulation of miRNAs. Here we present the first study to determine genome-wide miRNA expression patterns in uterine leiomyoma and myometrium using Solexa high-throughput sequencing. We found more than 50 miRNAs, which were differentially expressed, and furthermore we extend the list of putative new miRNA genes. The top five significantly de-regulated miRNAs in ULMs that we found in our libraries were miR-363, miR-490, miR-137, miR-217 and miR-4792. We also observed "isomiRs" with higher copy number than referenced mature miRNA specific for the leiomyoma libraries, which have a potential role in tumorigenesis. The microRNA transcriptomes obtained in this study deliver insights and further expand our understanding the role of small RNAs in uterine leiomyoma development.
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