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Mohammadi A, Mansoori B, Baradaran B. The role of microRNAs in colorectal cancer. Biomed Pharmacother 2016; 84:705-713. [PMID: 27701052 DOI: 10.1016/j.biopha.2016.09.099] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 01/30/2023] Open
Abstract
Colorectal cancer (CRC) is still the third most common cancer in the world. Mechanism of CRC tumorigenesis has been widely studied at the molecular levels, and has been recently entered the area of microRNAs. MicroRNAs are small 19 to 22 nucleotides of RNA that engage in the regulation of cell differentiation, apoptosis, and cell cycle progression. MicroRNAs are similar to small interfering RNA (siRNA), that post-transcriptionally regulate gene expression and control various cellular mechanisms. They are important factors in the carcinogenesis of CRC, one of the most important factors includes microRNA. MicroRNAs have been linked to CRC development, and these molecules have been recently studied as new potential biomarkers in diagnosis and treatment of CRC. Specific microRNA expression patterns help distinguish CRC from other colon related disease, and may be used as a prognostication factor in patients after treatment with different chemotherapy drugs. More over the newest molecular therapy via tumor suppressor micro RNA replacement can be new insight in molecular therapy of CRC. This review summarizes the potential roles of microRNAs as potential biomarkers for CRC diagnosis, and treatment.
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Affiliation(s)
- Ali Mohammadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Nasr R, Sleiman F, Awada Z, Zgheib NK. The pharmacoepigenetics of drug metabolism and transport in breast cancer: review of the literature and in silico analysis. Pharmacogenomics 2016; 17:1573-85. [DOI: 10.2217/pgs-2016-0081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The focus of this manuscript is on DNA methylation and miRNA regulation of drug-metabolizing enzymes and drug transporters involved in the disposition of drugs commonly used in breast cancer. We start with a review of the available scant literature and follow with an in silico analysis of the CpG islands and miRNA binding sites of genes of interest. We make the case that there is room for further research to include more genes and miRNAs despite the extensive sharing of miRNA targets by candidate genes of interest. We also stress on the role of peripheral blood as a source of pharmacoepigenetic biomarkers, and point out the lack of toxicoepigenetic studies in breast cancer.
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Affiliation(s)
- Rihab Nasr
- Department of Anatomy, Cell Biology & Physiology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
| | - Fatima Sleiman
- Department of Pharmacology & Toxicology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
| | - Zeinab Awada
- Department of Pharmacology & Toxicology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
| | - Natalie K Zgheib
- Department of Pharmacology & Toxicology, American University of Beirut Faculty of Medicine (AUBFM), Beirut, Lebanon
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Hervé M, Ibrahim EC. MicroRNA screening identifies a link between NOVA1 expression and a low level of IKAP in familial dysautonomia. Dis Model Mech 2016; 9:899-909. [PMID: 27483351 PMCID: PMC5007982 DOI: 10.1242/dmm.025841] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/22/2016] [Indexed: 12/20/2022] Open
Abstract
Familial dysautonomia (FD) is a rare neurodegenerative disease caused by a mutation in intron 20 of the IKBKAP gene (c.2204+6T>C), leading to tissue-specific skipping of exon 20 and a decrease in the synthesis of the encoded protein IKAP (also known as ELP1). Small non-coding RNAs known as microRNAs (miRNAs) are important post-transcriptional regulators of gene expression and play an essential role in the nervous system development and function. To better understand the neuronal specificity of IKAP loss, we examined expression of miRNAs in human olfactory ecto-mesenchymal stem cells (hOE-MSCs) from five control individuals and five FD patients. We profiled the expression of 373 miRNAs using microfluidics and reverse transcription coupled to quantitative PCR (RT-qPCR) on two biological replicate series of hOE-MSC cultures from healthy controls and FD patients. This led to the total identification of 26 dysregulated miRNAs in FD, validating the existence of a miRNA signature in FD. We then selected the nine most discriminant miRNAs for further analysis. The signaling pathways affected by these dysregulated miRNAs were largely within the nervous system. In addition, many targets of these dysregulated miRNAs had been previously demonstrated to be affected in FD models. Moreover, we found that four of our nine candidate miRNAs target the neuron-specific splicing factor NOVA1. We demonstrated that overexpression of miR-203a-3p leads to a decrease of NOVA1, counter-balanced by an increase of IKAP, supporting a potential interaction between NOVA1 and IKAP. Taken together, these results reinforce the choice of miRNAs as potential therapeutic targets and suggest that NOVA1 could be a regulator of FD pathophysiology. Summary: A miRNA screening conducted in olfactory stem cells from patients links the neuron-specific splicing factor NOVA1 to neurodegeneration in familial dysautonomia.
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Affiliation(s)
- Mylène Hervé
- CRN2M-UMR7286, Aix-Marseille Université, CNRS, Faculté de Médecine Nord, Marseille 13344, Cedex 15, France
| | - El Chérif Ibrahim
- CRN2M-UMR7286, Aix-Marseille Université, CNRS, Faculté de Médecine Nord, Marseille 13344, Cedex 15, France
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Abstract
MicroRNAs (miRNAs) are small, non-protein-coding, single-stranded RNAs. They function as posttranscriptional regulators of gene expression by interacting with target mRNAs. This process prevents translation of target mRNAs into a functional protein. miRNAs are considered to be functionally involved in virtually all physiologic processes, including differentiation and proliferation, metabolism, hemostasis, apoptosis, and inflammation. Many of these functions have important implications for anesthesiology and critical care medicine. Studies indicate that miRNA expression levels can be used to predict the risk for eminent organ injury or sepsis. Pharmacologic approaches targeting miRNAs for the treatment of human diseases are currently being tested in clinical trials. The present review highlights the important biological functions of miRNAs and their usefulness as perioperative biomarkers and discusses the pharmacologic approaches that modulate miRNA functions for disease treatment. In addition, the authors discuss the pharmacologic interactions of miRNAs with currently used anesthetics and their potential to impact anesthetic toxicity and side effects.
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Granata S, Dalla Gassa A, Carraro A, Brunelli M, Stallone G, Lupo A, Zaza G. Sirolimus and Everolimus Pathway: Reviewing Candidate Genes Influencing Their Intracellular Effects. Int J Mol Sci 2016; 17:ijms17050735. [PMID: 27187382 PMCID: PMC4881557 DOI: 10.3390/ijms17050735] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 04/21/2016] [Accepted: 05/06/2016] [Indexed: 02/07/2023] Open
Abstract
Sirolimus (SRL) and everolimus (EVR) are mammalian targets of rapamycin inhibitors (mTOR-I) largely employed in renal transplantation and oncology as immunosuppressive/antiproliferative agents. SRL was the first mTOR-I produced by the bacterium Streptomyces hygroscopicus and approved for several medical purposes. EVR, derived from SRL, contains a 2-hydroxy-ethyl chain in the 40th position that makes the drug more hydrophilic than SRL and increases oral bioavailability. Their main mechanism of action is the inhibition of the mTOR complex 1 and the regulation of factors involved in a several crucial cellular functions including: protein synthesis, regulation of angiogenesis, lipid biosynthesis, mitochondrial biogenesis and function, cell cycle, and autophagy. Most of the proteins/enzymes belonging to the aforementioned biological processes are encoded by numerous and tightly regulated genes. However, at the moment, the polygenic influence on SRL/EVR cellular effects is still not completely defined, and its comprehension represents a key challenge for researchers. Therefore, to obtain a complete picture of the cellular network connected to SRL/EVR, we decided to review major evidences available in the literature regarding the genetic influence on mTOR-I biology/pharmacology and to build, for the first time, a useful and specific “SRL/EVR genes-focused pathway”, possibly employable as a starting point for future in-depth research projects.
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Affiliation(s)
- Simona Granata
- Renal Unit, Department of Medicine, University/Hospital of Verona, 37126 Verona, Italy.
| | | | - Amedeo Carraro
- Liver Transplant Unit, Department of General Surgery and Odontoiatrics, University/Hospital of Verona, 37126 Verona, Italy.
| | - Matteo Brunelli
- Department of Pathology and Diagnostics, University of Verona, Azienda Ospedaliera Universitaria Integrata, 37126 Verona, Italy.
| | - Giovanni Stallone
- Nephrology, Dialysis and Transplantation Unit, University of Foggia, 71122 Foggia, Italy.
| | - Antonio Lupo
- Renal Unit, Department of Medicine, University/Hospital of Verona, 37126 Verona, Italy.
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, University/Hospital of Verona, 37126 Verona, Italy.
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Abstract
The discovery of small regulatory noncoding RNAs revolutionized our thinking on gene regulation. The class of microRNAs (miRs), a group of small noncoding RNAs (20-22 nt in length) that bind imperfectly to the 3'-untranslated region of target mRNA, has been insistently implicated in several pathological conditions including cancer. Indeed, major hallmarks of cancer, such as cell differentiation, cell proliferation, cell cycle, cell survival, and cell invasion, has been described as being regulated by miRs. Recent studies have also implicated miRs in cancer drug resistance. Regardless of the several studies done until now, drug resistance still is a burden for cancer therapy and patients' outcome, often resulting in more aggressive tumors that tend to metastasize to distant organs. Hence, with this review, we aim to summarize the miRs that influence molecular pathways that are involved in cancer drug resistance, such as drug metabolism, drug influx/efflux, DNA damage response (DDR), epithelial-to-mesenchymal transition (EMT), and cancer stem cells.
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Affiliation(s)
- Bruno Costa Gomes
- Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana 6, Edificio CEDOC II, Room 2.22-2.23, Lisbon, 1150-008, Portugal
| | - José Rueff
- Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana 6, Edificio CEDOC II, Room 2.22-2.23, Lisbon, 1150-008, Portugal
| | - António Sebastião Rodrigues
- Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana 6, Edificio CEDOC II, Room 2.22-2.23, Lisbon, 1150-008, Portugal.
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Koturbash I, Tolleson WH, Guo L, Yu D, Chen S, Hong H, Mattes W, Ning B. microRNAs as pharmacogenomic biomarkers for drug efficacy and drug safety assessment. Biomark Med 2015; 9:1153-76. [PMID: 26501795 PMCID: PMC5712454 DOI: 10.2217/bmm.15.89] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Much evidence has documented that microRNAs (miRNAs) play an important role in the modulation of interindividual variability in the production of drug metabolizing enzymes and transporters (DMETs) and nuclear receptors (NRs) through multidirectional interactions involving environmental stimuli/stressors, the expression of miRNA molecules and genetic polymorphisms. MiRNA expression has been reported to be affected by drugs and miRNAs themselves may affect drug metabolism and toxicity. In cancer research, miRNA biomarkers have been identified to mediate intrinsic and acquired resistance to cancer therapies. In drug safety assessment, miRNAs have been found associated with cardiotoxicity, hepatotoxicity and nephrotoxicity. This review article summarizes published studies to show that miRNAs can serve as early biomarkers for the evaluation of drug efficacy and drug safety.
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Affiliation(s)
- Igor Koturbash
- Department of Environmental & Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - William H Tolleson
- National Center for Toxicological Research, US Food & Drug Administration, Jefferson, AR 72079, USA
| | - Lei Guo
- National Center for Toxicological Research, US Food & Drug Administration, Jefferson, AR 72079, USA
| | - Dianke Yu
- National Center for Toxicological Research, US Food & Drug Administration, Jefferson, AR 72079, USA
| | - Si Chen
- National Center for Toxicological Research, US Food & Drug Administration, Jefferson, AR 72079, USA
| | - Huixiao Hong
- National Center for Toxicological Research, US Food & Drug Administration, Jefferson, AR 72079, USA
| | - William Mattes
- National Center for Toxicological Research, US Food & Drug Administration, Jefferson, AR 72079, USA
| | - Baitang Ning
- National Center for Toxicological Research, US Food & Drug Administration, Jefferson, AR 72079, USA
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Bian Q, Chen JJ, Gu JP, Xu J. Association between pre-miR-27a functional polymorphism and risk of colorectal cancer in north Chinese Han population. Onco Targets Ther 2015; 8:3003-7. [PMID: 26527885 PMCID: PMC4621200 DOI: 10.2147/ott.s89754] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
MicroRNA-27a (miR-27a) is deemed as an oncogene in malignancies including colorectal cancer (CRC), and rs895819 within pre-miR-27a may affect its secondary structure, leading to its aberrant expression and dysfunction of its targeted gene. We investigated genotype and allele frequencies of the locus in 412 I–III stage CRC cases and 412 age- and sex-matched healthy individuals to explore the possible association between them in the north of Chinese population. The results showed that frequencies of alleles A and G and genotypes GG, AG, and AA of the locus were 65.7%, 34.3%, 17.0%, 34.7%, and 48.3% in cases and 69.9%, 30.1%, 9.9%, 40.2%, and 49.8% in controls, respectively. GG genotype of the locus was positively associated with an increased risk of CRC in codominant (P=0.01, adjusted odds ratio =1.541, 95% confidence interval =1.110–2.239 for genotype GG vs AA) and recessive (P=0.003, adjusted odds ratio =1.855, 95% confidence interval =1.221–2.786 for genotype GG vs AA/GA) models, indicating that GG genotype of the locus might increase susceptibility to CRC. Moreover, genotypes AG and GG and allele G were significantly associated with III stage (P<0.001, P<0.001, and P=0.001, respectively), suggesting that the locus was associated with the progression of CRC. These results suggested that rs895819 within pre-miR-27a was involved in colorectal carcinogenesis and progression, genotype GG of the locus might be a susceptible factor for CRC, and allele G and allele G carrier (genotypes AG and GG) could predict CRC progression in north Chinese Han population.
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Affiliation(s)
- Quan Bian
- Department of General Surgery, Tianjin Hospital, Tianjin, People's Republic of China
| | - Jian-Jun Chen
- Department of General Surgery, Beijing Chaoyang Hospital, Beijing, People's Republic of China
| | - Jun-Ping Gu
- Department of General Surgery, Tianjin Hospital, Tianjin, People's Republic of China
| | - Jing Xu
- Department of Gastrointestinal Surgery, Union Medical Center of Tianjin, Nankai University Affiliated Hospital, Tianjin, People's Republic of China
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ZOFKOVA I, NEMCIKOVA P, KUKLIK M. Polymorphisms Associated With Low Bone Mass and High Risk of Atraumatic Fracture. Physiol Res 2015; 64:621-31. [DOI: 10.33549/physiolres.932973] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Osteoporosis is a serious disease characterized by high morbidity and mortality due to atraumatic fractures. In the pathogenesis of osteoporosis, except environment and internal factors, such as hormonal imbalance and genetic background, are also in play. In this study candidate genes for osteoporosis were classified according to metabolic or hormonal pathways, which regulate bone mineral density and bone quality (estrogen, RANKL/RANK/OPG axis, mevalonate, the canonical circuit and genes regulating the vitamin D system). COL1A1 and/or COL1A2 genes, which encode formation of the procollagen 1 molecule, were also studied. Mutations in these genes are well-known causes of the inborn disease ‘osteogenesis imperfecta’. In addition to this, polymorphisms in COL1A1 and/or COL1A2 have been found to be associated with parameters of bone quality in adult subjects. The authors discuss the perspectives for the practical utilization of pharmacogenetics (identification of single candidate genes using PCR) and pharmacogenomics (using genome wide association studies (GWAS) to choose optimal treatment for osteoporosis). Potential predictors of antiresorptive therapy efficacy include the following well established genes: ER, FDPS, Cyp19A1, VDR, Col1A1, and Col1A2, as well as the gene for the canonical (Wnt) pathway. Unfortunately, the positive outcomes seen in most association studies have not been confirmed by other researchers. The controversial results could be explained by the use of different methodological approaches in individual studies (different sample size, homogeneity of investigated groups, ethnic differences, or linkage disequilibrium between genes). The key pitfall of association studies is the low variability (7-10 %) of bone phenotypes associated with the investigated genes. Nevertheless, the identification of new genes and the verification of their association with bone density and/or quality (using both PCR and GWAS), remain a great challenge in the optimal prevention and treatment of osteoporosis.
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Affiliation(s)
- I. ZOFKOVA
- Institute of Endocrinology, Prague, Czech Republic
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Yu D, Green B, Tolleson WH, Jin Y, Mei N, Guo Y, Deng H, Pogribny I, Ning B. MicroRNA hsa-miR-29a-3p modulates CYP2C19 in human liver cells. Biochem Pharmacol 2015; 98:215-23. [PMID: 26296572 DOI: 10.1016/j.bcp.2015.08.094] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/14/2015] [Indexed: 12/12/2022]
Abstract
Cytochrome P450 2C19 (CYP2C19) is involved in the metabolism of many drugs. Extensive studies have demonstrated that genetic variants and endogenous and environmental factors play important roles in the expression of CYP2C19. However, the role of microRNAs (miRNAs) in controlling CYP2C19 expression has not been investigated completely. In the present study, we performed in silico analysis to rank putative miRNA/CYP2C19 hybrids with regards to the predicted stabilities of their duplexes and then we applied a series of biochemical and molecular assays to elucidate the underlying functional mechanisms for the regulation of CYP2C19 by miRNAs. In silico analysis indicated that hsa-miR-23a-3p and hsa-miR-29a-3p target the coding region of CYP2C19 with hybrid stabilities of -27.5kcal/mol and -23.3kcal/mol, respectively. RNA electrophoresis mobility shift assays showed that both hsa-miR-23a-3p and hsa-miR-29a-3p miRNAs were able to bind directly to their cognate targets in the CYP2C19 transcript. Further, a significant inverse correlation was found between chemically-induced up-regulation of hsa-miR-29a-3p and CYP2C19 expression in HepaRG cells. In addition, inverse correlations were also observed in human liver tissue samples between the level of CYP2C19 mRNA expression and both hsa-miR-23a-3p and hsa-miR-29a-3p levels. All these results demonstrated the suppressing role of hsa-miR-29a-3p on CYP2C19 expression.
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Affiliation(s)
- Dianke Yu
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Bridgett Green
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - William H Tolleson
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Yaqiong Jin
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Nan Mei
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Helen Deng
- Arkansas Department of Health, Little Rock, AR 72205, USA
| | - Igor Pogribny
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Baitang Ning
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
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Shen L, Huang F, Ye L, Zhu W, Zhang X, Wang S, Wang W, Ning G. Circulating microRNA predicts insensitivity to glucocorticoid therapy in Graves' ophthalmopathy. Endocrine 2015; 49:445-56. [PMID: 25588771 DOI: 10.1007/s12020-014-0487-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/18/2014] [Indexed: 12/21/2022]
Abstract
Glucocorticoid (GC) insensitivity occurs commonly in Graves' ophthalmopathy (GO), and GC therapy is associated with major adverse effects. A reliable and easily accessible biomarker is required to predict the outcome of GC therapy. This study aimed to evaluate the performance of circulating microRNA (miRNA) to predict GC insensitivity in GO patients. A total of 35 consecutive patients were included in this study. A cumulative dose of 4.5 g of methylprednisolone (MP) was administered intravenously for 12 weeks. Pretreatment serum miRNAs from the best- (N = 5) and worst- (N = 4) responding patients were profiled using miScript PCR arrays and validated by quantitative PCR in all patients. We calculated the predictive value of pretreatment assays of serum miRNAs with regard to GC insensitivity. We further investigated the roles of target miRNAs in modulating NF-κB activity and restoring transrepression of an NF-κB reporter by dexamethasone. Nine miRNAs displayed significant differences between responsive and resistant patients by miScript PCR arrays. Validation of the top two miRNAs in all 35 patients confirmed a significantly lower serum level of miR-224-5p (p = 0.0048) in resistant patients. A multivariate logistic regression model identified a composite biomarker combining baseline serum miR-224-5p and TRAb was independently associated with GC response (OR: 2.565, 95 % CI 1.011-6.505, p = 0.047). Receiver operating characteristic (ROC) curves analysis revealed the composite marker combining miR-224-5p and TRAb led to a 91.67 % positive prediction value (PPV) and a 69.56 % negative prediction value (NPV) with regard to GC resistance. Overexpression of miR-224-5p restored transrepression of the NF-κB reporter by dexamethasone under induced resistance, which may be via targeting GSK-3β to increase GR protein level. Our study demonstrated baseline serum miR-224-5p was associated with GC sensitivity in GO and in vitro overexpression of miR-224-5p restored GC sensitivity in a resistant cell model. A parameter combined serum miR-224-5p and TRAb could effectively predict GC sensitivity in GO patients.
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Affiliation(s)
- Liyun Shen
- Shanghai Key Laboratory for Endocrine Tumors, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases and Shanghai E-institute for Endocrinology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, 197 Ruijin 2nd Road, Shanghai, 200025, People's Republic of China
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Affiliation(s)
- David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 69978, Israel
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Insulin-like Growth Factor 1 Differentially Affects Lithium Sensitivity of Lymphoblastoid Cell Lines from Lithium Responder and Non-responder Bipolar Disorder Patients. J Mol Neurosci 2015; 56:681-7. [DOI: 10.1007/s12031-015-0523-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/11/2015] [Indexed: 01/08/2023]
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Mu W, Hu C, Zhang H, Qu Z, Cen J, Qiu Z, Li C, Ren H, Li Y, He X, Shi X, Hui L. miR-27b synergizes with anticancer drugs via p53 activation and CYP1B1 suppression. Cell Res 2015; 25:477-95. [PMID: 25698578 DOI: 10.1038/cr.2015.23] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/17/2014] [Accepted: 01/06/2015] [Indexed: 02/07/2023] Open
Abstract
Liver and kidney cancers are notorious for drug resistance. Due to the complexity, redundancy and interpatient heterogeneity of resistance mechanisms, most efforts targeting a single pathway were unsuccessful. Novel personalized therapies targeting multiple essential drug resistance pathways in parallel hold a promise for future cancer treatment. Exploiting the multitarget characteristic of microRNAs (miRNAs), we developed a new therapeutic strategy by the combinational use of miRNA and anticancer drugs to increase drug response. By a systems approach, we identified that miR-27b, a miRNA deleted in liver and kidney cancers, sensitizes cancer cells to a broad spectrum of anticancer drugs in vitro and in vivo. Functionally, miR-27b enhances drug response by activating p53-dependent apoptosis and reducing CYP1B1-mediated drug detoxification. Notably, miR-27b promotes drug response specifically in patients carrying p53-wild-type or CYP1B1-high signature. Together, we propose that miR-27b synergizes with anticancer drugs in a defined subgroup of liver and kidney cancer patients.
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Affiliation(s)
- Wenjing Mu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academic of Sciences, Shanghai 200031, China
| | - Chaobo Hu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academic of Sciences, Shanghai 200031, China
| | - Haibin Zhang
- Eastern Hepatobilliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Zengqiang Qu
- Eastern Hepatobilliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Jin Cen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academic of Sciences, Shanghai 200031, China
| | - Zhixin Qiu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academic of Sciences, Shanghai 200031, China
| | - Chao Li
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haozhen Ren
- Department of Hepatobiliary Surgery, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210000, China
| | - Yixue Li
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiaolei Shi
- Department of Hepatobiliary Surgery, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210000, China
| | - Lijian Hui
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academic of Sciences, Shanghai 200031, China
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Valenzuela-Miranda D, Nuñez-Acuña G, Valenzuela-Muñoz V, Asgari S, Gallardo-Escárate C. MicroRNA biogenesis pathway from the salmon louse (Caligus rogercresseyi): Emerging role in delousing drug response. Gene 2015; 555:231-41. [DOI: 10.1016/j.gene.2014.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/24/2014] [Accepted: 11/06/2014] [Indexed: 12/20/2022]
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Haenisch S, Werk AN, Cascorbi I. MicroRNAs and their relevance to ABC transporters. Br J Clin Pharmacol 2014; 77:587-96. [PMID: 24645868 DOI: 10.1111/bcp.12251] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/11/2013] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs, which regulate the expression of their target genes post-transcriptionally by RNA interference. They are involved in almost all cellular processes, including proliferation, differentiation, apoptosis, cell survival and the maintenance of tissue specificity. Recent findings also suggest that efflux pumps of the ABC (ATP-binding cassette) transporter family are subject to miRNA-mediated gene regulation. Moreover, it seems that ABC transporters are embedded in a concerted and miRNA-guided network of concurrently regulated proteins that mediate altered drug transport and cell survival in changing environmental conditions. In this review, we summarize recent findings of miRNAs interacting with ABC transporters, which have been connected with drug distribution as well as with drug resistance. Additionally, we specify findings of complex miRNA-protein pathways conferring increased drug export and cell survival.
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Affiliation(s)
- Sierk Haenisch
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Germany
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69
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Knake C, Stamp L, Bahn A. Molecular mechanism of an adverse drug–drug interaction of allopurinol and furosemide in gout treatment. Biochem Biophys Res Commun 2014; 452:157-62. [DOI: 10.1016/j.bbrc.2014.08.068] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 08/15/2014] [Indexed: 11/16/2022]
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MicroRNAs as key regulators of xenobiotic biotransformation and drug response. Arch Toxicol 2014; 89:1523-41. [PMID: 25079447 DOI: 10.1007/s00204-014-1314-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/08/2014] [Indexed: 12/11/2022]
Abstract
In the last decade, microRNAs have emerged as key factors that negatively regulate mRNA expression. It has been estimated that more than 50% of protein-coding genes are under microRNA control and each microRNA is predicted to repress several mRNA targets. In this respect, it is recognized that microRNAs play a vital role in various cellular and molecular processes and that, depending on the biological pathways in which they intervene, distorted expression of microRNAs can have serious consequences. It has recently been shown that specific microRNA species are also correlated with toxic responses induced by xenobiotics. Since the latter are primarily linked to the extent of detoxification in the liver by phase I and phase II biotransformation enzymes and influx and efflux drug transporters, the regulation of the mRNA levels of this particular set of genes through microRNAs is of great importance for the overall toxicological outcome. Consequently, in this paper, an overview of the current knowledge with respect to the complex interplay between microRNAs and the expression of biotransformation enzymes and drug transporters in the liver is provided. Nuclear receptors and transcription factors, known to be involved in the transcriptional regulation of these genes, are also discussed.
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71
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Li R, Li X, Ning S, Ye J, Han L, Kang C, Li X. Identification of a core miRNA-pathway regulatory network in glioma by therapeutically targeting miR-181d, miR-21, miR-23b, β-Catenin, CBP, and STAT3. PLoS One 2014; 9:e101903. [PMID: 25007077 PMCID: PMC4090169 DOI: 10.1371/journal.pone.0101903] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/12/2014] [Indexed: 11/24/2022] Open
Abstract
The application of microRNAs (miRNAs) in the therapeutics of glioma and other human diseases is an area of intense interest. However, it’s still a great challenge to interpret the functional consequences of using miRNAs in glioma therapy. Here, we examined paired deep sequencing expression profiles of miRNAs and mRNAs from human glioma cell lines after manipulating the levels of miRNAs miR-181d, -21, and -23b, as well as transcriptional regulators β-catenin, CBP, and STAT3. An integrated approach was used to identify functional miRNA-pathway regulatory networks (MPRNs) responding to each manipulation. MiRNAs were identified to regulate glioma related biological pathways collaboratively after manipulating the level of either post-transcriptional or transcriptional regulators, and functional synergy and crosstalk was observed between different MPRNs. MPRNs responsive to multiple interventions were found to occupy central positions in the comprehensive MPRN (cMPRN) generated by integrating all the six MPRNs. Finally, we identified a core module comprising 14 miRNAs and five pathways that could predict the survival of glioma patients and represent potential targets for glioma therapy. Our results provided novel insight into miRNA regulatory mechanisms implicated in therapeutic interventions and could offer more inspiration to miRNA-based glioma therapy.
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Affiliation(s)
- Ronghong Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiang Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jingrun Ye
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lei Han
- Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Laboratory of Neurotrauma, Variation and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin, China
| | - Chunsheng Kang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Laboratory of Neurotrauma, Variation and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin, China
- * E-mail: (XL); (CK)
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- * E-mail: (XL); (CK)
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Lopez-Lopez E, Gutierrez-Camino A, Bilbao-Aldaiturriaga N, Pombar-Gomez M, Martin-Guerrero I, Garcia-Orad A. Pharmacogenetics of childhood acute lymphoblastic leukemia. Pharmacogenomics 2014; 15:1383-98. [DOI: 10.2217/pgs.14.106] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the major pediatric cancer in developed countries. Although treatment outcome has improved owing to advances in chemotherapy, there is still a group of patients for which therapy fails while some patients experience severe toxicity. In the last few years, several pharmacogenetic studies have been performed to search for markers of outcome and toxicity in pediatric ALL. However, to date, TPMT is the only pharmacogenetic marker in ALL with clinical guidelines for drug dosing. In this article, we will provide an overview of the most important findings carried out in pharmacogenetics for pediatric ALL, such as the interest drawn by methotrexate transporters in the context of methotrexate treatment. Even if most of the studies are centered on coding genes, we will also point to new approaches focusing on noncoding regions and epigenetic variation that could be interesting for consideration in the near future.
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Affiliation(s)
- Elixabet Lopez-Lopez
- Department of Genetics, Physical Anthropology & Animal Physiology, Faculty of Medicine & Odontology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Angela Gutierrez-Camino
- Department of Genetics, Physical Anthropology & Animal Physiology, Faculty of Medicine & Odontology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Nerea Bilbao-Aldaiturriaga
- Department of Genetics, Physical Anthropology & Animal Physiology, Faculty of Medicine & Odontology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Maria Pombar-Gomez
- Department of Genetics, Physical Anthropology & Animal Physiology, Faculty of Medicine & Odontology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Idoia Martin-Guerrero
- Department of Genetics, Physical Anthropology & Animal Physiology, Faculty of Medicine & Odontology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Africa Garcia-Orad
- Department of Genetics, Physical Anthropology & Animal Physiology, Faculty of Medicine & Odontology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- BioCruces Health Research Institute, Leioa, Spain
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73
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Rukov JL, Wilentzik R, Jaffe I, Vinther J, Shomron N. Pharmaco-miR: linking microRNAs and drug effects. Brief Bioinform 2014; 15:648-59. [PMID: 23376192 PMCID: PMC4103536 DOI: 10.1093/bib/bbs082] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/19/2012] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are short regulatory RNAs that down-regulate gene expression. They are essential for cell homeostasis and active in many disease states. A major discovery is the ability of miRNAs to determine the efficacy of drugs, which has given rise to the field of 'miRNA pharmacogenomics' through 'Pharmaco-miRs'. miRNAs play a significant role in pharmacogenomics by down-regulating genes that are important for drug function. These interactions can be described as triplet sets consisting of a miRNA, a target gene and a drug associated with the gene. We have developed a web server which links miRNA expression and drug function by combining data on miRNA targeting and protein-drug interactions. miRNA targeting information derive from both experimental data and computational predictions, and protein-drug interactions are annotated by the Pharmacogenomics Knowledge base (PharmGKB). Pharmaco-miR's input consists of miRNAs, genes and/or drug names and the output consists of miRNA pharmacogenomic sets or a list of unique associated miRNAs, genes and drugs. We have furthermore built a database, named Pharmaco-miR Verified Sets (VerSe), which contains miRNA pharmacogenomic data manually curated from the literature, can be searched and downloaded via Pharmaco-miR and informs on trends and generalities published in the field. Overall, we present examples of how Pharmaco-miR provides possible explanations for previously published observations, including how the cisplatin and 5-fluorouracil resistance induced by miR-148a may be caused by miR-148a targeting of the gene KIT. The information is available at www.Pharmaco-miR.org.
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Lee H, Kim C, Ku JL, Kim W, Yoon SK, Kuh HJ, Lee JH, Nam SW, Lee EK. A long non-coding RNA snaR contributes to 5-fluorouracil resistance in human colon cancer cells. Mol Cells 2014; 37:540-6. [PMID: 25078450 PMCID: PMC4132306 DOI: 10.14348/molcells.2014.0151] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 12/11/2022] Open
Abstract
Several types of genetic and epigenetic regulation have been implicated in the development of drug resistance, one significant challenge for cancer therapy. Although changes in the expression of non-coding RNA are also responsible for drug resistance, the specific identities and roles of them remain to be elucidated. Long non-coding RNAs (lncRNAs) are a type of ncRNA (> 200 nt) that influence the regulation of gene expression in various ways. In this study, we aimed to identify differentially expressed lncRNAs in 5-fluorouracil-resistant colon cancer cells. Using two pairs of 5-FU-resistant cells derived from the human colon cancer cell lines SNU-C4 and SNU-C5, we analyzed the expression of 90 lncRNAs by qPCR-based profiling and found that 19 and 23 lncRNAs were differentially expressed in SNU-C4R and SNU-C5R cells, respectively. We confirmed that snaR and BACE1AS were downregulated in resistant cells. To further investigate the effects of snaR on cell growth, cell viability and cell cycle were analyzed after transfection of siRNAs targeting snaR. Down-regulation of snaR decreased cell death after 5-FU treatment, which indicates that snaR loss decreases in vitro sensitivity to 5-FU. Our results provide an important insight into the involvement of lncRNAs in 5-FU resistance in colon cancer cells.
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Affiliation(s)
- Heejin Lee
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
| | - Chongtae Kim
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
| | - Ja-Lok Ku
- Cancer Research Institute and Cancer Research Center, Seoul National University, Seoul 110-744, Korea
| | - Wook Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Sungjoo Kim Yoon
- Cancer Evolution Research Center, Catholic University of Korea, Seoul 137-701, Korea
- Department of Biomedical Science, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
| | - Hyo-Jeong Kuh
- Cancer Evolution Research Center, Catholic University of Korea, Seoul 137-701, Korea
- Department of Biomedical Science, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
| | - Jeong-Hwa Lee
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
- Cancer Evolution Research Center, Catholic University of Korea, Seoul 137-701, Korea
| | - Suk Woo Nam
- Cancer Evolution Research Center, Catholic University of Korea, Seoul 137-701, Korea
- Department of Pathology, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
| | - Eun Kyung Lee
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea
- Cancer Evolution Research Center, Catholic University of Korea, Seoul 137-701, Korea
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75
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Hsi E, Huang CF, Dai CY, Juo SHH, Chou WW, Huang JF, Yeh ML, Lin ZY, Chen SC, Wang LY, Chuang WL, Yu ML. Peripheral blood mononuclear cells microRNA predicts treatment outcome of hepatitis C virus genotype 1 infection. Antiviral Res 2014; 105:135-42. [PMID: 24637254 DOI: 10.1016/j.antiviral.2014.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/10/2014] [Accepted: 03/07/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUNDS Chronic hepatitis C virus (HCV) infection has been associated with induction of microRNAs (miRNAs) in peripheral blood mononuclear cells (PBMC). We aimed to evaluate the role of PBMC-miRNAs in the treatment outcome to antiviral therapy for HCV genotype 1 (HCV-1) patients. METHODS Treatment-naive chronic HCV-1 patients, including 13 in screening phase and 48 in validation phase, were treated with 48weeks of peginterferon/ribavirin. The primary end-point was the achievement of a sustained virological response (SVR, HCV RNA undetectable during 24weeks post-treatment follow-up). Expression profiling of PBMC-miRNAs was performed by quantitative PCR-based array in typical responders and null-responders. Then candidate PBMC-miRNAs were validated by quantitative PCR in an independent validation set. RESULTS PBMC-miR-125b was significantly predictive of an SVR, with expression levels of 5.28-fold lower in sustained responders versus null-responders (p=0.0163). In multivariate analysis, PBMC-miR-125b was significantly associated with the achievement of SVR (per 2-fold decrease, odds ratio/95% confidence interval (OR/CI): 2.07/1.14-6.31) independent of sex, age and interleukin-28B genotype. In patients who did not achieve a rapid virological response (RVR, undetectable HCV RNA at treatment week 4), PBMC-miR-125b was the only predictive factor of an SVR (per 2-fold decrease, OR/CI: 2.07/1.14-6.31). However, the circulating and hepatic miR-125b did not show significant difference between responders and non-responders. CONCLUSIONS PBMC-miR-125b expression levels were inversely related to the achievement of an SVR in HCV-1 patients, independent of interleukin-28B genotype, and was the single predictor of SVR in non-RVR patients.
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Affiliation(s)
- Edward Hsi
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Taiwan
| | - Chung-Feng Huang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Occupational Medicine, Kaohsiung Municipal Ta-Tung Hospital, Taiwan
| | - Chia-Yen Dai
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Suh-Hang Hank Juo
- Department of Medical Research, Kaohsiung Medical University Hospital, Taiwan; Department of Medical Genetics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Wen Chou
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Jee-Fu Huang
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Internal Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Lun Yeh
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Zu-Yau Lin
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shinn-Cherng Chen
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Liang-Yen Wang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wan-Long Chuang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Ming-Lung Yu
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
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76
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Song KH, Kim YH, Kim BY. Sho-saiko-to, a traditional herbal medicine, regulates gene expression and biological function by way of microRNAs in primary mouse hepatocytes. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 14:14. [PMID: 24410935 PMCID: PMC3893506 DOI: 10.1186/1472-6882-14-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/31/2013] [Indexed: 12/25/2022]
Abstract
BACKGROUND Sho-saiko-to (SST) (also known as so-shi-ho-tang or xiao-chai-hu-tang) has been widely prescribed for chronic liver diseases in traditional Oriental medicine. Despite the substantial amount of clinical evidence for SST, its molecular mechanism has not been clearly identified at a genome-wide level. METHODS By using a microarray, we analyzed the temporal changes of messenger RNA (mRNA) and microRNA expression in primary mouse hepatocytes after SST treatment. The pattern of genes regulated by SST was identified by using time-series microarray analysis. The biological function of genes was measured by pathway analysis. For the identification of the exact targets of the microRNAs, a permutation-based correlation method was implemented in which the temporal expression of mRNAs and microRNAs were integrated. The similarity of the promoter structure between temporally regulated genes was measured by analyzing the transcription factor binding sites in the promoter region. RESULTS The SST-regulated gene expression had two major patterns: (1) a temporally up-regulated pattern (463 genes) and (2) a temporally down-regulated pattern (177 genes). The integration of the genes and microRNA demonstrated that 155 genes could be the targets of microRNAs from the temporally up-regulated pattern and 19 genes could be the targets of microRNAs from the temporally down-regulated pattern. The temporally up-regulated pattern by SST was associated with signaling pathways such as the cell cycle pathway, whereas the temporally down-regulated pattern included drug metabolism-related pathways and immune-related pathways. All these pathways could be possibly associated with liver regenerative activity of SST. Genes targeted by microRNA were moreover associated with different biological pathways from the genes not targeted by microRNA. An analysis of promoter similarity indicated that co-expressed genes after SST treatment were clustered into subgroups, depending on the temporal expression patterns. CONCLUSIONS We are the first to identify that SST regulates temporal gene expression by way of microRNA. MicroRNA targets and non-microRNA targets moreover have different biological roles. This functional segregation by microRNA would be critical for the elucidation of the molecular activities of SST.
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77
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Vázquez O, Seitz O. Templated native chemical ligation: peptide chemistry beyond protein synthesis. J Pept Sci 2014; 20:78-86. [PMID: 24395765 DOI: 10.1002/psc.2602] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 11/22/2013] [Accepted: 11/22/2013] [Indexed: 12/11/2022]
Abstract
Native chemical ligation (NCL) is a powerful method for the convergent synthesis of proteins and peptides. In its original format, NCL between a peptide containing a C-terminal thioester and another peptide offering an N-terminal cysteine has been used to enable protein synthesis of unprotected peptide fragments. However, the applications of NCL extend beyond the scope of protein synthesis. For instance, NCL can be put under the control of template molecules. In such a scenario, NCL enables the design of conditional reaction systems in which, peptide bond formation occurs only when a specific third party molecule is present. In this review, we will show how templates can be used to control the reactivity and chemoselectivity of NCL reactions. We highlight peptide and nucleic-acid-templated NCL reactions and discuss potential applications in nucleic acid diagnosis, origin-of-life studies and gene-expression-specific therapies.
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Affiliation(s)
- Olalla Vázquez
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489, Berlin, Germany
| | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489, Berlin, Germany
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Lopez JP, Fiori LM, Gross JA, Labonte B, Yerko V, Mechawar N, Turecki G. Regulatory role of miRNAs in polyamine gene expression in the prefrontal cortex of depressed suicide completers. Int J Neuropsychopharmacol 2014; 17:23-32. [PMID: 24025154 DOI: 10.1017/s1461145713000941] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNA molecules that play an important role in the post-transcriptional regulation of mRNA. These molecules have been the subject of growing interest as they are believed to control the regulation of a large number of genes, including those expressed in the brain. Evidence suggests that miRNAs could be involved in the pathogenesis of neuropsychiatric disorders. Alterations in metabolic enzymes of the polyamine system have been reported to play a role in predisposition to suicidal behaviour. We have previously shown the expression of the polyamine genes SAT1 and SMOX to be down-regulated in the brains of suicide completers. In this study, we hypothesized that the dysregulation of these genes in depressed suicide completers could be influenced by miRNA post-transcriptional regulation. Using a stringent target prediction analysis, we identified several miRNAs that target the 3'UTR of SAT1 and SMOX. We profiled the expression of 10 miRNAs in the prefrontal cortex (BA44) of suicide completers (N = 15) and controls (N = 16) using qRT-PCR. We found that several miRNAs showed significant up-regulation in the prefrontal cortex of suicide completers compared to psychiatric healthy controls. Furthermore, we demonstrated a significant correlation between these miRNAs and the expression levels of both SAT1 and SMOX. Our results suggest a relationship between miRNAs and polyamine gene expression in the suicide brain, and postulate a mechanism for SAT1 and SMOX down-regulation by post-transcriptional activity of miRNAs.
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Affiliation(s)
- Juan Pablo Lopez
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, H4H 1R3, Canada
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Iudicibus SD, Lucafò M, Martelossi S, Pierobon C, Ventura A, Decorti G. MicroRNAs as tools to predict glucocorticoid response in inflammatory bowel diseases. World J Gastroenterol 2013; 19:7947-54. [PMID: 24307788 PMCID: PMC3848142 DOI: 10.3748/wjg.v19.i44.7947] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/16/2013] [Accepted: 10/19/2013] [Indexed: 02/06/2023] Open
Abstract
In spite of the introduction in therapy of highly effective biological agents, glucocorticoids (GCs) are still employed to induce remission in moderate to severe inflammatory bowel diseases (IBD), but considerable inter-individual differences in their efficacy and side effects have been reported. The effectiveness of these drugs is indeed very variable and side effects, particularly severe in pediatric patients, are common and often unpredictable: the understanding of the complex gene regulation mediated by GCs could shed light on the causes of this variability. In this context, microRNAs (miRNAs) represent a new and promising field of research. miRNAs are small non-coding RNA molecules that suppress gene expression at post-transcriptional level, and are fine-tuning regulators of diverse biological processes, including the development and function of the immune system, apoptosis, metabolism and inflammation. Emerging data have implicated the deregulated expression of certain miRNA networks in the pathogenesis of autoimmune and inflammatory diseases, such as IBD. There is a great interest in the identification of the role of miRNAs in the modulation of pharmacological response; however, the association between miRNA and GC response in patients with IBD has not yet been evaluated in a prospective clinical study. The identification of miRNAs differently expressed as a consequence of GC treatment in comparison to diagnosis, represents an important innovative approach that could be translated into clinical practice. In this review we highlight the altered regulation of proteins involved in GC molecular mechanism by miRNAs, and their potential role as molecular markers useful for predicting in advance GC response.
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80
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Erriquez D, Perini G, Ferlini A. Non-coding RNAs in muscle dystrophies. Int J Mol Sci 2013; 14:19681-704. [PMID: 24084719 PMCID: PMC3821580 DOI: 10.3390/ijms141019681] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/05/2013] [Accepted: 09/09/2013] [Indexed: 12/13/2022] Open
Abstract
ncRNAs are the most recently identified class of regulatory RNAs with vital functions in gene expression regulation and cell development. Among the variety of roles they play, their involvement in human diseases has opened new avenues of research towards the discovery and development of novel therapeutic approaches. Important data come from the field of hereditary muscle dystrophies, like Duchenne muscle dystrophy and Myotonic dystrophies, rare diseases affecting 1 in 7000-15,000 newborns and is characterized by severe to mild muscle weakness associated with cardiac involvement. Novel therapeutic approaches are now ongoing for these diseases, also based on splicing modulation. In this review we provide an overview about ncRNAs and their behavior in muscular dystrophy and explore their links with diagnosis, prognosis and treatments, highlighting the role of regulatory RNAs in these pathologies.
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Affiliation(s)
- Daniela Erriquez
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; E-Mail:
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; E-Mail:
- Health Sciences and Technologies–Interdepartmental Center for Industrial Research, University of Bologna, Bologna 40064, Italy
| | - Alessandra Ferlini
- Section of Microbiology and Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara 44100, Italy
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Yeon SE, No DY, Lee SH, Nam SW, Oh IH, Lee J, Kuh HJ. Application of concave microwells to pancreatic tumor spheroids enabling anticancer drug evaluation in a clinically relevant drug resistance model. PLoS One 2013; 8:e73345. [PMID: 24039920 PMCID: PMC3769301 DOI: 10.1371/journal.pone.0073345] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/19/2013] [Indexed: 12/11/2022] Open
Abstract
Intrinsic drug resistance of pancreatic ductal adenocarcinoma (PDAC) warrants studies using models that are more clinically relevant for identifying novel resistance mechanisms as well as for drug development. Tumor spheroids (TS) mimic in vivo tumor conditions associated with multicellular resistance and represent a promising model for efficient drug screening, however, pancreatic cancer cells often fail to form spheroids using conventional methods such as liquid overlay. This study describes the induction of TS of human pancreatic cancer cells (Panc-1, Aspc-1, Capan-2) in concave polydimethylsiloxane (PDMS) microwell plates and evaluation of their usefulness as an anticancer efficacy test model. All three cell lines showed TS formation with varying degree of necrosis inside TS. Among these, Panc-1 spheroid with spherical morphology, a rather rough surface, and unique adhesion structures were successfully produced with no notable necrosis in concave microwell plates. Panc-1 TS contained growth factors or enzymes such as TGF-β1, CTGF, and MT1-MMP, and extracellular matrix proteins such as collagen type I, fibronectin, and laminin. Panc-1 cells grown as TS showed changes in stem cell populations and in expression levels of miRNAs that may play roles in chemoresistance. Visualization of drug penetration and detection of viability indicators, such as Ki-67 and MitoSOX, were optimized for TS for quantitative analysis. Water-soluble tetrazolium (MTS) and acid phosphatase (APH) assays were also successfully optimized. Overall, we demonstrated that concave PDMS microwell plates are a novel platform for preparation of TS of weakly aggregating cells and that Panc-1 spheroids may represent a novel three-dimensional model for anti-pancreatic cancer drug screening.
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Affiliation(s)
- Sang-Eun Yeon
- Lab of Onco-Pharmacology and Experimental Therapeutics, Department of Biomedical Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Da Yoon No
- Department of Biomedical Engineering, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Sang-Hoon Lee
- Department of Biomedical Engineering, College of Health Science, Korea University, Seoul, Republic of Korea
| | - Suk Woo Nam
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Il-Hoan Oh
- Catholic High Performance Cell Therapy Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jaehwi Lee
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Hyo-Jeong Kuh
- Lab of Onco-Pharmacology and Experimental Therapeutics, Department of Biomedical Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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82
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Kang H, Kim C, Lee H, Kim W, Lee EK. Post-transcriptional controls by ribonucleoprotein complexes in the acquisition of drug resistance. Int J Mol Sci 2013; 14:17204-20. [PMID: 23965981 PMCID: PMC3759960 DOI: 10.3390/ijms140817204] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 07/31/2013] [Accepted: 08/09/2013] [Indexed: 01/03/2023] Open
Abstract
Acquisition of drug resistance leads to failure of anti-cancer treatments and therapies. Although several successive chemotherapies are available, along with efforts towards clinical applications of new anti-cancer drugs, it is generally realized that there is a long way to go to treat cancers. Resistance to anti-cancer drugs results from various factors, including genetic as well as epigenetic differences in tumors. Determining the molecular and cellular mechanisms responsible for the acquisition of drug resistance may be a helpful approach for the development of new therapeutic strategies to overcome treatment failure. Several studies have shown that the acquisition of drug resistance is tightly regulated by post-transcriptional regulators such as RNA binding proteins (RBPs) and microRNAs (miRNAs), which change the stability and translation of mRNAs encoding factors involved in cell survival, proliferation, epithelial-mesenchymal transition, and drug metabolism. Here, we review our current understanding of ribonucleoprotein complexes, including RBPs and miRNAs, which play critical roles in the acquisition of drug resistance and have potential clinical implications for cancer.
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Affiliation(s)
- Hoin Kang
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea; E-Mails: (H.K.); (C.K.); (H.L.)
| | - Chongtae Kim
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea; E-Mails: (H.K.); (C.K.); (H.L.)
| | - Heejin Lee
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea; E-Mails: (H.K.); (C.K.); (H.L.)
| | - Wook Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
- Authors to whom correspondence should be addressed; E-Mails: (W.K.); (E.K.L.); Tel.: +82-31-219-2513 (W.K.); +82-2-2258-7295 (E.K.L.); Fax: +82-31-219-1610 (W.K.); +82-2-596-4435 (E.K.L.)
| | - Eun Kyung Lee
- Department of Biochemistry, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea; E-Mails: (H.K.); (C.K.); (H.L.)
- Authors to whom correspondence should be addressed; E-Mails: (W.K.); (E.K.L.); Tel.: +82-31-219-2513 (W.K.); +82-2-2258-7295 (E.K.L.); Fax: +82-31-219-1610 (W.K.); +82-2-596-4435 (E.K.L.)
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83
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Mosakhani N, Mustjoki S, Knuutila S. Down-regulation of miR-181c in imatinib-resistant chronic myeloid leukemia. Mol Cytogenet 2013; 6:27. [PMID: 23866735 PMCID: PMC3751646 DOI: 10.1186/1755-8166-6-27] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/04/2013] [Indexed: 12/21/2022] Open
Abstract
The association of microRNA alterations with progression and treatment outcome has been revealed in different types of cancers. To find miRNAs involved in imatinib response we performed miRNA microarray followed by RT-qPCR verification of 9 available diagnostic bone marrow core biopsies from 9 CML patients including 4 imatinib-resistant and 5 imatinib-responder patients. Only one differentially expressed miRNA, miR-181c, was found when the imatinib-resistant group was compared with imatinib-responders. Significant down-regulation of miR-181c in imatinib-resistant versus imatinib-responders was confirmed by qRT-PCR. Some miR-181c target genes such as PBX3, HSP90B1, NMT2 and RAD21 have been associated with drug response.
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Affiliation(s)
- Neda Mosakhani
- Department of Pathology, Haartman Institute, and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
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84
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Mosakhani N, Räty R, Tyybäkinoja A, Karjalainen-Lindsberg ML, Elonen E, Knuutila S. MicroRNA profiling in chemoresistant and chemosensitive acute myeloid leukemia. Cytogenet Genome Res 2013; 141:272-6. [PMID: 23689423 DOI: 10.1159/000351219] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2013] [Indexed: 11/19/2022] Open
Abstract
MicroRNA (miRNA) deregulation is associated with progression and treatment outcome in various types of cancers. To identify miRNAs related to therapeutic response, we applied an miRNA microarray followed by PCR verification of 33 available diagnostic bone marrow core biopsies from 33 acute myeloid leukemia patients including 15 chemoresistant and 18 chemosensitive patients. We found 3 significantly upregulated miRNAs, miR-363, miR-532-5p and miR-342-3p, related to therapeutic response (q < 0.05). Further validation of miR-532-5p and miR-363 expression by quantitative RT-PCR confirmed microarray analysis results. Genes targeted by miR-363 include RGS17 and HIPK3, both reported to be associated with drug response.
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Affiliation(s)
- N Mosakhani
- Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
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85
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Abstract
Cytochrome P450 enzymes (CYPs) metabolize many drugs that act on the central nervous system (CNS), such as antidepressants and antipsychotics; drugs of abuse; endogenous neurochemicals, such as serotonin and dopamine; neurotoxins; and carcinogens. This takes place primarily in the liver, but metabolism can also occur in extrahepatic organs, including the brain. This is important for CNS-acting drugs, as variation in brain CYP-mediated metabolism may be a contributing factor when plasma levels do not predict drug response. This review summarizes the characterization of CYPs in the brain, using examples from the CYP2 subfamily, and discusses sources of variation in brain CYP levels and metabolism. Some recent experiments are described that demonstrate how changes in brain CYP metabolism can influence drug response, toxicity and drug-induced behaviours. Advancing knowledge of brain CYP-mediated metabolism may help us understand why patients respond differently to drugs used in psychiatry and predict risk for psychiatric disorders, including neurodegenerative diseases and substance abuse.
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Affiliation(s)
| | - Rachel F. Tyndale
- Correspondence to: R.F. Tyndale, Department of Pharmacology and Toxicology, 1 King’s College Circle, Toronto ON M5S 1A8;
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86
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Marini F, Brandi ML. The future of pharmacogenetics for osteoporosis. Pharmacogenomics 2013; 14:641-53. [DOI: 10.2217/pgs.13.40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The possibility to predict the outcome of medical treatments, both in terms of efficacy and development of adverse effects, is the main goal of modern personalized medicine. The principal aim of pharmacogenetics is to design specific predictive genetic tests, to be performed prior to any drug treatment, and to tailor the therapy for each patient based on the results of these tests. Few pharmacogenetic tests are today validated and commonly applied in clinical practice, and none in the area of osteoporosis and bone disorders. Surely, the complex regulation of bone metabolism and the involvement of numerous different molecular pathways makes it difficult to individuate responsible genes and polymorphisms involved in the modulation of anti-osteoporotic drug response and, subsequently, in designing specific predictive analyses.
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Affiliation(s)
- Francesca Marini
- Metabolic Bone Unit, Department of Surgery & Translation Medicine, University of Florence, Florence, Italy.
| | - Maria Luisa Brandi
- Metabolic Bone Unit, Department of Surgery & Translation Medicine, University of Florence, Florence, Italy
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87
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Totary-Jain H, Marks AR. MicroRNAs and the cellular response to rapamycin: potential role in diagnosis and therapy. Cell Cycle 2013; 12:861-2. [PMID: 23442794 PMCID: PMC3637337 DOI: 10.4161/cc.24100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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88
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Santarelli DM, Liu B, Duncan CE, Beveridge NJ, Tooney PA, Schofield PR, Cairns MJ. Gene-microRNA interactions associated with antipsychotic mechanisms and the metabolic side effects of olanzapine. Psychopharmacology (Berl) 2013; 227:67-78. [PMID: 23318695 PMCID: PMC3622003 DOI: 10.1007/s00213-012-2939-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/26/2012] [Indexed: 12/31/2022]
Abstract
RATIONALE Changes in the cortical expression of small non-coding microRNA (miRNA) have been observed in postmortem analysis of psychotic disorders. Antipsychotic drugs (APDs) are the most effective treatment option for these disorders and have been associated with changes in gene expression. MicroRNA regulate numerous genes involved in brain development and function. It is therefore plausible to question whether miRNA expression is also altered and hence whether they take part in the neuroleptic mechanism of action. OBJECTIVES We sought to investigate whether treatment with APDs induces changes in miRNA expression and query the functional implications of such changes. Furthermore, we investigated the possible functional interplay of miRNA-gene regulatory interactions. METHOD High-throughput miRNA profiling of the whole brain of C57BL/6 mice treated with haloperidol, olanzapine or clozapine for 7 days was performed. Functional analysis was conducted on the putative targets of altered microRNA. Significant miRNA-gene regulatory interactions were evaluated by the integration of genome-wide mRNA expression analysis using the Bayesian networks with splitting-averaging strategy and functional analysis conducted. RESULTS Small subsets of miRNA were altered with each treatment with potential neurologically relevant influence. Metabolic pathways were enriched in olanzapine and clozapine treatments, possibly associated with their weight gain side effects. Neurologically and metabolically relevant miRNA-gene interaction networks were identified in the olanzapine treatment group. CONCLUSION This study is the first to suggest a role for miRNA in the mechanism of APD action and the metabolic side effects of the atypical ADPs, and adds support for their consideration in pharmacogenomics.
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Affiliation(s)
- Danielle M. Santarelli
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, University Drive, Callaghan, NSW 2308 Australia ,Schizophrenia Research Institute, Sydney, NSW 2010 Australia ,Hunter Medical Research Institute, Lookout Road, New Lambton, NSW 2305 Australia
| | - Bing Liu
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, University Drive, Callaghan, NSW 2308 Australia ,Schizophrenia Research Institute, Sydney, NSW 2010 Australia ,Hunter Medical Research Institute, Lookout Road, New Lambton, NSW 2305 Australia
| | - Carlotta E. Duncan
- Schizophrenia Research Institute, Sydney, NSW 2010 Australia ,Neuroscience Research Australia, Sydney, NSW 2031 Australia ,School of Medical Sciences, The University of New South Wales, Sydney, NSW 2033 Australia
| | - Natalie J. Beveridge
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, University Drive, Callaghan, NSW 2308 Australia ,Schizophrenia Research Institute, Sydney, NSW 2010 Australia ,Hunter Medical Research Institute, Lookout Road, New Lambton, NSW 2305 Australia
| | - Paul A. Tooney
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, University Drive, Callaghan, NSW 2308 Australia ,Schizophrenia Research Institute, Sydney, NSW 2010 Australia ,Hunter Medical Research Institute, Lookout Road, New Lambton, NSW 2305 Australia
| | - Peter R. Schofield
- Schizophrenia Research Institute, Sydney, NSW 2010 Australia ,Neuroscience Research Australia, Sydney, NSW 2031 Australia ,School of Medical Sciences, The University of New South Wales, Sydney, NSW 2033 Australia
| | - Murray J. Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, University Drive, Callaghan, NSW 2308 Australia ,Schizophrenia Research Institute, Sydney, NSW 2010 Australia ,Hunter Medical Research Institute, Lookout Road, New Lambton, NSW 2305 Australia
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89
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Vincent M, Oved K, Morag A, Pasmanik-Chor M, Oron-Karni V, Shomron N, Gurwitz D. Genome-wide transcriptomic variations of human lymphoblastoid cell lines: insights from pairwise gene-expression correlations. Pharmacogenomics 2012; 13:1893-904. [DOI: 10.2217/pgs.12.179] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aims: Human lymphoblastoid cell lines (LCLs) are a rich resource of information on human interindividual genomic, transcriptomic, proteomic and phenomic variations, and are therefore gaining popularity for pharmacogenomic studies. In the present study we demonstrate that genome-wide transcriptomic data from a small LCL panel from unrelated individuals is sufficient for detecting pairs of genes that exhibit highly correlated expression levels and may thus convey insights about coregulated genes. Materials & methods: RNA samples were prepared from LCLs representing 12 unrelated healthy adult female Caucasian donors. Transcript levels were determined with the Affymetrix Human Gene arrays. Expression-level correlations were searched using Partek® Genomics Suite™ and the R environment. Sequences of detected correlated gene pairs were compared for shared conserved 3´-UTR miRNA binding. Results: Most of the approximately 33,000 transcripts covered by the Affymetrix arrays showed closely similar expression levels in LCLs from unrelated donors. However, the expression levels of some transcripts showed large inter-individual variations. When comparing the expression levels of each of the top 1000 genes showing the largest interindividual expression variations against the others, two sets containing 156 and 4438 correlated gene pairs with false-discovery rates of 0.01 and 0.05 were detected, respectively. Similar analysis of another gene-expression data set from LCLs (GSE11582) indicated that 61 and 39% of identified pairs matched the pairs detected from our transcriptomic data, respectively. Shared conserved 3´-UTR miRNA binding sites were noted for 14–17% of the top 100 gene pairs, suggesting that regulation by miRNA may contribute to their coordinated expression. Conclusion: Probing genome-wide transcriptomic data sets of LCLs from unrelated individuals may detect coregulated genes, adding insights on cellular regulation by miRNAs. Original submitted 11 July 2012; Revision submitted 4 September 2012
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Affiliation(s)
- Marc Vincent
- Université Paris Descartes, INSERM UMRS775, Paris, France
| | - Keren Oved
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Israel
- Department of Cell & Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Ayelet Morag
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, George Wise Faculty of Life Sciences, Tel-Aviv University, Israel
| | - Varda Oron-Karni
- Bioinformatics Unit, George Wise Faculty of Life Sciences, Tel-Aviv University, Israel
| | - Noam Shomron
- Department of Cell & Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - David Gurwitz
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Israel
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90
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Abstract
A new generation of technologies commonly named omics permits assessment of the entirety of the components of biological systems and produces an explosion of data and a major shift in our concepts of disease. These technologies will likely shape the future of health care. One aspect of these advances is that the data generated document the uniqueness of each human being in regard to disease risk and treatment response. These developments have reemphasized the concept of personalized medicine. Here we review the impact of omics technologies on one key aspect of personalized medicine: the individual drug response. We describe how knowledge of different omics may affect treatment decisions, namely drug choice and drug dose, and how it can be used to improve clinical outcomes.
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Affiliation(s)
- Urs A Meyer
- Division of Pharmacology and Neurobiology, Biozentrum of the University of Basel, CH-4056 Basel, Switzerland.
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91
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Kalabus JL, Cheng Q, Blanco JG. MicroRNAs differentially regulate carbonyl reductase 1 (CBR1) gene expression dependent on the allele status of the common polymorphic variant rs9024. PLoS One 2012; 7:e48622. [PMID: 23133646 PMCID: PMC3486798 DOI: 10.1371/journal.pone.0048622] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 10/02/2012] [Indexed: 01/25/2023] Open
Abstract
MicroRNAs (miRNAs) are small RNAs responsible for the post-transcriptional regulation of a variety of human genes. To date, their involvement in the regulation of CBR1 is unknown. This study reports for the first time the identification of microRNA-574-5p (hsa-miR-574-5p) and microRNA-921 (hsa-miR-921) as two miRNAs capable of interacting with the 3'-untranslated region (3'-UTR) of the CBR1 gene and downregulating CBR1 expression. Furthermore, we demonstrate that a common single-nucleotide polymorphism (SNP) in the CBR1 3'-UTR (rs9024, CBR1 1096G>A) differentially impacts the regulation of CBR1 by hsa-miR-574-5p and hsa-miR-921 dependent on genotype. First, four candidate miRNAs were selected based on bioinformatic analyses, and were tested in Chinese hamster ovary (CHO) cells transfected with CBR1 3'-UTR constructs harboring either the G or A allele for rs9024. We found that hsa-miR-574-5p and hsa-miR-921 significantly decreased luciferase activity in CHO cells transfected with the CBR1 3'-UTR construct carrying the major rs9024 G allele by 35% and 46%, respectively. The influence of these miRNAs was different in cells transfected with a CBR1 3'-UTR construct containing the minor rs9024 A allele in that only hsa-miR-574-5p had a demonstrable effect (i.e., 52% decrease in lucifersase activity). To further determine the functional effects of miRNA-mediated regulation of polymorphic CBR1, we assessed CBR1 protein expression and CBR1 enzymatic activity for the prototypical substrate menadione in human lymphoblastoid cell lines with distinct rs9024 genotypes. We found that hsa-miR-574-5p and hsa-miR-921 significantly decreased CBR1 protein (48% and 40%, respectively) and CBR1 menadione activity (54% and 18%, respectively) in lymphoblastoid cells homozygous for the major rs9024 G allele. In contrast, only hsa-miR-574-5p decreased CBR1 protein and CBR1 activity in cells homozygous for the minor rs9024 A allele, and did so by 49% and 56%, respectively. These results suggest that regulation of human CBR1 expression by hsa-miR-574-5p and hsa-miR-921 depends upon rs9024 genotype status.
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Affiliation(s)
- James L. Kalabus
- Department of Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Qiuying Cheng
- Department of Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Javier G. Blanco
- Department of Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, New York, United States of America
- * E-mail:
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92
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Ivanov M, Kacevska M, Ingelman-Sundberg M. Epigenomics and Interindividual Differences in Drug Response. Clin Pharmacol Ther 2012; 92:727-36. [DOI: 10.1038/clpt.2012.152] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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93
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MicroRNA profiling predicts survival in anti-EGFR treated chemorefractory metastatic colorectal cancer patients with wild-type KRAS and BRAF. Cancer Genet 2012; 205:545-51. [PMID: 23098991 DOI: 10.1016/j.cancergen.2012.08.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 08/17/2012] [Accepted: 08/23/2012] [Indexed: 02/07/2023]
Abstract
Anti-EGFR monoclonal antibodies (anti-EGFRmAb) serve in the treatment of metastatic colorectal cancer (mCRC), but patients with a mutation in KRAS/BRAF and nearly one-half of those without the mutation fail to respond. We performed microRNA (miRNA) analysis to find miRNAs predicting anti-EGFRmAb efficacy. Of the 99 mCRC patients, we studied differential miRNA expression by microarrays from primary tumors of 33 patients who had wild-type KRAS/BRAF and third- to sixth-line anti-EGFRmAb treatment, with/without irinotecan. We tested the association of each miRNA with overall survival (OS) by the Cox proportional hazards regression model. Significant miR-31* up-regulation and miR-592 down-regulation appeared in progressive disease versus disease control. miR-31* expression and down-regulation of its target genes SLC26A3 and ATN1 were verified by quantitative reverse transcriptase polymerase chain reaction. Clustering of patients based on miRNA expression revealed a significant difference in OS between patient clusters. Members of the let-7 family showed significant up-regulation in the patient cluster with poor OS. Additionally, miR-140-5p up-regulation and miR-1224-5p down-regulation were significantly associated with poor OS in both cluster analysis and the Cox proportional hazards regression model. In mCRC patients with wild-type KRAS/BRAF, miRNA profiling can efficiently predict the benefits of anti-EGFRmAb treatment. Larger series of patients are necessary for application of these miRNAs as predictive/prognostic markers.
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94
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Kacevska M, Ivanov M, Ingelman-Sundberg M. Epigenetic-dependent regulation of drug transport and metabolism: an update. Pharmacogenomics 2012; 13:1373-85. [DOI: 10.2217/pgs.12.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The pharmacokinetics of a drug are subject to large interindividual variability, which can result in lack of response or adverse drug reactions. In addition to genetic polymorphisms and drug interactions, key genes involved in the metabolism and transport of drugs are demonstrated to have epigenetic influences that can potentially affect interindividual variability in drug response. Emerging studies have focused on the importance of DNA methylation for ADME gene expression and for drug action and resistance, particularly in cancer. However, the epigenetic and ncRNA-dependent regulation of these genes, as well as the pharmacological consequences, is in need of greater attention. In the current review we provide an update of epigenetic and ncRNA-dependent regulation of ADME genes.
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Affiliation(s)
- Marina Kacevska
- Section of Pharmacogenetics, Department of Physiology & Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Maxim Ivanov
- Section of Pharmacogenetics, Department of Physiology & Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Magnus Ingelman-Sundberg
- Section of Pharmacogenetics, Department of Physiology & Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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95
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Schrattenholz A, Šoškić V, Schöpf R, Poznanović S, Klemm-Manns M, Groebe K. Protein biomarkers for in vitro testing of toxicology. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2012; 746:113-23. [DOI: 10.1016/j.mrgentox.2012.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 02/21/2012] [Indexed: 12/14/2022]
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96
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Le XF, Almeida MI, Mao W, Spizzo R, Rossi S, Nicoloso MS, Zhang S, Wu Y, Calin GA, Bast RC. Modulation of MicroRNA-194 and cell migration by HER2-targeting trastuzumab in breast cancer. PLoS One 2012; 7:e41170. [PMID: 22829924 PMCID: PMC3400637 DOI: 10.1371/journal.pone.0041170] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 06/18/2012] [Indexed: 12/27/2022] Open
Abstract
Trastuzumab, a humanized monoclonal antibody directed against the extracellular domain of the HER2 oncoprotein, can effectively target HER2-positive breast cancer through several mechanisms. Although the effects of trastuzumab on cancer cell proliferation, angiogenesis and apoptosis have been investigated in depth, the effect of trastuzumab on microRNA (miRNA) has not been extensively studied. We have performed miRNA microarray profiling before and after trastuzumab treatment in SKBr3 and BT474 human breast cancer cells that overexpress HER2. We found that trastuzumab treatment of SKBr3 cells significantly decreased five miRNAs and increased three others, whereas treatment of BT474 cells significantly decreased two miRNAs and increased nine. The only change in miRNA expression observed in both cell lines following trastuzumab treatment was upregulation of miRNA-194 (miR-194) that was further validated in vitro and in vivo. Forced expression of miR-194 in breast cancer cells that overexpress HER2 produced no effect on apoptosis, modest inhibition of proliferation, significant inhibition of cell migration/invasion in vitro and significant inhibition of xenograft growth in vivo. Conversely, knockdown of miR-194 promoted cell migration. Increased miR-194 expression markedly reduced levels of the cytoskeletal protein talin2 and specifically inhibited luciferase reporter activity of a talin2 wild-type 3'-untranslated region, but not that of a mutant reporter, indicating that talin2 is a direct downstream target of miR-194. Trastuzumab treatment inhibited breast cancer cell migration and reduced talin2 expression in vitro and in vivo. Knockdown of talin2 inhibited cell migration/invasion. Knockdown of trastuzumab-induced miR-194 expression with a miR-194 inhibitor compromised trastuzumab-inhibited cell migration in HER2-overexpressing breast cancer cells. Consequently, trastuzumab treatment upregulates miR-194 expression and may exert its cell migration-inhibitory effect through miR-194-mediated downregulation of cytoskeleton protein talin2 in HER2-overexpressing human breast cancer cells.
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Affiliation(s)
- Xiao-Feng Le
- Department of Experimental Therapeutics, the University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (XFL); (RCB)
| | - Maria I. Almeida
- Department of Experimental Therapeutics, the University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
| | - Weiqun Mao
- Department of Experimental Therapeutics, the University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Riccardo Spizzo
- Department of Experimental Therapeutics, the University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Simona Rossi
- Department of Experimental Therapeutics, the University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Milena S. Nicoloso
- Department of Experimental Therapeutics, the University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Shu Zhang
- Department of Experimental Therapeutics, the University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Yun Wu
- Department of Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - George A. Calin
- Department of Experimental Therapeutics, the University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Robert C. Bast
- Department of Experimental Therapeutics, the University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (XFL); (RCB)
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97
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Bell RE, Levy C. The three M's: melanoma, microphthalmia-associated transcription factor and microRNA. Pigment Cell Melanoma Res 2012; 24:1088-106. [PMID: 22004179 DOI: 10.1111/j.1755-148x.2011.00931.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Studies examining intratumor heterogeneity have indicated that several cancer types, including melanoma, can display phenotypic plasticity, corresponding to their capacity to undergo transient reversible cellular changes. Conceptual models constructed to explain the process of cancer propagation differ in their treatment of intratumor heterogeneity. Recent observations of reversible phenotypic heterogeneity in melanoma have led to the proposal of a novel 'phenotypic plasticity' model of cancer propagation. Microphthalmia-associated transcription factor (MITF), the melanocyte 'lineage-specific' transcription factor, has emerged as one of the central players in melanoma phenotypic plasticity. Here we discuss the conceptual models suggested to explain the relations between MITF and melanoma plasticity, in addition to the complex regulatory roles that MITF plays in melanocytes and melanoma development. Finally, we provide an in-depth literature survey of microRNAs (miRNAs) involved in MITF activity, melanoma propagation and metastasis, in addition to their potential use as agents of personalized therapy.
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Affiliation(s)
- Rachel E Bell
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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98
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Koturbash I, Beland FA, Pogribny IP. Role of microRNAs in the regulation of drug metabolizing and transporting genes and the response to environmental toxicants. Expert Opin Drug Metab Toxicol 2012; 8:597-606. [PMID: 22435483 DOI: 10.1517/17425255.2012.673587] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION MicroRNAs (miRNAs) comprise a family of short non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. Rapidly growing evidence indicates that miRNAs play a key role in drug (xenobiotic) metabolism. AREAS COVERED This review summarizes the current knowledge of the role of miRNAs in the regulation of drug (xenobiotic) metabolizing genes and the cellular responses to exposure to exogenous toxicants. The literature search was performed using the PubMed database (up to March 2012). EXPERT OPINION miRNAs play a major role in control of the proper functioning of the cellular drug metabolizing system. Emerging evidence indicates that exposure to environmental and occupational toxicants and therapeutic drugs may alter the expression of miRNAs, including those that regulate the expression of drug metabolizing genes. This suggests that drug-induced (xenobiotic-induced) miRNA abnormalities may be one of the underlying mechanisms in the pathogenesis of exposure-related pathologies, and that miRNAs may be potential non-invasive biomarkers of exposure and indicators of the severity of tissue injury induced by toxicants. Also, the evaluation of the expression of miRNAs may be applied for the chemical and drug safety assessment. Additionally, differences in the expression of miRNAs that target drug metabolizing genes may be important determinants for inter-individual differences in sensitivity to toxicants and can serve as critical biomarkers for identifying subpopulations sensitive to exposure.
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Affiliation(s)
- Igor Koturbash
- National Center for Toxicological Research, Division of Biochemical Toxicology, Jefferson, AR 72079, USA.
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99
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Isakov O, Ronen R, Kovarsky J, Gabay A, Gan I, Modai S, Shomron N. Novel insight into the non-coding repertoire through deep sequencing analysis. Nucleic Acids Res 2012; 40:e86. [PMID: 22406831 PMCID: PMC3367215 DOI: 10.1093/nar/gks228] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Non-coding RNAs (ncRNA) account for a large portion of the transcribed genomic output. This diverse family of untranslated RNA molecules play a crucial role in cellular function. The use of ‘deep sequencing’ technology (also known as ‘next generation sequencing’) to infer transcript expression levels in general, and ncRNA specifically, is becoming increasingly common in molecular and clinical laboratories. We developed a software termed ‘RandA’ (which stands for ncRNA Read-and-Analyze) that performs comprehensive ncRNA profiling and differential expression analysis on deep sequencing generated data through a graphical user interface running on a local personal computer. Using RandA, we reveal the complexity of the ncRNA repertoire in a given cell population. We further demonstrate the relevance of such an extensive ncRNA analysis by elucidating a multitude of characterizing features in pathogen infected mammalian cells. RandA is available for download at http://ibis.tau.ac.il/RandA.
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Affiliation(s)
- Ofer Isakov
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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100
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Targeting microRNAs in neurons: tools and perspectives. Exp Neurol 2011; 235:419-26. [PMID: 22085592 DOI: 10.1016/j.expneurol.2011.10.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/25/2011] [Accepted: 10/30/2011] [Indexed: 12/21/2022]
Abstract
In the past few years, the understanding of microRNA (miRNA) biogenesis, the molecular mechanisms by which miRNAs regulate gene expression, and the functional roles of miRNAs has been expanded. Interestingly, numerous miRNAs are expressed in a spatially and temporally controlled manner in the nervous system, suggesting that their post-transcriptional regulation may be particularly relevant in neural development and function. miRNA studies in neurobiology have shown their involvement in synaptic plasticity and brain diseases. Approaches for manipulating miRNA levels in neuronal cells in vitro and in vivo are described here. Recent applications of miRNA antisense oligonucleotides, miRNA gene knockout and miRNA sponges in neuronal cells are reviewed. Finally, miRNA-based therapies for neurological pathologies related to alterations in miRNA functions are discussed.
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