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Ono K, Okamoto S, Ninomiya C, Toji N, Kanazawa T, Ishiguro-Oonuma T, Takahashi T, Iga K, Kizaki K. Analysis of circulating microRNA during early gestation in Japanese black cattle. Domest Anim Endocrinol 2022; 79:106706. [PMID: 34973621 DOI: 10.1016/j.domaniend.2021.106706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022]
Abstract
Circulating microRNAs (miRNAs) have been used as biomarkers for various diseases and physiological conditions in humans and mice; studies in domestic animals, particularly cattle, are limited. The importance of early pregnancy diagnosis (especially within the 21-d cow estrous cycle) in the livestock industry is extremely high. This study compared the circulating miRNAs in bred non-pregnant and pregnant Japanese Black cows, explored miRNAs as biomarkers for early pregnancy diagnosis, and established a measurement system that included selecting an appropriate reference miRNA and determining the effect of hemolysis on miRNA quantification in plasma. miRNA was extracted from the plasma of Japanese Black cows on day 21 after artificial insemination and subjected to a customized bovine oligonucleotide microarray for expression analysis. Differentially expressed miRNAs and reference miRNA candidates were selected and validated using reverse transcription-quantitative PCR (RT-qPCR). An appropriate endogenous reference miRNA for normalization was selected using NormFinder software. To evaluate the effect of hemolysis on miRNA quantification, hemolyzed samples were prepared using plasma from four cows in the estrous cycle and subjected to RT-qPCR. A total of 124 miRNAs were detected in bovine plasma by microarray analysis in bred non-pregnant and pregnant cows. The levels of five circulating miRNAs were significantly higher in pregnant cows than in bred non-pregnant cows, and 24 miRNAs were detected only in the pregnant group. NormFinder analysis and RT-qPCR validation showed that miR-2455 was an appropriate reference miRNA in the plasma of bred non-pregnant and pregnant Japanese Black cows, and miR-19b, miR-25, miR-29a, and miR-148a were significantly higher in the pregnant group. These four circulating miRNAs did not change during the estrous cycle and were less affected by hemolysis. In the current study, we found four miRNAs, miR-19b, miR-25, miR-29a, and miR-148a, which were present at high levels in the plasma of pregnant Japanese Black cows. Since these miRNAs are less affected by hemolysis, they may potentially be used as biomarkers for early pregnancy diagnosis in cattle.
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Affiliation(s)
- K Ono
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - S Okamoto
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - C Ninomiya
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - N Toji
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - T Kanazawa
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - T Ishiguro-Oonuma
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - T Takahashi
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - K Iga
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Iwate 020-0198, Japan
| | - K Kizaki
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.
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Paesano L, Marmiroli M, Bianchi MG, White JC, Bussolati O, Zappettini A, Villani M, Marmiroli N. Differences in toxicity, mitochondrial function and miRNome in human cells exposed in vitro to Cd as CdS quantum dots or ionic Cd. JOURNAL OF HAZARDOUS MATERIALS 2020; 393:122430. [PMID: 32155524 DOI: 10.1016/j.jhazmat.2020.122430] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
Cadmium is toxic to humans, although Cd-based quantum dots exerts less toxicity. Human hepatocellular carcinoma cells (HepG2) and macrophages (THP-1) were exposed to ionic Cd, Cd(II), and cadmium sulfide quantum dots (CdS QDs), and cell viability, cell integrity, Cd accumulation, mitochondrial function and miRNome profile were evaluated. Cell-type and Cd form-specific responses were found: CdS QDs affected cell viability more in HepG2 than in THP-1; respective IC20 values were ∼3 and ∼50 μg ml-1. In both cell types, Cd(II) exerted greater effects on viability. Mitochondrial membrane function in HepG2 cells was reduced 70 % with 40 μg ml-1 CdS QDs but was totally inhibited by Cd(II) at corresponding amounts. In THP-1 cells, CdS QDs has less effect on mitochondrial function; 50 μg ml-1 CdS QDs or equivalent Cd(II) caused 30 % reduction or total inhibition, respectively. The different in vitro effects of CdS QDs were unrelated to Cd uptake, which was greater in THP-1 cells. For both cell types, changes in the expression of miRNAs (miR-222, miR-181a, miR-142-3p, miR-15) were found with CdS QDs, which may be used as biomarkers of hazard nanomaterial exposure. The cell-specific miRNome profiles were indicative of a more conservative autophagic response in THP-1 and as apoptosis as in HepG2.
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Affiliation(s)
- Laura Paesano
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Marta Marmiroli
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Massimiliano G Bianchi
- University of Parma, Department of Medicine and Surgery, Laboratory of General Pathology, Via Volturno 39, 43125 Parma, Italy
| | - Jason C White
- Department of Analytical Chemistry, The Connecticut Agricultural Experiment Station (CAES), New Haven, CT 06504, United States
| | - Ovidio Bussolati
- University of Parma, Department of Medicine and Surgery, Laboratory of General Pathology, Via Volturno 39, 43125 Parma, Italy
| | - Andrea Zappettini
- Institute of Materials for Electronics and Magnetism (IMEM-CNR), Parco Area delle Scienze 37/A, 43124 Parma, Italy
| | - Marco Villani
- Institute of Materials for Electronics and Magnetism (IMEM-CNR), Parco Area delle Scienze 37/A, 43124 Parma, Italy
| | - Nelson Marmiroli
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 11/A, 43124 Parma, Italy; National Interuniversity Consortium for Environmental Sciences (CINSA), Parco Area delle Scienze 93/A, 43124 Parma, Italy.
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3
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Mazzelli M, Maj C, Mariani N, Mora C, Begni V, Pariante CM, Riva MA, Cattaneo A, Cattane N. The Long-Term Effects of Early Life Stress on the Modulation of miR-19 Levels. Front Psychiatry 2020; 11:389. [PMID: 32499725 PMCID: PMC7243913 DOI: 10.3389/fpsyt.2020.00389] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/17/2020] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs), one of the major small non-coding RNA classes, have been proposed as regulatory molecules in neurodevelopment and stress response. Although alterations in miRNAs profiles have been implicated in several psychiatric and neurodevelopmental disorders, the contribution of individual miRNAs in brain development and function is still unknown. Recent studies have identified miR-19 as a key regulator of brain trajectories, since it drives the differentiation of neural stem cells into mature neurons. However, no findings are available on how vulnerability factors for these disorders, such as early life stress (ELS), can modulate the expression of miR-19 and its target genes. To reach our aim, we investigated miR-19 modulation in human hippocampal progenitor stem cells (HPCs) treated with cortisol during 3 days of proliferation and harvested immediately after the end of the treatment or after 20 days of differentiation into mature neurons. We also analyzed the long-term expression changes of miR-19 and of its validated target genes, involved in neurodevelopment and inflammation, in the hippocampus of adult rats exposed or not to prenatal stress (PNS). Interestingly, we observed a significant downregulation of miR-19 levels both in proliferating (FC = −1.59, p-value = 0.022 for miR-19a; FC = −1.79, p-value = 0.016 for miR-19b) as well as differentiated HPCs (FC = −1.28, p-value = 0.065 for miR-19a; FC = −1.75, p-value = 0.047 for miR-19b) treated with cortisol. Similarly, we found a long-term decrease of miR-19 levels in the hippocampus of adult PNS rats (FC = −1.35, p-value = 0.025 for miR-19a; FC = −1.43, p-value = 0.032 for miR-19b). Among all the validated target genes, we observed a significant increase of NRCAM (FC = 1.20, p-value = 0.027), IL4R (FC = 1.26, p-value = 0.046), and RAPGEF2 (FC = 1.23, p-value = 0.020).We suggest that ELS can cause a long-term downregulation of miR-19 levels, which may be responsible of alterations in neurodevelopmental pathways and in immune/inflammatory processes, leading to an enhanced risk for mental disorders later in life. Intervention strategies targeting miR-19 may prevent alterations in these pathways, reducing the ELS-related effects.
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Affiliation(s)
- Monica Mazzelli
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University Hospital, Bonn, Germany
| | - Nicole Mariani
- Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Cristina Mora
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Veronica Begni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Carmine M Pariante
- Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Marco A Riva
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Annamaria Cattaneo
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Nadia Cattane
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
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Zhang H, Wang Y, He Z. Glycine-Histidine-Lysine (GHK) Alleviates Neuronal Apoptosis Due to Intracerebral Hemorrhage via the miR-339-5p/VEGFA Pathway. Front Neurosci 2018; 12:644. [PMID: 30294253 PMCID: PMC6158323 DOI: 10.3389/fnins.2018.00644] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 08/29/2018] [Indexed: 01/17/2023] Open
Abstract
Glycine-histidine-lysine (GHK) is a human tripeptide that enhances wound healing, exerts neuroprotective effects against neurodegenerative disease, and improves tissue regeneration. This study examined whether GHK can alleviate injury due to intracerebral hemorrhage (ICH). Briefly, adult Wistar rats in GHK pretreatment groups were injected with GHK (1 or 10 mg/kg, i.p.) every 24 h for 3 days. Water content and intact neurons were detected in the rats 3 days after ICH, and the neurological deficit scores were examined in the rats at 4, 24, 72, and 168 h after ICH. Apoptosis was evaluated via caspase-3 immunohistochemistry, Nissl staining, and TUNEL assay. We also examined the effect of GHK on the expression of related proteins in SH-SY5Y cells via Western blotting. The expression of miR-339-5p was examined via real-time polymerase chain reaction analyses. GHK improved neurological deficits, reduced water content in the brain and inhibited neuronal apoptosis in ICH rats. It also prevented the apoptosis of SH-SY5Y cells with hemin treatment. Furthermore, GHK downregulated miR-339-5p expression, and overexpression of miR-339-5p partially reversed the anti-apoptotic effects of GHK in SH-SY5Y cells. Our findings suggest that the p38 MAPK pathway is involved in the GHK-induced downregulation of miR-339-5p, and that the miR-339-5p/VEGFA axis plays a role in preventing neuronal apoptosis following ICH injury. These findings indicate that GHK may represent a novel therapeutic strategy for ICH.
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Affiliation(s)
- Heyu Zhang
- Department of Neurology, The First Affiliated Hospital of China Medical University, Liaoning, China
| | - Yanzhe Wang
- Department of Neurology, The First Affiliated Hospital of China Medical University, Liaoning, China
| | - Zhiyi He
- Department of Neurology, The First Affiliated Hospital of China Medical University, Liaoning, China
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5
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Impact of miRNA-mRNA Profiling and Their Correlation on Medulloblastoma Tumorigenesis. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:490-503. [PMID: 30195786 PMCID: PMC6070673 DOI: 10.1016/j.omtn.2018.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 02/06/2023]
Abstract
Medulloblastoma (MB) is a clinically challenging, childhood brain tumor with a diverse genetic makeup and differential miRNA profile. Aiming to identify deregulated miRNAs in MB, the miRNA expression profile of human MB samples was compared to that of normal cerebellar tissues. As a result, 8 upregulated and 64 downregulated miRNAs were identified in MB samples. Although various algorithms have been developed to predict the interaction between miRNA-mRNA pairs, the complexity and fidelity of miRNA-mRNA remain a concern. Therefore, to identify the signatures of miRNA-mRNA interactions essential for MB pathogenesis, miRNA profiling, RNA sequencing, and ingenuity pathway analysis (IPA) were performed in the same primary human MB samples. Further, when miR-217 was inhibited, a significant upregulation of predicted target genes SIRT1, ROBO1, FOXO3, and SMAD7 in HDMB03 cells was observed, confirming the validity of our approach. Functional analysis revealed that the inhibition of miR-217 in HDMB03 cells suppresses colony formation, migration, invasion, promoted apoptosis, and arrested cell population in S phase, indicating that manipulation of miR-217 may have a therapeutic potential for MB patients. Therefore, our study provides an essential platform for future investigations of specific miRNAs responsible for MB pathogenesis.
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Taylor SC, Laperriere G, Germain H. Droplet Digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data. Sci Rep 2017; 7:2409. [PMID: 28546538 PMCID: PMC5445070 DOI: 10.1038/s41598-017-02217-x] [Citation(s) in RCA: 322] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/07/2017] [Indexed: 01/23/2023] Open
Abstract
Quantitative PCR (qPCR) has become the gold standard technique to measure cDNA and gDNA levels but the resulting data can be highly variable, artifactual and non-reproducible without appropriate verification and validation of both samples and primers. The root cause of poor quality data is typically associated with inadequate dilution of residual protein and chemical contaminants that variably inhibit Taq polymerase and primer annealing. The most susceptible, frustrating and often most interesting samples are those containing low abundant targets with small expression differences of 2-fold or lower. Here, Droplet Digital PCR (ddPCR) and qPCR platforms were directly compared for gene expression analysis using low amounts of purified, synthetic DNA in well characterized samples under identical reaction conditions. We conclude that for sample/target combinations with low levels of nucleic acids (Cq ≥ 29) and/or variable amounts of chemical and protein contaminants, ddPCR technology will produce more precise, reproducible and statistically significant results required for publication quality data. A stepwise methodology is also described to choose between these complimentary technologies to obtain the best results for any experiment.
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Affiliation(s)
- Sean C Taylor
- Bio-Rad Laboratories, Inc., Hercules, CA, 94547, USA.
| | - Genevieve Laperriere
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC, G9A 5H7, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC, G9A 5H7, Canada
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7
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Anauate AC, Leal MF, Wisnieski F, Santos LC, Gigek CO, Chen ES, Geraldis JC, Calcagno DQ, Assumpção PP, Demachki S, Arasaki CH, Lourenço LG, Artigiani R, Burbano RR, Smith MAC. Identification of suitable reference genes for miRNA expression normalization in gastric cancer. Gene 2017; 621:59-68. [PMID: 28411081 DOI: 10.1016/j.gene.2017.04.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Ana Carolina Anauate
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mariana Ferreira Leal
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil; Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, Brazil; Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Fernanda Wisnieski
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Leonardo Caires Santos
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Carolina Oliveira Gigek
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil; Disciplina de Gastroenterologia Cirúrgica, Departamento de Cirurgia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Elizabeth Suchi Chen
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Jaqueline Cruz Geraldis
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Danielle Queiroz Calcagno
- Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Paulo Pimentel Assumpção
- Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Samia Demachki
- Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Carlos Haruo Arasaki
- Disciplina de Gastroenterologia Cirúrgica, Departamento de Cirurgia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Laércio Gomes Lourenço
- Disciplina de Gastroenterologia Cirúrgica, Departamento de Cirurgia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ricardo Artigiani
- Departamento de Patologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rommel Rodríguez Burbano
- Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil; Laboratório de Citogenética Humana, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil; Laboratório de Biologia Molecular, Hospital Ophir Loyola, Belém, Brazil
| | - Marília Arruda Cardoso Smith
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil.
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Staal JA, Pei Y, Rood BR. A Proteogenomic Approach to Understanding MYC Function in Metastatic Medulloblastoma Tumors. Int J Mol Sci 2016; 17:ijms17101744. [PMID: 27775567 PMCID: PMC5085772 DOI: 10.3390/ijms17101744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/23/2016] [Accepted: 10/10/2016] [Indexed: 12/31/2022] Open
Abstract
Brain tumors are the leading cause of cancer-related deaths in children, and medulloblastoma is the most prevalent malignant childhood/pediatric brain tumor. Providing effective treatment for these cancers, with minimal damage to the still-developing brain, remains one of the greatest challenges faced by clinicians. Understanding the diverse events driving tumor formation, maintenance, progression, and recurrence is necessary for identifying novel targeted therapeutics and improving survival of patients with this disease. Genomic copy number alteration data, together with clinical studies, identifies c-MYC amplification as an important risk factor associated with the most aggressive forms of medulloblastoma with marked metastatic potential. Yet despite this, very little is known regarding the impact of such genomic abnormalities upon the functional biology of the tumor cell. We discuss here how recent advances in quantitative proteomic techniques are now providing new insights into the functional biology of these aggressive tumors, as illustrated by the use of proteomics to bridge the gap between the genotype and phenotype in the case of c-MYC-amplified/associated medulloblastoma. These integrated proteogenomic approaches now provide a new platform for understanding cancer biology by providing a functional context to frame genomic abnormalities.
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Affiliation(s)
- Jerome A Staal
- Multiple Sclerosis Department, Florey Institute of Neuroscience and Mental Health, Melbourne, VIC 3052, Australia.
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC 20010, USA.
| | - Yanxin Pei
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC 20010, USA.
| | - Brian R Rood
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC 20010, USA.
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9
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Bockmeyer CL, Säuberlich K, Wittig J, Eßer M, Roeder SS, Vester U, Hoyer PF, Agustian PA, Zeuschner P, Amann K, Daniel C, Becker JU. Comparison of different normalization strategies for the analysis of glomerular microRNAs in IgA nephropathy. Sci Rep 2016; 6:31992. [PMID: 27553688 PMCID: PMC4995590 DOI: 10.1038/srep31992] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/01/2016] [Indexed: 01/10/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) have been used for normalization in glomerular microRNA (miRNA) quantification without confirmation of validity. Our aim was to identify glomerular reference miRNAs in IgA nephropathy. We compared miRNAs in human paraffin-embedded renal biopsies from patients with cellular-crescentic IgA-GN (n = 5; crescentic IgA-GN) and non-crescentic IgA-GN (n = 5; IgA-GN) to mild interstitial nephritis without glomerular abnormalities (controls, n = 5). Laser-microdissected glomeruli were used for expression profiling of 762 miRNAs by low-density TaqMan arrays (cards A and B). The comparison of different normalization methods (GeNormPlus, NormFinder, global mean and snoRNAs) in crescentic IgA-GN, IgA-GN and controls yielded similar results. However, levels of significance and the range of relative expression differed. In median, two normalization methods demonstrated similar results. GeNormPlus and NormFinder gave different top ranked reference miRNAs. Stability ranking for snoRNAs varied between cards A and B. In conclusion, we suggest the geometric mean of the most stable reference miRNAs found in GeNormPlus (miR-26b-5p), NormFinder (miR-28-5p) and snoRNAs (RNU44) as reference. It should be considered that significant differences could be missed using one particular normalization method. As a starting point for glomerular miRNA studies in IgA nephropathy we provide a library of miRNAs.
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Affiliation(s)
- Clemens L Bockmeyer
- Department of Nephropathology, Friedrich Alexander University (FAU) Erlangen-Nuremberg, Erlangen, Germany.,Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Karen Säuberlich
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Juliane Wittig
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Marc Eßer
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Sebastian S Roeder
- Department of Nephropathology, Friedrich Alexander University (FAU) Erlangen-Nuremberg, Erlangen, Germany
| | - Udo Vester
- Children's Hospital, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Peter F Hoyer
- Children's Hospital, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Putri A Agustian
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Philip Zeuschner
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Kerstin Amann
- Department of Nephropathology, Friedrich Alexander University (FAU) Erlangen-Nuremberg, Erlangen, Germany
| | - Christoph Daniel
- Department of Nephropathology, Friedrich Alexander University (FAU) Erlangen-Nuremberg, Erlangen, Germany
| | - Jan U Becker
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
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10
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Juzėnas S, Saltenienė V, Kupcinskas J, Link A, Kiudelis G, Jonaitis L, Jarmalaite S, Kupcinskas L, Malfertheiner P, Skieceviciene J. Analysis of Deregulated microRNAs and Their Target Genes in Gastric Cancer. PLoS One 2015; 10:e0132327. [PMID: 26172537 PMCID: PMC4501563 DOI: 10.1371/journal.pone.0132327] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/13/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are widely studied non-coding RNAs that modulate gene expression. MiRNAs are deregulated in different tumors including gastric cancer (GC) and have potential diagnostic and prognostic implications. The aim of our study was to determine miRNA profile in GC tissues, followed by evaluation of deregulated miRNAs in plasma of GC patients. Using available databases and bioinformatics methods we also aimed to evaluate potential target genes of confirmed differentially expressed miRNA and validate these findings in GC tissues. METHODS The study included 51 GC patients and 51 controls. Initially, we screened miRNA expression profile in 13 tissue samples of GC and 12 normal gastric tissues with TaqMan low density array (TLDA). In the second stage, differentially expressed miRNAs were validated in a replication cohort using qRT-PCR in tissue and plasma samples. Subsequently, we analyzed potential target genes of deregulated miRNAs using bioinformatics approach, determined their expression in GC tissues and performed correlation analysis with targeting miRNAs. RESULTS Profiling with TLDA revealed 15 deregulated miRNAs in GC tissues compared to normal gastric mucosa. Replication analysis confirmed that miR-148a-3p, miR-204-5p, miR-223-3p and miR-375 were consistently deregulated in GC tissues. Analysis of GC patients' plasma samples showed significant down-regulation of miR-148a-3p, miR-375 and up-regulation of miR-223-3p compared to healthy subjects. Further, using bioinformatic tools we identified targets of replicated miRNAs and performed disease-associated gene enrichment analysis. Ultimately, we evaluated potential target gene BCL2 and DNMT3B expression by qRT-PCR in GC tissue, which correlated with targeting miRNA expression. CONCLUSIONS Our study revealed miRNA profile in GC tissues and showed that miR-148a-3p, miR-223-3p and miR-375 are deregulated in GC plasma samples, but these circulating miRNAs showed relatively weak diagnostic performance as sole biomarkers. Target gene analysis demonstrated that BCL2 and DNMT3B expression in GC tissue correlated with their targeting miRNA expression.
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Affiliation(s)
- Simonas Juzėnas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Violeta Saltenienė
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto von Guericke University, Magdeburg, Germany
| | - Gediminas Kiudelis
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Laimas Jonaitis
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Sonata Jarmalaite
- Division of Human Genome Research Centre, Faculty of Natural Sciences, Vilnius University, Vilnius, Lithuania
| | - Limas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto von Guericke University, Magdeburg, Germany
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
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Stability Assessment of Candidate Reference Genes in Urine Sediment of Prostate Cancer Patients for miRNA Applications. DISEASE MARKERS 2015; 2015:973597. [PMID: 26078486 PMCID: PMC4452852 DOI: 10.1155/2015/973597] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/30/2015] [Indexed: 12/19/2022]
Abstract
We aimed at assessing the stability of candidate reference genes in urine sediments of men subjected to digital rectal examination for suspected prostate cancer (PCa). Two microRNAs (miR-191 and miR-25) and 1 small nucleolar RNA (SNORD48) were assayed in 35 post-DRE urine sediments of men with PCa and in 26 subjects with histologically confirmed benign prostatic hyperplasia (BPH). The stability of candidate reference genes was assessed through BestKeeper algorithm and equivalence test. miR-200b and miR-452 were used to test for the effect of normalization on target genes. Our results proved miR-191 to be the most stable gene, showing the lowest degree of variation and the highest stability value. miR-25 and SNORD48 values fell beyond the cutoff of acceptability. In conclusion, we recommend the use of miR-191 for normalization purposes in post-DRE urine sediments.
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Johansen I, Andreassen R. Validation of miRNA genes suitable as reference genes in qPCR analyses of miRNA gene expression in Atlantic salmon (Salmo salar). BMC Res Notes 2014; 8:945. [PMID: 25533334 PMCID: PMC4308020 DOI: 10.1186/1756-0500-7-945] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) are an abundant class of endogenous small RNA molecules that downregulate gene expression at the post-transcriptional level. They play important roles by regulating genes that control multiple biological processes, and recent years there has been an increased interest in studying miRNA genes and miRNA gene expression. The most common method applied to study gene expression of single genes is quantitative PCR (qPCR). However, before expression of mature miRNAs can be studied robust qPCR methods (miRNA-qPCR) must be developed. This includes identification and validation of suitable reference genes. We are particularly interested in Atlantic salmon (Salmo salar). This is an economically important aquaculture species, but no reference genes dedicated for use in miRNA-qPCR methods has been validated for this species. Our aim was, therefore, to identify suitable reference genes for miRNA-qPCR methods in Salmo salar. Results We used a systematic approach where we utilized similar studies in other species, some biological criteria, results from deep sequencing of small RNAs and, finally, experimental validation of candidate reference genes by qPCR to identify the most suitable reference genes. Ssa-miR-25-3p was identified as most suitable single reference gene. The best combinations of two reference genes were ssa-miR-25-3p and ssa-miR-455-5p. These two genes were constitutively and stably expressed across many different tissues. Furthermore, infectious salmon anaemia did not seem to affect their expression levels. These genes were amplified with high specificity, good efficiency and the qPCR assays showed a good linearity when applying a simple cybergreen miRNA-PCR method using miRNA gene specific forward primers. Conclusions We have identified suitable reference genes for miRNA-qPCR in Atlantic salmon. These results will greatly facilitate further studies on miRNA genes in this species. The reference genes identified are conserved genes that are identical in their mature sequence in many aquaculture species. Therefore, they may also be suitable as reference genes in other teleosts. Finally, the systematic approach used in our study successfully identified suitable reference genes, suggesting that this may be a useful strategy to apply in similar validation studies in other aquaculture species. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-945) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Rune Andreassen
- Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway.
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13
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Vallelunga A, Ragusa M, Di Mauro S, Iannitti T, Pilleri M, Biundo R, Weis L, Di Pietro C, De Iuliis A, Nicoletti A, Zappia M, Purrello M, Antonini A. Identification of circulating microRNAs for the differential diagnosis of Parkinson's disease and Multiple System Atrophy. Front Cell Neurosci 2014; 8:156. [PMID: 24959119 PMCID: PMC4051126 DOI: 10.3389/fncel.2014.00156] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 05/19/2014] [Indexed: 11/13/2022] Open
Abstract
Background: Parkinson's disease (PD) is a progressive neurodegenerative disorder which may be misdiagnosed with atypical conditions such as Multiple System Atrophy (MSA), due to overlapping clinical features. MicroRNAs (miRNAs) are small non-coding RNAs with a key role in post-transcriptional gene regulation. We hypothesized that identification of a distinct set of circulating miRNAs (cmiRNAs) could distinguish patients affected by PD from MSA and healthy individuals. Results. Using TaqMan Low Density Array technology, we analyzed 754 miRNAs and found 9 cmiRNAs differentially expressed in PD and MSA patients compared to healthy controls. We also validated a set of 4 differentially expressed cmiRNAs in PD and MSA patients vs. controls. More specifically, miR-339-5p was downregulated, whereas miR-223*, miR-324-3p, and mir-24 were upregulated in both diseases. We found cmiRNAs specifically deregulated in PD (downregulation of miR-30c and miR-148b) and in MSA (upregulation of miR-148b). Finally, comparing MSA and PD, we identified 3 upregulated cmiRNAs in MSA serum (miR-24, miR-34b, miR-148b). Conclusions. Our results suggest that cmiRNA signatures discriminate PD from MSA patients and healthy controls and may be considered specific, non-invasive biomarkers for differential diagnosis.
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Affiliation(s)
- Annamaria Vallelunga
- Molecular Neurobiology Laboratory, Department for Parkinson's Disease, IRCCS Hospital San Camillo Venice, Italy
| | - Marco Ragusa
- Unit of Molecular, Genome and Complex Systems BioMedicine, Department Gian Filippo Ingrassia, University of Catania Catania, Italy
| | - Stefania Di Mauro
- Unit of Molecular, Genome and Complex Systems BioMedicine, Department Gian Filippo Ingrassia, University of Catania Catania, Italy
| | | | - Manuela Pilleri
- Molecular Neurobiology Laboratory, Department for Parkinson's Disease, IRCCS Hospital San Camillo Venice, Italy
| | - Roberta Biundo
- Molecular Neurobiology Laboratory, Department for Parkinson's Disease, IRCCS Hospital San Camillo Venice, Italy
| | - Luca Weis
- Molecular Neurobiology Laboratory, Department for Parkinson's Disease, IRCCS Hospital San Camillo Venice, Italy
| | - Cinzia Di Pietro
- Unit of Molecular, Genome and Complex Systems BioMedicine, Department Gian Filippo Ingrassia, University of Catania Catania, Italy
| | | | - Alessandra Nicoletti
- Section of Neuroscience University of Catania, Department GF Ingrassia, University of Catania Catania, Italy
| | - Mario Zappia
- Section of Neuroscience University of Catania, Department GF Ingrassia, University of Catania Catania, Italy
| | - Michele Purrello
- Unit of Molecular, Genome and Complex Systems BioMedicine, Department Gian Filippo Ingrassia, University of Catania Catania, Italy
| | - Angelo Antonini
- Molecular Neurobiology Laboratory, Department for Parkinson's Disease, IRCCS Hospital San Camillo Venice, Italy
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McDermott AM, Kerin MJ, Miller N. Identification and validation of miRNAs as endogenous controls for RQ-PCR in blood specimens for breast cancer studies. PLoS One 2013; 8:e83718. [PMID: 24391813 PMCID: PMC3877087 DOI: 10.1371/journal.pone.0083718] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 11/06/2013] [Indexed: 12/21/2022] Open
Abstract
Introduction A prerequisite to accurate interpretation of RQ-PCR data is robust data normalization. A commonly used method is to compare the cycle threshold (CT) of target miRNAs with those of a stably expressed endogenous (EC) miRNA(s) from the same sample. Despite the large number of studies reporting miRNA expression patterns, comparatively few appropriate ECs have been reported thus far. The purpose of this study was to identify stably expressed miRNAs with which to normalize RQ-PCR data derived from human blood specimens. Methods MiRNA profiling of approximately 380 miRNAs was performed on RNA derived from blood specimens from 10 women with breast cancer and 10 matched controls. Analysis of mean expression values across the dataset (GME) identified stably expressed candidates. Additional candidates were selected from the literature and analyzed by the geNorm algorithm. Further validation of three candidate ECs by RQ-PCR was performed in a larger cohort (n = 40 cancer, n = 20 control) was performed, including analysis by geNorm and NormFinder algorithms. Results Microarray screening identified 10 candidate ECs with expression patterns closest to the global mean. Geometric averaging of candidate ECs from the literature using geNorm identified miR-425 as the most stably expressed miRNA. MiR-425 and miR-16 were the best combination, achieving the lowest V-value of 0.185. Further validation by RQ-PCR confirmed that miR-16 and miR-425 were the most stably expressed ECs overall. Their combined use to normalize expression data enabled the detection of altered target miRNA expression that reliably differentiated between cancers and controls in human blood specimens. Conclusion This study identified that the combined use of 2 miRNAs, (miR-16 and miR-425) to normalize RQ-PCR data generated more reliable results than using either miRNA alone, or use of U6. Further investigation into suitable ECs for use in miRNA RQ-PCR studies is warranted.
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Affiliation(s)
- Ailbhe M. McDermott
- Discipline of Surgery, School of Medicine, National University of Ireland, Galway, Ireland
- * E-mail:
| | - Michael J. Kerin
- Discipline of Surgery, School of Medicine, National University of Ireland, Galway, Ireland
| | - Nicola Miller
- Discipline of Surgery, School of Medicine, National University of Ireland, Galway, Ireland
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15
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Zheng G, Wang H, Zhang X, Yang Y, Wang L, Du L, Li W, Li J, Qu A, Liu Y, Wang C. Identification and validation of reference genes for qPCR detection of serum microRNAs in colorectal adenocarcinoma patients. PLoS One 2013; 8:e83025. [PMID: 24349425 PMCID: PMC3859607 DOI: 10.1371/journal.pone.0083025] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/06/2013] [Indexed: 12/14/2022] Open
Abstract
Serum microRNAs (miRNAs) have become a highlighted research hotspot, especially for their great potential as a novel promising non-invasive biomarker in cancer diagnosis. The most frequently used approach for serum miRNAs detection is quantitative real time polymerase chain reaction (qPCR). In order to obtain reliable qPCR data of miRNAs expression, the use of reference genes as endogenous control is undoubtly necessary. However, no systematic evaluation and validation of reference genes for normalizing qPCR analysis of serum miRNAs has been reported in colorectal adenocarcinoma. We firstly profiled pooled serum of colorectal adenocarcinoma, colorectal adenoma and healthy controls and selected a list of 13 miRNAs as candidate reference genes. U6 snRNA (U6) and above-mentioned 13 miRNAs were included in further confirmation by qPCR. As a result, 5 miRNAs (miR-151a-3p, miR-4446-3p, miR-221-3p, miR-93-5p and miR-3184-3p) were not detected in all samples and 2 miRNAs (miR-197-3p and miR-26a-5p) were relatively low with median Cq more than 35, and were excluded from further stability analysis. Then variable stability of other 6 miRNAs (miR-103b, miR-484, miR-16-5p, miR-3615, miR-18a-3p and miR-191-5p) and U6 were evaluated using two algorithms: geNorm and NormFinder which both identified miR-191-5p as the most stably expressed reference gene and selected miR-191-5p and U6 as the most stable pair of reference genes. After validating in an independent large cohorts and selecting miR-92a-3p as target miRNA to evaluate the effect of reference gene, we propose that combination of miR-191-5p and U6 could be used as reference genes for serum microRNAs qPCR data in colorectal adenocarcinoma, colorectal adenoma and healthy controls.
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Affiliation(s)
- Guixi Zheng
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Haiyan Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Yongmei Yang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Lili Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Lutao Du
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Wei Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Juan Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Ailin Qu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Yimin Liu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong Province, China
- * E-mail:
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Crottini A, Bollen A, Weldon C, Dalton DL, Kotzé A, Noël J, Iambana B, Andreone F. Amphibian survey and current absence of Batrachochytrium dendrobatidis (Bd) in Ivoloina Park, Toamasina (eastern Madagascar). AFR J HERPETOL 2013. [DOI: 10.1080/21564574.2013.833994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Angelica Crottini
- CIBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal
| | | | - Ché Weldon
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Desiré L. Dalton
- National Zoological Gardens of South Africa, Pretoria, South Africa
- Genetics Department, University of the Free State, Bloemfontein, South Africa
| | - Antoinette Kotzé
- National Zoological Gardens of South Africa, Pretoria, South Africa
- Genetics Department, University of the Free State, Bloemfontein, South Africa
| | - Jean Noël
- Madagascar Fauna Group, Toamasina, Madagascar
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Qiao G, Li Q, Peng G, Ma J, Fan H, Li Y. Similarity on neural stem cells and brain tumor stem cells in transgenic brain tumor mouse models. Neural Regen Res 2013; 8:2360-9. [PMID: 25206546 PMCID: PMC4146040 DOI: 10.3969/j.issn.1673-5374.2013.25.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 08/25/2013] [Indexed: 11/29/2022] Open
Abstract
Although it is believed that glioma is derived from brain tumor stem cells, the source and molecular signal pathways of these cells are still unclear. In this study, we used stable doxycycline-inducible transgenic mouse brain tumor models (c-myc+/SV40Tag+/Tet-on+) to explore the malignant trans-formation potential of neural stem cells by observing the differences of neural stem cells and brain tumor stem cells in the tumor models. Results showed that chromosome instability occurred in brain tumor stem cells. The numbers of cytolysosomes and autophagosomes in brain tumor stem cells and induced neural stem cells were lower and the proliferative activity was obviously stronger than that in normal neural stem cells. Normal neural stem cells could differentiate into glial fibrillary acidic protein-positive and microtubule associated protein-2-positive cells, which were also negative for nestin. However, glial fibrillary acidic protein/nestin, microtubule associated protein-2/nestin, and glial fibrillary acidic protein/microtubule associated protein-2 double-positive cells were found in induced neural stem cells and brain tumor stem cells. Results indicate that induced neural stem cells are similar to brain tumor stem cells, and are possibly the source of brain tumor stem cells.
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Affiliation(s)
- Guanqun Qiao
- Department of Neurosurgery, the Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Qingquan Li
- Department of Neurosurgery, the Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Gang Peng
- Department of Neurosurgery, the Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Jun Ma
- Department of Neurosurgery, the Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Hongwei Fan
- Department of Pharmacology, the Third Affiliated Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
| | - Yingbin Li
- Department of Neurosurgery, the Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, Jiangsu Province, China
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18
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miR-218 is downregulated and directly targets SH3GL1 in childhood medulloblastoma. Mol Med Rep 2013; 8:1111-7. [DOI: 10.3892/mmr.2013.1639] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/08/2013] [Indexed: 11/05/2022] Open
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Li B, Matter EK, Hoppert HT, Grayson BE, Seeley RJ, Sandoval DA. Identification of optimal reference genes for RT-qPCR in the rat hypothalamus and intestine for the study of obesity. Int J Obes (Lond) 2013; 38:192-7. [PMID: 23736358 DOI: 10.1038/ijo.2013.86] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 03/28/2013] [Accepted: 04/28/2013] [Indexed: 02/02/2023]
Abstract
BACKGROUND Obesity has a complicated metabolic pathology, and defining the underlying mechanisms of obesity requires integrative studies with molecular end points. Real-time quantitative PCR (RT-qPCR) is a powerful tool that has been widely utilized. However, the importance of using carefully validated reference genes in RT-qPCR seems to have been overlooked in obesity-related research. The objective of this study was to select a set of reference genes with stable expressions to be used for RT-qPCR normalization in rats under fasted vs re-fed and chow vs high-fat diet (HFD) conditions. DESIGN Male long-Evans rats were treated under four conditions: chow/fasted, chow/re-fed, HFD/fasted and HFD/re-fed. Expression stabilities of 13 candidate reference genes were evaluated in the rat hypothalamus, duodenum, jejunum and ileum using the ReFinder software program. The optimal number of reference genes needed for RT-qPCR analyses was determined using geNorm. RESULTS Using geNorm analysis, we found that it was sufficient to use the two most stably expressed genes as references in RT-qPCR analyses for each tissue under specific experimental conditions. B2M and RPLP0 in the hypothalamus, RPS18 and HMBS in the duodenum, RPLP2 and RPLP0 in the jejunum and RPS18 and YWHAZ in the ileum were the most suitable pairs for a normalization study when the four aforementioned experimental conditions were considered. CONCLUSIONS Our study demonstrates that gene expression levels of reference genes commonly used in obesity-related studies, such as ACTB or RPS18, are altered by changes in acute or chronic energy status. These findings underline the importance of using reference genes that are stable in expression across experimental conditions when studying the rat hypothalamus and intestine, because these tissues have an integral role in the regulation of energy homeostasis. It is our hope that this study will raise awareness among obesity researchers on the essential need for reference gene validation in gene expression studies.
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Affiliation(s)
- B Li
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - E K Matter
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - H T Hoppert
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - B E Grayson
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - R J Seeley
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - D A Sandoval
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
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WANG LISHUI, LIU YIMIN, DU LUTAO, LI JUAN, JIANG XIUMEI, ZHENG GUIXI, QU AILIN, WANG HAIYAN, WANG LILI, ZHANG XIN, LIU HUI, PAN HONGWEI, YANG YONGMEI, WANG CHUANXIN. Identification and validation of reference genes for the detection of serum microRNAs by reverse transcription-quantitative polymerase chain reaction in patients with bladder cancer. Mol Med Rep 2012; 12:615-22. [DOI: 10.3892/mmr.2015.3428] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 01/22/2015] [Indexed: 11/06/2022] Open
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