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Unkovič A, Boštjančič E, Belič A, Perše M. Selection and Evaluation of mRNA and miRNA Reference Genes for Expression Studies (qPCR) in Archived Formalin-Fixed and Paraffin-Embedded (FFPE) Colon Samples of DSS-Induced Colitis Mouse Model. BIOLOGY 2023; 12:biology12020190. [PMID: 36829468 PMCID: PMC9952917 DOI: 10.3390/biology12020190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023]
Abstract
The choice of appropriate reference genes is essential for correctly interpreting qPCR data and results. However, the majority of animal studies use a single reference gene without any prior evaluation. Therefore, many qPCR results from rodent studies can be misleading, affecting not only reproducibility but also translatability. In this study, the expression stability of reference genes for mRNA and miRNA in archived FFPE samples of 117 C57BL/6JOlaHsd mice (males and females) from 9 colitis experiments (dextran sulfate sodium; DSS) were evaluated and their expression analysis was performed. In addition, we investigated whether normalization reduced/neutralized the influence of inter/intra-experimental factors which we systematically included in the study. Two statistical algorithms (NormFinder and Bestkeeper) were used to determine the stability of reference genes. Multivariate analysis was made to evaluate the influence of normalization with different reference genes on target gene expression in regard to inter/intra-experimental factors. Results show that archived FFPE samples are a reliable source of RNA and imply that the FFPE procedure does not change the ranking of stability of reference genes obtained in fresh tissues. Multivariate analysis showed that the histological picture is an important factor affecting the expression levels of target genes.
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Affiliation(s)
- Ana Unkovič
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Emanuela Boštjančič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleš Belič
- Statistics and Modelling, Technical Development Biologics, Novartis Technical Research & Development, Lek Pharmaceuticals d.d., 1000 Ljubljana, Slovenia
| | - Martina Perše
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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2
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Analysis of miR-143, miR-1, miR-210 and let-7e Expression in Colorectal Cancer in Relation to Histopathological Features. Genes (Basel) 2022; 13:genes13050875. [PMID: 35627259 PMCID: PMC9141994 DOI: 10.3390/genes13050875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/18/2022] Open
Abstract
Background: MicroRNAs (miRNAs) are small RNA molecules involved in the control of the expression of many genes and are responsible for, among other things, cell death, differentiation and the control of their division. Changes in miRNA expression profiles have been observed in colorectal cancer. This discovery significantly enriches our knowledge of the pathogenesis of colorectal cancer and offers new goals in diagnostics and therapy. Aim: The aim of this study was to analyze the expression of four miRNA sequences—miR-143, miR-1, miR-210 and let-7e—and to investigate their significance in the risk of developing colorectal cancer. Materials and methods: miRNA sequences were investigated in formalin-fixed, paraffin-embedded (FFPE) tissue in colorectal cancer patients (n = 150) and in cancer-free controls (n = 150). The real-time PCR method was used. Results: This study revealed a lower expression of miR-143 in colorectal cancer patients than in the controls. miR-143 was positively correlated with the degree of tumor differentiation (grading). Three out of four analyzed miRNA (miR-1, miR-210 and let-7e) were found to be statistically insignificant in terms of colorectal carcinoma risk. Conclusions: miR-143 may be associated with the development of colorectal cancer.
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3
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Sun Y, Cui B, Ye L, Hu Y, Pan Y. Pramipexole Inhibits Neuronal Apoptosis in Rats with Parkinson's Disease. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:7002630. [PMID: 35463692 PMCID: PMC9020956 DOI: 10.1155/2022/7002630] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/12/2022] [Accepted: 03/17/2022] [Indexed: 11/23/2022]
Abstract
To explore the inhibition of pramipexole on the neuronal apoptosis and its influences on the expressions of brain tissue brain-derived neurotrophic factor (BDNF), and serum miR-103a and miR-30b and inflammatory factors in rats with Parkinson's disease. A total of 36 Sprague-Dawley rats were randomly divided into normal group (n = 12), model group (n = 12) and pramipexole group (n = 12). Compared with that in normal group, the positive expression of BDNF was substantially increased in model group and pramipexole group, and its positive expression in pramipexole group was notably higher than that in model group. The WB results revealed that compared with those in normal group, the relative protein expression levels of Bax and Bcl-2 were markedly increased and decreased, respectively, in the other two groups, and that pramipexole group exhibited a remarkable decline in the relative protein expression level of Bax and a considerable increase in that of Bcl-2, compared with model group. The relative expression levels of miR-103a and miR-30b in model and pramipexole groups were markedly higher than those in normal group, and pramipexole group had remarkably higher relative expression levels of miR-103a and miR-30b than model group. It was found through ELISA that model and pramipexole groups had markedly raised IL-1β and IL-18 content compared with normal group, and their content in pramipexole group was remarkably lower than that in model group. Based on the TUNEL results, compared with that in normal group, the apoptosis rate of cells rose substantially in the other two groups, and the apoptosis rate in pramipexole group was notably lower than that in model group. Pramipexole may up-regulate the expressions of BDNF, miR-103a and miR-30b to inhibit the apoptosis and inflammation in Parkinson's disease model rats.
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Affiliation(s)
- Yongqi Sun
- Department of Neurology, Guangdong 999 Brain Hospital, Guangzhou, China
| | - Baohong Cui
- Laboratory Medicine, The Third Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lin Ye
- Department of Rehabilitation, Xuanwu Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yunxin Hu
- Department of Neurology, Guangdong 999 Brain Hospital, Guangzhou, China
| | - Yujun Pan
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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Schofield AL, Brown JP, Brown J, Wilczynska A, Bell C, Glaab WE, Hackl M, Howell L, Lee S, Dear JW, Remes M, Reeves P, Zhang E, Allmer J, Norris A, Falciani F, Takeshita LY, Seyed Forootan S, Sutton R, Park BK, Goldring C. Systems analysis of miRNA biomarkers to inform drug safety. Arch Toxicol 2021; 95:3475-3495. [PMID: 34510227 PMCID: PMC8492583 DOI: 10.1007/s00204-021-03150-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
microRNAs (miRNAs or miRs) are short non-coding RNA molecules which have been shown to be dysregulated and released into the extracellular milieu as a result of many drug and non-drug-induced pathologies in different organ systems. Consequently, circulating miRs have been proposed as useful biomarkers of many disease states, including drug-induced tissue injury. miRs have shown potential to support or even replace the existing traditional biomarkers of drug-induced toxicity in terms of sensitivity and specificity, and there is some evidence for their improved diagnostic and prognostic value. However, several pre-analytical and analytical challenges, mainly associated with assay standardization, require solutions before circulating miRs can be successfully translated into the clinic. This review will consider the value and potential for the use of circulating miRs in drug-safety assessment and describe a systems approach to the analysis of the miRNAome in the discovery setting, as well as highlighting standardization issues that at this stage prevent their clinical use as biomarkers. Highlighting these challenges will hopefully drive future research into finding appropriate solutions, and eventually circulating miRs may be translated to the clinic where their undoubted biomarker potential can be used to benefit patients in rapid, easy to use, point-of-care test systems.
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Affiliation(s)
- Amy L Schofield
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Joseph P Brown
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Jack Brown
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Ania Wilczynska
- bit.bio, Babraham Research Campus, The Dorothy Hodgkin Building, Cambridge, CB22 3FH, UK
| | - Catherine Bell
- CVRM Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Warren E Glaab
- Merck & Co., Inc, 770 Sumneytown Pike, West Point, PA, 19486, USA
| | | | - Lawrence Howell
- GlaxoSmithKline (GSK), Stevenage, Greater Cambridge Area, UK
| | - Stephen Lee
- ABHI, 1 Duchess St, 4th Floor, Suite 2, London, W1W 6AN, UK
| | - James W Dear
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mika Remes
- Genomics EMEA, QIAGEN Aarhus, Prismet, Silkeborgvej 2, 8000, Aarhus C, Denmark
| | - Paul Reeves
- Arcis Biotechnology Limited, Suite S07, Techspace One, Sci-tech Daresbury, Keckwick Lane, Daresbury, Warrington, WA4 4AB, UK
| | - Eunice Zhang
- Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK
| | - Jens Allmer
- Applied Bioinformatics, Bioscience, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB, Wageningen, The Netherlands
| | - Alan Norris
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Francesco Falciani
- Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Louise Y Takeshita
- Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Shiva Seyed Forootan
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Robert Sutton
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - B Kevin Park
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Chris Goldring
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK.
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Ferneza S, Fetsych M, Shuliak R, Makukh H, Volodko N, Yarema R, Fetsych T. Clinical significance of microRNA-200 and let-7 families expression assessment in patients with ovarian cancer. Ecancermedicalscience 2021; 15:1249. [PMID: 34267805 PMCID: PMC8241451 DOI: 10.3332/ecancer.2021.1249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Indexed: 11/30/2022] Open
Abstract
Ovarian cancer (OC) represents the most lethal malignancy in gynaecologic oncology practice and shows a high recurrence rate due to its early chemoresistance to first-line chemotherapy. Yet, timely selection of the correct treatment strategy is likely to prolong a patient's survival. MicroRNAs (miRNAs) are a class of short non-coding RNAs responsible for the expression of 30%-60% of human genes. In numerous studies, miRNAs have been used to provide the overall prognosis for patients and analyse the process's prevalence and responses to chemotherapy. In particular, miRNAs as markers for predicting the sensitivity of OC to platinum- and taxane-based chemotherapeutics can significantly improve the treatment efficacy. This article highlights two families of miRNAs: miR-200 and let-7, which are promising for further research on OC and its chemosensitivity.
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Affiliation(s)
- Severyn Ferneza
- Department of Oncology and Radiology FPGE, Danylo Halytsky Lviv National Medical University, Hasheka 2A str., Lviv 79000, Ukraine
| | - Markiyan Fetsych
- Department of Oncology and Radiology FPGE, Danylo Halytsky Lviv National Medical University, Hasheka 2A str., Lviv 79000, Ukraine
| | - Roman Shuliak
- Department of Microinvasive Surgery, Lviv State Regional Oncology Treatment and Diagnostic Center, Hasheka 2A str., Lviv 79000, Ukraine
| | - Halyna Makukh
- Institute of Hereditary Pathology, National Academy of Medical Sciences of Ukraine, Lviv 79000, Ukraine
| | - Natalia Volodko
- Department of Oncology and Radiology FPGE, Danylo Halytsky Lviv National Medical University, Hasheka 2A str., Lviv 79000, Ukraine
| | - Roman Yarema
- Department of Oncology and Radiology FPGE, Danylo Halytsky Lviv National Medical University, Hasheka 2A str., Lviv 79000, Ukraine
| | - Taras Fetsych
- Department of Oncology and Radiology FPGE, Danylo Halytsky Lviv National Medical University, Hasheka 2A str., Lviv 79000, Ukraine
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miRNA as promising theragnostic biomarkers for predicting radioresistance in cancer: A systematic review and meta-analysis. Crit Rev Oncol Hematol 2020; 157:103183. [PMID: 33310279 DOI: 10.1016/j.critrevonc.2020.103183] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 02/08/2023] Open
Abstract
Radioresistance remains as an obstacle in cancer treatment. This systematic review and meta-analysis aimed to evaluate the association between the expression of miRNAs and responses to radiotherapy and the prognosis of different tumors. In total, 77 miRNAs in 19 cancer types were studied, in which 24 miRNAs were upregulated and 58 miRNAs were downregulated in cancer patients. Five miRNAs were differentially expressed. Moreover, 75 miRNAs were found to be related to radioresistance, while 5 were observed to be related to radiosensitivity. The pooled HR and 95 % confidence interval for the combined studies was 1.135 (0.819-1.574; P-value = 0.4). The HR values of the subgroup analysis for miR-21 (HR = 2.344; 95 % CI: 1.927-2.850; P-value = 0.000), nasopharyngeal carcinoma (HR = 0.448; 95 % CI: 0.265-0.760; P = 0.003) and breast cancer (HR = 1.131; 95 % CI: 0.311-4.109; P = .85) were obtained. Our results highlighted that across the published literature, miRNAs can modulate tumor radioresistance or sensitivity by affecting radiation-related signaling pathways. It seems that miRNAs could be considered as a theragnostic biomarker to predict and monitor clinical response to radiotherapy. Thus, the prediction of radioresistance in malignant patients will improve radiotherapy outcomes and radiotherapeutic resistance.
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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8
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Decmann A, Perge P, Turai PI, Patócs A, Igaz P. Non-Coding RNAs in Adrenocortical Cancer: From Pathogenesis to Diagnosis. Cancers (Basel) 2020; 12:cancers12020461. [PMID: 32079166 PMCID: PMC7072220 DOI: 10.3390/cancers12020461] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNA molecules including microRNAs and long non-coding RNAs (lncRNA) have been implicated in the pathogenesis of several tumors and numerous data support their applicability in diagnosis as well. Despite recent advances, the pathogenesis of adrenocortical cancer still remains elusive and there are no reliable blood-borne markers of adrenocortical malignancy, either. Several findings show the potential applicability of microRNAs as biomarkers of malignancy and prognosis, and there are some data on lncRNA as well. In this review, we present a synopsis on the potential relevance of non-coding RNA molecules in adrenocortical pathogenesis and their applicability in diagnosis from tissue and blood.
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Affiliation(s)
- Abel Decmann
- 2nd Department of Internal Medicine, Faculty of Medicine, Semmelweis University, Szentkirályi Str. 46., H-1088 Budapest, Hungary; (A.D.); (P.P.); (P.I.T.)
| | - Pál Perge
- 2nd Department of Internal Medicine, Faculty of Medicine, Semmelweis University, Szentkirályi Str. 46., H-1088 Budapest, Hungary; (A.D.); (P.P.); (P.I.T.)
| | - Peter Istvan Turai
- 2nd Department of Internal Medicine, Faculty of Medicine, Semmelweis University, Szentkirályi Str. 46., H-1088 Budapest, Hungary; (A.D.); (P.P.); (P.I.T.)
| | - Attila Patócs
- MTA-SE Lendület Hereditary Endocrine Tumors Research Group, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary
| | - Peter Igaz
- 2nd Department of Internal Medicine, Faculty of Medicine, Semmelweis University, Szentkirályi Str. 46., H-1088 Budapest, Hungary; (A.D.); (P.P.); (P.I.T.)
- MTA-SE Molecular Medicine Research Group, H-1088 Budapest, Hungary
- Correspondence: ; Tel./Fax: +36-1-266-0816
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MicroRNAs Which Can Prognosticate Aggressiveness of Bladder Cancer. Cancers (Basel) 2019; 11:cancers11101551. [PMID: 31615011 PMCID: PMC6826751 DOI: 10.3390/cancers11101551] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/09/2019] [Accepted: 10/09/2019] [Indexed: 12/18/2022] Open
Abstract
Bladder cancer (BC) is still characterized by a very high death rate in patients with this disease. One of the reasons for this is the lack of adequate markers which could help determine the biological potential of the tumor to develop into its invasive stage. It has been found that some microRNAs (miRNAs) correlate with disease progression. The purpose of this study was to identify which miRNAs can accurately predict the presence of BC and can differentiate low grade (LG) tumors from high grade (HG) tumors. The study included 55 patients with diagnosed bladder cancer and 30 persons belonging to the control group. The expression of seven selected miRNAs was estimated with the real-time PCR technique according to miR-103-5p (for the normalization of the results). Receiver operating characteristics (ROC) curves and the area under the curve (AUC) were used to evaluate the feasibility of using selected markers as biomarkers for detecting BC and discriminating non-muscle invasive BC (NMIBC) from muscle invasive BC (MIBC). For HG tumors, the relevant classifiers are miR-205-5p and miR-20a-5p, whereas miR-205-5p and miR-182-5p are for LG (AUC = 0.964 and AUC = 0.992, respectively). NMIBC patients with LG disease are characterized by significantly higher miR-130b-3p expression values compared to patients in HG tumors.
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Buonpane C, Ares G, Benyamen B, Yuan C, Hunter CJ. Identification of suitable reference microRNA for qPCR analysis in pediatric inflammatory bowel disease. Physiol Genomics 2019; 51:169-175. [PMID: 30978148 DOI: 10.1152/physiolgenomics.00126.2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Pediatric inflammatory bowel disease (IBD) accounts for 10-15% of IBD and is associated with considerable morbidity for patients. Dysregulated microRNAs (miRNA, miR), small noncoding RNA molecules that modulate gene expression, have been the target of research in IBD diagnosis, surveillance, and therapy. Proper selection of reference genes, which are a prerequisite for accurate measurement of miRNA expression, is currently lacking. We hypothesize that appropriate normalization requires unique reference genes for different tissue and disease types. Through the study of 28 pediatric intestinal samples, we sought to create a protocol for selection of suitable endogenous reference genes. Candidate reference genes (miR-16, 193a, 27a, 103a, 191) were analyzed by RT-quantitative (q)PCR. Criteria used for designation of suitable reference genes were as follows: 1) ubiquitous: present in all tissue samples with quantification cycle value 15-35; 2) uniform expression: no differential expression between control and disease samples (P > 0.05); 3) stability: stability value <0.5 by NormFinder. Our results suggest the use of miR-27a/191 for Crohn's disease small bowel, none of the five candidate genes for Crohn's disease colon, and miR-16/27a for ulcerative colitis. Additionally, target miR-874 had differential expression when normalized with different reference genes. Our results demonstrate that reference gene choice for qPCR analysis has a significant effect on study results and that proper data normalization is imperative.
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Affiliation(s)
- Christie Buonpane
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University , Chicago, Illinois.,Ann and Robert H. Lurie Children's Hospital of Chicago , Chicago, Illinois
| | - Guillermo Ares
- Ann and Robert H. Lurie Children's Hospital of Chicago , Chicago, Illinois.,Department of Surgery, University of Illinois at Chicago , Chicago, Illinois
| | - Beshoy Benyamen
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University , Chicago, Illinois.,Ann and Robert H. Lurie Children's Hospital of Chicago , Chicago, Illinois
| | - Carrie Yuan
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University , Chicago, Illinois
| | - Catherine J Hunter
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University , Chicago, Illinois.,Ann and Robert H. Lurie Children's Hospital of Chicago , Chicago, Illinois
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Wang J, Zhang H, Zhou X, Wang T, Zhang J, Zhu W, Zhu H, Cheng W. Five serum-based miRNAs were identified as potential diagnostic biomarkers in gastric cardia adenocarcinoma. Cancer Biomark 2019; 23:193-203. [PMID: 30198863 DOI: 10.3233/cbm-181258] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Circulating microRNAs (miRNAs) have been implicated as novel biomarkers for various types of cancers. The aim of the study is to identify serum miRNAs with potential in detecting gastric cardia adenocarcinoma (GCA). METHODS A three-phase study was designed with 102 GCA patients and 84 cancer-free controls. In the screening phase (3 GCA pools vs. 1 normal control (NC) pool), a total of 35 miRNAs were identified using quantitative reverse transcription polymerase chain reaction (qRT-PCR) based Exiqon panel. Subsequently, these miRNAs were further assessed by qRT-PCR in the training phase (30 GCAs vs. 30 NCs) and testing phase (72 GCAs vs. 54 NCs). Finally, the expression levels of the identified miRNAs were assessed in GCA tissues and exosomes. RESULTS Five up-regulated miRNAs (miR-200a-3p, miR-296-5p, miR-132-3p, miR-485-3p and miR-22-5p) were identified in serum of the GCA patients compared with NCs. The areas under the receiver operating characteristic curve (AUCs) of the five-miRNA panel were 0.766 and 0.724 for the training and testing phases, respectively. In addition, miR-200a-3p, miR-296-5p, miR-485-3p and miR-22-5p were significantly up-regulated in GCA tissues. However, none of the miRNAs in the exosomes showed different expression between GCA patients and NCs. CONCLUSIONS We identified a five-miRNA panel in peripheral serum samples as a non-invasive biomarker in detection of GCA.
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Affiliation(s)
- Juan Wang
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China.,Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Huo Zhang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China.,Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Xin Zhou
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China.,Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Tongshan Wang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - JinYing Zhang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Wei Zhu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Hong Zhu
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Wenfang Cheng
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
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Zhang H, Zhu M, Shan X, Zhou X, Wang T, Zhang J, Tao J, Cheng W, Chen G, Li J, Liu P, Wang Q, Zhu W. A panel of seven-miRNA signature in plasma as potential biomarker for colorectal cancer diagnosis. Gene 2018; 687:246-254. [PMID: 30458288 DOI: 10.1016/j.gene.2018.11.055] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/02/2018] [Accepted: 11/16/2018] [Indexed: 12/11/2022]
Abstract
Colorectal cancer (CRC) has been one of the most commonly diagnosed cancers in global. The differential expression profiles of microRNAs (miRNAs) in CRC plasma of patients have the potential to serve as a diagnostic biomarker. We conducted a four-stage study to identify the potential plasma miRNAs for CRC detection. In the initial screening phase, Exiqon panel (miRCURY-Ready-to-Use-PCR-Human-panel-I + II-V1.M) including 3 CRC pools and 1 normal controls (NCs) pool were applied to acquire miRNA profiles. In the training stage (30 CRC VS. 30 NCs) and testing stage (79 CRC VS. 76 NCs), quantitative real-time polymerase chain reaction (qRT-PCR) was utilized to conduct candidate miRNA profiles. Then the identified miRNAs were verified in external validation stage (30 CRC VS. 26 NCs). Expression levels of identified miRNAs were assessed in tissue samples (24 pairs) and plasma exosomes (18 CRC VS. 18 NCs). Receiver operating characteristic (ROC) curves were constructed to evaluate the diagnostic accuracy. Seven miRNAs (miR-103a-3p, miR-127-3p, miR-151a-5p, miR-17-5p, miR-181a-5p, miR-18a-5p and miR-18b-5p) were significantly overexpressed in CRC compared with NCs. Area under the ROC curve of the seven-miRNA signature was 0.762, 0.824 and 0.895 for the training, testing and the external validation stages, respectively. Additionally, miR-103a-3p, miR-127-3p, miR-17-5p and miR-18a-5p were discovered significantly up-regulated in CRC tissues; while miR-17-5p, miR-181a-5p, miR-18a-5p and miR-18b-5p were significantly elevated in CRC plasma exosomes. In conclusion, we established a seven-miRNA signature in the peripheral plasma for CRC detection.
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Affiliation(s)
- Huo Zhang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Mingxia Zhu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China; Department of Radiation Oncology, The First Affiliated Hospital of Soochow University, Suzhou 215006, PR China
| | - Xia Shan
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China; Department of Respiration, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing 210000, PR China
| | - Xin Zhou
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Tongshan Wang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Jinying Zhang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Jinsong Tao
- Department of Cardiology, The Affiliated Jiangyin Hospital of Southeast University, Jiangyin 214400, PR China
| | - Wenfang Cheng
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Gang Chen
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China; Department of Oncology, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing 210000, PR China
| | - Jian Li
- Department of Cardiology, The Affiliated Jiangyin Hospital of Southeast University, Jiangyin 214400, PR China
| | - Ping Liu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China.
| | - Qiang Wang
- Department of General Surgery, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou 215000, PR China.
| | - Wei Zhu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China; Department of Oncology, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou 215000, PR China.
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13
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Ammerlaan W, Trouet J, Sachs MC, Guan P, Carithers L, Lambert P, Frasquilho S, Antunes L, Kofanova O, Rohrer D, Valley DR, Blanski A, Jewell S, Moore H, Betsou F. Small Nucleolar RNA Score: An Assay to Detect Formalin-Overfixed Tissue. Biopreserv Biobank 2018; 16:467-476. [PMID: 30234371 PMCID: PMC6308291 DOI: 10.1089/bio.2018.0042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Although there are millions of formalin-fixed paraffin-embedded (FFPE) tissue blocks potentially available for scientific research, many are of questionable quality, partly due to unknown fixation conditions. We analyzed FFPE tissue biospecimens as part of the NCI Biospecimen Preanalytical Variables (BPV) program to identify microRNA (miRNA) markers for fixation time. miRNA was extracted from kidney and ovary tumor FFPE blocks (19 patients, cold ischemia ≤2 hours) with 6, 12, 24, and 72 hours fixation times, then analyzed using the WaferGen SmartChip platform (miRNA chip with 1036 miRNA targets). For fixation time, principal component analysis of miRNA chip expression data separated 72 hours fixed samples from 6 to 24 hours fixed samples. A set of small nuclear RNA (snRNA) targets was identified that best determines fixation time and was validated using a second independent cohort of seven different tissue types. A customized assay was then developed, based on a set of 24 miRNA and snRNA targets, and a simple “snoRNA score” defined. This score detects FFPE tissue samples with fixation for 72 hours or more, with 79% sensitivity and 80% specificity. It can therefore be used to assess the fitness-for-purpose of FFPE samples for DNA or RNA-based research or clinical assays, which are known to be of limited robustness to formalin overfixation.
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Affiliation(s)
| | | | - Michael C Sachs
- Biostatistics Unit, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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14
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Gaffney EF, Riegman PH, Grizzle WE, Watson PH. Factors that drive the increasing use of FFPE tissue in basic and translational cancer research. Biotech Histochem 2018; 93:373-386. [PMID: 30113239 DOI: 10.1080/10520295.2018.1446101] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The decision to use 10% neutral buffered formalin fixed, paraffin embedded (FFPE) archival pathology material may be dictated by the cancer research question or analytical technique, or may be governed by national ethical, legal and social implications (ELSI), biobank, and sample availability and access policy. Biobanked samples of common tumors are likely to be available, but not all samples will be annotated with treatment and outcomes data and this may limit their application. Tumors that are rare or very small exist mostly in FFPE pathology archives. Pathology departments worldwide contain millions of FFPE archival samples, but there are challenges to availability. Pathology departments lack resources for retrieving materials for research or for having pathologists select precise areas in paraffin blocks, a critical quality control step. When samples must be sourced from several pathology departments, different fixation and tissue processing approaches create variability in quality. Researchers must decide what sample quality and quality tolerance fit their specific purpose and whether sample enrichment is required. Recent publications report variable success with techniques modified to examine all common species of molecular targets in FFPE samples. Rigorous quality management may be particularly important in sample preparation for next generation sequencing and for optimizing the quality of extracted proteins for proteomics studies. Unpredictable failures, including unpublished ones, likely are related to pre-analytical factors, unstable molecular targets, biological and clinical sampling factors associated with specific tissue types or suboptimal quality management of pathology archives. Reproducible results depend on adherence to pre-analytical phase standards for molecular in vitro diagnostic analyses for DNA, RNA and in particular, extracted proteins. With continuing adaptations of techniques for application to FFPE, the potential to acquire much larger numbers of FFPE samples and the greater convenience of using FFPE in assays for precision medicine, the choice of material in the future will become increasingly biased toward FFPE samples from pathology archives. Recognition that FFPE samples may harbor greater variation in quality than frozen samples for several reasons, including variations in fixation and tissue processing, requires that FFPE results be validated provided a cohort of frozen tissue samples is available.
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Affiliation(s)
- E F Gaffney
- a Biobank Ireland Trust , Malahide , Co Dublin , Ireland
| | - P H Riegman
- b Erasmus Medical Centre , Department of Pathology , Rotterdam , The Netherlands
| | - W E Grizzle
- c Department of Pathology , University of Alabama at Birmingham (UAB) , Birmingham , Alabama , USA
| | - P H Watson
- d BC Cancer Agency , Vancouver Island Center , Victoria , BC , Canada
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15
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Inada K, Okoshi Y, Cho-Isoda Y, Ishiguro S, Suzuki H, Oki A, Tamaki Y, Shimazui T, Saito H, Hori M, Iijima T, Kojima H. Endogenous reference RNAs for microRNA quantitation in formalin-fixed, paraffin-embedded lymph node tissue. Sci Rep 2018; 8:5918. [PMID: 29651113 PMCID: PMC5897550 DOI: 10.1038/s41598-018-24338-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/28/2018] [Indexed: 12/18/2022] Open
Abstract
Lymph node metastasis is one of the most important factors for tumor dissemination. Quantifying microRNA (miRNA) expression using real-time PCR in formalin-fixed, paraffin-embedded (FFPE) lymph node can provide valuable information regarding the biological research for cancer metastasis. However, a universal endogenous reference gene has not been identified in FFPE lymph node. This study aimed to identify suitable endogenous reference genes for miRNA expression analysis in FFPE lymph node. FFPE lymph nodes were obtained from 41 metastatic cancer and from 16 non-cancerous tissues. We selected 10 miRNAs as endogenous reference gene candidates using the global mean method. The stability of candidate genes was assessed by the following four statistical tools: BestKeeper, geNorm, NormFinder, and the comparative ΔCt method. miR-103a was the most stable gene among candidate genes. However, the use of a single miR-103a was not recommended because its stability value exceeded the reference value. Thus, we combined stable genes and investigated the stability and the effect of gene normalization. The combination of miR-24, miR-103a, and let-7a was identified as one of the most stable sets of endogenous reference genes for normalization in FFPE lymph node. This study may provide a basis for miRNA expression analysis in FFPE lymph node tissue.
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Affiliation(s)
- Katsushige Inada
- Department of Hematology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan.
| | - Yasushi Okoshi
- Department of Hematology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan.,Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yukiko Cho-Isoda
- Department of Medical Oncology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Shingo Ishiguro
- Department of Medical Oncology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Hisashi Suzuki
- Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Department of Thoracic Surgery, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Akinori Oki
- Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Department of Obstetrics and Gynecology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Yoshio Tamaki
- Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Department of Radiation Oncology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Toru Shimazui
- Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Department of Urology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Hitoaki Saito
- Department of Pathology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Mitsuo Hori
- Department of Hematology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Tatsuo Iijima
- Department of Pathology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
| | - Hiroshi Kojima
- Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Department of Medical Oncology, Ibaraki Prefectural Central Hospital, Ibaraki, Japan
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16
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Differential expression levels of plasma microRNA in Hashimoto's disease. Gene 2018; 642:152-158. [DOI: 10.1016/j.gene.2017.10.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/16/2017] [Indexed: 12/20/2022]
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17
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Reference miRNAs for colorectal cancer: analysis and verification of current data. Sci Rep 2017; 7:8413. [PMID: 28827728 PMCID: PMC5567181 DOI: 10.1038/s41598-017-08784-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 07/13/2017] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) hold great promise in cancer research. The use of appropriate reference miRNAs for normalization of qPCR data is crucial for accurate expression analysis. We present here analysis and verification of current data, proposing a workflow strategy for identification of reference miRNAs in colorectal cancer (CRC). We performed a systematic review of studies aimed to identify stable reference miRNAs in CRC through high-throughput screening. Among the candidate miRNAs selected from the literature we excluded those predicted to target oncogenes or tumor suppressor gene. We then assessed the expression levels of the remaining candidates in exosomes, plasma and tissue samples from CRC patients and healthy controls. The expression stability was evaluated by box-plot, ∆Cq analysis, NormFinder and BestKeeper statistical algorithms. The effects of normalisers on the relative quantification of the oncogenic miR-1290 was also assessed. Our results consistently showed that different combinations of miR-520d, miR-1228 and miR-345 provided the most stably expressed reference miRNAs in the three biological matrices. We identified suitable reference miRNAs for future miRNA expression studies in exosomes plasma and tissues CRC samples. We also provided a novel conceptual framework that overcome the need of performing ex novo identification of suitable reference genes in single experimental systems.
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18
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Fit for genomic and proteomic purposes: Sampling the fitness of nucleic acid and protein derivatives from formalin fixed paraffin embedded tissue. PLoS One 2017; 12:e0181756. [PMID: 28742856 PMCID: PMC5526578 DOI: 10.1371/journal.pone.0181756] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 07/06/2017] [Indexed: 11/19/2022] Open
Abstract
The demand for nucleic acid and protein derivatives from formalin-fixed paraffin-embedded (FFPE) tissue has greatly increased due to advances in extraction and purification methods, making these derivatives available for numerous genomic and proteomic platforms. Previously, DNA, RNA, microRNA (miRNA), or protein derived from FFPE tissue blocks were considered "unfit" for such platforms, as the process of tissue immobilization by FFPE resulted in cross-linked, fragmented, and chemically modified macromolecules. We conducted a systematic examination of nucleic acids and proteins co-extracted from 118 FFPE blocks sampled from the AIDS and Cancer Specimen Resource (ACSR) at The George Washington University after stratification by storage duration and the three most common tumor tissue types at the ACSR (adenocarcinoma, squamous cell carcinoma, and papillary carcinoma). DNA, RNA, miRNA, and protein could be co-extracted from 98% of the FFPE blocks sampled, with DNA and miRNA "fit" for diverse genomic purposes including sequencing. While RNA was the most labile of the FFPE derivatives, especially when assessed by RNA integrity number (RIN), it was still "fit" for genomic methods that use smaller sequence lengths, e.g., quantitative PCR. While more than half of the protein derivatives were fit for proteomic purposes, our analyses indicated a significant interaction effect on the absorbance values for proteins derived from FFPE, implying that storage duration may affect protein derivatives differently by tumor tissue type. The mean absorbance value for proteins derived from more recently stored FFPE was greater than protein derived from older FFPE, with the exception of adenocarcinoma tissue. Finally, the fitness of one type of derivative was weakly associated with the fitness of derivatives co-extracted from the same FFPE block. The current study used several novel quality assurance approaches and metrics to show that archival FFPE tissue blocks are a valuable resource for contemporary genomic and proteomic platforms.
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Colorectal Cancer: From the Genetic Model to Posttranscriptional Regulation by Noncoding RNAs. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7354260. [PMID: 28573140 PMCID: PMC5442347 DOI: 10.1155/2017/7354260] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/16/2017] [Indexed: 12/11/2022]
Abstract
Colorectal cancer is the third most common form of cancer in developed countries and, despite the improvements achieved in its treatment options, remains as one of the main causes of cancer-related death. In this review, we first focus on colorectal carcinogenesis and on the genetic and epigenetic alterations involved. In addition, noncoding RNAs have been shown to be important regulators of gene expression. We present a general overview of what is known about these molecules and their role and dysregulation in cancer, with a special focus on the biogenesis, characteristics, and function of microRNAs. These molecules are important regulators of carcinogenesis, progression, invasion, angiogenesis, and metastases in cancer, including colorectal cancer. For this reason, miRNAs can be used as potential biomarkers for diagnosis, prognosis, and efficacy of chemotherapeutic treatments, or even as therapeutic agents, or as targets by themselves. Thus, this review highlights the importance of miRNAs in the development, progression, diagnosis, and therapy of colorectal cancer and summarizes current therapeutic approaches for the treatment of colorectal cancer.
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20
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Negoi I, Hostiuc S, Sartelli M, Negoi RI, Beuran M. MicroRNA-21 as a prognostic biomarker in patients with pancreatic cancer - A systematic review and meta-analysis. Am J Surg 2017; 214:515-524. [PMID: 28477839 DOI: 10.1016/j.amjsurg.2017.03.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/22/2017] [Accepted: 03/31/2017] [Indexed: 02/08/2023]
Abstract
OBJECTIVES The aim of this systematic review and meta-analysis is to summarize the current knowledge regarding microRNA-21 and to evaluate its prognostic impact in patients with pancreatic cancer. METHODS We conducted an electronic literature search to identify all published studies in PubMed/MEDLINE, Scopus and Google Scholar databases from 2000 until August 2016. RESULTS A total of 17 studies involving 1471 patients met the inclusion criteria for the quantitative synthesis. The microRNA-21 upregulation was significantly associated with poorer overall survival, disease-free survival, and progression-free survival. The subgroup analysis revealed that microRNA-21 overexpression has a significant higher prognostic value for patients who receive adjuvant chemotherapy. Increased microRNA-21 was associated with a statistically significant higher rate of metastatic lymph nodes and poorly differentiated tumors. CONCLUSIONS MicroRNA-21 upregulation in pancreatic cancer is associated with a significantly poorer overall survival, disease-free survival, and progression-free survival. MicroRNA-21 may be a useful prognostic biomarker, allowing stratification for chemotherapy administration, and being a component of precision medicine in patients with pancreatic cancer.
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Affiliation(s)
- Ionut Negoi
- Carol Davila University of Medicine and Pharmacy Bucharest, Romania; Department of General Surgery, Emergency Hospital of Bucharest, Romania.
| | - Sorin Hostiuc
- Carol Davila University of Medicine and Pharmacy Bucharest, Romania; Department of Legal Medicine and Bioethics, National Institute of Legal Medicine Mina Minovici, Romania
| | | | | | - Mircea Beuran
- Carol Davila University of Medicine and Pharmacy Bucharest, Romania; Department of General Surgery, Emergency Hospital of Bucharest, Romania
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21
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Wang X, Li Y, Zhang J, Zhang Q, Liu X, Li Z. De novo characterization of microRNAs in oriental fruit moth Grapholita molesta and selection of reference genes for normalization of microRNA expression. PLoS One 2017; 12:e0171120. [PMID: 28158242 PMCID: PMC5291412 DOI: 10.1371/journal.pone.0171120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/16/2017] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are a group of endogenous non-coding small RNAs that have critical regulatory functions in almost all known biological processes at the post-transcriptional level in a variety of organisms. The oriental fruit moth Grapholita molesta is one of the most serious pests in orchards worldwide and threatens the production of Rosacea fruits. In this study, a de novo small RNA library constructed from mixed stages of G. molesta was sequenced through Illumina sequencing platform and a total of 536 mature miRNAs consisting of 291 conserved and 245 novel miRNAs were identified. Most of the conserved and novel miRNAs were detected with moderate abundance. The miRNAs in the same cluster normally showed correlated expressional profiles. A comparative analysis of the 79 conserved miRNA families within 31 arthropod species indicated that these miRNA families were more conserved among insects and within orders of closer phylogenetic relationships. The KEGG pathway analysis and network prediction of target genes indicated that the complex composed of miRNAs, clock genes and developmental regulation genes may play vital roles to regulate the developmental circadian rhythm of G. molesta. Furthermore, based on the sRNA library of G. molesta, suitable reference genes were selected and validated for study of miRNA transcriptional profile in G. molesta under two biotic and six abiotic experimental conditions. This study systematically documented the miRNA profile in G. molesta, which could lay a foundation for further understanding of the regulatory roles of miRNAs in the development and metabolism in this pest and might also suggest clues to the development of genetic-based techniques for agricultural pest control.
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Affiliation(s)
- Xiu Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Yisong Li
- Department of Entomology, China Agricultural University, Beijing, China
- Department of Plant Protection, Shihezi University, Shihezi, China
| | - Jing Zhang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Qingwen Zhang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xiaoxia Liu
- Department of Entomology, China Agricultural University, Beijing, China
- * E-mail: (ZL); (XXL)
| | - Zhen Li
- Department of Entomology, China Agricultural University, Beijing, China
- * E-mail: (ZL); (XXL)
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22
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Variability in, variability out: best practice recommendations to standardize pre-analytical variables in the detection of circulating and tissue microRNAs. ACTA ACUST UNITED AC 2017; 55:608-621. [DOI: 10.1515/cclm-2016-0471] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/05/2016] [Indexed: 01/02/2023]
Abstract
Abstract:microRNAs (miRNAs) hold promise as biomarkers for a variety of disease processes and for determining cell differentiation. These short RNA species are robust, survive harsh treatment and storage conditions and may be extracted from blood and tissue. Pre-analytical variables are critical confounders in the analysis of miRNAs: we elucidate these and identify best practices for minimizing sample variation in blood and tissue specimens. Pre-analytical variables addressed include patient-intrinsic variation, time and temperature from sample collection to storage or processing, processing methods, contamination by cells and blood components, RNA extraction method, normalization, and storage time/conditions. For circulating miRNAs, hemolysis and blood cell contamination significantly affect profiles; samples should be processed within 2 h of collection; ethylene diamine tetraacetic acid (EDTA) is preferred while heparin should be avoided; samples should be “double spun” or filtered; room temperature or 4 °C storage for up to 24 h is preferred; miRNAs are stable for at least 1 year at –20 °C or –80 °C. For tissue-based analysis, warm ischemic time should be <1 h; cold ischemic time (4 °C) <24 h; common fixative used for all specimens; formalin fix up to 72 h prior to processing; enrich for cells of interest; validate candidate biomarkers with in situ visualization. Most importantly, all specimen types should have standard and common workflows with careful documentation of relevant pre-analytical variables.
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23
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Shen J, Wang Q, Gurvich I, Remotti H, Santella RM. Evaluating normalization approaches for the better identification of aberrant microRNAs associated with hepatocellular carcinoma. ACTA ACUST UNITED AC 2016; 2:305-315. [PMID: 28393113 DOI: 10.20517/2394-5079.2016.28] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
AIM Dysregulated microRNAs (miRNAs) have been identified in hepatocellular carcinoma (HCC), but only a small proportion have been confirmed. An appropriate normalizer is crucial to determining the accuracy and reliability of data from miRNA studies. METHODS Different normalization strategies were used to validate genome-wide miRNA profiles in HCC tumor and non-tumor tissues, and to determine the consistency and discrepancy of data on dysregulated miRNAs. RESULTS Two sets of stable miRNAs (miR-30c/miR-30b and miR-30c/miR-126) were identified in HCC tissues by geNorm and NormFinder tools, respectively. The mean of global miRNAs also showed good stability for ranking the top 1-2 miRNAs, but the stabilities of the manufacturer-recommended ncRNAs controls were poor. Four panels of miRNAs were significantly associated with HCC by separately using various normalizers, and 14 miRNAs were consistently identified by three normalization strategies. Although fewer miRNAs (17-26) were dysregulated in HCC using the global mean or the 2 stable miRNAs as normalizers, perfect clustering of tissues was also obtained with only 1 to 2 misclassifications, suggesting the efficiency of the miRNA panels. Using global mean as the normalizer, the authors identified 7 miRNAs, including 2 novel (miR-324-5p and miR-550) significantly upregulated in HCC that were omitted when using 3 endogenous controls as the normalizer. CONCLUSION An optimal normalization strategy to identify biologically important miRNAs in HCC tissue studies of miRNA may be the combination of global mean and 2 stable miRNAs. Selection of appropriate normalization strategies to adjust miRNAs levels is particularly important for epidemiological studies dealing with large data sets and covering multiple experimental batches.
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Affiliation(s)
- Jing Shen
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032, USA
| | - Qiao Wang
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032, USA
| | - Irina Gurvich
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032, USA
| | - Helen Remotti
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Regina M Santella
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032, USA
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