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Khan MM, Sharma V, Serajuddin M. Emerging role of miRNA in prostate cancer: A future era of diagnostic and therapeutics. Gene 2023; 888:147761. [PMID: 37666374 DOI: 10.1016/j.gene.2023.147761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/17/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Prostate cancer (PCa) is the most common cancer in men (20%) and is responsible for 6.8% (1/5) of all cancer-related deaths in men around the world. The development and spread of prostate cancer are driven by a wide variety of genomic changes and extensive epigenetic events. Because of this, the MicroRNA (miRNA) and associated molecular mechanisms involved in PCa genesis and aggressive were only partially identified until today. The miRNAs are a newly discovered category of regulatorsthat have recently been recognized to have a significant role in regulating numerous elements of cancer mechanisms, such as proliferation, differentiation, metabolism, and apoptosis. The miRNAs are a type of small (22-24 nucleotides), non-coding, endogenous, single-stranded RNA and work as potent gene regulators. Various types of cancer, including PCa, have found evidence that miRNA genes, which are often located in cancer-related genetic regions or fragile locations, have a role in the primary steps of tumorigenesis, either as oncogenes or tumorsuppressors. To explain the link between miRNAs and their function in the initiation and advancement of PCa, we conducted a preliminary assessment. The purpose of this research was to enhance our understanding of the connection between miRNA expression profiles and PCa by elucidating the fundamental processes of miRNA expression and the target genes.
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Affiliation(s)
- Mohd Mabood Khan
- Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India.
| | - Vineeta Sharma
- Department of Medicine, Vanderbilt University Medical Center, Nashville 37232, TN, USA
| | - Mohammad Serajuddin
- Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
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2
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Bonin S, D’Errico S, Medeot C, Moreschi C, Ciglieri SS, Peruch M, Concato M, Azzalini E, Previderè C, Fattorini P. Evaluation of a Set of miRNAs in 26 Cases of Fatal Traumatic Brain Injuries. Int J Mol Sci 2023; 24:10836. [PMID: 37446013 PMCID: PMC10341445 DOI: 10.3390/ijms241310836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
In forensic medicine, identifying novel biomarkers for use as diagnostic tools to ascertain causes of death is challenging because of sample degradation. To that aim, a cohort (n = 26) of fatal traumatic brain injuries (TBIs) were tested for three candidate miRNAs (namely, miR-124-3p, miR-138-5p, and miR144-3p). For each case, three FFPE specimens (coup area (CA), contrecoup area (CCA), and the corpus callosum (CC)) were investigated, whereas the FFPE brain tissues of 45 subjects (deceased due to acute cardiovascular events) were used as controls. Relative quantification via the ∆∆Ct method returned significantly higher expression levels of the three candidate miRNAs (p < 0.01) in the TBI cases. No difference was detected in the expression levels of any miRNA investigated in the study among the CA, CCA, and CC. Furthermore, the analyzed miRNAs were unrelated to the TBI samples' post-mortem intervals (PMIs). On the contrary, has-miR-124-3p ahashsa-miR-144-3p were significantly correlated (p < 0.01) with the agonal time in TBI deaths. Since the RNA was highly degraded in autoptic FFPE tissues, it was impossible to analyze the mRNA targets of the miRNAs investigated in the present study, highlighting the necessity of standardizing pre-analytical processes even for autopsy tissues.
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Affiliation(s)
- Serena Bonin
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Stefano D’Errico
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Caterina Medeot
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Carlo Moreschi
- DAME—Department of Medical Area, University of Udine, 33100 Udine, Italy;
| | - Solange Sorçaburu Ciglieri
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Michela Peruch
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Monica Concato
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Eros Azzalini
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
| | - Carlo Previderè
- Department of Public Health, Experimental, and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, 27100 Pavia, Italy;
| | - Paolo Fattorini
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (S.B.); (C.M.); (S.S.C.); (M.P.); (M.C.); (E.A.); (P.F.)
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3
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Vazifehmand R, Ali DS, Othman Z, Chau DM, Stanslas J, Shafa M, Sekawi Z. The evaluation expression of non-coding RNAs in response to HSV-G47∆ oncolytic virus infection in glioblastoma multiforme cancer stem cells. J Neurovirol 2022; 28:566-582. [PMID: 35951174 DOI: 10.1007/s13365-022-01089-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 01/13/2023]
Abstract
Glioblastoma multiforme is the most aggressive astrocytes brain tumor. Glioblastoma cancer stem cells and hypoxia conditions are well-known major obstacles in treatment. Studies have revealed that non-coding RNAs serve a critical role in glioblastoma progression, invasion, and resistance to chemo-radiotherapy. The present study examined the expression levels of microRNAs (in normoxic condition) and long non-coding RNAs (in normoxic and hypoxic conditions) in glioblastoma stem cells treated with the HSV-G47∆. The expression levels of 43 miRNAs and 8 lncRNAs isolated from U251-GBM-CSCs were analyzed using a miRCURY LNA custom PCR array and a quantitative PCR assay, respectively. The data revealed that out of 43 miRNAs that only were checked in normoxic condition, the only 8 miRNAs, including miR-7-1, miR-let-7b, miR-130a, miR-137, miR-200b, miR-221, miR-222, and miR-874, were markedly upregulated. The expression levels of lncRNAs, including LEF1 antisense RNA 1 (LEF1-AS1), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), long intergenic non-protein coding RNA 470 (LINC00470), tumor suppressor candidate 7 (TUSC7), HOX transcript antisense RNA (HOTAIR), nuclear paraspeckle assembly transcript 1 (NEAT1), and X inactive specific transcript (XIST), were markedly downregulated in the hypoxic microenvironment, and H19-imprinted maternally expressed transcript (H19) was not observed to be dysregulated in this environment. Under normoxic conditions, LEF1-AS1, MALAT1, LINC00470, H19, HOTAIR, NEAT1, and XIST were downregulated and TUSC7 was not targeted by HSV-G47∆. Overall, the present data shows HSVG47Δ treatment deregulates non-coding RNA expression in GBM-CSC tumor microenvironments.
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Affiliation(s)
- Reza Vazifehmand
- Department of Medical Microbiology & Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor Darul Ehsan, 43400, Malaysia
| | - Dhuha Saeed Ali
- Halal Products Research Institute, Universiti Putra Malaysia UPM, Serdang, Selangor, 43400, Malaysia
| | - Zulkefley Othman
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor Darul Ehsan, 43400, Malaysia
| | - De-Ming Chau
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor Darul Ehsan, 43400, Malaysia
| | - Johnson Stanslas
- Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia UPM, Serdang, Selangor, 43400, Malaysia
| | - Mehdi Shafa
- Cell Therapy process development, Lonza Houston Inc, Houston, TX, USA
| | - Zamberi Sekawi
- Department of Medical Microbiology & Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor Darul Ehsan, 43400, Malaysia.
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Veryaskina YA, Titov SE, Kometova VV, Rodionov VV, Zhimulev IF. Intratumoral Heterogeneity of Expression of 16 miRNA in Luminal Cancer of the Mammary Gland. Noncoding RNA 2020; 6:ncrna6020016. [PMID: 32403384 PMCID: PMC7344477 DOI: 10.3390/ncrna6020016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/16/2020] [Accepted: 05/07/2020] [Indexed: 12/16/2022] Open
Abstract
The purpose of this work is to determine the intratumoral distribution of miRNA expression profiles in luminal breast cancer (BC). The study included 33 certain BC cases of the luminal A or luminal B (Her2-) subtypes. The relative expression levels of miRNA-20a; -21; -125b; -126; -200b; -181a; -205; -221; -222; -451a; -99a; -145; -200a; -214; -30a; -191; and small nuclear RNAs U6, U54, and U58 were measured by RT-qPCR in four intratumor areas in each of 33 luminal BC specimens and in surrounding normal mammary gland tissues. Comparative analysis of miRNA expression levels between normal mammary gland tissue and different intratumor areas revealed that only four miRNAs (miRNA-21, -200b, -200a, -191) appear as consistently differentiating markers. A comparative analysis of miRNA expression levels between normal mammary gland tissue and the tumor border revealed statistically significant differences for ten miRNAs; 10 miRNAs show differential expression between normal mammary gland tissue and central tumor specimens; 9 miRNAs show differential expression between normal mammary gland tissue and tumor periphery 1; 13 miRNAs show differential expression between normal mammary gland tissue and tumor periphery 2. After comparing the tumor periphery 1 and tumor center, we found statistically significant differences in expression between five miRNAs and after comparing the tumor periphery 2 and tumor center, differences were observed for 12 miRNAs. MiRNA expression levels are subject to considerable variation, depending on the intratumor area. This may explain the inconsistency in miRNA expression estimates in BC coming from different laboratories.
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Affiliation(s)
- Yuliya A. Veryaskina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (S.E.T.); (I.F.Z.)
- Correspondence:
| | - Sergei E. Titov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (S.E.T.); (I.F.Z.)
- AO Vector-Best, 630117 Novosibirsk, Russia
| | - Vlada V. Kometova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov of the Ministry of Healthcare of the Russian Federation, 117997 Moscow, Russia; (V.V.K.); (V.V.R.)
| | - Valerii V. Rodionov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov of the Ministry of Healthcare of the Russian Federation, 117997 Moscow, Russia; (V.V.K.); (V.V.R.)
| | - Igor F. Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (S.E.T.); (I.F.Z.)
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Ramakrishnan V, Xu B, Akers J, Nguyen T, Ma J, Dhawan S, Ning J, Mao Y, Hua W, Kokkoli E, Furnari F, Carter BS, Chen CC. Radiation-induced extracellular vesicle (EV) release of miR-603 promotes IGF1-mediated stem cell state in glioblastomas. EBioMedicine 2020; 55:102736. [PMID: 32361246 PMCID: PMC7195524 DOI: 10.1016/j.ebiom.2020.102736] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 01/28/2023] Open
Abstract
Background Recurrence after radiation therapy is nearly universal for glioblastomas, the most common form of adult brain cancer. The study aims to define clinically pertinent mechanisms underlying this recurrence. Methods microRNA (miRNA) profiling was performed using matched pre- and post-radiation treatment glioblastoma specimens from the same patients. All specimens harbored unmethylated O6-methylguanine-DNA methyltransferase promoters (umMGMT) and wild-type isocitrate dehydrogenase (wtIDH). The most altered miRNA, miR-603, was characterized. Findings While nearly all miRNAs remained unchanged after treatment, decreased levels of few, select miRNAs in the post-treatment specimens were observed, the most notable of which involved miR-603. Unbiased profiling of miR-603 targets revealed insulin-like growth factor 1 (IGF1) and IGF1 receptor (IGF1R). Ionizing radiation (IR) induced cellular export of miR-603 through extracellular vesicle (EV) release, thereby de-repressing IGF1 and IGF1R. This de-repression, in turn, promoted cancer stem-cell (CSC) state and acquired radiation resistance in glioblastomas. Export of miR-603 additionally de-repressed MGMT, a DNA repair protein responsible for detoxifying DNA alkylating agents, to promote cross-resistance to these agents. Ectopic miR-603 expression overwhelmed cellular capacity for miR-603 export and synergized with the tumoricidal effects of IR and DNA alkylating agents. Interpretation Profiling of matched pre- and post-treatment glioblastoma specimens revealed altered homeostasis of select miRNAs in response to radiation. Radiation-induced EV export of miR-603 simultaneously promoted the CSC state and up-regulated DNA repair to promote acquired resistance. These effects were abolished by exogenous miR-603 expression, suggesting potential for clinical translation. Funding NIH 1R01NS097649-01, 9R44GM128223-02, 1R01CA240953-01, the Doris Duke Charitable Foundation Clinical Scientist Development Award, The Sontag Foundation Distinguished Scientist Award, the Kimmel Scholar Award, and BWF 1006774.01 (C.C.C).
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Affiliation(s)
- Valya Ramakrishnan
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Beibei Xu
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Thien Nguyen
- School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jun Ma
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sanjay Dhawan
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jianfang Ning
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Wei Hua
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Efrosini Kokkoli
- Department of Chemical and Biomolecular Engineering, Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Frank Furnari
- Ludwig Institute of Cancer Research, University of California, San Diego, CA 92093, USA
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Clark C Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA.
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Combined proteomics/miRNomics of dendritic cell immunotherapy-treated glioblastoma patients as a screening for survival-associated factors. NPJ Vaccines 2020; 5:5. [PMID: 31969991 PMCID: PMC6965118 DOI: 10.1038/s41541-019-0149-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma is the most prevalent and aggressive brain cancer. With a median overall survival of ~15–20 months under standard therapy, novel treatment approaches are desperately needed. A recent phase II clinical trial with a personalized immunotherapy based on tumor lysate-charged dendritic cell (DC) vaccination, however, failed to prolong survival. Here, we investigated tumor tissue from trial patients to explore glioblastoma survival-related factors. We followed an innovative approach of combining mass spectrometry-based quantitative proteomics (n = 36) with microRNA sequencing plus RT-qPCR (n = 38). Protein quantification identified, e.g., huntingtin interacting protein 1 (HIP1), retinol-binding protein 1 (RBP1), ferritin heavy chain (FTH1) and focal adhesion kinase 2 (FAK2) as factor candidates correlated with a dismal prognosis. MicroRNA analysis identified miR-216b, miR-216a, miR-708 and let-7i as molecules potentially associated with favorable tissue characteristics as they were enriched in patients with a comparably longer survival. To illustrate the utility of integrated miRNomics and proteomics findings, focal adhesion was studied further as one example for a pathway of potential general interest. Taken together, we here mapped possible drivers of glioblastoma outcome under immunotherapy in one of the largest DC vaccination tissue analysis cohorts so far—demonstrating usefulness and feasibility of combined proteomics/miRNomics approaches. Future research should investigate agents that sensitize glioblastoma to (immuno)therapy—potentially building on insights generated here. Glioblastoma is an aggressive form of brain cancer and effective immunotherapeutics are limited, with treatment currently based on chemotherapy and radiotherapy. A recent phase II clinical trial tested a personalized, targeted dendritic cell-based immunotherapy but there was no observed improvement in patient survival or progression-free survival compared to standard-of-care therapy. Here, Carmen Visus and colleagues have used tumor tissue samples from glioblastoma patients involved in this trial and receiving immunotherapy. Using a combination of mass spectrometry-based proteomics, microRNA sequencing and RT-qPCR they identified factors associated with survival or poor prognosis. Proteomics associated poor prognosis with various proteins including focal adhesion kinase 2 (FAK2), whilst microRNAs, miR-216b, miR-216a, miR-708 and let-7i, were associated with longer survival. Focussing on one pathway, FAK2, they integrated the proteomic and microRNA datasets and saw a negative association with overall survival across all patients. To test this, they added an FAK inhibitor to glioblastoma cell lines, including cells isolated from trial patients, and observed inhibition of gliomaspheres in treated cells, providing insights into potential immunotherapy targets.
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Muñoz JJ, Anauate AC, Amaral AG, Ferreira FM, Meca R, Ormanji MS, Boim MA, Onuchic LF, Heilberg IP. Identification of housekeeping genes for microRNA expression analysis in kidney tissues of Pkd1 deficient mouse models. Sci Rep 2020; 10:231. [PMID: 31937827 PMCID: PMC6959247 DOI: 10.1038/s41598-019-57112-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/21/2019] [Indexed: 12/11/2022] Open
Abstract
Polycystic kidney disease is a complex clinical entity which comprises a group of genetic diseases that leads to renal cyst development. We evaluated the most suitable housekeeping genes for microRNA expression by RT-qPCR analyses of kidney tissues in Pkd1-deficient mouse models from a panel of five candidates genes (miR-20a, miR-25, miR-26a, miR-191 and U6) and 3 target genes (miR-17, miR-21 and let-7a) using samples from kidneys of cystic mice (Pkd1flox/flox:Nestincre, CY), non-cystic controls (Pkd1flox/flox, NC), Pkd1-haploinsufficient (Pkd1+/−, HT), wild-type controls (Pkd1+/+, WT), severely cystic mice (Pkd1V/V, SC), wild-type controls (CO). The stability of the candidate genes was investigated using NormFinder, GeNorm, BestKeeper, DataAssist, and RefFinder software packages and the comparative ΔCt method. The analyses identified miR-26a as the most stable housekeeping gene for all kidney samples, miR-20a for CY and NC, miR-20a and miR-26a for HT and WT, and miR-25 and miR-26a for SC and CO. Expression of miR-21 was upregulated in SC compared to CO and trends of miR-21 upregulation and let-7a downregulation in CY and HT compared to its control kidneys, when normalized by different combinations of miR-20a, miR-25 and miR-26a. Our findings established miR-20a, miR-25, and miR-26a as the best housekeeping genes for miRNA expression analyses by RT-qPCR in kidney tissues of Pkd1-deficient mouse models.
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Affiliation(s)
- J J Muñoz
- Nephrology Division, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - A C Anauate
- Nephrology Division, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - A G Amaral
- Divisions of Molecular Medicine and Nephrology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - F M Ferreira
- Laboratory of Immunology, Heart Institute, University of São Paulo School of Medicine, São Paulo, Brazil
| | - R Meca
- Nephrology Division, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - M S Ormanji
- Nephrology Division, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - M A Boim
- Nephrology Division, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - L F Onuchic
- Divisions of Molecular Medicine and Nephrology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - I P Heilberg
- Nephrology Division, Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil.
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Lv Y, Li S, Li Z, Tao R, Shao Y, Chen Y. Quantitative analysis of noncoding RNA from paired fresh and formalin-fixed paraffin-embedded brain tissues. Int J Legal Med 2019; 134:873-884. [PMID: 31788707 DOI: 10.1007/s00414-019-02210-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 11/13/2019] [Indexed: 12/30/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are commonly used both clinically and in forensic pathology. Recently, noncoding RNA (ncRNA) has attracted interest among molecular medical researchers. However, it remains unclear whether newly identified ncRNAs, such as long noncoding RNA (lncRNA) and circular RNA (circRNA), remain stable for downstream molecular analysis in FFPE tissues. Here, we assessed the feasibility of using autoptic FFPE brain tissues from eight individuals to perform quantitative molecular analyses. Selected RNA targets (9 mRNAs and 15 ncRNAs) with different amplicon lengths were studied by RT-qPCR in paired fresh and FFPE specimens. For RNA quality assessment, RNA purity and yield were comparable between the two sample cohorts; however, the RNA integrity number decreased significantly during FFPE sampling. Amplification efficiency also displayed certain variability related with amplicon length and RNA species. We found molecular evidence that short amplicons of mRNA, lncRNA, and circRNA were amplified more efficiently than long amplicons. With the assistance of RefFinder, 5S, SNORD48, miR-103a, and miR-125b were selected as reference genes given their high stability. After normalization, we found that short amplicon markers (e.g., ACTB mRNA and MALAT1 lncRNA) exhibited high consistency of quantification in paired fresh/FFPE samples. In particular, circRNAs (XPO1, HIPK3, and TMEM56) presented relatively consistent and stable expression profiles in FFPE tissues compared with their corresponding linear transcripts. Additionally, we evaluated the influence of prolonged storage time on the amplification of gene transcripts and found that short amplicons still work effectively in archived FFPE biospecimens. In conclusion, our findings demonstrate the possibility of performing accurate quantitative analysis of ncRNAs using short amplicons and standardized RT-qPCR assays in autopsy-derived FFPE samples.
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Affiliation(s)
- Yehui Lv
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China. .,School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China.
| | - Shiying Li
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Zhihong Li
- School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China
| | - Ruiyang Tao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China.,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yu Shao
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yijiu Chen
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China.
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9
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Li X, Kleeman S, Coburn SB, Fumagalli C, Perner J, Jammula S, Pfeiffer RM, Orzolek L, Hao H, Taylor PR, Miremadi A, Galeano-Dalmau N, Lao-Sirieix P, Tennyson M, MacRae S, Cook MB, Fitzgerald RC. Selection and Application of Tissue microRNAs for Nonendoscopic Diagnosis of Barrett's Esophagus. Gastroenterology 2018; 155:771-783.e3. [PMID: 29906417 PMCID: PMC6120784 DOI: 10.1053/j.gastro.2018.05.050] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/27/2018] [Accepted: 05/31/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS MicroRNA (miRNA) is highly stable in biospecimens and provides tissue-specific profiles, making it a useful biomarker of carcinogenesis. We aimed to discover a set of miRNAs that could accurately discriminate Barrett's esophagus (BE) from normal esophageal tissue and to test its diagnostic accuracy when applied to samples collected by a noninvasive esophageal cell sampling device. METHODS We analyzed miRNA expression profiles of 2 independent sets of esophageal biopsy tissues collected during endoscopy from 38 patients with BE and 26 patients with normal esophagus (controls) using Agilent microarray and Nanostring nCounter assays. Consistently up-regulated miRNAs were quantified by real-time polymerase chain reaction in esophageal tissues collected by Cytosponge from patients with BE vs without BE. miRNAs were expressed from plasmids and antisense oligonucleotides were expressed in normal esophageal squamous cells; effects on proliferation and gene expression patterns were analyzed. RESULTS We identified 15 miRNAs that were significantly up-regulated in BE vs control tissues. Of these, 11 (MIR215, MIR194, MIR 192, MIR196a, MIR199b, MIR10a, MIR145, MIR181a, MIR30a, MIR7, and MIR199a) were validated in Cytosponge samples. The miRNAs with the greatest increases in BE tissues (7.9-fold increase in expression or more, P < .0001: MIR196a, MIR192, MIR194, and MIR215) each identified BE vs control tissues with area under the curve (AUC) values of 0.82 or more. We developed an optimized multivariable logistic regression model, based on expression levels of 6 miRNAs (MIR7, MIR30a, MIR181a, MIR192, MIR196a, and MIR199a), that identified patients with BE with an AUC value of 0.89, 86.2% sensitivity, and 91.6% specificity. Expression level of MIR192, MIR196a, MIR199a, combined that of trefoil factor 3, identified patients with BE with an AUC of 0.93, 93.1% sensitivity, and 93.7% specificity. Hypomethylation was observed in the promoter region of the highly up-regulated cluster MIR192-MIR194. Overexpression of these miRNAs in normal esophageal squamous cells increased their proliferation, via GRHL3 and PTEN signaling. CONCLUSIONS In analyses of miRNA expression patterns of BE vs non-BE tissues, we identified a profile that can identify Cytosponge samples from patients with BE with an AUC of 0.93. Expression of MIR194 is increased in BE samples via epigenetic mechanisms that might be involved in BE pathogenesis.
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Affiliation(s)
- Xiaodun Li
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Sam Kleeman
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Sally B. Coburn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland
| | - Carlo Fumagalli
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Juliane Perner
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sriganesh Jammula
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ruth M. Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland
| | - Linda Orzolek
- Johns Hopkins Medical Institutions Deep Sequencing and Microarray Core, Baltimore, Maryland
| | - Haiping Hao
- Johns Hopkins Medical Institutions Deep Sequencing and Microarray Core, Baltimore, Maryland
| | - Philip R. Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland
| | | | - Núria Galeano-Dalmau
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Pierre Lao-Sirieix
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Maria Tennyson
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Shona MacRae
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Michael B. Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland,Reprint requests Address requests for reprints to: Michael B. Cook, PhD, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Rebecca C. Fitzgerald
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK,Rebecca C. Fitzgerald, MD, MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, UK CB2 0XZ.
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10
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xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells. Sci Rep 2018; 8:9783. [PMID: 29955168 PMCID: PMC6023933 DOI: 10.1038/s41598-018-28198-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/19/2018] [Indexed: 01/09/2023] Open
Abstract
Accurate, RNA-seq based, microRNA (miRNA) expression estimates from primary cells have recently been described. However, this in vitro data is mainly obtained from cell culture, which is known to alter cell maturity/differentiation status, significantly changing miRNA levels. What is needed is a robust method to obtain in vivo miRNA expression values directly from cells. We introduce expression microdissection miRNA small RNA sequencing (xMD-miRNA-seq), a method to isolate cells directly from formalin fixed paraffin-embedded (FFPE) tissues. xMD-miRNA-seq is a low-cost, high-throughput, immunohistochemistry-based method to capture any cell type of interest. As a proof-of-concept, we isolated colon epithelial cells from two specimens and performed low-input small RNA-seq. We generated up to 600,000 miRNA reads from the samples. Isolated epithelial cells, had abundant epithelial-enriched miRNA expression (miR-192; miR-194; miR-200b; miR-200c; miR-215; miR-375) and overall similar miRNA expression patterns to other epithelial cell populations (colonic enteroids and flow-isolated colon epithelium). xMD-derived epithelial cells were generally not contaminated by other adjacent cells of the colon as noted by t-SNE analysis. xMD-miRNA-seq allows for simple, economical, and efficient identification of cell-specific miRNA expression estimates. Further development will enhance rapid identification of cell-specific miRNA expression estimates in health and disease for nearly any cell type using archival FFPE material.
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11
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A Noninvasive Test for MicroRNA Expression in Oral Squamous Cell Carcinoma. Int J Mol Sci 2018; 19:ijms19061789. [PMID: 29914173 PMCID: PMC6032413 DOI: 10.3390/ijms19061789] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/07/2018] [Accepted: 06/13/2018] [Indexed: 01/10/2023] Open
Abstract
MicroRNAs have recently been proposed as non-invasive biomarkers in Oral Squamous Cell Carcinoma (OSCC). The aim of this study was to analyze the expression of a panel of miRNAs in epithelial cells collected by oral brushing from OSCCs from regenerative areas after OSCC surgical resection and from their respective normal distant mucosa. Oral brushing specimens were collected from 24 healthy donors, 14 OSCC patients with specimens from tumour and normal distant mucosa, and from 13 patients who had OSCC resection, with samples from regenerative areas after OSCC resection and normal distant mucosa. Expression levels of eight targets (miR-21, miR-375, miR-345, miR-181b, miR-146a, miR-649, miR-518b, and miR-191) were evaluated by real-time Polymerase Chain Reaction (PCR). A highly significant between-group difference was found for miR-21 (F = 6.58, p < 0.001), miR-146a (F = 6.974, p < 0.001), and miR-191 (F = 17.07, p < 0.001). The major difference was observed between samples from healthy donors and from OSCC brushing, whereas no significant differences were observed between areas infiltrated by OSCC and their respective normal distant mucosa. Furthermore, altered expression of miR-146a and miR-191 was also observed in regenerative areas after OSCC resection. CONCLUSIONS Oral brushing could be proposed as a noninvasive method to study microRNA expression in oral mucosa in OSCC patients.
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12
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Bongaarts A, Prabowo AS, Arena A, Anink JJ, Reinten RJ, Jansen FE, Spliet WGM, Thom M, Coras R, Blümcke I, Kotulska K, Jozwiak S, Grajkowska W, Söylemezoğlu F, Pimentel J, Schouten-van Meeteren AYN, Mills JD, Iyer AM, van Vliet EA, Mühlebner A, Aronica E. MicroRNA519d and microRNA4758 can identify gangliogliomas from dysembryoplastic neuroepithelial tumours and astrocytomas. Oncotarget 2018; 9:28103-28115. [PMID: 29963264 PMCID: PMC6021349 DOI: 10.18632/oncotarget.25563] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/19/2018] [Indexed: 12/28/2022] Open
Abstract
Glioneuronal tumours, including gangliogliomas and dysembryoplastic neuroepithelial tumours, represent the most common low-grade epilepsy-associated brain tumours and are a well-recognized cause of intractable focal epilepsy in children and young adults. Classification is predominantly based on histological features, which is difficult due to the broad histological spectrum of these tumours. The aim of the present study was to find molecular markers that can be used to identify entities within the histopathology spectrum of glioneuronal tumours. The focus of this study was on microRNAs (miRNAs). miRNAs are important post-transcriptional regulators of gene expression and are involved in the pathogenesis of different neurological diseases and oncogenesis. Using a miRNA array, miR-519d and miR-4758 were found to be upregulated in gangliogliomas (n=26) compared to control cortex (n=17), peritumoural tissue (n=7), dysembryoplastic neuroepithelial tumours (n=9) and astrocytomas (grade I-IV; subependymal giant cell astrocytomas, n=10; pilocytic astrocytoma, n=15; diffuse astrocytoma grade II, n=10; grade III, n=14 and glioblastoma n=15). Furthermore, the PI3K/AKT3/P21 pathway, which is predicated to be targeted by miR-519d and miR-4758, was deregulated in gangliogliomas. Functionally, overexpression of miR-519d in an astrocytic cell line resulted in a downregulation of CDKN1A (P21) and an increase in cell proliferation, whereas co-transfection with miR-4758 counteracted this effect. These results suggest that miR-519d and miR-4758 might work in concert as regulators of the cell cycle in low grade gliomas. Furthermore, these miRNAs could be used to distinguish gangliogliomas from dysembryoplastic neuroepithelial tumours and other low and high grade gliomas and may lead to more targeted therapy.
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Affiliation(s)
- Anika Bongaarts
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Avanita S Prabowo
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Andrea Arena
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Jasper J Anink
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Roy J Reinten
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Floor E Jansen
- Department of Pediatric Neurology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wim G M Spliet
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maria Thom
- Neuropathology Department, University College London, Institute of Neurology, London, UK
| | - Roland Coras
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Ingmar Blümcke
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, Children's Memorial Health Institute, Warsaw, Poland
| | - Sergiusz Jozwiak
- Department of Neurology and Epileptology, Children's Memorial Health Institute, Warsaw, Poland.,Department of Child Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Wieslawa Grajkowska
- Department of Pathology, Children's Memorial Health Institute, Warsaw, Poland
| | - Figen Söylemezoğlu
- Department of Pathology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - José Pimentel
- Department of Neurology, Hospital de Santa Maria, Lisbon, Portugal
| | | | - James D Mills
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Anand M Iyer
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Erwin A van Vliet
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Angelika Mühlebner
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Stichting Epilepsie Instellingen Nederland, Heemstede, The Netherlands
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13
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Sim J, Kim Y, Kim H, Shin SJ, Kim DH, Paik SS, Jang K. Identification of recurrence-associated microRNAs in stage I lung adenocarcinoma. Medicine (Baltimore) 2018; 97:e10996. [PMID: 29923982 PMCID: PMC6024484 DOI: 10.1097/md.0000000000010996] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is the most common cause of cancer-associated death worldwide. Postoperative relapse and subsequent metastasis result in a high mortality rate, even in early stage lung cancer. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level and are frequently dysregulated in various cancers. The aim of this study was to identify recurrence-associated miRNAs in early stage lung cancer. To screen for differentially expressed miRNAs related to postoperative recurrence, miRNA microarray data derived from stage I lung adenocarcinoma formalin-fixed paraffin-embedded (FFPE) tissue samples (n = 6) and publically available the Cancer Genome Atlas (TCGA) data were analyzed. An independent sample (n = 29) was used to validate candidate miRNAs by quantitative real-time polymerase chain reaction (qRT-PCR). In miRNA expression profiling, we identified 60 significantly dysregulated miRNAs in the relapsed group. Additionally, 20 dysregulated miRNAs were found using TCGA data set. Three miRNAs (let-7g-5p, miR-143-3p, and miR-374a-5p) were associated with postoperative recurrence in both microarray and TCGA data sets. All 3 candidate miRNAs were validated in the independent cohort of stage I adenocarcinoma by qRT-PCR. We discovered 3 recurrence-associated miRNAs of stage I lung adenocarcinoma samples using FFPE tissue, which showed possible clinical utility as biomarkers predicting recurrence after curative surgery. Further investigation of the functional properties of these miRNAs is needed.
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Affiliation(s)
- Jongmin Sim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Yeseul Kim
- Department of Pathology, Hanyang University College of Medicine
| | - Hyunsung Kim
- Department of Pathology, Hanyang University College of Medicine
| | - Su-Jin Shin
- Department of Pathology, Hanyang University College of Medicine
| | - Dong-Hoon Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seung Sam Paik
- Department of Pathology, Hanyang University College of Medicine
| | - Kiseok Jang
- Department of Pathology, Hanyang University College of Medicine
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14
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Vojtechova Z, Zavadil J, Klozar J, Grega M, Tachezy R. Comparison of the miRNA expression profiles in fresh frozen and formalin-fixed paraffin-embedded tonsillar tumors. PLoS One 2017; 12:e0179645. [PMID: 28644855 PMCID: PMC5482461 DOI: 10.1371/journal.pone.0179645] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/01/2017] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs are considered as promising prognostic and diagnostic biomarkers of human cancer since their profiles differ between tumor types. Most of the tumor profiling studies were performed on rarely available fresh frozen (FF) samples. Alternatively, archived formalin-fixed paraffin-embedded (FFPE) tissue samples are also well applicable to larger-scale retrospective miRNA profiling studies. The aim of this study was to perform systematic comparison of the miRNA expression profiles between FF and macrodissected FFPE tonsillar tumors using the TaqMan Low Density Array system, with the data processed by different software programs and two types of normalization methods. We observed a marked correlation between the miRNA expression profiles of paired FF and FFPE samples; however, only 27-38% of the differentially deregulated miRNAs overlapped between the two source systems. The comparison of the results with regard to the distinct modes of data normalization revealed an overlap in 58-67% of differentially expressed miRNAs, with no influence of the choice of software platform. Our study highlights the fact that for an accurate comparison of the miRNA expression profiles from published studies, it is important to use the same type of clinical material and to test and select the best-performing normalization method for data analysis.
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Affiliation(s)
- Zuzana Vojtechova
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Immunology, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jiri Zavadil
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - Jan Klozar
- Department of Otorhinolaryngology and Head and Neck Surgery, 1 Faculty of Medicine, Charles University, Motol University Hospital, Prague, Czech Republic
| | - Marek Grega
- Department of Pathology and Molecular Medicine, 2 Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ruth Tachezy
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Immunology, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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15
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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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16
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Baldin E, Testoni S, de Pasqua S, Ferro S, Albani F, Baruzzi A, D’Alessandro R. Incidence of neuroepithelial primary brain tumors among adult population of Emilia-Romagna Region, Italy. Neurol Sci 2016; 38:255-262. [DOI: 10.1007/s10072-016-2747-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 10/20/2016] [Indexed: 01/30/2023]
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17
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Boisen MK, Dehlendorff C, Linnemann D, Schultz NA, Jensen BV, Høgdall EVS, Johansen JS. MicroRNA Expression in Formalin-fixed Paraffin-embedded Cancer Tissue: Identifying Reference MicroRNAs and Variability. BMC Cancer 2015; 15:1024. [PMID: 26714641 PMCID: PMC4696166 DOI: 10.1186/s12885-015-2030-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/17/2015] [Indexed: 01/06/2023] Open
Abstract
Background Archival formalin-fixed paraffin-embedded (FFPE) cancer tissue samples are a readily available resource for microRNA (miRNA) biomarker identification. No established standard for reference miRNAs in FFPE tissue exists. We sought to identify stable reference miRNAs for normalization of miRNA expression in FFPE tissue samples from patients with colorectal (CRC) and pancreatic (PC) cancer and to quantify the variability associated with sample age and fixation. Methods High-throughput miRNA profiling results from 203 CRC and 256 PC FFPE samples as well as from 37 paired frozen/FFPE samples from nine other CRC tumors (methodological samples) were used. Candidate reference miRNAs were identified by their correlation with global mean expression. The stability of reference genes was analyzed according to published methods. The association between sample age and global mean miRNA expression was tested using linear regression. Variability was described using correlation coefficients and linear mixed effects models. Normalization effects were determined by changes in standard deviation and by hierarchical clustering. Results We created lists of 20 miRNAs with the best correlation to global mean expression in each cancer type. Nine of these miRNAs were present in both lists, and miR-103a-3p was the most stable reference miRNA for both CRC and PC FFPE tissue. The optimal number of reference miRNAs was 4 in CRC and 10 in PC. Sample age had a significant effect on global miRNA expression in PC (50 % reduction over 20 years) but not in CRC. Formalin fixation for 2–6 days decreased miRNA expression 30–65 %. Normalization using global mean expression reduced variability for technical and biological replicates while normalization using the expression of the identified reference miRNAs reduced variability only for biological replicates. Normalization only had a minor impact on clustering results. Conclusions We identified suitable reference miRNAs for future miRNA expression experiments using CRC- and PC FFPE tissue samples. Formalin fixation decreased miRNA expression considerably, while the effect of increasing sample age was estimated to be negligible in a clinical setting. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-2030-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mogens Karsbøl Boisen
- Department of Oncology, Herlev and Gentofte Hospital, Herlev Ringvej 75, DK-2730, Herlev, Denmark.
| | - Christian Dehlendorff
- Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Copenhagen, Denmark.
| | - Dorte Linnemann
- Department of Pathology, Herlev and Gentofte Hospital, Herlev, Denmark.
| | | | - Benny Vittrup Jensen
- Department of Oncology, Herlev and Gentofte Hospital, Herlev Ringvej 75, DK-2730, Herlev, Denmark.
| | | | - Julia Sidenius Johansen
- Department of Oncology, Herlev and Gentofte Hospital, Herlev Ringvej 75, DK-2730, Herlev, Denmark. .,Department of Medicine, Herlev and Gentofte Hospital, Herlev, Denmark. .,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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18
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Visani M, Acquaviva G, Fiorino S, Bacchi Reggiani ML, Masetti M, Franceschi E, Fornelli A, Jovine E, Fabbri C, Brandes AA, Tallini G, Pession A, de Biase D. Contribution of microRNA analysis to characterisation of pancreatic lesions: a review. J Clin Pathol 2015; 68:859-69. [PMID: 26314585 DOI: 10.1136/jclinpath-2015-203246] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/05/2015] [Indexed: 02/05/2023]
Abstract
Pancreatic tumours are usually very aggressive cancer with a poor prognosis. A limitation of pancreatic imaging techniques is that lesions are often of ambiguous relevance. The inability to achieve a definitive diagnosis based on cytological evaluation of specimens, due to sampling error, paucicellular samples or coexisting inflammation, might lead to delay in clinical management. Given the morbidity associated with pancreatectomy, a proper selection of patients for surgery is fundamental. Many studies have been conducted in order to identify specific markers that could support the early diagnosis of pancreatic lesions, but, to date, none of them allow to diagnose pancreatic cancer with high sensitivity and specificity. MicroRNAs (miRNA) are small non-coding RNAs (19-25 nucleotides) that regulate gene expression interacting with mRNA targets. It is now established that each tissue shows a characteristic miRNA expression pattern that could be modified in association with a number of different diseases including neoplasia. Due to their key role in the regulation of gene expression, in the last years several studies have investigated miRNA tissue-specific expression, quantification and functional analysis to understand their peculiar involvement in cellular processes. The aim of this review is to focus on miRNA expression in pancreatic cancer and their putative role in early characterisation of pancreatic lesions.
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Affiliation(s)
- Michela Visani
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Acquaviva
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Bologna, Italy
| | - Sirio Fiorino
- Operative Unit of Medicine, Budrio Hospital, Budrio, Italy
| | - Maria Letizia Bacchi Reggiani
- Department of Experimental, Diagnostic and Specialty Medicine, Cardiology Unit, University of Bologna, Bologna, Italy
| | | | - Enrico Franceschi
- Medical Oncology Department, Bellaria Hospital, Azienda USL/ IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Adele Fornelli
- Anatomic Pathology Unit, Maggiore Hospital, Bologna, Italy
| | - Elio Jovine
- Surgery Unit, Maggiore Hospital, Bologna, Italy
| | - Carlo Fabbri
- Endoscopy Unit, Maggiore Hospital, Bologna, Italy
| | - Alba A Brandes
- Medical Oncology Department, Bellaria Hospital, Azienda USL/ IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Giovanni Tallini
- Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Bologna, Italy
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19
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Prabowo AS, van Scheppingen J, Iyer AM, Anink JJ, Spliet WGM, van Rijen PC, Schouten-van Meeteren AYN, Aronica E. Differential expression and clinical significance of three inflammation-related microRNAs in gangliogliomas. J Neuroinflammation 2015; 12:97. [PMID: 25986346 PMCID: PMC4446114 DOI: 10.1186/s12974-015-0315-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 04/30/2015] [Indexed: 01/18/2023] Open
Abstract
PURPOSE miR21, miR146, and miR155 represent a trio of microRNAs which has been shown to play a key role in the regulation of immune and inflammatory responses. In the present study, we investigated the differential expression and clinical significance of these three miRNAs in glioneuronal tumors (gangliogliomas, GGs) which are characterized by prominent activation of the innate immune response. METHODS The expression levels of miR21, miR146, and miR155 were evaluated using Taqman PCR in 34 GGs, including 15 cases with sufficient amount of perilesional cortex. Their expression was correlated with the tumor features and the clinical history of epilepsy. In addition, in situ hybridization was used to evaluate their cellular distribution in both tumor and peritumoral cortex. RESULTS Increased expression of miR146a was observed in both tumor and peritumoral cortex compared to control samples. miR146a was detected in both neuronal and astroglial cells. Tumor and peritumoral miR146a expression was negatively correlated with frequency of seizures and the density of activated microglial cells. Neuronal and astroglial expression was observed for both miR21 and miR155 with increased expression of miR21 within the tumor and miR155 in the peritumoral region. Negative correlations were observed between the miRNA levels and the expression of putative targets within the astroglial component of the tumor. CONCLUSION We report a differential regulation of three miRNAs, known to be related to inflammation, in both tumor and peritumoral cortex of patients with GG. Moreover, our findings suggest a functional relationship between miR146a expression and epilepsy, either directly in epileptogenesis or as modulation of seizure activity.
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Affiliation(s)
- A S Prabowo
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - J van Scheppingen
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - A M Iyer
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - J J Anink
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - W G M Spliet
- Department of Pathology, Rudolf Magnus Institute for Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - P C van Rijen
- Department of Neurosurgery, Rudolf Magnus Institute for Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - A Y N Schouten-van Meeteren
- Department of Pediatric Oncology, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - E Aronica
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. .,SEIN - Stichting Epilepsie Instellingen Nederland, Heemstede, The Netherlands. .,Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam, The Netherlands.
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20
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How C, Pintilie M, Bruce JP, Hui ABY, Clarke BA, Wong P, Yin S, Yan R, Waggott D, Boutros PC, Fyles A, Hedley DW, Hill RP, Milosevic M, Liu FF. Developing a prognostic micro-RNA signature for human cervical carcinoma. PLoS One 2015; 10:e0123946. [PMID: 25880806 PMCID: PMC4399941 DOI: 10.1371/journal.pone.0123946] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 03/09/2015] [Indexed: 12/15/2022] Open
Abstract
Cervical cancer remains the third most frequently diagnosed and fourth leading cause of cancer death in women worldwide. We sought to develop a micro-RNA signature that was prognostic for disease-free survival, which could potentially allow tailoring of treatment for cervical cancer patients. A candidate prognostic 9-micro-RNA signature set was identified in the training set of 79 frozen specimens. However, three different approaches to validate this signature in an independent cohort of 87 patients with formalin-fixed paraffin-embedded (FFPE) specimens, were unsuccessful. There are several challenges and considerations associated with developing a prognostic micro-RNA signature for cervical cancer, namely: tumour heterogeneity, lack of concordance between frozen and FFPE specimens, and platform selection for global micro-RNA expression profiling in this disease. Our observations provide an important cautionary tale for future miRNA signature studies for cervical cancer, which can also be potentially applicable to miRNA profiling studies involving other types of human malignancies.
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Affiliation(s)
- Christine How
- Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Melania Pintilie
- Division of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jeff P. Bruce
- Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Angela B. Y. Hui
- Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Blaise A. Clarke
- Department of Pathology, University Health Network, Toronto, ON, Canada
| | - Philip Wong
- Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Shaoming Yin
- Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Rui Yan
- Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Daryl Waggott
- Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Paul C. Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Anthony Fyles
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - David W. Hedley
- Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Richard P. Hill
- Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Michael Milosevic
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Fei-Fei Liu
- Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
- * E-mail:
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Henriksen M, Johnsen KB, Andersen HH, Pilgaard L, Duroux M. MicroRNA expression signatures determine prognosis and survival in glioblastoma multiforme--a systematic overview. Mol Neurobiol 2014; 50:896-913. [PMID: 24619503 PMCID: PMC4225053 DOI: 10.1007/s12035-014-8668-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 02/25/2014] [Indexed: 12/21/2022]
Abstract
Despite advances in our knowledge about glioblastoma multiforme (GBM) pathology, clinical challenges still lie ahead with respect to treatment in GBM due to high prevalence, poor prognosis, and frequent tumor relapse. The implication of microRNAs (miRNAs) in GBM is a rapidly expanding field of research with the aim to develop more targeted molecular therapies. This review aims to present a comprehensive overview of all the available literature, evaluating miRNA signatures as a function of prognosis and survival in GBM. The results are presented with a focus on studies derived from clinical data in databases and independent tissue cohorts where smaller samples sizes were investigated. Here, miRNA associated to longer survival (protective) and miRNA with shorter survival (risk-associated) have been identified and their signatures based on different prognostic attributes are described. Finally, miRNAs associated with disease progression or survival in several studies are identified and functionally described. These miRNAs may be valuable for future determination of patient prognosis and could possibly serve as targets for miRNA-based therapies, which hold a great potential in the treatment of this severe malignant disease.
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Affiliation(s)
- Michael Henriksen
- Laboratory for Cancer Biology, Institute of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220 Aalborg Ø, Denmark
| | - Kasper Bendix Johnsen
- Laboratory for Cancer Biology, Institute of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220 Aalborg Ø, Denmark
| | - Hjalte Holm Andersen
- Laboratory for Cancer Biology, Institute of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220 Aalborg Ø, Denmark
| | - Linda Pilgaard
- Laboratory for Cancer Biology, Institute of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220 Aalborg Ø, Denmark
| | - Meg Duroux
- Laboratory for Cancer Biology, Institute of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220 Aalborg Ø, Denmark
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22
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Visani M, de Biase D, Marucci G, Cerasoli S, Nigrisoli E, Bacchi Reggiani ML, Albani F, Baruzzi A, Pession A. Expression of 19 microRNAs in glioblastoma and comparison with other brain neoplasia of grades I-III. Mol Oncol 2014; 8:417-30. [PMID: 24412053 PMCID: PMC5528554 DOI: 10.1016/j.molonc.2013.12.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/09/2013] [Accepted: 12/16/2013] [Indexed: 02/08/2023] Open
Abstract
Several biomarkers have been proposed as useful parameters to better specify the prognosis or to delineate new target therapy strategies for glioblastoma patients. MicroRNAs could represent putative target molecules, considering their role in tumorigenesis, cancer progression and their specific tissue expression. Although several studies have tried to identify microRNA signature for glioblastoma, a microRNA profile is still far from being well-defined. In this work the expression of 19 microRNAs (miR-7, miR-9, miR-9∗, miR-10a, miR-10b, miR-17, miR-20a, miR-21, miR-26a, miR-27a, miR-31, miR-34a, miR-101, miR-137, miR-182, miR-221, miR-222, miR-330, miR-519d) was evaluated in sixty formalin-fixed and paraffin-embedded glioblastoma samples using a locked nucleic acid real-time PCR. Moreover, a comparison of miRNA expressions was performed between primary brain neoplasias of different grades (grades IV-I). The analysis of 14 validated miRNA expression in the 60 glioblastomas, using three different non-neoplastic references as controls, revealed a putative miRNA signature: mir-10b and miR-21 were up-regulated, while miR-7, miR-31, miR-101, miR-137, miR-222 and miR-330 were down-regulated in glioblastomas. Comparing miRNA expression between glioblastoma group and gliomas of grades I-III, 3 miRNAs (miR-10b, mir-34a and miR-101) showed different regulation statuses between high-grade and low-grade tumors. miR-10b was up-regulated in high grade and significantly down-regulated in low-grade gliomas, suggesting that could be a candidate for a GBM target therapy. This study provides further data for the identification of a miRNA profile for glioblastoma and suggests that different-grade neoplasia could be characterized by different expression of specific miRNAs.
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Affiliation(s)
- Michela Visani
- Department of Pharmacy and Biotechnology, FaBiT, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, FaBiT, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy; Department of Experimental, Diagnostic and Specialty Medicine, DIMES, Anatomic Pathology at Bellaria Hospital, University of Bologna, via Altura 3, 40139 Bologna, Italy.
| | - Gianluca Marucci
- Department of Biomedical Science and Neuromotor Sciences, DIBINEM, Anatomic Pathology, Bellaria Hospital, University of Bologna, via Altura 3, 40139 Bologna, Italy
| | - Serenella Cerasoli
- Anatomic Pathology, M. Bufalini Hospital, Viale Ghirotti 286, 47023 Cesena (FC), Italy
| | - Evandro Nigrisoli
- Anatomic Pathology, M. Bufalini Hospital, Viale Ghirotti 286, 47023 Cesena (FC), Italy
| | - Maria Letizia Bacchi Reggiani
- Department of Experimental, Diagnostic and Specialty Medicine, DIMES, University of Bologna, Via Massarenti 9, 40100 Bologna, Italy
| | - Fiorenzo Albani
- IRCCS Istituto delle Scienze Neurologiche, via Altura 3, 40139 Bologna, Italy; Department of Biomedical & Neuromotor Sciences, University of Bologna, via Altura 3, 40139 Bologna, Italy
| | - Agostino Baruzzi
- IRCCS Istituto delle Scienze Neurologiche, via Altura 3, 40139 Bologna, Italy; Department of Biomedical & Neuromotor Sciences, University of Bologna, via Altura 3, 40139 Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology, FaBiT, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
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Koshkin PA, Chistiakov DA, Nikitin AG, Konovalov AN, Potapov AA, Usachev DY, Pitskhelauri DI, Kobyakov GL, Shishkina LV, Chekhonin VP. Analysis of expression of microRNAs and genes involved in the control of key signaling mechanisms that support or inhibit development of brain tumors of different grades. Clin Chim Acta 2014; 430:55-62. [PMID: 24412320 DOI: 10.1016/j.cca.2014.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 12/31/2013] [Accepted: 01/01/2014] [Indexed: 01/13/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are a class of small non-coding RNA molecules involved in the regulation of key biological processes. Different miRNAs with pro-oncogenic and anti-oncogenic properties have been identified in glioblastomas. We decided to analyze expression profiles of 10 mature miRNAs (miR-7-1, miR-10а, miR-17, miR-20а, miR-21, miR-23а, miR-26а, miR-137, and miR-222) in post-surgery glioma specimens of different grades in order to find whether the expression level correlates with tumor grades. We also measured expression of six key genes such as PTEN, p21/CDKN1A, MDR1, ABCG2, BAX, and BCL-2 involved in the regulation of critical glioma signaling pathways to establish the effect of miRNAs on these signaling mechanisms. METHODS Using RT-PCR, we performed expression analysis of 25 tumor fresh samples (grades II-IV). RESULTS We found gradual increase in miR-21 and miR-23a levels in all tumor grades whereas miR-7 and miR-137 were significantly down-regulated depending on the glioma grade. MDR, ABCG2, and p21/CDKN1A levels were significantly up-regulated while expression of PTEN was down-regulated in tumor samples compared to the normal brain tissue. CONCLUSIONS These observations provide new insights into molecular pathogenic mechanisms of glioma progression and suggest about a potential value of miRNAs as a putative diagnostic marker of brain tumors.
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Affiliation(s)
| | | | - Alexey Georgievich Nikitin
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | | | | | | | | | | | - Vladimir Pavlovich Chekhonin
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, Moscow, Russia; Department of Fundamental and Applied Neurobiology, Serbsky State Scientific Center for Social and Forensic Psychiatry, Moscow, Russia
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24
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MicroRNA expression profiles in human testicular tissues of infertile men with different histopathologic patterns. Fertil Steril 2014; 101:78-86.e2. [DOI: 10.1016/j.fertnstert.2013.09.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 09/01/2013] [Accepted: 09/05/2013] [Indexed: 12/14/2022]
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25
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Miele E, Buttarelli FR, Arcella A, Begalli F, Garg N, Silvano M, Po A, Baldi C, Carissimo G, Antonelli M, Spinelli GP, Capalbo C, Donofrio V, Morra I, Nozza P, Gulino A, Giangaspero F, Ferretti E. High-throughput microRNA profiling of pediatric high-grade gliomas. Neuro Oncol 2013; 16:228-40. [PMID: 24305714 PMCID: PMC3895388 DOI: 10.1093/neuonc/not215] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND High-grade gliomas (HGGs) account for 15% of all pediatric brain tumors and are a leading cause of cancer-related mortality and morbidity. Pediatric HGGs (pHGGs) are histologically indistinguishable from their counterpart in adulthood. However, recent investigations indicate that differences occur at the molecular level, thus suggesting that the molecular path to gliomagenesis in childhood is distinct from that of adults. MicroRNAs (miRNAs) have been identified as key molecules in gene expression regulation, both in development and in cancer. miRNAs have been investigated in adult high-grade gliomas (aHGGs), but scant information is available for pHGGs. METHODS We explored the differences in microRNAs between pHGG and aHGG, in both fresh-frozen and paraffin-embedded tissue, by high-throughput miRNA profiling. We also evaluated the biological effects of miR-17-92 cluster silencing on a pHGG cell line. RESULTS Comparison of miRNA expression patterns in formalin versus frozen specimens resulted in high correlation between both types of samples. The analysis of miRNA profiling revealed a specific microRNA pattern in pHGG with an overexpression and a proliferative role of the miR-17-92 cluster. Moreover, we highlighted a possible quenching function of miR-17-92 cluster on its target gene PTEN, together with an activation of tumorigenic signaling such as sonic hedgehog in pHGG. CONCLUSIONS Our results suggest that microRNA profiling represents a tool to distinguishing pediatric from adult HGG and that miR-17-92 cluster sustains pHGG.
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Affiliation(s)
- Evelina Miele
- Corresponding author: Elisabetta Ferretti, MD, PhD, Department of Experimental Medicine, Sapienza University, Rome, Italy. Viale Regina Elena, 291 - 00161 Rome, Italy.
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26
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Molecular markers for prostate cancer in formalin-fixed paraffin-embedded tissues. BIOMED RESEARCH INTERNATIONAL 2013; 2013:283635. [PMID: 24371818 PMCID: PMC3859157 DOI: 10.1155/2013/283635] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 10/10/2013] [Indexed: 12/14/2022]
Abstract
Prostate cancer (PCa) is the most frequently diagnosed type of cancer in developed countries. The decisive method of diagnosis is based on the results of biopsies, morphologically evaluated to determine the presence or absence of cancer. Although this approach leads to a confident diagnosis in most cases, it can be improved by using the molecular markers present in the tissue. Both miRNAs and proteins are considered excellent candidates for biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues, due to their stability over long periods of time. In the last few years, a concerted effort has been made to develop the necessary tools for their reliable measurement in these types of samples. Furthermore, the use of these kinds of markers may also help in establishing tumor grade and aggressiveness, as well as predicting the possible outcomes in each particular case for the different treatments available. This would aid clinicians in the decision-making process. In this review, we attempt to summarize and discuss the potential use of microRNA and protein profiles in FFPE tissue samples as markers to better predict PCa diagnosis, progression, and response to therapy.
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27
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Akers JC, Ramakrishnan V, Kim R, Skog J, Nakano I, Pingle S, Kalinina J, Hua W, Kesari S, Mao Y, Breakefield XO, Hochberg FH, Van Meir EG, Carter BS, Chen CC. MiR-21 in the extracellular vesicles (EVs) of cerebrospinal fluid (CSF): a platform for glioblastoma biomarker development. PLoS One 2013; 8:e78115. [PMID: 24205116 PMCID: PMC3804457 DOI: 10.1371/journal.pone.0078115] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 09/09/2013] [Indexed: 01/22/2023] Open
Abstract
Glioblastoma cells secrete extra-cellular vesicles (EVs) containing microRNAs (miRNAs). Analysis of these EV miRNAs in the bio-fluids of afflicted patients represents a potential platform for biomarker development. However, the analytic algorithm for quantitative assessment of EV miRNA remains under-developed. Here, we demonstrate that the reference transcripts commonly used for quantitative PCR (including GAPDH, 18S rRNA, and hsa-miR-103) were unreliable for assessing EV miRNA. In this context, we quantitated EV miRNA in absolute terms and normalized this value to the input EV number. Using this method, we examined the abundance of miR-21, a highly over-expressed miRNA in glioblastomas, in EVs. In a panel of glioblastoma cell lines, the cellular levels of miR-21 correlated with EV miR-21 levels (p<0.05), suggesting that glioblastoma cells actively secrete EVs containing miR-21. Consistent with this hypothesis, the CSF EV miR-21 levels of glioblastoma patients (n=13) were, on average, ten-fold higher than levels in EVs isolated from the CSF of non-oncologic patients (n=13, p<0.001). Notably, none of the glioblastoma CSF harbored EV miR-21 level below 0.25 copies per EV in this cohort. Using this cut-off value, we were able to prospectively distinguish CSF derived from glioblastoma and non-oncologic patients in an independent cohort of twenty-nine patients (Sensitivity=87%; Specificity=93%; AUC=0.91, p<0.01). Our results suggest that CSF EV miRNA analysis of miR-21 may serve as a platform for glioblastoma biomarker development.
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Affiliation(s)
- Johnny C. Akers
- Center for Theoretical and Applied Neuro-Oncology, University of California, San Diego, California, United States of America
| | - Valya Ramakrishnan
- Center for Theoretical and Applied Neuro-Oncology, University of California, San Diego, California, United States of America
| | - Ryan Kim
- Center for Theoretical and Applied Neuro-Oncology, University of California, San Diego, California, United States of America
| | - Johan Skog
- Exosome Diagnostics, New York, New York, United States of America
| | - Ichiro Nakano
- Dardinger Laboratory for Neurosciences, Department of Neurosurgery, Ohio State University,Columbus, Ohio, United States of America
| | - Sandeep Pingle
- Department of Neurosciences, University of California, San Diego, California, United States of America
| | - Juliya Kalinina
- Department of Neurosurgery and Hematology & Medical Oncology, School of Medicine and Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
| | - Wei Hua
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Santosh Kesari
- Department of Neurosciences, University of California, San Diego, California, United States of America
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xandra O. Breakefield
- Neurology Service, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Fred H. Hochberg
- Neurology Service, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erwin G. Van Meir
- Department of Neurosurgery and Hematology & Medical Oncology, School of Medicine and Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
| | - Bob S. Carter
- Center for Theoretical and Applied Neuro-Oncology, University of California, San Diego, California, United States of America
| | - Clark C. Chen
- Center for Theoretical and Applied Neuro-Oncology, University of California, San Diego, California, United States of America
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Michelucci R, Pasini E, Meletti S, Fallica E, Rizzi R, Florindo I, Chiari A, Monetti C, Cremonini AM, Forlivesi S, Albani F, Baruzzi A. Epilepsy in primary cerebral tumors: the characteristics of epilepsy at the onset (results from the PERNO study--Project of Emilia Romagna Region on Neuro-Oncology). Epilepsia 2013; 54 Suppl 7:86-91. [PMID: 24099060 DOI: 10.1111/epi.12314] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
PURPOSE To present new information on the semiology and short-term evolution of seizures associated with primary brain tumors (PBTs) in a prospective study. METHODS This study is a section of the PERNO study--Project of Emilia Romagna Region on Neuro-Oncology, the main aim of which is to collect prospectively all cases of PBTs occurring in the Emilia-Romagna region, northeast Italy (3,983,346 population) from January 2009 to December 2011, to allow epidemiologic, clinical, and biomolecular studies. The epilepsy section of the PERNO study included all the patients who experienced seizures, either as first symptom of the tumor or appearing during the course of the disease. Each patient was interviewed by the referring neurologist with a specific interest in epilepsy. The patients who entered the study were followed up with visits on a quarterly basis. KEY FINDINGS We collected 100 cases with full clinical, neuroradiologic, and pathologic data. The majority (79%) had high grade PBTs (glioblastoma in 50 cases), whereas the remaining patients had low-grade gliomas, mostly localized in the frontal (60%), temporal (38%), and parietal (28%) lobes. Seizures were the first symptom of the tumor in 72 cases. Overall, the initial seizures were tonic-clonic (48%) (without clear initial focal signs in more than half of the patients), focal motor (26%), complex partial (10%), and somatosensitive (8%). The majority of cases (60%) had isolated seizures or a low seizure frequency at the onset of the disease, whereas a high seizure frequency or status epilepticus was observed in 18% and 12% of cases, respectively. Ninety-two patients underwent surgical removal of the tumor, which was either radical (38%) or partial (53%). Seven patients underwent only cerebral biopsy. In the 72 patients in whom seizures were the first symptom, the mean time to the surgical treatment was 174 days, with a significant difference between high grade (95 days) and low grade (481 days) gliomas. At the time of our first observation, the majority of patients (69%) had already undergone surgical removal, with a mean follow-up of 3 months after the procedure. Overall, 39 patients (56%) were seizure free after tumor removal. The good outcome did not depend on presurgical seizure frequency or tumor type, although there was a trend for better results with low-grade PBTs. SIGNIFICANCE These data provide evidence that seizures are strictly linked to the tumoral lesion: They are the initial symptom of the tumor, reflect the tumor location and type, are usually resistant to antiepileptic treatment, and may disappear after the treatment of the lesion.
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Affiliation(s)
- Roberto Michelucci
- IRCCS - Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy
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29
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Meng W, McElroy JP, Volinia S, Palatini J, Warner S, Ayers LW, Palanichamy K, Chakravarti A, Lautenschlaeger T. Comparison of microRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues. PLoS One 2013; 8:e64393. [PMID: 23696889 PMCID: PMC3655971 DOI: 10.1371/journal.pone.0064393] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 04/13/2013] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs regulate several aspects of tumorigenesis and cancer progression. Most cancer tissues are archived formalin-fixed and paraffin-embedded (FFPE). While microRNAs are a more stable form of RNA thought to withstand FFPE-processing and degradation there is only limited evidence for the latter assumption. We examined whether microRNA profiling can be successfully conducted on FFPE cancer tissues using SOLiD ligation based sequencing. Tissue storage times (2-9 years) appeared to not affect the number of detected microRNAs in FFPE samples compared to matched frozen samples (paired t-test p>0.7). Correlations of microRNA expression values were very high across microRNAs in a given sample (Pearson's r = 0.71-0.95). Higher variance of expression values among samples was associated with higher correlation coefficients between FFPE and frozen tissues. One of the FFPE samples in this study was degraded for unknown reasons with a peak read length of 17 nucleotides compared to 21 in all other samples. The number of detected microRNAs in this sample was within the range of microRNAs detected in all other samples. Ligation-based microRNA deep sequencing on FFPE cancer tissues is feasible and RNA degradation to the degree observed in our study appears to not affect the number of microRNAs that can be quantified.
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Affiliation(s)
- Wei Meng
- Department of Radiation Oncology, Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Joseph P. McElroy
- Center for Biostatistics, The Ohio State University, Columbus, Ohio, United States of America
| | - Stefano Volinia
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Jeff Palatini
- Microarray Shared Resource, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Sarah Warner
- Microarray Shared Resource, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Leona W. Ayers
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Kamalakannan Palanichamy
- Department of Radiation Oncology, Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Arnab Chakravarti
- Department of Radiation Oncology, Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (AC); (TL)
| | - Tim Lautenschlaeger
- Department of Radiation Oncology, Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (AC); (TL)
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30
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Visani M, de Biase D, Marucci G, Taccioli C, Baruzzi A, Pession A. Definition of miRNAs expression profile in glioblastoma samples: the relevance of non-neoplastic brain reference. PLoS One 2013; 8:e55314. [PMID: 23383149 PMCID: PMC3558478 DOI: 10.1371/journal.pone.0055314] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 12/21/2012] [Indexed: 02/05/2023] Open
Abstract
Glioblastoma is the most aggressive brain tumor that may occur in adults. Regardless of the huge improvements in surgery and molecular therapy, the outcome of neoplasia remains poor. MicroRNAs are small molecules involved in several cellular processes, and their expression is altered in the vast majority of tumors. Several studies reported the expression of different miRNAs in glioblastoma, but one of the most critical point in understanding glioblastoma miRNAs profile is the comparison of these studies. In this paper, we focused our attention on the non-neoplastic references used for determining miRNAs expression. The aim of this study was to investigate if using three different non-neoplastic brain references (normal adjacent the tumor, commercial total RNA, and epileptic specimens) could provide discrepant results. The analysis of 19 miRNAs was performed using Real-Time PCR, starting from the set of samples described above and the expression values compared. Moreover, the three different normal RNAs were used to determine the miRNAs profile in 30 glioblastomas. The data showed that different non-neoplastic controls could lead to different results and emphasize the importance of comparing miRNAs profiles obtained using the same experimental condition.
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Affiliation(s)
- Michela Visani
- Department of Experimental Pathology, University of Bologna, Bologna, Italy
| | - Dario de Biase
- Department of Experimental Pathology, University of Bologna, Bologna, Italy
- Department of Hematologic and Oncological Sciences, University of Bologna, Bologna, Italy
- * E-mail:
| | - Gianluca Marucci
- Department of Hematologic and Oncological Sciences, University of Bologna, Bologna, Italy
| | - Cristian Taccioli
- Department of Cancer Biology, Paul O'Gorman Cancer Institute, University College London, London, United Kingdom
| | - Agostino Baruzzi
- Department of Biomedical & Neuromotor Sciences, University of Bologna and IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Annalisa Pession
- Department of Experimental Pathology, University of Bologna, Bologna, Italy
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Larne O, Martens-Uzunova E, Hagman Z, Edsjö A, Lippolis G, den Berg MSVV, Bjartell A, Jenster G, Ceder Y. miQ--a novel microRNA based diagnostic and prognostic tool for prostate cancer. Int J Cancer 2012. [PMID: 23184647 DOI: 10.1002/ijc.27973] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Today, the majority of prostate tumors are detected at early stages with uncertain prognosis. Therefore, we set out to identify early predictive markers of prostate cancer with aggressive progression characteristics. We measured the expression of microRNAs (miRNA) using qRT-PCR in formalin fixed and paraffin embedded prostatic tissue samples from a Swedish cohort of 49 patients with prostate cancer and 25 without cancer and found seven of 13 preselected miRNAs to discriminate between the two groups. Subsequently, four discriminatory miRNAs were combined to a quota, denoted the miRNA index quote (miQ); ((miR-96-5p × miR-183-5p)/(miR-145-5p × miR221-5p)). The advantage of using a quote is increased discrimination, no need for house-keepings, and most important it may be an advantage considering the heterogeneity of the disease. miQ was found to successfully predict diagnosis (p < 0.0001) with high accuracy (area under the curve, AUC = 0.931) that was verified in an independent Dutch cohort and three external cohorts, and significantly outperforming prostate-specific antigen. Importantly, miQ also has prognostic power to predict aggressiveness of tumors (AUC = 0.895), metastatic statues (AUC = 0.827) and overall survival (p = 0.0013, Wilcoxon test HR = 6.5, median survival 2 vs. 5 years), verified in the Dutch cohort. In this preliminary study, we propose that miQ has potential to be used as a clinical tool for prostate cancer diagnosis and as a prognostic marker of disease progression.
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Affiliation(s)
- Olivia Larne
- Department of Laboratory Medicine, Clinical Chemistry, Lund University, Malmö, Sweden
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