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Mirabbasi R, Ebrahimi SO, Tavakoli F, Reiisi S. Novel polymorphism rs12402181 in the mature sequence of hsa-miR-3117-3p has a protective effect against breast cancer development by affecting miRNA processing and function. 3 Biotech 2023; 13:349. [PMID: 37780804 PMCID: PMC10541378 DOI: 10.1007/s13205-023-03765-y] [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: 04/17/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
The current study aimed to investigate how the rs12402181 variant in the miR-3117-3p seed region affects miRNA processing and binding ability to the target sequences and breast cancer susceptibility. To study the role of rs12402181 polymorphism in breast cancer, blood samples were examined to investigate the possible association between the genetic variant in the miR-3117 and breast cancer susceptibility. The miR-3117 gene variant was genotyped using PCR-RFLP. The pre-miR-3117 and parts of the flanking region with GG or AA genotype were inserted into a pEGFPN1 expression vector and followed by qPCR to evaluate the effect of SNP on miR-3117-3p expression levels and function. Cell proliferation and migration properties investigated by MTT and wound healing assay. Web server databases were used for further investigation of potential changes in miRNA function. Genotype frequency study in breast cancer patients and healthy controls showed that rs12402181 polymorphism (G > A) is inversely associated with susceptibility to breast cancer (P = 0.03, OR 0.551). The variant allele led to increased production of mature miR-3117 and reduced cell proliferation and migration in MCF7 and T47D cells. These findings suggest that A allele in miR-3117-3p affects the processing of miRNA, causing an increase in the miRNA mature form which can negatively regulate tumor development and migration. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03765-y.
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Affiliation(s)
- Razieh Mirabbasi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Seyed Omar Ebrahimi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Fatemeh Tavakoli
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Somayeh Reiisi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
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2
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van der Wijngaart H, Jagga S, Dekker H, de Goeij R, Piersma SR, Pham TV, Knol JC, Zonderhuis BM, Holland HJ, Jiménez CR, Verheul HMW, Vanapalli S, Labots M. Advancing wide implementation of precision oncology: A liquid nitrogen-free snap freezer preserves molecular profiles of biological samples. Cancer Med 2023; 12:10979-10989. [PMID: 36916528 DOI: 10.1002/cam4.5781] [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: 12/12/2022] [Revised: 02/18/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
PURPOSE In precision oncology, tumor molecular profiles guide selection of therapy. Standardized snap freezing of tissue biospecimens is necessary to ensure reproducible, high-quality samples that preserve tumor biology for adequate molecular profiling. Quenching in liquid nitrogen (LN2 ) is the golden standard method, but LN2 has several limitations. We developed a LN2 -independent snap freezer with adjustable cold sink temperature. To benchmark this device against the golden standard, we compared molecular profiles of biospecimens. METHODS Cancer cell lines and core needle normal tissue biopsies from five patients' liver resection specimens were used to compare mass spectrometry (MS)-based global phosphoproteomic and RNA sequencing profiles and RNA integrity obtained by both freezing methods. RESULTS Unsupervised cluster analysis of phosphoproteomic and transcriptomic profiles of snap freezer versus LN2 -frozen K562 samples and liver biopsies showed no separation based on freezing method (with Pearson's r 0.96 (range 0.92-0.98) and >0.99 for K562 profiles, respectively), while samples with +2 h bench-time formed a separate cluster. RNA integrity was also similar for both snap freezing methods. Molecular profiles of liver biopsies were clearly identified per individual patient regardless of the applied freezing method. Two to 25 s freezing time variations did not induce profiling differences in HCT116 samples. CONCLUSION The novel snap freezer preserves high-quality biospecimen and allows identification of individual patients' molecular profiles, while overcoming important limitations of the use of LN2 . This snap freezer may provide a useful tool in clinical cancer research and practice, enabling a wider implementation of (multi-)omics analyses for precision oncology.
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Affiliation(s)
- Hanneke van der Wijngaart
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sahil Jagga
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Henk Dekker
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Richard de Goeij
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Babs M Zonderhuis
- Department of Surgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Harry J Holland
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Srinivas Vanapalli
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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3
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HNRNPA2B1-Mediated MicroRNA-92a Upregulation and Section Acts as a Promising Noninvasive Diagnostic Biomarker in Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15051367. [PMID: 36831695 PMCID: PMC9954252 DOI: 10.3390/cancers15051367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
MicroRNA-92a (miR-92a) may serve as a novel promising biomarker in multiple cancers, including colorectal cancer (CRC); however, the diagnostic accuracy and the underlying molecular mechanism of miR-92a in CRC is poorly understood. We first carried out meta-analysis and found that serum/plasma miR-92a yield better diagnostic efficacy when compared to stool samples and CRC tissues, and this finding was validated by our independent study through stool sample. Multiple bioinformatics assay indicated that miR-92a expression was positively correlated with heterogeneous nuclear ribonucleoproteins A2/B1 (HNRNPA2B1) expression and closely related with the clinical characteristics of CRC. Experimental evidence showed that knockdown of HNRNPA2B1 could significantly decrease miR-92a expression and secretion in RKO cells. HNRNPA2B1 mediated miR-92a via m6A RNA modification. These findings indicate that HNRNPA2B1-m6A RNA modification-derived MicroRNA-92a upregulation and section from the local CRC acts a candidate noninvasive serum biomarker in colorectal cancer. Our study provides a novel insight into miR-92a mechanisms in relation to both expression and secretion for CRC diagnosis.
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4
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van Nee MM, van de Brug T, van de Wiel MA. Fast Marginal Likelihood Estimation of Penalties for Group-Adaptive Elastic Net. J Comput Graph Stat 2022; 32:950-960. [PMID: 38013849 PMCID: PMC10511031 DOI: 10.1080/10618600.2022.2128809] [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: 07/29/2021] [Accepted: 09/12/2022] [Indexed: 10/10/2022]
Abstract
Elastic net penalization is widely used in high-dimensional prediction and variable selection settings. Auxiliary information on the variables, for example, groups of variables, is often available. Group-adaptive elastic net penalization exploits this information to potentially improve performance by estimating group penalties, thereby penalizing important groups of variables less than other groups. Estimating these group penalties is, however, hard due to the high dimension of the data. Existing methods are computationally expensive or not generic in the type of response. Here we present a fast method for estimation of group-adaptive elastic net penalties for generalized linear models. We first derive a low-dimensional representation of the Taylor approximation of the marginal likelihood for group-adaptive ridge penalties, to efficiently estimate these penalties. Then we show by using asymptotic normality of the linear predictors that this marginal likelihood approximates that of elastic net models. The ridge group penalties are then transformed to elastic net group penalties by matching the ridge prior variance to the elastic net prior variance as function of the group penalties. The method allows for overlapping groups and unpenalized variables, and is easily extended to other penalties. For a model-based simulation study and two cancer genomics applications we demonstrate a substantially decreased computation time and improved or matching performance compared to other methods. Supplementary materials for this article are available online.
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Affiliation(s)
- Mirrelijn M. van Nee
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Tim van de Brug
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Mark A. van de Wiel
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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5
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Adam RS, Poel D, Ferreira Moreno L, Spronck JMA, de Back TR, Torang A, Gomez Barila PM, ten Hoorn S, Markowetz F, Wang X, Verheul HMW, Buffart TE, Vermeulen L. Development of a miRNA-based classifier for detection of colorectal cancer molecular subtypes. Mol Oncol 2022; 16:2693-2709. [PMID: 35298091 PMCID: PMC9297751 DOI: 10.1002/1878-0261.13210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Previously, colorectal cancer (CRC) has been classified into four distinct molecular subtypes based on transcriptome data. These consensus molecular subtypes (CMSs) have implications for our understanding of tumor heterogeneity and the prognosis of patients. So far, this classification has been based on the use of messenger RNAs (mRNAs), although microRNAs (miRNAs) have also been shown to play a role in tumor heterogeneity and biological differences between CMSs. In contrast to mRNAs, miRNAs have a smaller size and increased stability, facilitating their detection. Therefore, we built a miRNA-based CMS classifier by converting the existing mRNA-based CMS classification using machine learning (training dataset of n = 271). The performance of this miRNA-assigned CMS classifier (CMS-miRaCl) was evaluated in several datasets, achieving an overall accuracy of ~ 0.72 (0.6329-0.7987) in the largest dataset (n = 158). To gain insight into the biological relevance of CMS-miRaCl, we evaluated the most important features in the classifier. We found that miRNAs previously reported to be relevant in microsatellite-instable CRCs or Wnt signaling were important features for CMS-miRaCl. Following further studies to validate its robustness, this miRNA-based alternative might simplify the implementation of CMS classification in clinical workflows.
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Affiliation(s)
- Ronja S. Adam
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Dennis Poel
- Department of Medical OncologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Leandro Ferreira Moreno
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Joey M. A. Spronck
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Tim R. de Back
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Arezo Torang
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Patricia M. Gomez Barila
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Sanne ten Hoorn
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | | | - Xin Wang
- Department of Biomedical SciencesCity University of Hong KongKowloon TongHong Kong
- Shenzhen Research InstituteCity University of Hong KongShenzhenChina
| | - Henk M. W. Verheul
- Department of Medical OncologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Tineke E. Buffart
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Department of Gastrointestinal OncologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
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6
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Ferris WF. The Role and Interactions of Programmed Cell Death 4 and its Regulation by microRNA in Transformed Cells of the Gastrointestinal Tract. Front Oncol 2022; 12:903374. [PMID: 35847932 PMCID: PMC9277020 DOI: 10.3389/fonc.2022.903374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/30/2022] [Indexed: 11/26/2022] Open
Abstract
Data from GLOBOCAN 2020 estimates that there were 19.3 million new cases of cancer and 10.0 million cancer-related deaths in 2020 and that this is predicted to increase by 47% in 2040. The combined burden of cancers of the gastrointestinal (GI) tract, including oesophageal-, gastric- and colorectal cancers, resulted in 22.6% of the cancer-related deaths in 2020 and 18.7% of new diagnosed cases. Understanding the aetiology of GI tract cancers should have a major impact on future therapies and lessen this substantial burden of disease. Many cancers of the GI tract have suppression of the tumour suppressor Programmed Cell Death 4 (PDCD4) and this has been linked to the expression of microRNAs which bind to the untranslated region of PDCD4 mRNA and either inhibit translation or target the mRNA for degradation. This review highlights the properties of PDCD4 and documents the evidence for the regulation of PDCD4 expression by microRNAs in cancers of the GI tract.
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7
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Høye E, Fromm B, Böttger PHM, Domanska D, Torgunrud A, Lund-Andersen C, Abrahamsen TW, Fretland Å, Dagenborg VJ, Lorenz S, Edwin B, Hovig E, Flatmark K. A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer. NAR Cancer 2022; 4:zcab051. [PMID: 35047825 PMCID: PMC8759566 DOI: 10.1093/narcan/zcab051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 11/24/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022] Open
Abstract
Although microRNAs (miRNAs) contribute to all hallmarks of cancer, miRNA dysregulation in metastasis remains poorly understood. The aim of this work was to reliably identify miRNAs associated with metastatic progression of colorectal cancer (CRC) using novel and previously published next-generation sequencing (NGS) datasets generated from 268 samples of primary (pCRC) and metastatic CRC (mCRC; liver, lung and peritoneal metastases) and tumor adjacent tissues. Differential expression analysis was performed using a meticulous bioinformatics pipeline, including only bona fide miRNAs, and utilizing miRNA-tailored quality control and processing. Five miRNAs were identified as up-regulated at multiple metastatic sites Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p [mir-141–3p], Mir-1307_5p and Mir-155_5p. Several have previously been implicated in metastasis through involvement in epithelial-to-mesenchymal transition and hypoxia, while other identified miRNAs represent novel findings. The use of a publicly available pipeline facilitates reproducibility and allows new datasets to be added as they become available. The set of miRNAs identified here provides a reliable starting-point for further research into the role of miRNAs in metastatic progression.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Kjersti Flatmark
- To whom correspondence should be addressed. Tel: +47 22 78 18 63;
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8
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Marei HE, Althani A, Afifi N, Hasan A, Caceci T, Pozzoli G, Morrione A, Giordano A, Cenciarelli C. p53 signaling in cancer progression and therapy. Cancer Cell Int 2021; 21:703. [PMID: 34952583 PMCID: PMC8709944 DOI: 10.1186/s12935-021-02396-8] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/06/2021] [Indexed: 12/21/2022] Open
Abstract
The p53 protein is a transcription factor known as the "guardian of the genome" because of its critical function in preserving genomic integrity. The TP53 gene is mutated in approximately half of all human malignancies, including those of the breast, colon, lung, liver, prostate, bladder, and skin. When DNA damage occurs, the TP53 gene on human chromosome 17 stops the cell cycle. If p53 protein is mutated, the cell cycle is unrestricted and the damaged DNA is replicated, resulting in uncontrolled cell proliferation and cancer tumours. Tumor-associated p53 mutations are usually associated with phenotypes distinct from those caused by the loss of the tumor-suppressing function exerted by wild-type p53protein. Many of these mutant p53 proteins have oncogenic characteristics, and therefore modulate the ability of cancer cells to proliferate, escape apoptosis, invade and metastasize. Because p53 deficiency is so common in human cancer, this protein is an excellent option for cancer treatment. In this review, we will discuss some of the molecular pathways by which mutant p53 proteins might perform their oncogenic activities, as well as prospective treatment methods based on restoring tumor suppressive p53 functions.
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Affiliation(s)
- Hany E Marei
- Department of Cytology and Histology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35116, Egypt.
| | - Asmaa Althani
- Biomedical Research Center, Qatar University, Doha, Qatar
| | | | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha, Qatar
| | - Thomas Caceci
- Biomedical Sciences, Virginia Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Giacomo Pozzoli
- Pharmacology Unit, Fondazione Policlinico A. Gemelli, IRCCS, Rome, Italy
| | - Andrea Morrione
- Sbarro Institute for Cancer Research and Molecular Medicine. Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine. Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
- Department of Medical Biotechnology, University of Siena, Siena, Italy
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9
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Abstract
Recent studies have revealed the significant dysregulation of m6A level in peripheral blood in several cancer types and its value in diagnosis. Nonetheless, a biomarker for accurate screening of multiple cancer types has not been established based on the perspective of m6A modification. In this study, we aimed to develop a serum diagnostic signature based on the m6A target miRNAs for the mass detection of cancer. A total of 14965 serum samples with 12 cancer types were included. Based on training cohort (n=7299), we developed the m6A-miRNAs signature using a support vector machine algorithm for cancer detection. The m6A-miRNAs signature showed high accuracy, and its area under the curve (AUC) in the training, internal validation and external validation cohort reached 0.979 (95%CI 0.976 - 0.982), 0.976 (95%CI 0.973 - 0.979) and 0.936 (95%CI 0.922 - 0.951), respectively. In the performance of distinguishing cancer types, the m6A-miRNAs signature showed superior sensitivity in each cancer type and presented a satisfactory AUC in identifying lung cancer, gastric cancer and hepatocellular carcinoma. Additionally, the diagnostic performance of m6A-miRNAs was not interfered by the gender, age and benign disease. In short, this study revealed the value of serum circulating m6A miRNAs in cancer detection and provided a new direction and strategy for the development of novel biomarkers with high accuracy, low cost and less invasiveness for mass cancer screening, such as RNA modification.
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10
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van Nee MM, Wessels LFA, van de Wiel MA. Flexible co-data learning for high-dimensional prediction. Stat Med 2021; 40:5910-5925. [PMID: 34438466 PMCID: PMC9292202 DOI: 10.1002/sim.9162] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 05/18/2021] [Accepted: 07/29/2021] [Indexed: 02/06/2023]
Abstract
Clinical research often focuses on complex traits in which many variables play a role in mechanisms driving, or curing, diseases. Clinical prediction is hard when data is high-dimensional, but additional information, like domain knowledge and previously published studies, may be helpful to improve predictions. Such complementary data, or co-data, provide information on the covariates, such as genomic location or P-values from external studies. We use multiple and various co-data to define possibly overlapping or hierarchically structured groups of covariates. These are then used to estimate adaptive multi-group ridge penalties for generalized linear and Cox models. Available group adaptive methods primarily target for settings with few groups, and therefore likely overfit for non-informative, correlated or many groups, and do not account for known structure on group level. To handle these issues, our method combines empirical Bayes estimation of the hyperparameters with an extra level of flexible shrinkage. This renders a uniquely flexible framework as any type of shrinkage can be used on the group level. We describe various types of co-data and propose suitable forms of hypershrinkage. The method is very versatile, as it allows for integration and weighting of multiple co-data sets, inclusion of unpenalized covariates and posterior variable selection. For three cancer genomics applications we demonstrate improvements compared to other models in terms of performance, variable selection stability and validation.
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Affiliation(s)
- Mirrelijn M van Nee
- Epidemiology & Data Science
- Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Computational Cancer Biology, Oncode Institute, Amsterdam, The Netherlands.,Intelligent Systems, Delft University of Technology, Delft, The Netherlands
| | - Mark A van de Wiel
- Epidemiology & Data Science
- Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands.,MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
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11
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Münch MM, Peeters CFW, Van Der Vaart AW, Van De Wiel MA. Adaptive group-regularized logistic elastic net regression. Biostatistics 2021; 22:723-737. [PMID: 31886488 PMCID: PMC8596493 DOI: 10.1093/biostatistics/kxz062] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/27/2022] Open
Abstract
In high-dimensional data settings, additional information on the features is often
available. Examples of such external information in omics research are: (i)
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}{}$p$\end{document}-values from a previous study and (ii) omics
annotation. The inclusion of this information in the analysis may enhance classification
performance and feature selection but is not straightforward. We propose a
group-regularized (logistic) elastic net regression method, where each penalty parameter
corresponds to a group of features based on the external information. The method, termed
gren, makes use of the Bayesian formulation of logistic elastic
net regression to estimate both the model and penalty parameters in an approximate
empirical–variational Bayes framework. Simulations and applications to three cancer
genomics studies and one Alzheimer metabolomics study show that, if the partitioning of
the features is informative, classification performance, and feature selection are indeed
enhanced.
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Affiliation(s)
- Magnus M Münch
- Department of Epidemiology & Biostatistics, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, PO Box 7057, 1007 MB Amsterdam, The Netherlands and Mathematical Institute, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
| | - Carel F W Peeters
- Department of Epidemiology & Biostatistics, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Aad W Van Der Vaart
- Mathematical Institute, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
| | - Mark A Van De Wiel
- Department of Epidemiology & Biostatistics, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, PO Box 7057, 1007 MB Amsterdam, The Netherlands and MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
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12
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Hozaka Y, Kita Y, Yasudome R, Tanaka T, Wada M, Idichi T, Tanabe K, Asai S, Moriya S, Toda H, Mori S, Kurahara H, Ohtsuka T, Seki N. RNA-Sequencing Based microRNA Expression Signature of Colorectal Cancer: The Impact of Oncogenic Targets Regulated by miR-490-3p. Int J Mol Sci 2021; 22:ijms22189876. [PMID: 34576039 PMCID: PMC8469425 DOI: 10.3390/ijms22189876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/24/2022] Open
Abstract
To elucidate novel aspects of the molecular pathogenesis of colorectal cancer (CRC), we have created a new microRNA (miRNA) expression signature based on RNA-sequencing. Analysis of the signature showed that 84 miRNAs were upregulated, and 70 were downregulated in CRC tissues. Interestingly, our signature indicated that both guide and passenger strands of some miRNAs were significantly dysregulated in CRC tissues. These findings support our earlier data demonstrating the involvement of miRNA passenger strands in cancer pathogenesis. Our study focused on downregulated miR-490-3p and investigated its tumor-suppressive function in CRC cells. We successfully identified a total of 38 putative oncogenic targets regulated by miR-490-3p in CRC cells. Among these targets, the expression of three genes (IRAK1: p = 0.0427, FUT1: p = 0.0468, and GPRIN2: p = 0.0080) significantly predicted 5-year overall survival of CRC patients. Moreover, we analyzed the direct regulation of IRAK1 by miR-490-3p, and its resultant oncogenic function in CRC cells. Thus, we have clarified a part of the molecular pathway of CRC based on the action of tumor-suppressive miR-490-3p. This new miRNA expression signature of CRC will be a useful tool for elucidating new molecular pathogenesis in this disease.
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Affiliation(s)
- Yuto Hozaka
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.H.); (Y.K.); (R.Y.); (T.T.); (M.W.); (T.I.); (K.T.); (H.T.); (S.M.); (H.K.); (T.O.)
| | - Yoshiaki Kita
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.H.); (Y.K.); (R.Y.); (T.T.); (M.W.); (T.I.); (K.T.); (H.T.); (S.M.); (H.K.); (T.O.)
| | - Ryutaro Yasudome
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.H.); (Y.K.); (R.Y.); (T.T.); (M.W.); (T.I.); (K.T.); (H.T.); (S.M.); (H.K.); (T.O.)
| | - Takako Tanaka
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.H.); (Y.K.); (R.Y.); (T.T.); (M.W.); (T.I.); (K.T.); (H.T.); (S.M.); (H.K.); (T.O.)
| | - Masumi Wada
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.H.); (Y.K.); (R.Y.); (T.T.); (M.W.); (T.I.); (K.T.); (H.T.); (S.M.); (H.K.); (T.O.)
| | - Tetsuya Idichi
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.H.); (Y.K.); (R.Y.); (T.T.); (M.W.); (T.I.); (K.T.); (H.T.); (S.M.); (H.K.); (T.O.)
| | - Kan Tanabe
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.H.); (Y.K.); (R.Y.); (T.T.); (M.W.); (T.I.); (K.T.); (H.T.); (S.M.); (H.K.); (T.O.)
| | - Shunichi Asai
- Department of Functional Genomics, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan;
| | - Shogo Moriya
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan;
| | - Hiroko Toda
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.H.); (Y.K.); (R.Y.); (T.T.); (M.W.); (T.I.); (K.T.); (H.T.); (S.M.); (H.K.); (T.O.)
| | - Shinichiro Mori
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.H.); (Y.K.); (R.Y.); (T.T.); (M.W.); (T.I.); (K.T.); (H.T.); (S.M.); (H.K.); (T.O.)
| | - Hiroshi Kurahara
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.H.); (Y.K.); (R.Y.); (T.T.); (M.W.); (T.I.); (K.T.); (H.T.); (S.M.); (H.K.); (T.O.)
| | - Takao Ohtsuka
- Department of Digestive Surgery, Breast and Thyroid Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (Y.H.); (Y.K.); (R.Y.); (T.T.); (M.W.); (T.I.); (K.T.); (H.T.); (S.M.); (H.K.); (T.O.)
| | - Naohiko Seki
- Department of Functional Genomics, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan;
- Correspondence: ; Tel.: +81-43-226-2971
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13
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Sarabandi S, Sattarifard H, Kiumarsi M, Karami S, Taheri M, Hashemi M, Bahari G, Ghavami S. Association between Genetic Polymorphisms of miR-1307, miR- 1269, miR-3117 and Breast Cancer Risk in a Sample of South East Iranian Women. Asian Pac J Cancer Prev 2021; 22:201-208. [PMID: 33507700 PMCID: PMC8184203 DOI: 10.31557/apjcp.2021.22.1.201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION MicroRNAs (miRNAs) play an essential role in the susceptibility and development of cancer cells. OBJECTIVE Examining the dependency of breast cancer risk with genetic polymorphisms of miR-1307, miR-1269, and miR-3117 in a sample of Iranian women (southeast region). METHODS The case-control study consisted of 520 individuals (260 diagnosed BC patients, 260 healthy individuals). The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used for genotyping of miR-1307 rs7911488, miR-1269 rs73239138, and miR-3117 (rs4655646 and rs7512692) polymorphisms. RESULTS AND CONCLUSION This study provided evidence that miR-1307 rs7911488 polymorphism significantly reduced the risk of BC in heterozygous AG genotype, as well as dominant (AG+GG) genotype and G allele. A significant correlation was found between dominant (AA+AG) genotype, the A allele and protection against BC due to miR-1269 rs73239138 in the sample of study. In contrast, our findings suggested that AG genotype and G allele of miR-3117 rs4655646 polymorphism could increase BC's susceptibility among the southeastern Iranian females. The miR-3117 rs7512692 variant also increased the risk of BC in codominant, dominant and recessive models, as well as the T allele. The possible dependency of miR-1307, miR-1269, and miR-3117 variants with patients' clinicopathological characteristics and BC was also studied. It was concluded that there is a correlation between miR-3117 rs7512692 variant and tumor grade (p=0.031); also, a correlation between miR-1269 rs73239138 variant and progesterone receptor status (p=0.006). The current investigation revealed that miR-1307, miR-1269, and miR-3117 polymorphisms might play a crucial role in the Iranian population's vulnerability to BC.<br />.
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Affiliation(s)
- Sahel Sarabandi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hedieh Sattarifard
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Mohammad Kiumarsi
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Shima Karami
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohsen Taheri
- Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohammad Hashemi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Gholamreza Bahari
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.,Children and Adolescent Health Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada.,Faculty of Medicine, Katowice School of Technology, 40-555 Katowice, Poland.,Autophagy Research Center, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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14
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Poel D, Gootjes EC, Bakkerus L, Trypsteen W, Dekker H, van der Vliet HJ, van Grieken NCT, Verhoef C, Buffart TE, Verheul HMW. A specific microRNA profile as predictive biomarker for systemic treatment in patients with metastatic colorectal cancer. Cancer Med 2020; 9:7558-7571. [PMID: 32864858 PMCID: PMC7571833 DOI: 10.1002/cam4.3371] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 07/15/2020] [Accepted: 07/22/2020] [Indexed: 12/24/2022] Open
Abstract
Background Palliative systemic therapy is currently standard of care for patients with extensive metastatic colorectal cancer (mCRC). A biomarker predicting chemotherapy benefit which prevents toxicity from ineffective treatment is urgently needed. Therefore, a previously developed tissue‐derived microRNA profile to predict clinical benefit from chemotherapy was evaluated in tissue biopsies and serum from patients with mCRC. Methods Samples were prospectively collected from patients (N = 132) who were treated with capecitabine or 5‐FU/LV with oxaliplatin ± bevacizumab. Response evaluation was performed according to RECIST 1.1 after three or four cycles, respectively. Baseline tissue and serum miRNAs expression levels of miR‐17‐5p, miR‐20a‐5p, miR‐30a‐5p, miR‐92a‐3p, miR‐92b‐3p, and miR‐98‐5p were quantified with RT‐qPCR and droplet digital PCR, respectively. Combined predictive performance of selected variables was tested using logistic regression analysis. Results From 132 patients, 81 fresh frozen tissue biopsies from metastases and 93 serum samples were available. Based on expression levels of miRNAs in tissue, progressive disease could be predicted with an AUC of 0.85 (95% CI:0.72‐0.91) and response could be predicted with an AUC of 0.70 (95% CI:0.56‐0.80). This did not outperform clinical parameters alone (respectively P = .14 and P = .27). Expression levels of miR‐92a‐3p and miR‐98‐5p in serum significantly improved the predictive value of clinical parameters for response to chemotherapy (AUC 0.74, 95% CI:0.64‐0.84, P = .003) in this cohort. Conclusions The additive predictive value to clinical parameters of the tissue‐derived six miRNA profile for clinical benefit could not be validated in patients with mCRC treated with first‐line systemic therapy. Although miR‐92a‐3p and miR‐98‐5p serum levels improved the predictive value of clinical parameters, it remained insufficient for clinical decision‐making.
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Affiliation(s)
- Dennis Poel
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU Universiteit Medical Center Amsterdam, Amsterdam, the Netherlands.,Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elske C Gootjes
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU Universiteit Medical Center Amsterdam, Amsterdam, the Netherlands.,Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lotte Bakkerus
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU Universiteit Medical Center Amsterdam, Amsterdam, the Netherlands.,Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wim Trypsteen
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, HIV Cure Research Center, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Henk Dekker
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU Universiteit Medical Center Amsterdam, Amsterdam, the Netherlands
| | - Hans J van der Vliet
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU Universiteit Medical Center Amsterdam, Amsterdam, the Netherlands
| | - Nicole C T van Grieken
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, VU Universiteit Medical Center Amsterdam, Amsterdam, the Netherlands
| | - Cornelis Verhoef
- Division of Surgical Oncology, Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Tineke E Buffart
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU Universiteit Medical Center Amsterdam, Amsterdam, the Netherlands.,Department of Gastrointestinal Oncology, Antoni van Leeuwenhoek, Amsterdam, the Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU Universiteit Medical Center Amsterdam, Amsterdam, the Netherlands.,Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
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15
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Poel D, Rustenburg F, Sie D, van Essen HF, Eijk PP, Bloemena E, Elhorst Benites T, van den Berg MC, Vergeer MR, Leemans RC, Buffart TE, Ylstra B, Brakenhoff RH, Verheul HM, Voortman J. Expression of let-7i and miR-192 is associated with resistance to cisplatin-based chemoradiotherapy in patients with larynx and hypopharynx cancer. Oral Oncol 2020; 109:104851. [PMID: 32585557 DOI: 10.1016/j.oraloncology.2020.104851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/18/2020] [Accepted: 06/07/2020] [Indexed: 12/16/2022]
Abstract
OBJECTIVES The majority of patients with locally advanced larynx or hypopharynx squamous cell carcinoma are treated with organ-preserving chemoradiotherapy (CRT). Clinical outcome following CRT varies greatly. We hypothesized that tumor microRNA (miRNA) expression is predictive for outcome following CRT. METHODS Next-generation sequencing (NGS) miRNA profiling was performed on 37 formalin-fixed paraffin-embedded (FFPE) tumor samples. Patients with a recurrence-free survival (RFS) of less than 2 years and patients with late/no recurrence within 2 years were compared by differential expression analysis. Tumor-specific miRNAs were selected based on normal mucosa miRNA expression data from The Cancer Genome Atlas database. A model was constructed to predict outcome using group-regularized penalized logistic ridge regression. Candidate miRNAs were validated by RT-qPCR in the initial sample set as well as in 46 additional samples. RESULTS Thirteen miRNAs were differentially expressed (p < 0.05, FDR < 0.1) according to outcome group. Initial class prediction in the NGS cohort (n = 37) resulted in a model combining five miRNAs and disease stage, able to predict CRT outcome with an area under the curve (AUC) of 0.82. In the RT-qPCR cohort (n = 83), 25 patients (30%) experienced early recurrence (median RFS 8 months; median follow-up 42 months). Class prediction resulted in a model combining let-7i-5p, miR-192-5p and disease stage, able to discriminate patients with good versus poor clinical outcome (AUC:0.80). CONCLUSION The combined miRNA expression and disease stage prediction model for CRT outcome is superior to using either factor alone. This study indicates NGS miRNA profiling using FFPE specimens is feasible, resulting in clinically relevant biomarkers.
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Affiliation(s)
- Dennis Poel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, the Netherlands; Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - François Rustenburg
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurosurgery, Cancer Center Amsterdam, the Netherlands
| | - Daoud Sie
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, the Netherlands
| | - Hendrik F van Essen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, the Netherlands
| | - Paul P Eijk
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, the Netherlands
| | - Elisabeth Bloemena
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, the Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Maxillofacial Surgery/Oral Pathology, Academic Center for Dentistry Amsterdam (ACTA), the Netherlands
| | - Teresita Elhorst Benites
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, the Netherlands
| | - Madeleine C van den Berg
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, the Netherlands
| | - Marije R Vergeer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Radiation Oncology, Cancer Center Amsterdam, the Netherlands
| | - René C Leemans
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Otolaryngology-Head and Neck Surgery, Cancer Center Amsterdam, the Netherlands
| | - Tineke E Buffart
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, the Netherlands; Antoni van Leeuwenhoek Hospital, Department of Gastrointestinal Oncology, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, the Netherlands
| | - Ruud H Brakenhoff
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Otolaryngology-Head and Neck Surgery, Cancer Center Amsterdam, the Netherlands
| | - Henk M Verheul
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, the Netherlands; Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jens Voortman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, the Netherlands.
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16
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Agupitan AD, Neeson P, Williams S, Howitt J, Haupt S, Haupt Y. P53: A Guardian of Immunity Becomes Its Saboteur through Mutation. Int J Mol Sci 2020; 21:E3452. [PMID: 32414156 PMCID: PMC7278985 DOI: 10.3390/ijms21103452] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/06/2020] [Accepted: 05/11/2020] [Indexed: 02/06/2023] Open
Abstract
Awareness of the importance of immunity in controlling cancer development triggered research into the impact of its key oncogenic drivers on the immune response, as well as their value as targets for immunotherapy. At the heart of tumour suppression is p53, which was discovered in the context of viral infection and now emerges as a significant player in normal and cancer immunity. Wild-type p53 (wt p53) plays fundamental roles in cancer immunity and inflammation. Mutations in p53 not only cripple wt p53 immune functions but also sinisterly subvert the immune function through its neomorphic gain-of-functions (GOFs). The prevalence of mutant p53 across different types of human cancers, which are associated with inflammatory and immune dysfunction, further implicates mutant p53 in modulating cancer immunity, thereby promoting tumorigenesis, metastasis and invasion. In this review, we discuss several mutant p53 immune GOFs in the context of the established roles of wt p53 in regulating and responding to tumour-associated inflammation, and regulating innate and adaptive immunity. We discuss the capacity of mutant p53 to alter the tumour milieu to support immune dysfunction, modulate toll-like receptor (TLR) signalling pathways to disrupt innate immunity and subvert cell-mediated immunity in favour of immune privilege and survival. Furthermore, we expose the potential and challenges associated with mutant p53 as a cancer immunotherapy target and underscore existing therapies that may benefit from inquiry into cancer p53 status.
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Affiliation(s)
- Arjelle Decasa Agupitan
- Tumour Suppression Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne 3000, Victoria, Australia; (A.D.A.); (S.H.)
| | - Paul Neeson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville 3010, Victoria, Australia;
- Cancer Immunology Research, Peter MacCallum Cancer Centre, Melbourne 3000, Victoria, Australia
| | - Scott Williams
- Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne 3000, Victoria, Australia;
| | - Jason Howitt
- School of Health Sciences, Swinburne University, Melbourne 3122, Victoria, Australia;
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Sue Haupt
- Tumour Suppression Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne 3000, Victoria, Australia; (A.D.A.); (S.H.)
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville 3010, Victoria, Australia;
| | - Ygal Haupt
- Tumour Suppression Laboratory, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne 3000, Victoria, Australia; (A.D.A.); (S.H.)
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville 3010, Victoria, Australia;
- Department of Clinical Pathology, University of Melbourne, Parkville 3010, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne 3800, Victoria, Australia
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17
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Duran-Sanchon S, Moreno L, Augé JM, Serra-Burriel M, Cuatrecasas M, Moreira L, Martín A, Serradesanferm A, Pozo À, Costa R, Lacy A, Pellisé M, Lozano JJ, Gironella M, Castells A. Identification and Validation of MicroRNA Profiles in Fecal Samples for Detection of Colorectal Cancer. Gastroenterology 2020; 158:947-957.e4. [PMID: 31622624 DOI: 10.1053/j.gastro.2019.10.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/01/2019] [Accepted: 10/05/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND & AIMS Screening for colorectal cancer (CRC) is effective in the population at average risk. The most extended strategy in organized programs involves the fecal immunochemical test, which is limited by low sensitivity for the detection of advanced adenomas (AAs). We aimed to identify microRNA (miRNA) signatures in fecal samples that identify patients with AAs or CRC and might be used in noninvasive screening. METHODS Our study comprised 4 stages. In the discovery phase, we performed genome-wide miRNA expression profiling of 124 fresh, paired colorectal tumor and nontumor samples (30 CRC; 32 AAs) from patients in Spain. In the technical validation stage, miRNAs with altered expression levels in tumor vs nontumor tissues were quantified by reverse-transcription polymerase chain reaction in fecal samples from a subset of patients included in the discovery phase (n = 39) and individuals without colorectal neoplasms (controls, n = 39). In the clinical validation stage, the miRNAs found to be most significantly up-regulated by quantitative reverse transcription polymerase chain reaction analysis were measured in an independent set of fecal samples (n = 767) from patients with positive results from fecal immunochemical tests in a CRC screening program. Finally, we developed a model to identify patients with advanced neoplasms (CRCs or AAs) based on their miRNA profiles, using findings from colonoscopy as the reference standard. RESULTS Among 200 and 324 miRNAs significantly deregulated in CRC and AA tissues, respectively, 7 and 5 of these miRNAs were also found to be deregulated in feces (technical validation). Of them, MIR421, MIR130b-3p, and MIR27a-3p were confirmed to be upregulated in fecal samples from patients with advanced neoplasms. In our model, the combination of fecal level of MIR421, MIR27a-3p, and hemoglobin identified patients with CRC with an area under the curve (AUC) of 0.93, compared with an AUC of 0.67 for fecal hemoglobin concentration alone. CONCLUSIONS We found that increased levels of 2 miRNAs and hemoglobin in feces can identify patients with AAs or CRC more accurately than fecal hemoglobin concentration alone. Assays for these miRNAs might be added to fecal tests for the detection of CRC or AAs.
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Affiliation(s)
- Saray Duran-Sanchon
- Gastroenterology Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Catalonia, Spain
| | - Lorena Moreno
- Gastroenterology Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Catalonia, Spain
| | - Josep M Augé
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Catalonia, Spain
| | - Miquel Serra-Burriel
- Center for Research in Health and Economics, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Míriam Cuatrecasas
- Pathology Department and Tumour Bank-Biobank, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Catalonia, Spain
| | - Leticia Moreira
- Gastroenterology Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Catalonia, Spain
| | - Agatha Martín
- Gastroenterology Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Catalonia, Spain
| | - Anna Serradesanferm
- Preventive Medicine and Hospital Epidemiology Department, Hospital Clínic, Barcelona, Catalonia, Spain
| | - Àngels Pozo
- Preventive Medicine and Hospital Epidemiology Department, Hospital Clínic, Barcelona, Catalonia, Spain
| | - Rosa Costa
- Gastroenterology Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Catalonia, Spain
| | - Antonio Lacy
- Gastrointestinal Surgery Department, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Catalonia, Spain
| | - Maria Pellisé
- Gastroenterology Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Catalonia, Spain
| | - Juan José Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Catalonia, Spain
| | - Meritxell Gironella
- Gastroenterology Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Catalonia, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Catalonia, Spain.
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18
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Liu L, Zhang H, Mao H, Li X, Hu Y. Exosomal miR-320d derived from adipose tissue-derived MSCs inhibits apoptosis in cardiomyocytes with atrial fibrillation (AF). ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2020; 47:3976-3984. [PMID: 31591913 DOI: 10.1080/21691401.2019.1671432] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) play a key role in various pathological processes like atrial fibrillation (AF), which is a common cardiac arrhythmia. Exosomes are essential information carrier in the intercellular communication. Therefore, this study aimed to investigate the effects of exosomal miR-320d on cardiomyocytes with AF and related mechanisms. To do this, AMSCs were transfected with miR-320d mimics, AMSCs-derived exosomes were co-cultured with cardiomyocytes with AF. MTT, TUNEL staining, flow cytometry, real-time PCR, western blots, and luciferase reporter assays were performed. The results revealed that miR-320d expression was decreased in AF cardiomyocytes. AF increased apoptosis and reduced cell viability in cardiomyocytes. By transfection with miR-320d mimics, the miR-320d level was increased in AMSCs, exosomes and cardiomyocytes, which reversed the effect of AF on cardiomyocytes. STAT3 was down-regulated in AF cardiomyocytes and was a direct target gene of miR-320d. Inhibition of STAT3 abolished the effect of modified exosomes in cardiomyocytes, causing decreased apoptosis and increased cell viability. Taken together, the results suggested that exosomal miR-320d was associated with AF cardiomyocytes apoptosis and cell viability and that the effect of miR-320d on cardiomyocytes is STAT3-dependent. Therefore, this study provides a novel understanding of the molecular basis of AF and provides insight into therapeutic strategies for AF.
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Affiliation(s)
- Lina Liu
- Department of Cardiovascular Medicine, Cangzhou Central Hospital , Cangzhou , China
| | - Haoran Zhang
- Nephrology Department, Cangzhou Central Hospital , Cangzhou , China
| | - Hongyu Mao
- Department of Cardiovascular Medicine, Cangzhou Central Hospital , Cangzhou , China
| | - Xiaohong Li
- Department of Cardiovascular Medicine, Cangzhou Central Hospital , Cangzhou , China
| | - Yamin Hu
- Department of Cardiovascular Medicine, Cangzhou Central Hospital , Cangzhou , China
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19
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Liu H, Ma L, Wang L, Yang Y. MicroRNA-937 is overexpressed and predicts poor prognosis in patients with colon cancer. Diagn Pathol 2019; 14:136. [PMID: 31856857 PMCID: PMC6923914 DOI: 10.1186/s13000-019-0920-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022] Open
Abstract
Background Colon cancer is a heterogeneous tumor and a leading cause of cancer-related mortality. MicroRNA (miRNA) has been proposed as the biomarker in cancers. The aim of this study was to investigate the clinical significance and potential functional role of miR-937 in colon cancer. Methods In the present study, reverse transcription-quantitative polymerase chain reaction (qRT-PCR) was conducted to examine the expression levels of miR-937 in colon cancer tissues and cell lines. Kaplan-Meier curve and Cox regression analyses were used to determine the prognostic impact of miR-937 on survival. Cell Counting Kit-8 and Transwell assays were performed to examine cell proliferation, migration, and invasion, respectively. Results miR-937 was significantly upregulated in colon cancer tissues and cell lines. Clinical analysis results showed that miR-937 expression was associated with lymph node metastasis and TNM stage. Patients with high miR-937 expression predicted a shorter overall survival rate. Functionally, overexpression of miR-937 promoted cell proliferation, migration, and invasion, while inhibition of miR-937 inhibited these cellular behaviors in vitro. Conclusions These results suggested that miR-937 may act as a prognostic biomarker and a potential target for therapeutic strategy, as well as promote proliferation, migration, and invasion of colon cancer.
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Affiliation(s)
- Huiya Liu
- Department of Gastroenterology, Heze Municipal Hospital, Heze, 274400, Shandong, China
| | - Lin Ma
- Department of Laboratory Medicine, Heze Municipal Hospital, Heze, 274400, Shandong, China
| | - Ling Wang
- Department of Cardiac Intervention, Heze Municipal Hospital, Heze, 274400, Shandong, China
| | - Yizuo Yang
- Department of Geriatrics, Heze Municipal Hospital, No. 2888, Caozhou Road, Heze, 274400, Shandong, China.
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20
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Huang Y, Xiao W, Jiang X, Li H. MicroRNA-935 acts as a prognostic marker and promotes cell proliferation, migration, and invasion in colorectal cancer. Cancer Biomark 2019; 26:229-237. [PMID: 31524145 DOI: 10.3233/cbm-190183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ying Huang
- Department of Oncology, Shengli Oilfield Central Hospital, Shandong, China
| | - Wenfeng Xiao
- Department of Magnetic Rsonance Emination, Shengli Oilfield Central Hospital, Shandong, China
| | - Xiuli Jiang
- Xunshan Street Health Center, Rongcheng, Weihai, Shandong, China
| | - Honglei Li
- Department of Medical, Shengli Oilfield Central Hospital, Shandong, China
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21
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Poel D, Boyd LN, Beekhof R, Schelfhorst T, Pham TV, Piersma SR, Knol JC, Jimenez CR, Verheul HM, Buffart TE. Proteomic Analysis of miR-195 and miR-497 Replacement Reveals Potential Candidates that Increase Sensitivity to Oxaliplatin in MSI/P53wt Colorectal Cancer Cells. Cells 2019; 8:cells8091111. [PMID: 31546954 PMCID: PMC6770888 DOI: 10.3390/cells8091111] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 12/17/2022] Open
Abstract
Most patients with advanced colorectal cancer (CRC) eventually develop resistance to systemic combination therapy. miR-195-5p and miR-497-5p are downregulated in CRC tissues and associated with drug resistance. Sensitization to 5-FU, oxaliplatin, and irinotecan by transfection with miR-195-5p and miR-497-5p mimics was studied using cell viability and clonogenic assays in cell lines HCT116, RKO, DLD-1, and SW480. In addition, proteomic analysis of transfected cells was implemented to identify potential targets. Significantly altered proteins were subjected to STRING (protein-protein interaction networks) database analysis to study the potential mechanisms of drug resistance. Cell viability analysis of transfected cells revealed increased sensitivity to oxaliplatin in microsatellite instable (MSI)/P53 wild-type HCT116 and RKO cells. HCT116 transfected cells formed significantly fewer colonies when treated with oxaliplatin. In sensitized cells, proteomic analysis showed 158 and 202 proteins with significantly altered expression after transfection with miR-195-5p and miR-497-5p mimics respectively, of which CHUK and LUZP1 proved to be coinciding downregulated proteins. Resistance mechanisms of these proteins may be associated with nuclear factor kappa-B signaling and G1 cell-cycle arrest. In conclusion, miR-195-5p and miR-497-5p replacement enhanced sensitivity to oxaliplatin in treatment naïve MSI/P53 wild-type CRC cells. Proteomic analysis revealed potential miRNA targets associated with the cell-cycle which possibly bare a relation with chemotherapy sensitivity.
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Affiliation(s)
- Dennis Poel
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
- Department of Medical Oncology, Radboud University medical center, 6525GA Nijmegen, The Netherlands
| | - Lenka N.C. Boyd
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Robin Beekhof
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Tim Schelfhorst
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Jaco C. Knol
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Connie R. Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Henk M.W. Verheul
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
- Department of Medical Oncology, Radboud University medical center, 6525GA Nijmegen, The Netherlands
| | - Tineke E. Buffart
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
- Antoni van Leeuwenhoek, Department of Gastrointestinal Oncology, 1066CX Amsterdam, The Netherlands
- Correspondence: ; Tel.: +20-5122-566
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22
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Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples. mSystems 2019; 4:4/5/e00289-19. [PMID: 31530647 PMCID: PMC6749105 DOI: 10.1128/msystems.00289-19] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The characteristics of microbial small RNA transcription are largely unknown, while it is of primary importance for a better identification of molecules with functional activities in the gut niche under both healthy and disease conditions. By performing combined analyses of metagenomic and small RNA sequencing (sRNA-Seq) data, we characterized both the human and microbial small RNA contents of stool samples from healthy individuals and from patients with colorectal carcinoma or adenoma. With the integrative analyses of metagenomic and sRNA-Seq data, we identified a human and microbial small RNA signature which can be used to improve diagnosis of the disease. Our analysis of human and gut microbiome small RNA expression is relevant to generation of the first hypotheses about the potential molecular interactions occurring in the gut of CRC patients, and it can be the basis for further mechanistic studies and clinical tests. Dysbiotic configurations of the human gut microbiota have been linked to colorectal cancer (CRC). Human small noncoding RNAs are also implicated in CRC, and recent findings suggest that their release in the gut lumen contributes to shape the gut microbiota. Bacterial small RNAs (bsRNAs) may also play a role in carcinogenesis, but their role has been less extensively explored. Here, we performed small RNA and shotgun sequencing on 80 stool specimens from patients with CRC or with adenomas and from healthy subjects collected in a cross-sectional study to evaluate their combined use as a predictive tool for disease detection. We observed considerable overlap and a correlation between metagenomic and bsRNA quantitative taxonomic profiles obtained from the two approaches. We identified a combined predictive signature composed of 32 features from human and microbial small RNAs and DNA-based microbiome able to accurately classify CRC samples separately from healthy and adenoma samples (area under the curve [AUC] = 0.87). In the present study, we report evidence that host-microbiome dysbiosis in CRC can also be observed by examination of altered small RNA stool profiles. Integrated analyses of the microbiome and small RNAs in the human stool may provide insights for designing more-accurate tools for diagnostic purposes. IMPORTANCE The characteristics of microbial small RNA transcription are largely unknown, while it is of primary importance for a better identification of molecules with functional activities in the gut niche under both healthy and disease conditions. By performing combined analyses of metagenomic and small RNA sequencing (sRNA-Seq) data, we characterized both the human and microbial small RNA contents of stool samples from healthy individuals and from patients with colorectal carcinoma or adenoma. With the integrative analyses of metagenomic and sRNA-Seq data, we identified a human and microbial small RNA signature which can be used to improve diagnosis of the disease. Our analysis of human and gut microbiome small RNA expression is relevant to generation of the first hypotheses about the potential molecular interactions occurring in the gut of CRC patients, and it can be the basis for further mechanistic studies and clinical tests.
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23
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Circulating MiR-210 and MiR-1246 as Potential Biomarkers for Differentiating Hepatocellular Carcinoma from Metastatic Tumors in the Liver. J Med Biochem 2019; 38:109-117. [PMID: 30867638 PMCID: PMC6411000 DOI: 10.2478/jomb-2018-0010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/17/2018] [Indexed: 12/16/2022] Open
Abstract
Background To date few reports have pointed out the role of circulating miRNAs in discriminating metastatic liver tumors from primary hepatocellular (HCC) tumors. Such discrimination will have significant therapeutic and prognostic implications. The purpose of this study was to evaluate the potential value of a panel of HCC-related circulating miRNAs (miR-142, miR-182, miR-200a, mir-210, miR-211, miR-302b, miR-324, miR-338, miR-340 and miR-1246) as noninvasive biomarkers for discriminating primary HCC from metastatic tumors in the liver. Methods The expression level of the selected miRNAs was quantified by quantitative real time PCR in 33 patients with HCC, 22 patients with metastatic tumors in the liver, and 30 healthy volunteers as control. Mann-Whitney U test was used to evaluate the difference in miRNAs expression between primary and metastatic liver tumors and to study the associations between their relative expression levels and the clinicopathological factors. Receiver operating characteristic curve was used to evaluate the diagnostic value of the individual miRNAs. Results Statistical analyses revealed a differential expression in the level of serum miR-210 and miR-1246 between the two groups of patients. The sensitivity and specificity of miR-210, for differentiating HCC from metastatic malignancies in the liver were found to be 73.7% and 64.28%, respectively. Whilst, of miR-1246 were 72.2% and 67.8%, respectively. In addition, the differential expression of the two miRNAs was also found to be associated with clinicopathological parameters in the two studied groups. Conclusions Serum miR-210 and miR-1246 have some diagnostic value for discriminating patients with metastatic tumors to patients with primary HCC
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24
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Mjelle R, Sjursen W, Thommesen L, Sætrom P, Hofsli E. Small RNA expression from viruses, bacteria and human miRNAs in colon cancer tissue and its association with microsatellite instability and tumor location. BMC Cancer 2019; 19:161. [PMID: 30786859 PMCID: PMC6381638 DOI: 10.1186/s12885-019-5330-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/29/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNA) and other small RNAs are frequently dysregulated in cancer and are promising biomarkers for colon cancer. Here we profile human, virus and bacteria small RNAs in normal and tumor tissue from early stage colon cancer and correlate the expression with clinical parameters. METHODS Small RNAs from colon cancer tissue and adjacent normal mucosa of 48 patients were sequenced using Illumina high-throughput sequencing. Clinical parameters were correlated with the small RNA expression data using linear models. We performed a meta-analysis by comparing publicly available small RNA sequencing datasets with our original sequencing data to confirm the main findings. RESULTS We identified 331 differentially expressed miRNAs between tumor and normal samples. We found that the major changes in miRNA expression between left and right colon are due to miRNAs located within the Hox-developmental genes, including miR-10b, miR-196b and miR-615. Further, we identified new miRNAs associated with microsatellite instability (MSI), including miR-335, miR-26 and miR-625. We performed a meta-analysis on all publicly available miRNA-seq datasets and identified 117 common miRNAs that were differentially expressed between tumor and normal tissue. The miRNAs miR-135b and miR-31 were the most significant upregulated miRNA in tumor across all datasets. The miRNA miR-133a was the most strongly downregulated miRNA in our dataset and also showed consistent downregulation in the other datasets. The miRNAs associated with MSI and tumor location in our data showed similar changes in the other datasets. Finally, we show that small RNAs from Epstein-Barr virus and Fusobacterium nucleatum are differentially expressed between tumor and normal adjacent tissue. CONCLUSIONS Small RNA profiling in colon cancer tissue revealed novel RNAs associated with MSI and tumor location. We show that Fusobacterium nucleatum are detectable at the RNA-level in colon tissue, and that both Fusobacterium nucleatum and Epstein-Barr virus separate tumor and normal tissue.
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Affiliation(s)
- Robin Mjelle
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.
| | - Wenche Sjursen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Department of Medical Genetics, St Olavs Hospital, Trondheim Norway, Erling Skjalgssons gt 1, 7030, Trondheim, Norway
| | - Liv Thommesen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Department of Biomedical Laboratory Science, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Department of Computer and Information Science, Norwegian University of Science and Technology, NTNU, Sem Sælandsvei 9, 7491, Trondheim, Norway.,Bioinformatics core facility-BioCore, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Eva Hofsli
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,The Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
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25
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Bhullar DS, Barriuso J, Mullamitha S, Saunders MP, O'Dwyer ST, Aziz O. Biomarker concordance between primary colorectal cancer and its metastases. EBioMedicine 2019; 40:363-374. [PMID: 30733075 PMCID: PMC6413540 DOI: 10.1016/j.ebiom.2019.01.050] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/13/2019] [Accepted: 01/24/2019] [Indexed: 12/17/2022] Open
Abstract
Background The use of biomarkers to target anti-EGFR treatments for metastatic colorectal cancer (CRC) is well-established, requiring molecular analysis of primary or metastatic biopsies. We aim to review concordance between primary CRC and its metastatic sites. Methods A systematic review and meta-analysis of all published studies (1991–2018) reporting on biomarker concordance between primary CRC and its metastatic site(s) was undertaken according to PRISMA guidelines using several medical databases. Studies without matched samples or using peripheral blood for biomarker analysis were excluded. Findings 61 studies including 3565 patient samples were included. Median biomarker concordance for KRAS (n = 50) was 93.7% [[67], [68], [69], [70], [71], [72], [73], [74], [75], [76], [77], [78], [79], [80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]], NRAS (n = 11) was 100% [[90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]], BRAF (n = 22) was 99.4% [[80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]], and PIK3CA (n = 17) was 93% [[42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66], [67], [68], [69], [70], [71], [72], [73], [74], [75], [76], [77], [78], [79], [80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]]. Meta-analytic pooled discordance was 8% for KRAS (95% CI = 5–10%), 8% for BRAF (95% CI = 5–10%), 7% for PIK3CA (95% CI = 2–13%), and 28% overall (95% CI = 14–44%). The liver was the most commonly biopsied metastatic site (n = 2276), followed by lung (n = 438), lymph nodes (n = 1123), and peritoneum (n = 132). Median absolute concordance in multiple biomarkers was 81% (5–95%). Interpretation Metastatic CRC demonstrates high concordance across multiple biomarkers, suggesting that molecular testing of either the primary or liver and lung metastasis is adequate. More research on colorectal peritoneal metastases is required.
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Affiliation(s)
- D S Bhullar
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - J Barriuso
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - S Mullamitha
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - M P Saunders
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - S T O'Dwyer
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - O Aziz
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK.
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26
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Blank A, Roberts DE, Dawson H, Zlobec I, Lugli A. Tumor Heterogeneity in Primary Colorectal Cancer and Corresponding Metastases. Does the Apple Fall Far From the Tree? Front Med (Lausanne) 2018; 5:234. [PMID: 30234115 PMCID: PMC6128217 DOI: 10.3389/fmed.2018.00234] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/01/2018] [Indexed: 01/05/2023] Open
Abstract
Colorectal cancer harbors tremendous heterogeneity, with temporal and spatial differences in genetic mutations, epigenetic regulation, and tumor microenvironment. Analyzing the distribution and frequency of genetic, epigenetic, and microenvironment differences within a given tumor and between different sites of a metastatic tumor has been used as a powerful tool to investigate tumorigenesis, tumor progression, and to yield insight into various models of tumor development. A better understanding of tumor heterogeneity would have tremendous clinical relevance, which may manifest most clearly when genetic analyses to inform treatment decisions are performed on a very limited sample of a large tumor. This review summarizes the current concepts of tumor heterogeneity, with a focus on primary colorectal cancers and their corresponding metastases as well as potential clinical implications.
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Affiliation(s)
- Annika Blank
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States.,Clinical Pathology Division, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Daniel Edward Roberts
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Heather Dawson
- Clinical Pathology Division, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Inti Zlobec
- Translational Research Unit, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Alessandro Lugli
- Clinical Pathology Division, Institute of Pathology, University of Bern, Bern, Switzerland
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27
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Neerincx M, Poel D, Sie DLS, van Grieken NCT, Shankaraiah RC, van der Wolf - de Lijster FSW, van Waesberghe JHTM, Burggraaf JD, Eijk PP, Verhoef C, Ylstra B, Meijer GA, van de Wiel MA, Buffart TE, Verheul HMW. Combination of a six microRNA expression profile with four clinicopathological factors for response prediction of systemic treatment in patients with advanced colorectal cancer. PLoS One 2018; 13:e0201809. [PMID: 30075027 PMCID: PMC6075783 DOI: 10.1371/journal.pone.0201809] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/22/2018] [Indexed: 12/19/2022] Open
Abstract
Background First line chemotherapy is effective in 75 to 80% of patients with metastatic colorectal cancer (mCRC). We studied whether microRNA (miR) expression profiles can predict treatment outcome for first line fluoropyrimidine containing systemic therapy in patients with mCRC. Methods MiR expression levels were determined by next generation sequencing from snap frozen tumor samples of 88 patients with mCRC. Predictive miRs were selected with penalized logistic regression and posterior forward selection. The prediction co-efficients of the miRs were re-estimated and validated by real-time quantitative PCR in an independent cohort of 81 patients with mCRC. Results Expression levels of miR-17-5p, miR-20a-5p, miR-30a-5p, miR-92a-3p, miR-92b-3p and miR-98-5p in combination with age, tumor differentiation, adjuvant therapy and type of systemic treatment, were predictive for clinical benefit in the training cohort with an AUC of 0.78. In the validation cohort the addition of the six miR signature to the four clinicopathological factors demonstrated a significant increased AUC for predicting treatment response versus those with stable disease (SD) from 0.79 to 0.90. The increase for predicting treatment response versus progressive disease (PD) and for patients with SD versus those with PD was not significant. in the validation cohort. MiR-17-5p, miR-20a-5p and miR-92a-3p were significantly upregulated in patients with treatment response in both the training and validation cohorts. Conclusion A six miR expression signature was identified that predicted treatment response to fluoropyrimidine containing first line systemic treatment in patients with mCRC when combined with four clinicopathological factors. Independent validation demonstrated added predictive value of this miR-signature for predicting treatment response versus SD. However, added predicted value for separating patients with PD could not be validated. The clinical relevance of the identified miRs for predicting treatment response has to be further explored.
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Affiliation(s)
- Maarten Neerincx
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Dennis Poel
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Daoud L. S. Sie
- Department of Pathology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Nicole C. T. van Grieken
- Department of Pathology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Ram C. Shankaraiah
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | | | | | | | - Paul P. Eijk
- Department of Pathology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Cornelis Verhoef
- Department of Surgical Oncology, Erasmus Medical Center Cancer Institute, Rotterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mark A. van de Wiel
- Department of Epidemiology and Biostatistics, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
- Department of Mathematics, VU University, Amsterdam, The Netherlands
| | - Tineke E. Buffart
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M. W. Verheul
- Department of Medical Oncology, VUmc Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
- * E-mail:
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28
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Arvidsson Y, Rehammar A, Bergström A, Andersson E, Altiparmak G, Swärd C, Wängberg B, Kristiansson E, Nilsson O. miRNA profiling of small intestinal neuroendocrine tumors defines novel molecular subtypes and identifies miR-375 as a biomarker of patient survival. Mod Pathol 2018; 31:1302-1317. [PMID: 29487354 DOI: 10.1038/s41379-018-0010-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 12/08/2017] [Accepted: 12/08/2017] [Indexed: 12/30/2022]
Abstract
The aim of this study was to define the miRNA profile of small intestinal neuroendocrine tumors and to search for novel molecular subgroups and prognostic biomarkers. miRNA profiling was conducted on 42 tumors from 37 patients who underwent surgery for small intestinal neuroendocrine tumors. Unsupervised hierarchical clustering analysis of miRNA profiles identified two groups of tumor metastases, denoted cluster M1 and M2. The smaller cluster M1 was associated with shorter overall survival and contained tumors with higher grade (WHO grade G2/3) and multiple chromosomal gains including gain of chromosome 14. Tumors of cluster M1 had elevated expression of miR-1246 and miR-663a, and reduced levels of miR-488-3p. Pathway analysis predicted Wnt signaling to be the most significantly altered signaling pathway between clusters M1 and M2. Analysis of miRNA expression in relation to tumor proliferation rate showed significant alterations including downregulation of miR-137 and miR-204-5p in tumors with Ki67 index above 3%. Similarly, tumor progression was associated with significant alterations in miRNA expression, e.g. higher expression of miR-95 and miR-210, and lower expression of miR-378a-3p in metastases. Pathway analysis predicted Wnt signaling to be altered during tumor progression, which was supported by decreased nuclear translocation of β-catenin in metastases. Survival analysis revealed that downregulation of miR-375 was associated with shorter overall survival. We performed in situ hybridization on biopsies from an independent cohort of small intestinal neuroendocrine tumors using tissue microarrays. Expression of miR-375 was found in 578/635 (91%) biopsies and survival analysis confirmed that there was a correlation between downregulation of miR-375 in tumor metastases and shorter patient survival. We conclude that miRNA profiling defines novel molecular subgroups of metastatic small intestinal neuroendocrine tumors and identifies miRNAs associated with tumor proliferation rate and progression. miR-375 is highly expressed in small intestinal neuroendocrine tumors and may be used as a prognostic biomarker.
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Affiliation(s)
- Yvonne Arvidsson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.
| | - Anna Rehammar
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Anders Bergström
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Ellinor Andersson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Gülay Altiparmak
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Christina Swärd
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Bo Wängberg
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Ola Nilsson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
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29
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eNOS expression and NO release during hypoxia is inhibited by miR-200b in human endothelial cells. Angiogenesis 2018; 21:711-724. [PMID: 29737439 PMCID: PMC6208887 DOI: 10.1007/s10456-018-9620-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/03/2018] [Indexed: 02/07/2023]
Abstract
The nitric oxide (NO) secreted by vascular endothelium is required for the maintenance of cardiovascular homeostasis. Diminished release of NO generated by endothelial NO synthase contributes to endothelial dysfunction. Hypoxia and ischemia reduce endothelial eNOS expression via posttranscriptional mechanisms that result in NOS3 transcript destabilization. Here, we examine whether microRNAs contribute to this mechanism. We followed the kinetics of hypoxia-induced changes in NOS3 mRNA and eNOS protein levels in primary human umbilical vein endothelial cells (HUVECs). Utilizing in silico predictive protocols to identify potential miRNAs that regulate eNOS expression, we identified miR-200b as a candidate. We established the functional miR-200b target sequence within the NOS3 3′UTR, and demonstrated that manipulation of the miRNA levels during hypoxia using miR-200b mimics and antagomirs regulates eNOS levels, and established that miR-200b physiologically limits eNOS expression during hypoxia. Furthermore, we demonstrated that the specific ablation of the hypoxic induction of miR-200b in HUVECs restored eNOS-driven hypoxic NO release to the normoxic levels. To determine whether miR-200b might be the only miRNA that had this effect, we utilized Next Generation Sequencing (NGS) to follow hypoxia-induced changes in the miRNA levels in HUVECS and found 83 novel hypoxamiRs, with two candidate miRNAs besides miR-200b that could potentially influence eNOS levels. Taken together, the data establish miR-200b-eNOS regulation as a first hypoxamiR-based mechanism that limits NO bioavailability during hypoxia in endothelial cells, and show that hypoxamiRs could become useful therapeutic targets for cardiovascular diseases and other hypoxic-related diseases including various types of cancer.
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30
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Wu J, Ding J, Yang J, Guo X, Zheng Y. MicroRNA Roles in the Nuclear Factor Kappa B Signaling Pathway in Cancer. Front Immunol 2018; 9:546. [PMID: 29616037 PMCID: PMC5868594 DOI: 10.3389/fimmu.2018.00546] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/02/2018] [Indexed: 12/19/2022] Open
Abstract
Nuclear factor kappa B (NF-κB) is a pluripotent and crucial dimer transcription factor that orchestrates various physiological and pathological processes, especially cell proliferation, inflammation, and cancer development and progression. NF-κB expression is transient and tightly regulated in normal cells, but it is activated in cancer cells. Recently, numerous studies have demonstrated microRNAs (miRNAs) play a vital role in the NF-κB signaling pathway and NF-κB-associated immune responses, radioresistance and drug resistance of cancer, some acting as inhibitors and the others as activators. Although it is still in infancy, targeting NF-κB or the NF-κB signaling pathway by miRNAs is becoming a promising strategy of cancer treatment.
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Affiliation(s)
- Jin’en Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute (CAAS), Lanzhou, China
| | - Juntao Ding
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Jing Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute (CAAS), Lanzhou, China
| | - Xiaola Guo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute (CAAS), Lanzhou, China
| | - Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute (CAAS), Lanzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
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31
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Poel D, Buffart TE, Oosterling-Jansen J, Verheul HM, Voortman J. Evaluation of several methodological challenges in circulating miRNA qPCR studies in patients with head and neck cancer. Exp Mol Med 2018. [PMID: 29520111 PMCID: PMC5898892 DOI: 10.1038/emm.2017.288] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Circulating microRNAs (ci-miRNAs) in blood have emerged as promising diagnostic, prognostic and predictive biomarkers in cancer. Many clinical studies currently incorporate studies that assess ci-miRNAs. Validation of the clinical significance of candidate biomarker miRNAs has proven to be difficult, potentially resulting from vast discrepancies in the detection methodology as well as biological variability. In the current study, the influence of several methodological factors on ci-miRNA detection was evaluated as well as short-term biological variability in patients with head and neck cancer. RNA was isolated from 124 serum and plasma samples originating from patients with head and neck cancer and healthy volunteers. The miRNA levels were measured using RT-qPCR and the influence of pre-analytical factors, different normalization strategies and temporal reproducibility was assessed. RNA carriers improved ci-miRNA detection in serum and plasma specimens. A prolonged pre-processing time correlated with an increased hemolytic index in serum samples only. Hemolysis differentially affected the detection of individual miRNAs. Optimal normalization was achieved using the averaged detection values of spike-in cel-miR-39-3p and endogenous miR-16-5p. Comparing biological replicates from patients with head and neck cancer, the intra-individual miRNA levels were relatively stable (average interval 7 days). Differences in the ci-miRNA detection methodology and limitations of currently used technologies can greatly affect the results and may explain inconsistent outcomes between studies. Prior to the implementation of ci-miRNAs as useful clinical biomarkers, further advances in the standardization of the detection methodology and reduction of technical variability are needed.
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Affiliation(s)
- Dennis Poel
- Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Tineke E Buffart
- Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Jolanda Oosterling-Jansen
- Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Henk Mw Verheul
- Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Jens Voortman
- Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, The Netherlands
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32
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Schrijver WAME, van Diest PJ, Moelans CB. Unravelling site-specific breast cancer metastasis: a microRNA expression profiling study. Oncotarget 2018; 8:3111-3123. [PMID: 27902972 PMCID: PMC5356868 DOI: 10.18632/oncotarget.13623] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/21/2016] [Indexed: 01/07/2023] Open
Abstract
Distant metastasis is still the main cause of death from breast cancer. MicroRNAs (miRs) are important regulators of many physiological and pathological processes, including metastasis. Molecular breast cancer subtypes are known to show a site-specific pattern of metastases formation. In this study, we set out to determine the underlying molecular mechanisms of site-specific breast cancer metastasis by microRNA expression profiling. To identify a miR signature for metastatic breast carcinoma that could predict metastatic localization, we compared global miR expression in 23 primary breast cancer specimens with their corresponding multiple distant metastases to ovary (n=9), skin (n=12), lung (n=10), brain (n=4) and gastrointestinal tract (n=10) by miRCURY microRNA expression arrays. For validation, we performed quantitative real-time (qRT) PCR on the discovery cohort and on an independent validation cohort of 29 primary breast cancer specimens and their matched metastases. miR expression was highly patient specific and miR signatures in the primary tumor were largely retained in the metastases, with the exception of several differentially expressed, location specific miRs. Validation with qPCR demonstrated that hsa-miR-106b-5p was predictive for the development of lung metastases. In time, the second metastasis often showed a miR upregulation compared to the first metastasis. This study discovered a metastatic site-specific miR and found miR expression to be highly patient specific. This may lead to novel biomarkers predicting site of distant metastases, and to adjuvant, personalized targeted therapy strategies that could prevent such metastases from becoming clinically manifest.
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Affiliation(s)
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
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33
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Cooks T, Pateras IS, Jenkins LM, Patel KM, Robles AI, Morris J, Forshew T, Appella E, Gorgoulis VG, Harris CC. Mutant p53 cancers reprogram macrophages to tumor supporting macrophages via exosomal miR-1246. Nat Commun 2018; 9:771. [PMID: 29472616 PMCID: PMC5823939 DOI: 10.1038/s41467-018-03224-w] [Citation(s) in RCA: 340] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 01/30/2018] [Indexed: 02/06/2023] Open
Abstract
TP53 mutants (mutp53) are involved in the pathogenesis of most human cancers. Specific mutp53 proteins gain oncogenic functions (GOFs) distinct from the tumor suppressor activity of the wild-type protein. Tumor-associated macrophages (TAMs), a hallmark of solid tumors, are typically correlated with poor prognosis. Here, we report a non-cell-autonomous mechanism, whereby human mutp53 cancer cells reprogram macrophages to a tumor supportive and anti-inflammatory state. The colon cancer cells harboring GOF mutp53 selectively shed miR-1246-enriched exosomes. Uptake of these exosomes by neighboring macrophages triggers their miR-1246-dependent reprogramming into a cancer-promoting state. Mutp53-reprogammed TAMs favor anti-inflammatory immunosuppression with increased activity of TGF-β. These findings, associated with poor survival in colon cancer patients, strongly support a microenvironmental GOF role for mutp53 in actively engaging the immune system to promote cancer progression and metastasis. p53 gain of function mutants (mutp53) are involved in the pathogenesis of most human cancers. Here, the authors show that mutp53 regulates the tumor microenvironment by inducing the release of specific exosomes containing miR-1246 that once received by macrophages turns them into tumor supportive macrophages.
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Affiliation(s)
- Tomer Cooks
- Laboratory of Human Carcinogenesis, NCI-CCR, National Institutes of Health, Bethesda, 20892-4258, MD, USA
| | - Ioannis S Pateras
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias St, Athens, GR-11527, Greece
| | - Lisa M Jenkins
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, 20892-4258, MD, USA
| | - Keval M Patel
- Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, NCI-CCR, National Institutes of Health, Bethesda, 20892-4258, MD, USA
| | - James Morris
- Cancer Research UK, Cambridge Research Institute, Robinsons Way, Cambridge, CB2 0RE, UK
| | - Tim Forshew
- UCL Cancer Institute, Huntley St, Camden Town, London, WC1E 6DD, UK
| | - Ettore Appella
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, 20892-4258, MD, USA
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias St, Athens, GR-11527, Greece.,Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou St., GR-11527, Athens, Greece.,Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health, Science Centre, Wilmslow Road, Manchester, M20 4QL, UK
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, NCI-CCR, National Institutes of Health, Bethesda, 20892-4258, MD, USA.
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34
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Shao Y, Shen Y, Chen T, Xu F, Chen X, Zheng S. The functions and clinical applications of tumor-derived exosomes. Oncotarget 2018; 7:60736-60751. [PMID: 27517627 PMCID: PMC5312416 DOI: 10.18632/oncotarget.11177] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/1969] [Accepted: 07/13/2016] [Indexed: 02/06/2023] Open
Abstract
Exosomes are extracellular vesicles with diameters ranging from 30 to 150 nm. They can be secreted by all cell types and transfer information in the form of their contents, which include proteins, lipids and nucleic acids, to other cells throughout the body. They have roles in normal physiological processes as well as in disease development. Here, we review recent findings regarding tumor-derived exosomes, including methods for their extraction and preservation. We also describe the actions of exosomes in tumorigenesis. The exosomal antigen-presenting effect during antitumor immune responses and its suppressive function in immune tolerance are discussed. Finally, we describe the potential application of exosomes to cancer therapy and liquid biopsy.
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Affiliation(s)
- Yingkuan Shao
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanwei Shen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ting Chen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fei Xu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xuewen Chen
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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35
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El Bairi K, Tariq K, Himri I, Jaafari A, Smaili W, Kandhro AH, Gouri A, Ghazi B. Decoding colorectal cancer epigenomics. Cancer Genet 2018; 220:49-76. [PMID: 29310839 DOI: 10.1016/j.cancergen.2017.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/01/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is very heterogeneous and presents different types of epigenetic alterations including DNA methylation, histone modifications and microRNAs. These changes are considered as characteristics of various observed clinical phenotypes. Undoubtedly, the discovery of epigenetic pathways with novel epigenetic-related mechanisms constitutes a promising advance in cancer biomarker discovery. In this review, we provide an evidence-based discussing of the current understanding of CRC epigenomics and its role in initiation, epithelial-to-mesenchymal transition and metastasis. We also discuss the recent findings regarding the potential clinical perspectives of these alterations as potent biomarkers for CRC diagnosis, prognosis, and therapy in the era of liquid biopsy.
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Affiliation(s)
- Khalid El Bairi
- Independent Research Team in Cancer Biology and Bioactive Compounds, Mohamed 1(st) University, Oujda, Morocco.
| | - Kanwal Tariq
- B-10 Jumani Center, Garden East, Karachi 74400, Pakistan
| | - Imane Himri
- Laboratory of Biochemistry, Faculty of Sciences, Mohamed I(st) Universiy, Oujda, Morocco; Delegation of the Ministry of Health, Oujda, Morocco
| | - Abdeslam Jaafari
- Laboratoire de Génie Biologique, Equipe d'Immunopharmacologie, Faculté des Sciences et Techniques, Université Sultan Moulay Slimane, Beni Mellal, Maroc
| | - Wiam Smaili
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohamed V, Rabat, Maroc; Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Maroc
| | - Abdul Hafeez Kandhro
- Department of Biochemistry, Healthcare Molecular and Diagnostic Laboratory, Hyderabad, Pakistan
| | - Adel Gouri
- Laboratory of Medical Biochemistry, Ibn Rochd University Hospital, Annaba, Algeria
| | - Bouchra Ghazi
- National Laboratory of Reference, Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
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36
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Del Vecchio F, Mastroiaco V, Di Marco A, Compagnoni C, Capece D, Zazzeroni F, Capalbo C, Alesse E, Tessitore A. Next-generation sequencing: recent applications to the analysis of colorectal cancer. J Transl Med 2017; 15:246. [PMID: 29221448 PMCID: PMC5723063 DOI: 10.1186/s12967-017-1353-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023] Open
Abstract
Since the establishment of the Sanger sequencing method, scientists around the world focused their efforts to progress in the field to produce the utmost technology. The introduction of next-generation sequencing (NGS) represents a revolutionary step and promises to lead to massive improvements in our understanding on the role of nucleic acids functions. Cancer research began to use this innovative and highly performing method, and interesting results started to appear in colorectal cancer (CRC) analysis. Several studies produced high-quality data in terms of mutation discovery, especially about actionable or less frequently mutated genes, epigenetics, transcriptomics. Analysis of results is unveiling relevant perspectives aiding to evaluate the response to therapies. Novel evidences have been presented also in other directions such as gut microbiota or CRC circulating tumor cells. However, despite its unquestioned potential, NGS poses some issues calling for additional studies. This review intends to offer a view of the state of the art of NGS applications to CRC through examination of the most important technologies and discussion of recent published results.
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Affiliation(s)
- Filippo Del Vecchio
- Division of Cancer Sciences, University of Southampton, Southampton, Hampshire, SO16 6YD UK
| | - Valentina Mastroiaco
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Antinisca Di Marco
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Daria Capece
- Department of Medicine, Centre for Cell Signaling and Inflammation, Imperial College London, London, W12 0NN UK
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, La Sapienza University, Rome, 00161 Italy
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
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37
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Ragusa M, Barbagallo C, Cirnigliaro M, Battaglia R, Brex D, Caponnetto A, Barbagallo D, Di Pietro C, Purrello M. Asymmetric RNA Distribution among Cells and Their Secreted Exosomes: Biomedical Meaning and Considerations on Diagnostic Applications. Front Mol Biosci 2017; 4:66. [PMID: 29046875 PMCID: PMC5632685 DOI: 10.3389/fmolb.2017.00066] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/20/2017] [Indexed: 12/17/2022] Open
Abstract
Over the past few years, exosomes and their RNA cargo have been extensively studied because of the fascinating biological roles they play in cell-to-cell communication, including the signal exchange among cancer, stromal, and immune cells, leading to modifications of tumor microenvironment. RNAs, especially miRNAs, stored within exosomes, seem to be among the main determinants of such signaling: their sorting into exosomes appears to be cell-specific and related to cellular physiopathology. Accordingly, the identification of exosomal miRNAs in body fluids from pathological patients has become one of the most promising activity in the field of biomarker discovery. Several analyses on the qualitative and quantitative distribution of RNAs between cells and their secreted exosomes have given rise to questions on whether and how accurately exosomal RNAs would represent the transcriptomic snapshot of the physiological and pathological status of secreting cells. Although the exact molecular mechanisms of sorting remain quite elusive, many papers have reported an evident asymmetric quantitative distribution of RNAs between source cells and their exosomes. This phenomenon could depend both on passive and active sorting mechanisms related to: (a) RNA turnover; (b) maintaining the cytoplasmic miRNA:target equilibrium; (c) removal of RNAs not critical or even detrimental for normal or diseased cells. These observations represent very critical issues in the exploitation of exosomal miRNAs as cancer biomarkers. In this review, we will discuss how much the exosomal and corresponding donor cell transcriptomes match each other, to better understand the actual reliability of exosomal RNA molecules as pathological biomarkers reflecting a diseased status of the cells.
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Affiliation(s)
- Marco Ragusa
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy.,IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Italy
| | - Cristina Barbagallo
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Matilde Cirnigliaro
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Rosalia Battaglia
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Duilia Brex
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Angela Caponnetto
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Davide Barbagallo
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Cinzia Di Pietro
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Michele Purrello
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of BioMedical Sciences and Biotechnology, University of Catania, Catania, Italy
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38
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Mjelle R, Sellæg K, Sætrom P, Thommesen L, Sjursen W, Hofsli E. Identification of metastasis-associated microRNAs in serum from rectal cancer patients. Oncotarget 2017; 8:90077-90089. [PMID: 29163812 PMCID: PMC5685733 DOI: 10.18632/oncotarget.21412] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 08/31/2017] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are promising prognostic and diagnostic biomarkers due to their high stability in blood. Here we investigate the expression of miRNAs and other noncoding (nc) RNAs in serum of rectal cancer patients. Serum from 96 rectal cancer patients was profiled using small RNA sequencing and expression of small RNAs was correlated with the clinicopathological characteristics of the patients. Multiple classes of RNAs were detected, including miRNAs and fragments of tRNAs, snoRNAs, long ncRNAs, and other classes of RNAs. Several miRNAs, miRNA variants (isomiRs) and other ncRNAs were differentially expressed between Stage IV and Stage I-III rectal cancer patients, including several members of the miR-320 family. Furthermore, we show that high expression of miR-320d as well as one tRNA fragment is associated with poor survival. We also show that several miRNAs and isomiRs are differentially expressed between patients receiving preoperative chemoradiotherapy and patients who did not receive any treatment before serum collection. In summary, our study shows that the expression of miRNAs and other small ncRNAs in serum may be used to predict distant metastasis and survival in rectal cancer.
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Affiliation(s)
- Robin Mjelle
- Department of Clinical and Molecular Medicine, NO-7491 Trondheim, Norway
| | - Kjersti Sellæg
- Department of Clinical and Molecular Medicine, NO-7491 Trondheim, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, NO-7491 Trondheim, Norway.,Department of Computer Science, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Liv Thommesen
- Department of Biomedical Science, Norwegian University of Science and Technology, 7030 Trondheim Norway
| | - Wenche Sjursen
- Department of Clinical and Molecular Medicine, NO-7491 Trondheim, Norway.,Department of Medical Genetics, St. Olavs Hospital, Norwegian University of Science and Technology, 7030 Trondheim Norway
| | - Eva Hofsli
- Department of Clinical and Molecular Medicine, NO-7491 Trondheim, Norway.,The Cancer Clinic, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
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Singh MP, Rai S, Suyal S, Singh SK, Singh NK, Agarwal A, Srivastava S. Genetic and epigenetic markers in colorectal cancer screening: recent advances. Expert Rev Mol Diagn 2017; 17:665-685. [PMID: 28562109 DOI: 10.1080/14737159.2017.1337511] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Colorectal cancer (CRC) is a heterogenous disease which develops from benign intraepithelial lesions known as adenomas to malignant carcinomas. Acquired alterations in Wnt signaling, TGFβ, MAPK pathway genes and clonal propagation of altered cells are responsible for this transformation. Detection of adenomas or early stage cancer in asymptomatic patients and better prognostic and predictive markers is important for improving the clinical management of CRC. Area covered: In this review, the authors have evaluated the potential of genetic and epigenetic alterations as markers for early detection, prognosis and therapeutic predictive potential in the context of CRC. We have discussed molecular heterogeneity present in CRC and its correlation to prognosis and response to therapy. Expert commentary: Molecular marker based CRC screening methods still fail to gain trust of clinicians. Invasive screening methods, molecular heterogeneity, chemoresistance and low quality test samples are some key challenges which need to be addressed in the present context. New sequencing technologies and integrated omics data analysis of individual or population cohort results in GWAS. MPE studies following a GWAS could be future line of research to establish accurate correlations between CRC and its risk factors. This strategy would identify most reliable biomarkers for CRC screening and management.
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Affiliation(s)
- Manish Pratap Singh
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Sandhya Rai
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Shradha Suyal
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Sunil Kumar Singh
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Nand Kumar Singh
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
| | - Akash Agarwal
- b Department of Surgical Oncology , Dr. Ram Manohar Lohia Institute of Medical Sciences (DRMLIMS) , Lucknow , India
| | - Sameer Srivastava
- a Department of Biotechnology , Motilal Nehru National Institute of Technology (MNNIT) Allahabad , India
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Qin CZ, Lv QL, Yang YT, Zhang JM, Zhang XJ, Zhou HH. Downregulation of MicroRNA-320d predicts poor overall survival and promotes the growth and invasive abilities in glioma. Chem Biol Drug Des 2016; 89:806-814. [PMID: 27862991 DOI: 10.1111/cbdd.12906] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 10/20/2016] [Accepted: 10/31/2016] [Indexed: 01/02/2023]
Abstract
Previous studies have demonstrated that miRNAs play an important role in tumor development and progression. The role of miR-320d has been studied in several cancers except for glioma. The aim of the study was to investigate the expression levels, biological function, and mechanism of miR-320d in glioma. The expression levels of miR-320d were detected in glioma tissues and cell lines (U87 and U251) by RT-qPCR. Cell proliferation, colony formation, apoptosis, cell cycle, and transwell assays were performed in glioma cell lines transfected with miR-320d mimics or controls to evaluate the effects of miR-320d in vitro. The expression levels of invasive-related proteins were determined by Western blot analysis. Results showed that the expression of miR-320d was significantly decreased in glioma tissues and cell lines. Overexpression of miR-320d could significantly suppress cell growth, migration and invasion, and induced cell apoptosis as well as cell cycle at G0/G1 arrest in U87 and U251 cell lines. Additionally, expression levels of MMP-2, MMP-9, N-cadherin, and integrin-β1 reduced, while E-cadherin increased in miR-320d mimic group. Overall, this study is the first to demonstrate that miR-320d may serve as an independent prognostic factor, indicating that miR-320d is a biomarker for prognosis and therapy in glioma.
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Affiliation(s)
- Chong-Zhen Qin
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiao-Li Lv
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Yan-Tao Yang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing-Min Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiao-Jian Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
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Cui X, Li Q, He Y. miR-3117 regulates hepatocellular carcinoma cell proliferation by targeting PHLPPL. Mol Cell Biochem 2016; 424:195-201. [PMID: 27822662 DOI: 10.1007/s11010-016-2855-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 10/22/2016] [Indexed: 01/01/2023]
Abstract
Altered microRNA expression is associated with tumor proliferation, metastasis, and tumorigenesis. In this study, we studied the role of miR-3117 in hepatocellular carcinoma (HCC) cell proliferation and found that miR-3117 was upregulated in HCC tissues and cells. MTT assay, soft agar growth assay, BrdU assay, and cell cycle assay revealed that miR-3117 overexpression promoted HCC HepG2 cell proliferation and that knockdown of miR-3117 suppressed HepG2 proliferation. Mechanism analysis suggested PH domain and leucine-rich repeat protein phosphatase-like (PHLPPL) as the target of miR-3117. Luciferase reporter assay suggested that miR-3117 directly binds to the 3'UTR of PHLPPL. Double knockdown of miR-3117 and PHLPPL copied the phenotypes caused by miR-3117 overexpression, suggesting that miR-3117 contributes to the proliferation of HepG2 by targeting PHLPPL. Our study provided a target for HCC therapy.
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Affiliation(s)
- Xia Cui
- Department of Hepatopathy, Liaocheng People's Hospital, 67 Dongchang West Road, Liaocheng, 252000, China
| | - Qingyan Li
- Department of Hepatopathy, Liaocheng People's Hospital, 67 Dongchang West Road, Liaocheng, 252000, China
| | - Yukai He
- Department of Hepatopathy, Liaocheng People's Hospital, 67 Dongchang West Road, Liaocheng, 252000, China.
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Shigeyasu K, Okugawa Y, Toden S, Boland CR, Goel A. Exportin-5 Functions as an Oncogene and a Potential Therapeutic Target in Colorectal Cancer. Clin Cancer Res 2016; 23:1312-1322. [PMID: 27553833 DOI: 10.1158/1078-0432.ccr-16-1023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/13/2016] [Accepted: 08/16/2016] [Indexed: 12/12/2022]
Abstract
Purpose: Dysregulated expression of miRNAs has emerged as a hallmark feature in human cancers. Exportin-5 (XPO5), a karyopherin family member, is a key protein responsible for transporting precursor miRNAs from the nucleus to the cytoplasm. Although XPO5 is one of the key regulators of miRNA biogenesis, its functional role and potential clinical significance in colorectal cancer remains unclear.Experimental Design: The expression levels of XPO5 were initially assessed in three genomic datasets, followed by determination and validation of the relationship between XPO5 expression and clinicopathologic features in two independent colorectal cancer patient cohorts. A functional characterization of XPO5 in colorectal cancer was examined by targeted gene silencing in colorectal cancer cell lines and a xenograft animal model.Results: XPO5 is upregulated, both at mRNA and protein levels, in colorectal cancers compared with normal tissues. High XPO5 expression is associated with worse clinicopathologic features and poor survival in colorectal cancer patient cohorts. The siRNA knockdown of XPO5 resulted in reduced cellular proliferation, attenuated invasion, induction of G1-S cell-cycle arrest, and downregulation of key oncogenic miRNAs in colorectal cancer cells. These findings were confirmed in a xenograft animal model, wherein silencing of XPO5 resulted in the attenuation of tumor growth.Conclusions: XPO5 acts like an oncogene in colorectal cancer by regulating the expression of miRNAs and may be a potential therapeutic target in colorectal cancer. Clin Cancer Res; 23(5); 1312-22. ©2016 AACR.
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Affiliation(s)
- Kunitoshi Shigeyasu
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention, and Cancer Genomics, Baylor Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention, and Cancer Genomics, Baylor Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Shusuke Toden
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention, and Cancer Genomics, Baylor Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - C Richard Boland
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention, and Cancer Genomics, Baylor Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Epigenetics, Cancer Prevention, and Cancer Genomics, Baylor Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas.
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Abstract
Since their discovery in 1993, microRNAs (miRNAs) have been identified as important gene regulators in many biological processes and as key molecular players in human disease, including cancer where they show specific pathogenic deregulation. Their remarkable chemical stability, the availability of very sensitive miRNA detection methods and the fact that miRNAs can be extracted from and detected in various kinds of clinically relevant samples, such as solid tissues, body fluids and secretions make them excellent candidate biomarkers. However, no miRNA has yet entered the level of practical clinical relevance. We present a brief background and some key aspects and challenges of miRNAs as cancer biomarkers, we discuss shortfalls and identify possible routes towards the use of miRNAs as reliable biomarkers for cancer.
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Affiliation(s)
- Kjersti Flatmark
- a Department of Gastroenterological Surgery , Norwegian Radium Hospital, Oslo University Hospital , Oslo , Norway ;,b Department of Tumor Biology , Norwegian Radium Hospital, Oslo University Hospital , Oslo , Norway ;,c Institute of Clinical Medicine , University of Oslo , Oslo , Norway
| | - Eirik Høye
- b Department of Tumor Biology , Norwegian Radium Hospital, Oslo University Hospital , Oslo , Norway
| | - Bastian Fromm
- b Department of Tumor Biology , Norwegian Radium Hospital, Oslo University Hospital , Oslo , Norway
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Bobowicz M, Skrzypski M, Czapiewski P, Marczyk M, Maciejewska A, Jankowski M, Szulgo-Paczkowska A, Zegarski W, Pawłowski R, Polańska J, Biernat W, Jaśkiewicz J, Jassem J. Prognostic value of 5-microRNA based signature in T2-T3N0 colon cancer. Clin Exp Metastasis 2016; 33:765-773. [PMID: 27485175 PMCID: PMC5110606 DOI: 10.1007/s10585-016-9810-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/06/2016] [Indexed: 01/07/2023]
Abstract
The role of adjuvant chemotherapy in stage T2-T3N0 colon cancer (CC) is controversial and there are currently no reliable factors allowing for individual selection of patients with high risk of relapse for such therapy. We searched for microRNA-based signature with prognostic significance in this group. We assessed by qRT-PCR expression of 754 microRNAs (miRNAs) in tumour samples from 85 stage pT2-3N0 CC patients treated with surgery alone. MiRNA expression was compared between two groups of patients: 40 and 45 patients who did and did not develop distant metastases after resection, respectively. Additionally, miRNA expression was compared between CC and normal colon mucosa samples and between the mismatch repair (MMR) competent and deficient tumours. Low expression of miR-1300 and miR-939 was significantly correlated with shorter distant metastasis-free survival (DMFS) in Cox univariate analysis (p.adjusted = 0.049). The expression signature of five miRNAs (miR-1296, miR-135b, miR-539, miR-572 and miR-185) was found to be prognostic [p = 1.28E−07, HR 8.4 (95 % CI: 3.81–18.52)] for DMFS and cross-validated in a leave-one-out analysis, with the sensitivity and specificity of 74 and 78 %, respectively. The expression of miR-592 was significantly associated with the MMR status (p.adjusted <0.01). The expression of several novel miRNAs were found to be tumour specific, e.g. miR-888, miR-523, miR-18b, miR-302a, miR-423-5p, miR-582-3p (p < 0.05). We developed a miRNA expression signature that may be predictive for the risk of distant relapse in early stage CC and confirmed previously reported association between miR-592 expression and MMR status.
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Affiliation(s)
- Maciej Bobowicz
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Marcin Skrzypski
- Department of Oncology and Radiotherapy, Medical University of Gdansk, 7 Dębinki St., 80-211, Gdańsk, Poland.
| | - Piotr Czapiewski
- Department of Pathomorfology, Medical University of Gdansk, Gdańsk, Poland
| | - Michał Marczyk
- Institute of Automatic Control, Data Mining Group, Silesian University of Technology, Gliwice, Poland
| | | | - Michał Jankowski
- Department and Clinic of Oncologic Surgery, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | | | - Wojciech Zegarski
- Department and Clinic of Oncologic Surgery, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Ryszard Pawłowski
- Institute of Forensic Medicine, Medical University of Gdansk, Gdańsk, Poland
| | - Joanna Polańska
- Institute of Automatic Control, Data Mining Group, Silesian University of Technology, Gliwice, Poland
| | - Wojciech Biernat
- Department of Pathomorfology, Medical University of Gdansk, Gdańsk, Poland
| | - Janusz Jaśkiewicz
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Jacek Jassem
- Department of Oncology and Radiotherapy, Medical University of Gdansk, 7 Dębinki St., 80-211, Gdańsk, Poland
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Verma M. Genome-wide association studies and epigenome-wide association studies go together in cancer control. Future Oncol 2016; 12:1645-64. [PMID: 27079684 PMCID: PMC5551540 DOI: 10.2217/fon-2015-0035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/22/2016] [Indexed: 02/07/2023] Open
Abstract
Completion of the human genome a decade ago laid the foundation for: using genetic information in assessing risk to identify individuals and populations that are likely to develop cancer, and designing treatments based on a person's genetic profiling (precision medicine). Genome-wide association studies (GWAS) completed during the past few years have identified risk-associated single nucleotide polymorphisms that can be used as screening tools in epidemiologic studies of a variety of tumor types. This led to the conduct of epigenome-wide association studies (EWAS). This article discusses the current status, challenges and research opportunities in GWAS and EWAS. Information gained from GWAS and EWAS has potential applications in cancer control and treatment.
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Affiliation(s)
- Mukesh Verma
- Methods & Technologies Branch, Epidemiology & Genomics Research Program, Division of Cancer Control & Population Sciences, National Cancer Institute (NCI), NIH, 9609 Medical Center Drive, Suite 4E102, Rockville, MD 20850, USA
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Schou JV, Johansen JS, Nielsen D, Rossi S. Circulating microRNAs as Prognostic and Predictive Biomarkers in Patients with Colorectal Cancer. Noncoding RNA 2016; 2:ncrna2020005. [PMID: 29657263 PMCID: PMC5831904 DOI: 10.3390/ncrna2020005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 03/23/2016] [Accepted: 05/20/2016] [Indexed: 12/22/2022] Open
Abstract
MiRNAs are suggested as promising cancer biomarkers. They are stable and extractable from a variety of clinical tissue specimens (fresh frozen or formalin fixed paraffin embedded tissue) and a variety of body fluids (e.g., blood, urine, saliva). However, there are several challenges that need to be solved, considering their potential as biomarkers in cancer, such as lack of consistency between biomarker panels in independent studies due to lack of standardized sample handling and processing, use of inconsistent normalization approaches, and differences in patients populations. Focusing on colorectal cancer (CRC), divergent results regarding circulating miRNAs as prognostic or predictive biomarkers are reported in the literature. In the present review, we summarize the current data on circulating miRNAs as prognostic/predictive biomarkers in patients with localized and metastatic CRC (mCRC).
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Affiliation(s)
- Jakob Vasehus Schou
- Department of Oncology, Herlev & Gentofte Hospital, DK-2730 Herlev, Denmark.
| | - Julia Sidenius Johansen
- Department of Oncology, Herlev & Gentofte Hospital, DK-2730 Herlev, Denmark.
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørregade 10, DK-1165 Copenhagen, Denmark.
| | - Dorte Nielsen
- Department of Oncology, Herlev & Gentofte Hospital, DK-2730 Herlev, Denmark.
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørregade 10, DK-1165 Copenhagen, Denmark.
| | - Simona Rossi
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Via Vela 6, CH-6500 Bellinzona, Switzerland.
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Ahmadi S, Sharifi M, Salehi R. Locked nucleic acid inhibits miR-92a-3p in human colorectal cancer, induces apoptosis and inhibits cell proliferation. Cancer Gene Ther 2016; 23:199-205. [PMID: 27199220 DOI: 10.1038/cgt.2016.10] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 03/02/2016] [Accepted: 03/02/2016] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are a type of small noncoding RNAs that have a vital role in basic biological processes such as cellular growth, division and apoptosis. A change in the expression of miRNAs can induce many diseases. Recently, the role of miRNA in some of the cancers as a tumor suppressor and oncogene has been recognized. Several studies have proved that miR-92a-3p acts as an oncogene in colorectal cancer (CRC). We studied CRC by inhibiting miR-92a-3p in SW48 cells (human colorectal cancer cell line) that were transfected with locked nucleic acid (LNA). At different times, the expression level of miR-92a-3p, cell vitality, apoptosis and necrosis were studied by qRT-PCR, MTT, Annexin-V and propidiumiodide. Our results showed that the expression of miR-92a-3p and proliferation of SW48 cells were decreased, and also a high percentage of SW48 cells were exposed to apoptosis and necrosis (P⩽0.005). Our study showed that the inhibition of miR-92a-3p with LNA inhibited cell proliferation and induced apoptosis and necrosis in CRC.
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Affiliation(s)
- S Ahmadi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - M Sharifi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - R Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Mancuso G, Bovio E, Rena O, Rrapaj E, Mercalli F, Veggiani C, Paganotti A, Andorno S, Boldorini R. Prognostic impact of a 3-MicroRNA signature in cytological samples of small cell lung cancer. Cancer Cytopathol 2016; 124:621-9. [DOI: 10.1002/cncy.21729] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/19/2016] [Accepted: 02/11/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Giuseppe Mancuso
- Department of Health Science, School of Medicine; Amedeo Avogadro University of Eastern Piedmont; Novara Italy
| | - Enrica Bovio
- Unit of Pathology; Maggiore della Carità Hospital; Novara Italy
| | - Ottavio Rena
- Unit of Thoracic Surgery; Maggiore della Carità Hospital; Novara Italy
| | - Eltjona Rrapaj
- Department of Health Science, School of Medicine; Amedeo Avogadro University of Eastern Piedmont; Novara Italy
| | | | | | | | - Silvano Andorno
- Department of Health Science, School of Medicine; Amedeo Avogadro University of Eastern Piedmont; Novara Italy
| | - Renzo Boldorini
- Department of Health Science, School of Medicine; Amedeo Avogadro University of Eastern Piedmont; Novara Italy
- Unit of Pathology; Maggiore della Carità Hospital; Novara Italy
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Lee WY, Do JT, Park C, Kim JH, Chung HJ, Kim KW, Gil CH, Kim NH, Song H. Identification of Putative Biomarkers for the Early Stage of Porcine Spermatogonial Stem Cells Using Next-Generation Sequencing. PLoS One 2016; 11:e0147298. [PMID: 26800048 PMCID: PMC4723225 DOI: 10.1371/journal.pone.0147298] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/02/2016] [Indexed: 01/15/2023] Open
Abstract
To identify putative biomarkers of porcine spermatogonial stem cells (pSSCs), total RNA sequencing (RNA-seq) analysis was performed on 5- and 180-day-old porcine testes and on pSSC colonies that were established under low temperature culture conditions as reported previously. In total, 10,184 genes were selected using Cufflink software, followed by a logarithm and quantile normalization of the pairwise scatter plot. The correlation rates of pSSCs compared to 5- and 180-day-old testes were 0.869 and 0.529, respectively and that between 5- and 180-day-old testes was 0.580. Hierarchical clustering data revealed that gene expression patterns of pSSCs were similar to 5-day-old testis. By applying a differential expression filter of four fold or greater, 607 genes were identified between pSSCs and 5-day-old testis, and 2118 genes were identified between the 5- and 180-day-old testes. Among these differentially expressed genes, 293 genes were upregulated and 314 genes were downregulated in the 5-day-old testis compared to pSSCs, and 1106 genes were upregulated and 1012 genes were downregulated in the 180-day-old testis compared to the 5-day-old testis. The following genes upregulated in pSSCs compared to 5-day-old testes were selected for additional analysis: matrix metallopeptidase 9 (MMP9), matrix metallopeptidase 1 (MMP1), glutathione peroxidase 1 (GPX1), chemokine receptor 1 (CCR1), insulin-like growth factor binding protein 3 (IGFBP3), CD14, CD209, and Kruppel-like factor 9 (KLF9). Expression levels of these genes were evaluated in pSSCs and in 5- and 180-day-old porcine testes. In addition, immunohistochemistry analysis confirmed their germ cell-specific expression in 5- and 180-day-old testes. These finding may not only be useful in facilitating the enrichment and sorting of porcine spermatogonia, but may also be useful in the study of the early stages of spermatogenic meiosis.
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Affiliation(s)
- Won-Young Lee
- Department of Food Bioscience, Research Institute for Biomedical & Health Science, College of Biomedical & Health Science, Konkuk University, Chung-ju 380–701, Republic of Korea
| | - Jeong Tae Do
- Department of Animal Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143–701, Republic of Korea
| | - Chankyu Park
- Department of Animal Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143–701, Republic of Korea
| | - Jin Hoi Kim
- Department of Animal Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143–701, Republic of Korea
| | - Hak-Jae Chung
- Animal Biotechnology Division, National Institute of Animal Science, RDA, Wanju-gun 565–851, Republic of Korea
| | - Kyung-Woon Kim
- Animal Biotechnology Division, National Institute of Animal Science, RDA, Wanju-gun 565–851, Republic of Korea
| | - Chang-Hyun Gil
- School of Medicine, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143–701, Republic of Korea
| | - Nam-Hyung Kim
- Department of Animal Science, College of Agriculture, Chungbuk National University, Choung-ju 361–763, Republic of Korea
| | - Hyuk Song
- Department of Animal Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143–701, Republic of Korea
- * E-mail:
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