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Torang A, van de Weerd S, Lammers V, van Hooff S, van den Berg I, van den Bergh S, Koopman M, IJzermans JN, Roodhart JML, Koster J, Medema JP. NanoCMSer: a consensus molecular subtype stratification tool for fresh-frozen and paraffin-embedded colorectal cancer samples. Mol Oncol 2025; 19:1332-1346. [PMID: 39720854 PMCID: PMC12077266 DOI: 10.1002/1878-0261.13781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 10/03/2024] [Accepted: 11/28/2024] [Indexed: 12/26/2024] Open
Abstract
Colorectal cancer (CRC) is a significant contributor to cancer-related mortality, emphasizing the need for advanced biomarkers to guide treatment. As part of an international consortium, we previously categorized CRCs into four consensus molecular subtypes (CMS1-CMS4), showing promise for outcome prediction. To facilitate clinical integration of CMS classification in settings where formalin-fixed paraffin-embedded (FFPE) samples are routinely used, we developed NanoCMSer, a NanoString-based CMS classifier using 55 genes. NanoCMSer achieved high accuracy rates, with 95% for fresh-frozen samples from the MATCH cohort and 92% for FFPE samples from the CODE cohort, marking the highest reported accuracy for FFPE tissues to date. Additionally, it demonstrated 96% accuracy across a comprehensive collection of 23 RNAseq-based datasets, compiled in this study, surpassing the performance of existing models. Classifying with only 55 genes, the CMS predictions were still biologically relevant, recognizing CMS-specific biology upon enrichment analysis. Additionally, we observed substantial differences in recurrence-free survival curves when comparing CMS2/3 patients in stage III versus II. Probability of recurrence after 5 years increased by 21% in CMS2 and 31% in CMS3 for patients in stage III, whereas this difference was less pronounced for CMS1 and CMS4, with 11% and 10%, respectively. We posit NanoCMSer as a robust tool for subtyping CRCs for both tumor biology and clinical practice, accessible via nanocmser r package (https://github.com/LEXORlab/NanoCMSer) and Shinyapp (https://atorang.shinyapps.io/NanoCMSer).
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Affiliation(s)
- Arezo Torang
- Amsterdam UMC, Center for Experimental and Molecular Medicine, Cancer Center AmsterdamUniversity of AmsterdamThe Netherlands
- Oncode Institute, Amsterdam UMCUniversity of AmsterdamThe Netherlands
| | - Simone van de Weerd
- Amsterdam UMC, Center for Experimental and Molecular Medicine, Cancer Center AmsterdamUniversity of AmsterdamThe Netherlands
- Oncode Institute, Amsterdam UMCUniversity of AmsterdamThe Netherlands
- Department of PathologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Veerle Lammers
- Amsterdam UMC, Center for Experimental and Molecular Medicine, Cancer Center AmsterdamUniversity of AmsterdamThe Netherlands
- Oncode Institute, Amsterdam UMCUniversity of AmsterdamThe Netherlands
| | - Sander van Hooff
- Amsterdam UMC, Center for Experimental and Molecular Medicine, Cancer Center AmsterdamUniversity of AmsterdamThe Netherlands
- Oncode Institute, Amsterdam UMCUniversity of AmsterdamThe Netherlands
| | - Inge van den Berg
- Department of Surgery, Erasmus MCUniversity Medical Center RotterdamThe Netherlands
- Department of Medical Oncology, University Medical Center UtrechtUtrecht UniversityThe Netherlands
| | - Saskia van den Bergh
- Amsterdam UMC, Center for Experimental and Molecular Medicine, Cancer Center AmsterdamUniversity of AmsterdamThe Netherlands
- Oncode Institute, Amsterdam UMCUniversity of AmsterdamThe Netherlands
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center UtrechtUtrecht UniversityThe Netherlands
| | - Jan N. IJzermans
- Department of Surgery, Erasmus MCUniversity Medical Center RotterdamThe Netherlands
| | - Jeanine M. L. Roodhart
- Department of Medical Oncology, University Medical Center UtrechtUtrecht UniversityThe Netherlands
| | - Jan Koster
- Amsterdam UMC, Center for Experimental and Molecular Medicine, Cancer Center AmsterdamUniversity of AmsterdamThe Netherlands
| | - Jan Paul Medema
- Amsterdam UMC, Center for Experimental and Molecular Medicine, Cancer Center AmsterdamUniversity of AmsterdamThe Netherlands
- Oncode Institute, Amsterdam UMCUniversity of AmsterdamThe Netherlands
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Lella RK, Malarkannan S. IQGAP1 promotes early B cell development, is essential for the development of marginal zone (MZ) B cells, and is critical for both T-dependent and T-independent antibody responses. Cell Mol Life Sci 2024; 81:462. [PMID: 39585462 PMCID: PMC11589066 DOI: 10.1007/s00018-024-05509-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 10/23/2024] [Accepted: 11/13/2024] [Indexed: 11/26/2024]
Abstract
IQGAP1 is a multi-functional scaffold protein. However, its role in B cell development and function is unknown. Here, we show IQGAP1 as an essential scaffold that regulates early B cell development and function. Iqgap1-/- mice contained significantly increased numbers of B220+ B, B220+IgM- pro/pre-B, and B220LowIgM+ immature-B cells in the bone marrow. In the spleens of the Iqgap1-/- mice, newly formed and follicular B cell numbers were increased, while the marginal zone B cell numbers were significantly reduced. Lack of IQGAP1 reduced T-dependent and T-independent humoral responses. Mechanistically, the lack of IQGAP1 considerably decreased the phosphorylation of Mek1/2, Erk1/2, and Jnk1/2. B cells from Iqgap1-/- mice failed to suppress IL-7R-mediated activation of Stat5a/b, an essential step for cell-cycle exit and initiate light-chain recombination, reducing RS rearrangement frequency. Our study provides the first evidence that IQGAP1-based signalosome is necessary for the development and functions of B cells.
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Affiliation(s)
- Ravi K Lella
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Versiti, Milwaukee, WI, USA
- Abdi Bio, Abdi Ibrahim Pharmaceuticals, Orhan Gazi Mahallesi Tunc Caddesi No. 3, Esenyurt, Istanbul, Turkey
| | - Subramaniam Malarkannan
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Versiti, Milwaukee, WI, USA.
- Departments of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.
- Departments of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.
- Departments of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
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3
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Love CG, Coombs L, Van Laar R. RNA-seq validation of microRNA expression signatures for precision melanoma diagnosis and prognostic stratification. BMC Med Genomics 2024; 17:256. [PMID: 39456086 PMCID: PMC11515382 DOI: 10.1186/s12920-024-02028-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 10/11/2024] [Indexed: 10/28/2024] Open
Abstract
BACKGROUND New diagnostic tools are needed to improve the diagnosis and risk stratification of cutaneous melanoma. Disease-specific microRNA signatures have been previously described via NanoString profiling of solid biopsy tissue and plasma. This study validated these signatures via next-generation sequencing technology and compared their performance against clinical metrics and other published melanoma signatures. METHODS RNA from 64 plasma and 60 FFPE biopsy samples from individuals with invasive melanoma or related benign/control phenotypes was extracted and enriched for microRNA. RNA sequencing was performed to compute MEL38/MEL12 signature scores. The results were evaluated with published NanoString and RNA sequencing datasets, comprising 548 solid tissue samples and 217 plasma samples, to predict disease status and patient outcome. RESULTS The MEL38 diagnostic signature classifies patients into discrete diagnostic groups via RNA sequencing in either solid tissue or plasma (P < 0.001). In solid tissue, the prognostic MEL12 signature stratifies patients into low-, intermediate- and high-risk groups, independent of clinical covariates. The hazard ratios for 10-year overall survival, based on observed survival intervals, were 2.2 (MEL12 high-risk vs low-risk, P < 0.001) and 1.8 (intermediate-risk vs low-risk, P < 0.001), outperforming other published prognostic models. MEL12 also exhibited prognostic significance in the plasma of 42 patients with invasive disease. CONCLUSIONS The MEL38 and MEL12 signatures can be assessed in either solid tissue or plasma using RNA-seq and are strong predictors of disease state and patient outcome. Compared with other genomic methods, MEL12 was shown to be the strongest predictor of poor prognosis. MicroRNA expression profiling offers objective, accurate genomic information about a patient's likelihood of invasive melanoma and prognosis.
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Affiliation(s)
| | - Lauren Coombs
- Australian Clinical Laboratories, Clayton, VIC, Australia
| | - Ryan Van Laar
- Geneseq Biosciences, Melbourne, VIC, Australia
- Australian Clinical Laboratories, Clayton, VIC, Australia
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Block I, Burton M, Sørensen KP, Larsen MJ, Do TTN, Bak M, Cold S, Thomassen M, Tan Q, Kruse TA. Ensemble-based classification using microRNA expression identifies a breast cancer patient subgroup with an ultralow long-term risk of metastases. Cancer Med 2024; 13:e7089. [PMID: 38676390 PMCID: PMC11053369 DOI: 10.1002/cam4.7089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/28/2023] [Accepted: 01/18/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Current clinical markers overestimate the recurrence risk in many lymph node negative (LNN) breast cancer (BC) patients such that a majority of these low-risk patients unnecessarily receive systemic treatments. We tested if differential microRNA expression in primary tumors allows reliable identification of indolent LNN BC patients to provide an improved classification tool for overtreatment reduction in this patient group. METHODS We collected freshly frozen primary tumors of 80 LNN BC patients with recurrence and 80 recurrence-free patients (mean follow-up: 20.9 years). The study comprises solely systemically untreated patients to exclude that administered treatments confound the metastasis status. Samples were pairwise matched for clinical-pathological characteristics to minimize dependence of current markers. Patients were classified into risk-subgroups according to the differential microRNA expression of their tumors via classification model building with cross-validation using seven classification methods and a voting scheme. The methodology was validated using available data of two independent cohorts (n = 123, n = 339). RESULTS Of the 80 indolent patients (who would all likely receive systemic treatments today) our ultralow-risk classifier correctly identified 37 while keeping a sensitivity of 100% in the recurrence group. Multivariable logistic regression analysis confirmed independence of voting results from current clinical markers. Application of the method in two validation cohorts confirmed successful classification of ultralow-risk BC patients with significantly prolonged recurrence-free survival. CONCLUSION Profiles of differential microRNAs expression can identify LNN BC patients who could spare systemic treatments demanded by currently applied classifications. However, further validation studies are required for clinical implementation of the applied methodology.
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Affiliation(s)
- Ines Block
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
- Present address:
Department of Mathematics and Computer ScienceUniversity of MarburgMarburgGermany
| | - Mark Burton
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
- Human Genetics, Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
- Clinical Genome CenterUniversity of Southern Denmark and Region of Southern DenmarkOdenseDenmark
| | | | - Martin J. Larsen
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
- Human Genetics, Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | - Thi T. N. Do
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
- Human Genetics, Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | - Martin Bak
- Department of PathologyOdense University HospitalOdenseDenmark
- Department of PathologyHospital of Southwest JutlandEsbjergDenmark
| | - Søren Cold
- Department of OncologyOdense University HospitalOdenseDenmark
| | - Mads Thomassen
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
- Human Genetics, Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
- Clinical Genome CenterUniversity of Southern Denmark and Region of Southern DenmarkOdenseDenmark
| | - Qihua Tan
- Human Genetics, Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
- Clinical Genome CenterUniversity of Southern Denmark and Region of Southern DenmarkOdenseDenmark
- Epidemiology, Department of Public HealthUniversity of Southern DenmarkOdenseDenmark
| | - Torben A. Kruse
- Department of Clinical GeneticsOdense University HospitalOdenseDenmark
- Human Genetics, Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
- Clinical Genome CenterUniversity of Southern Denmark and Region of Southern DenmarkOdenseDenmark
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Khan MM, Sharma V, Serajuddin M. Emerging role of miRNA in prostate cancer: A future era of diagnostic and therapeutics. Gene 2023; 888:147761. [PMID: 37666374 DOI: 10.1016/j.gene.2023.147761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/17/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Prostate cancer (PCa) is the most common cancer in men (20%) and is responsible for 6.8% (1/5) of all cancer-related deaths in men around the world. The development and spread of prostate cancer are driven by a wide variety of genomic changes and extensive epigenetic events. Because of this, the MicroRNA (miRNA) and associated molecular mechanisms involved in PCa genesis and aggressive were only partially identified until today. The miRNAs are a newly discovered category of regulatorsthat have recently been recognized to have a significant role in regulating numerous elements of cancer mechanisms, such as proliferation, differentiation, metabolism, and apoptosis. The miRNAs are a type of small (22-24 nucleotides), non-coding, endogenous, single-stranded RNA and work as potent gene regulators. Various types of cancer, including PCa, have found evidence that miRNA genes, which are often located in cancer-related genetic regions or fragile locations, have a role in the primary steps of tumorigenesis, either as oncogenes or tumorsuppressors. To explain the link between miRNAs and their function in the initiation and advancement of PCa, we conducted a preliminary assessment. The purpose of this research was to enhance our understanding of the connection between miRNA expression profiles and PCa by elucidating the fundamental processes of miRNA expression and the target genes.
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Affiliation(s)
- Mohd Mabood Khan
- Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India.
| | - Vineeta Sharma
- Department of Medicine, Vanderbilt University Medical Center, Nashville 37232, TN, USA
| | - Mohammad Serajuddin
- Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
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MicroRNA Expression Profiling Using Agilent One-Color Microarray. Methods Mol Biol 2023; 2595:49-64. [PMID: 36441453 DOI: 10.1007/978-1-0716-2823-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MicroRNA (miRNA) expression profiling is an important tool to identify miRNA regulation in physiological or pathological states. This technique has a large number of molecular diagnostic applications, including cancer, cardiovascular and autoimmune diseases, and forensics. To date, a multitude of high-throughput genomic approaches have been developed. Here, we focus on miRNA expression profiling by microarray using SurePrint technology, providing a description of both the workflow and methods for expression profiling by Agilent One-Color Microarray.
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van Baardwijk M, Cristoferi I, Ju J, Varol H, Minnee RC, Reinders MEJ, Li Y, Stubbs AP, Clahsen-van Groningen MC. A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel. Front Immunol 2022; 13:841519. [PMID: 35619722 PMCID: PMC9128066 DOI: 10.3389/fimmu.2022.841519] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/11/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction A decentralized and multi-platform-compatible molecular diagnostic tool for kidney transplant biopsies could improve the dissemination and exploitation of this technology, increasing its clinical impact. As a first step towards this molecular diagnostic tool, we developed and validated a classifier using the genes of the Banff-Human Organ Transplant (B-HOT) panel extracted from a historical Molecular Microscope® Diagnostic system microarray dataset. Furthermore, we evaluated the discriminative power of the B-HOT panel in a clinical scenario. Materials and Methods Gene expression data from 1,181 kidney transplant biopsies were used as training data for three random forest models to predict kidney transplant biopsy Banff categories, including non-rejection (NR), antibody-mediated rejection (ABMR), and T-cell-mediated rejection (TCMR). Performance was evaluated using nested cross-validation. The three models used different sets of input features: the first model (B-HOT Model) was trained on only the genes included in the B-HOT panel, the second model (Feature Selection Model) was based on sequential forward feature selection from all available genes, and the third model (B-HOT+ Model) was based on the combination of the two models, i.e. B-HOT panel genes plus highly predictive genes from the sequential forward feature selection. After performance assessment on cross-validation, the best-performing model was validated on an external independent dataset based on a different microarray version. Results The best performances were achieved by the B-HOT+ Model, a multilabel random forest model trained on B-HOT panel genes with the addition of the 6 most predictive genes of the Feature Selection Model (ST7, KLRC4-KLRK1, TRBC1, TRBV6-5, TRBV19, and ZFX), with a mean accuracy of 92.1% during cross-validation. On the validation set, the same model achieved Area Under the ROC Curve (AUC) of 0.965 and 0.982 for NR and ABMR respectively. Discussion This kidney transplant biopsy classifier is one step closer to the development of a decentralized kidney transplant biopsy classifier that is effective on data derived from different gene expression platforms. The B-HOT panel proved to be a reliable highly-predictive panel for kidney transplant rejection classification. Furthermore, we propose to include the aforementioned 6 genes in the B-HOT panel for further optimization of this commercially available panel.
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Affiliation(s)
- Myrthe van Baardwijk
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Division of HPB and Transplant Surgery, Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Companion Diagnostics and Personalised Healthcare, Omnigen BV, Delft, Netherlands
| | - Iacopo Cristoferi
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Division of HPB and Transplant Surgery, Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jie Ju
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Hilal Varol
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Robert C Minnee
- Division of HPB and Transplant Surgery, Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marlies E J Reinders
- Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Yunlei Li
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Andrew P Stubbs
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marian C Clahsen-van Groningen
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands.,Institute of Experimental Medicine and Systems Biology, Rheinish-Westphalian Technical University Aachen University (RWTH), Aachen, Germany
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Sebestyén E, Nagy Á, Marosvári D, Rajnai H, Kajtár B, Deák B, Matolcsy A, Brandner S, Storhoff J, Chen N, Bagó AG, Bödör C, Reiniger L. Distinct miRNA Expression Signatures of Primary and Secondary Central Nervous System Lymphomas. J Mol Diagn 2021; 24:224-240. [DOI: 10.1016/j.jmoldx.2021.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 01/07/2023] Open
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O'Reilly JJ, Barak S, Penn AA. A new pipeline for clinico-pathological and molecular placental research utilizing FFPE tissues. Placenta 2021; 112:185-188. [PMID: 34375913 PMCID: PMC11832072 DOI: 10.1016/j.placenta.2021.07.301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/26/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022]
Abstract
The placenta is at the core of many pregnancy pathologies, but we have limited knowledge about placental function because of two key research barriers: 1) lack of guidelines for sample collection and pathologic diagnosis; and 2) limited tools are available for molecular analysis of stored placental samples. We aimed to create a searchable, population-based placental database of pathologic diagnoses, and to validate molecular methods for gene expression studies of matching formalin fixed paraffin embedded (FFPE) placental blocks. Our database has over 1000 pregnancies coded for clinical diagnosis with corresponding FFPE blocks that are available for gene expression studies. RNA harvested from FFPE tissues is of sufficient quality for downstream applications. We successfully used this pipeline to identify FFPE placenta from term and preterm pregnancies, and compared their gene expression. The establishment of this platform, which links clinicopathological data and molecular gene expression, will increase our understanding of obstetrical diseases.
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Affiliation(s)
- Jiaqi J O'Reilly
- Department of Pediatrics, Columbia University, New York-Presbyterian Morgan Stanley Children's Hospital, New York, NY, USA
| | - Stephanie Barak
- Department of Pathology, The George Washington University School of Medicine & Health Sciences, Washington, DC, USA
| | - Anna A Penn
- Department of Pediatrics, Columbia University, New York-Presbyterian Morgan Stanley Children's Hospital, New York, NY, USA.
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Tejos-Bravo M, Oakley RH, Whirledge SD, Corrales WA, Silva JP, García-Rojo G, Toledo J, Sanchez W, Román-Albasini L, Aliaga E, Aguayo F, Olave F, Maracaja-Coutinho V, Cidlowski JA, Fiedler JL. Deletion of hippocampal Glucocorticoid receptors unveils sex-biased microRNA expression and neuronal morphology alterations in mice. Neurobiol Stress 2021; 14:100306. [PMID: 33665240 PMCID: PMC7906897 DOI: 10.1016/j.ynstr.2021.100306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/18/2021] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Sex differences in the brain have prompted many researchers to investigate the underlying molecular actors, such as the glucocorticoid receptor (GR). This nuclear receptor controls gene expression, including microRNAs (miRNAs), in non-neuronal cells. Here, we investigated sex-biased effects of GR on hippocampal miRNA expression and neuronal morphology by generating a neuron-specific GR knockout mouse (Emx1-Nr3c1−/−). The levels of 578 mature miRNAs were assessed using NanoString technology and, in contrast to males, female Emx1-Nr3c1−/− mice showed a substantially higher number of differentially expressed miRNAs, confirming a sex-biased effect of GR ablation. Based on bioinformatic analyses we identified several transcription factors potentially involved in miRNA regulation. Functional enrichment analyses of the miRNA-mRNA interactions revealed pathways related to neuronal arborization and both spine morphology and density in both sexes. Two recognized regulators of dendritic morphology, CAMKII-α and GSK-3β, increased their protein levels by GR ablation in female mice hippocampus, without changes in males. Additionally, sex-specific effects of GR deletion were observed on CA1 neuronal arborization and dendritic spine features. For instance, a reduced density of mushroom spines in apical dendrites was evidenced only in females, while a decreased length in basal dendrites was noted only in males. However, length and arborization of apical dendrites were reduced by GR ablation irrespective of the sex. Overall, our study provides new insights into the sex-biased GR actions, especially in terms of miRNAs expression and neuronal morphology in the hippocampus.
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Affiliation(s)
- Macarena Tejos-Bravo
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia, 8380492, Santiago, Chile
| | - Robert H Oakley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Shannon D Whirledge
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Wladimir A Corrales
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia, 8380492, Santiago, Chile
| | - Juan P Silva
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia, 8380492, Santiago, Chile
| | - Gonzalo García-Rojo
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia, 8380492, Santiago, Chile.,Carrera de Odontología. Facultad de Ciencias, Universidad de La Serena, La Serena, Chile
| | - Jorge Toledo
- Laboratory of Scientific Image Analysis (SCIAN-Lab), Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8380453, Chile
| | - Wendy Sanchez
- Laboratory of Scientific Image Analysis (SCIAN-Lab), Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8380453, Chile
| | - Luciano Román-Albasini
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia, 8380492, Santiago, Chile
| | - Esteban Aliaga
- Department of Kinesiology and the Neuropsychology and Cognitive Neurosciences Research Center (CINPSI-Neurocog), Faculty of Health Sciences, Universidad Católica del Maule, Talca, Chile
| | - Felipe Aguayo
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia, 8380492, Santiago, Chile
| | - Felipe Olave
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia, 8380492, Santiago, Chile
| | - Vinicius Maracaja-Coutinho
- Advanced Center for Chronic Diseases -ACCDiS. Faculty of Chemical and Pharmaceutical Sciences. Department of Biochemistry and Molecular Biology. Universidad de Chile, Independencia, 8380492, Santiago, Chile
| | - John A Cidlowski
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Jenny L Fiedler
- Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Independencia, 8380492, Santiago, Chile
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11
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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: 0.4] [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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12
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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13
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Cacheux J, Bancaud A, Leichlé T, Cordelier P. Technological Challenges and Future Issues for the Detection of Circulating MicroRNAs in Patients With Cancer. Front Chem 2019; 7:815. [PMID: 31850308 PMCID: PMC6894013 DOI: 10.3389/fchem.2019.00815] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022] Open
Abstract
In the era of precision medicine, the success of clinical trials, notably for patients diagnosed with cancer, strongly relies on biomarkers with pristine clinical value but also on robust and versatile analytical technologies to ensure proper patients' stratification and treatment. In this review, we will first address whether plasmatic and salivary microRNAs can be considered as a reliable source of biomarkers for cancer diagnosis and prognosis. We will then discuss the pre-analytical steps preceding miRNA quantification (from isolation to purification), and how such process could be biased and time-consuming. Next, we will review the most recent tools derived from micro- and nano-technologies for microRNA detection available to date and how they may compete with current standards. This review will prioritize publications using relevant biological samples. The significance of various physical transduction schemes (mechanical, optical, electrical, etc.) for biological detection will be compared, and pros and cons of each method will be widely discussed. Finally, we will debate on how micro and nanotechnologies could widespread the use of biomarkers in modern medicine, to help manage patients with serious diseases such as cancer.
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Affiliation(s)
- Jean Cacheux
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France.,Université Fédérale de Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, CRCT, Toulouse, France
| | | | | | - Pierre Cordelier
- Université Fédérale de Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, CRCT, Toulouse, France
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14
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Yu L, Bhayana S, Jacob NK, Fadda P. Comparative studies of two generations of NanoString nCounter System. PLoS One 2019; 14:e0225505. [PMID: 31751415 PMCID: PMC6874068 DOI: 10.1371/journal.pone.0225505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/06/2019] [Indexed: 11/24/2022] Open
Abstract
The NanoString nCounter System has been widely used in basic science and translational science research for the past decade. The System consists of two instruments: the PrepStation and the Digital Analyzer, and both have been continuously improved with evolving technologies. A great amount of research data have been generated at multiple research laboratories with the employment of different generations of the System. With the need of integrating multiple datasets, researchers are interested to know whether signals are comparable between different generations of the System. Toward this end, we designed a profiling study to compare performance of two generations of the NanoString nCounter System using a common set of biological samples. Using graphical tools and statistical models, we found that two different generations of NanoString nCounter System produced equivalent signals and signal deviations are in the range of random background noises for the medium-high expression levels.
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Affiliation(s)
- Lianbo Yu
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (LY); (PF)
| | - Sagar Bhayana
- Department of Radiation Oncology, The Ohio State University, Columbus, Ohio, United States of America
| | - Naduparambil K. Jacob
- Department of Radiation Oncology, The Ohio State University, Columbus, Ohio, United States of America
| | - Paolo Fadda
- Genomics Shared Resource, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (LY); (PF)
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15
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Multi-gene technical assessment of qPCR and NanoString n-Counter analysis platforms in cynomolgus monkey cardiac allograft recipients. Cell Immunol 2019; 347:104019. [PMID: 31744596 DOI: 10.1016/j.cellimm.2019.104019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/17/2022]
Abstract
Quantitative gene expression profiling of cardiac allografts characterizes the phenotype of the alloimmune response, yields information regarding differential effects that may be associated with various anti-rejection drug regimens, and generates testable hypotheses regarding the pathogenesis of the chronic rejection lesions typically observed in non-human primate heart transplant models. The goal of this study was to assess interplatform performance and variability between the relatively novel NanoString nCounter Analysis System, ΔΔCT (relative) RT-qPCR, and standard curve (absolute) RT-qPCR utilizing cynomolgus monkey cardiac allografts. Methods for RNA isolation and preamplification were also systematically evaluated and effective methods are proposed. In this study, we demonstrate strong correlation between the two RT-qPCR methods, but variable and, at times, weak correlation between RT-qPCR and NanoString. NanoString fold change results demonstrate less sensitivity to small changes in gene expression than RT-qPCR. These findings appear to be driven by technical aspects of each platform that influence the conditions under which each technique is ideal. Collectively, our data contribute to the general effort to optimally utilize gene expression profiling techniques, not only for transplanted tissues, but for many other applications where accurate rank-order of gene expression versus precise quantification of absolute gene transcript number may be relatively valuable.
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16
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Abstract
Objectives: Firefighters have elevated cancer incidence and mortality rates. MicroRNAs play prominent roles in carcinogenesis, but have not been previously evaluated in firefighters. Methods: Blood from 52 incumbent and 45 new recruit nonsmoking firefighters was analyzed for microRNA expression, and the results adjusted for age, obesity, ethnicity, and multiple comparisons. Results: Nine microRNAs were identified with at least a 1.5-fold significant difference between groups. All six microRNAs with decreased expression in incumbent firefighters have been reported to have tumor suppressor activity or are associated with cancer survival, and two of the three microRNAs with increased expression in incumbent firefighters have activities consistent with cancer promotion, with the remaining microRNA associated with neurological disease. Conclusion: Incumbent firefighters showed differential microRNA expression compared with new recruits, providing potential mechanisms for increased cancer risk in firefighters.
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17
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Lindberg T, Forreryd A, Bergendorff O, Lindstedt M, Zeller KS. In vitro assessment of mechanistic events induced by structurally related chemical rubber sensitizers. Toxicol In Vitro 2019; 60:144-153. [PMID: 31082492 DOI: 10.1016/j.tiv.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/30/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
Abstract
Allergic contact dermatitis (ACD) is one of the most common forms of immunotoxicity, and increased understanding of how chemicals trigger these adverse reactions is needed in order to treat or design testing strategies to identify and subsequently avoid exposure to such substances. In this study, we investigated the cellular response induced by rubber chemicals in a dendritic cell (DC) model, focusing on the structurally similar chemicals diethylthiocarbamylbenzothiazole sulfide and dimethylthiocarbamylbenzothiazole sulfide, with regard to regulation of microRNA, and messenger RNA expression. Only a few miRNAs were found to be commonly regulated by both rubber chemicals, among them miR1973, while the overall miRNA expression profiles were diverse. Similarly, out of approximately 500 differentially regulated transcripts for each chemical, about 60% overlapped, while remaining were unique. The pathways predicted to be enriched in the cell model by stimulation with the rubber chemicals were linked to immunological events, relevant in the context of ACD. These results suggest that small structural differences can trigger specific activation of the immune system in response to chemicals. The here presented mechanistic data can be valuable in explaining the immunotoxicological events in DC activation after exposure to skin sensitizing chemicals, and can contribute to understanding, preventing and treating ACD.
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Affiliation(s)
- Tim Lindberg
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
| | - Andy Forreryd
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
| | - Ola Bergendorff
- Department of Occupational and Environmental Dermatology, Skåne University Hospital, Lund University, 20502 Malmö, Sweden.
| | - Malin Lindstedt
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
| | - Kathrin S Zeller
- Department of Immunotechnology, Medicon Village (406), 22381 Lund, Sweden.
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18
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Pillar N, Haguel D, Grad M, Shapira G, Yoffe L, Shomron N. Characterization of MicroRNA and Gene Expression Profiles Following Ricin Intoxication. Toxins (Basel) 2019; 11:E250. [PMID: 31052539 PMCID: PMC6563297 DOI: 10.3390/toxins11050250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/23/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022] Open
Abstract
Ricin, derived from the castor bean plant, is a highly potent toxin, classified as a potential bioterror agent. Current methods for early detection of ricin poisoning are limited in selectivity. MicroRNAs (miRNAs), which are naturally occurring, negative gene expression regulators, are known for their tissue specific pattern of expression and their stability in tissues and blood. While various approaches for ricin detection have been investigated, miRNAs remain underexplored. We evaluated the effect of pulmonary exposure to ricin on miRNA expression profiles in mouse lungs and peripheral blood mononuclear cells (PBMCs). Significant changes in lung tissue miRNA expression levels were detected following ricin intoxication, specifically regarding miRNAs known to be involved in innate immunity pathways. Transcriptome analysis of the same lung tissues revealed activation of several immune regulation pathways and immune cell recruitment. Our work contributes to the understanding of the role of miRNAs and gene expression in ricin intoxication.
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Affiliation(s)
- Nir Pillar
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Danielle Haguel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Meitar Grad
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Guy Shapira
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Liron Yoffe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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19
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Piskol R, Huw L, Sergin I, Kljin C, Modrusan Z, Kim D, Kljavin N, Tam R, Patel R, Burton J, Penuel E, Qu X, Koeppen H, Sumiyoshi T, de Sauvage F, Lackner MR, de Sousa e Melo F, Kabbarah O. A Clinically Applicable Gene-Expression Classifier Reveals Intrinsic and Extrinsic Contributions to Consensus Molecular Subtypes in Primary and Metastatic Colon Cancer. Clin Cancer Res 2019; 25:4431-4442. [DOI: 10.1158/1078-0432.ccr-18-3032] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/29/2019] [Accepted: 04/15/2019] [Indexed: 01/10/2023]
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20
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Factors affecting RNA quantification from tissue long-term stored in formalin. J Pharmacol Toxicol Methods 2019; 96:61-66. [DOI: 10.1016/j.vascn.2019.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/29/2019] [Accepted: 02/03/2019] [Indexed: 11/18/2022]
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21
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Zhang J, Ye Y, Chang DW, Lin SH, Huang M, Tannir NM, Matin S, Karam JA, Wood CG, Chen ZN, Wu X. Global and Targeted miRNA Expression Profiling in Clear Cell Renal Cell Carcinoma Tissues Potentially Links miR-155-5p and miR-210-3p to both Tumorigenesis and Recurrence. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:2487-2496. [PMID: 30201497 PMCID: PMC6207099 DOI: 10.1016/j.ajpath.2018.07.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/26/2018] [Accepted: 07/10/2018] [Indexed: 12/23/2022]
Abstract
About 30% of patients undergoing nephrectomy for renal cell carcinoma (RCC) experience disease recurrence. We profiled miRNAs dysregulated in clear-cell (cc) RCC tumor tissues and predictive of recurrence. The expression levels of 800 miRNAs were assessed in paired tumor and normal tissues from a discovery cohort of 18 ccRCC patients. miRNAs found to be differentially expressed were examined in a validation set of 205 patients, using real-time quantitative PCR. Tumor-normal data from 64 patients in The Cancer Genome Atlas were used for external validation. Twenty-eight miRNAs were consistently dysregulated in tumor tissues. On dichotomized analysis, patients with high levels of miR-155-5p and miR-210-3p displayed an increased risk for ccRCC recurrence (hazard ratio, 2.64; 95% CI, 1.49 to 4.70; P = 0.0009; and hazard ratio, 1.80; 95% CI, 1.04 to 3.12; P = 0.036, respectively) and a shorter median recurrence-free survival time than did patients with low levels [P < 0.01 (log rank test)]. A risk score was generated based on the expression levels of miR-155-5p and miR-210-3p, and the trend test was significant (P = 0.005). On pathway analysis, target genes regulated by miR-155-5p and miR-210-3p were mainly enriched in inflammation-related pathways. We identified and validated multiple miRNAs dysregulated in ccRCC tissues; miR-155-5p and miR-210-3p were predictive of ccRCC recurrence, pointing to potential utility as biomarkers and underlying biological mechanisms.
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Affiliation(s)
- Jinhua Zhang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas; College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David W Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shu-Hong Lin
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Surena Matin
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jose A Karam
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher G Wood
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhi-Nan Chen
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China; Cell Engineering Research Center and Department of Cell Biology, State Key Laboratory of Cancer, Fourth Military Medical University, Xi'an, China
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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22
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Li X, Kleeman S, Coburn SB, Fumagalli C, Perner J, Jammula S, Pfeiffer RM, Orzolek L, Hao H, Taylor PR, Miremadi A, Galeano-Dalmau N, Lao-Sirieix P, Tennyson M, MacRae S, Cook MB, Fitzgerald RC. Selection and Application of Tissue microRNAs for Nonendoscopic Diagnosis of Barrett's Esophagus. Gastroenterology 2018; 155:771-783.e3. [PMID: 29906417 PMCID: PMC6120784 DOI: 10.1053/j.gastro.2018.05.050] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/27/2018] [Accepted: 05/31/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS MicroRNA (miRNA) is highly stable in biospecimens and provides tissue-specific profiles, making it a useful biomarker of carcinogenesis. We aimed to discover a set of miRNAs that could accurately discriminate Barrett's esophagus (BE) from normal esophageal tissue and to test its diagnostic accuracy when applied to samples collected by a noninvasive esophageal cell sampling device. METHODS We analyzed miRNA expression profiles of 2 independent sets of esophageal biopsy tissues collected during endoscopy from 38 patients with BE and 26 patients with normal esophagus (controls) using Agilent microarray and Nanostring nCounter assays. Consistently up-regulated miRNAs were quantified by real-time polymerase chain reaction in esophageal tissues collected by Cytosponge from patients with BE vs without BE. miRNAs were expressed from plasmids and antisense oligonucleotides were expressed in normal esophageal squamous cells; effects on proliferation and gene expression patterns were analyzed. RESULTS We identified 15 miRNAs that were significantly up-regulated in BE vs control tissues. Of these, 11 (MIR215, MIR194, MIR 192, MIR196a, MIR199b, MIR10a, MIR145, MIR181a, MIR30a, MIR7, and MIR199a) were validated in Cytosponge samples. The miRNAs with the greatest increases in BE tissues (7.9-fold increase in expression or more, P < .0001: MIR196a, MIR192, MIR194, and MIR215) each identified BE vs control tissues with area under the curve (AUC) values of 0.82 or more. We developed an optimized multivariable logistic regression model, based on expression levels of 6 miRNAs (MIR7, MIR30a, MIR181a, MIR192, MIR196a, and MIR199a), that identified patients with BE with an AUC value of 0.89, 86.2% sensitivity, and 91.6% specificity. Expression level of MIR192, MIR196a, MIR199a, combined that of trefoil factor 3, identified patients with BE with an AUC of 0.93, 93.1% sensitivity, and 93.7% specificity. Hypomethylation was observed in the promoter region of the highly up-regulated cluster MIR192-MIR194. Overexpression of these miRNAs in normal esophageal squamous cells increased their proliferation, via GRHL3 and PTEN signaling. CONCLUSIONS In analyses of miRNA expression patterns of BE vs non-BE tissues, we identified a profile that can identify Cytosponge samples from patients with BE with an AUC of 0.93. Expression of MIR194 is increased in BE samples via epigenetic mechanisms that might be involved in BE pathogenesis.
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Affiliation(s)
- Xiaodun Li
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Sam Kleeman
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Sally B. Coburn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland
| | - Carlo Fumagalli
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Juliane Perner
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sriganesh Jammula
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ruth M. Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland
| | - Linda Orzolek
- Johns Hopkins Medical Institutions Deep Sequencing and Microarray Core, Baltimore, Maryland
| | - Haiping Hao
- Johns Hopkins Medical Institutions Deep Sequencing and Microarray Core, Baltimore, Maryland
| | - Philip R. Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland
| | | | - Núria Galeano-Dalmau
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Pierre Lao-Sirieix
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Maria Tennyson
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Shona MacRae
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Michael B. Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland,Reprint requests Address requests for reprints to: Michael B. Cook, PhD, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD
| | - Rebecca C. Fitzgerald
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK,Rebecca C. Fitzgerald, MD, MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, UK CB2 0XZ.
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23
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High-throughput chemical screening to discover new modulators of microRNA expression in living cells by using graphene-based biosensor. Sci Rep 2018; 8:11413. [PMID: 30061704 PMCID: PMC6065314 DOI: 10.1038/s41598-018-29633-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/16/2018] [Indexed: 12/30/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulatory RNAs that control gene expression in various biological processes. Therefore, control over the disease-related miRNA expression is important both for basic research and for a new class of therapeutic modality to treat serious diseases such as cancer. Here, we present a high-throughput screening strategy to identify small molecules that modulate miRNA expression in living cells. The screen enables simultaneous monitoring of the phenotypic cellular changes associated with the miRNA expression by measuring quantitative fluorescent signals corresponding to target miRNA level in living cells based on a novel biosensor composed of peptide nucleic acid and nano-sized graphene oxide. In this study, the biosensor based cellular screening of 967 compounds (including FDA-approved drugs, enzyme inhibitors, agonists, and antagonists) in cells identified four different classes of small molecules consisting of (i) 70 compounds that suppress both miRNA-21 (miR-21) expression and cell proliferation, (ii) 65 compounds that enhance miR-21 expression and reduce cell proliferation, (iii) 2 compounds that suppress miR-21 expression and increase cell proliferation, and (iv) 21 compounds that enhance both miR-21 expression and cell proliferation. We further investigated the hit compounds to correlate cell morphology changes and cell migration ability with decreased expression of miR-21.
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24
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Sim J, Kim Y, Kim H, Shin SJ, Kim DH, Paik SS, Jang K. Identification of recurrence-associated microRNAs in stage I lung adenocarcinoma. Medicine (Baltimore) 2018; 97:e10996. [PMID: 29923982 PMCID: PMC6024484 DOI: 10.1097/md.0000000000010996] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is the most common cause of cancer-associated death worldwide. Postoperative relapse and subsequent metastasis result in a high mortality rate, even in early stage lung cancer. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level and are frequently dysregulated in various cancers. The aim of this study was to identify recurrence-associated miRNAs in early stage lung cancer. To screen for differentially expressed miRNAs related to postoperative recurrence, miRNA microarray data derived from stage I lung adenocarcinoma formalin-fixed paraffin-embedded (FFPE) tissue samples (n = 6) and publically available the Cancer Genome Atlas (TCGA) data were analyzed. An independent sample (n = 29) was used to validate candidate miRNAs by quantitative real-time polymerase chain reaction (qRT-PCR). In miRNA expression profiling, we identified 60 significantly dysregulated miRNAs in the relapsed group. Additionally, 20 dysregulated miRNAs were found using TCGA data set. Three miRNAs (let-7g-5p, miR-143-3p, and miR-374a-5p) were associated with postoperative recurrence in both microarray and TCGA data sets. All 3 candidate miRNAs were validated in the independent cohort of stage I adenocarcinoma by qRT-PCR. We discovered 3 recurrence-associated miRNAs of stage I lung adenocarcinoma samples using FFPE tissue, which showed possible clinical utility as biomarkers predicting recurrence after curative surgery. Further investigation of the functional properties of these miRNAs is needed.
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Affiliation(s)
- Jongmin Sim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Yeseul Kim
- Department of Pathology, Hanyang University College of Medicine
| | - Hyunsung Kim
- Department of Pathology, Hanyang University College of Medicine
| | - Su-Jin Shin
- Department of Pathology, Hanyang University College of Medicine
| | - Dong-Hoon Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seung Sam Paik
- Department of Pathology, Hanyang University College of Medicine
| | - Kiseok Jang
- Department of Pathology, Hanyang University College of Medicine
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25
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Wu CW, Evans JM, Huang S, Mahoney DW, Dukek BA, Taylor WR, Yab TC, Smyrk TC, Jen J, Kisiel JB, Ahlquist DA. A Comprehensive Approach to Sequence-oriented IsomiR annotation (CASMIR): demonstration with IsomiR profiling in colorectal neoplasia. BMC Genomics 2018; 19:401. [PMID: 29801434 PMCID: PMC5970459 DOI: 10.1186/s12864-018-4794-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/14/2018] [Indexed: 01/14/2023] Open
Abstract
Background MicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conventional profiling methods, limitations in assay and analysis platforms may compromise isomiR interrogation. Results We introduce a comprehensive approach to sequence-oriented isomiR annotation (CASMIR) to allow unbiased identification of global isomiRs from small RNA sequencing data. In this approach, small RNA reads are maintained as independent sequences instead of being summarized under miRNA names. IsomiR features are identified through step-wise local alignment against canonical forms and precursor sequences. Through customizing the reference database, CASMIR is applicable to isomiR annotation across species. To demonstrate its application, we investigated isomiR profiles in normal and neoplastic human colorectal epithelia. We also ran miRDeep2, a popular miRNA analysis algorithm to validate isomiRs annotated by CASMIR. With CASMIR, specific and biologically relevant isomiR patterns could be identified. We note that specific isomiRs are often more abundant than their canonical forms. We identify isomiRs that are commonly up-regulated in both colorectal cancer and advanced adenoma, and illustrate advantages in targeting isomiRs as potential biomarkers over canonical forms. Conclusions Studying miRNAs at the isomiR level could reveal new insight into miRNA biology and inform assay design for specific isomiRs. CASMIR facilitates comprehensive annotation of isomiR features in small RNA sequencing data for isomiR profiling and differential expression analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4794-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chung Wah Wu
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jared M Evans
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Shengbing Huang
- Division of Bioinformatics and Computational Biology, University of Minnesota Rochester, Rochester, MN, USA
| | - Douglas W Mahoney
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Brian A Dukek
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Thomas C Smyrk
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jin Jen
- Genome Analysis Core, Medical Genome Facility, Mayo Clinic, Rochester, MN, USA.,Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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26
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Loudig O, Liu C, Rohan T, Ben-Dov IZ. Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens. J Vis Exp 2018. [PMID: 29781987 DOI: 10.3791/57471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays. MicroRNAs (miRNAs), however, which represent a small class of RNA molecules spanning only up to ~18-24 nucleotides, have been shown to withstand long-term storage and have been successfully analyzed in FFPE samples. Here we present a 3' barcoded complementary DNA (cDNA) library preparation protocol specifically optimized for the analysis of small RNAs extracted from archived tissues, which was recently demonstrated to be robust and highly reproducible when using archived clinical specimens stored for up to 35 years. This library preparation is well adapted to the multiplex analysis of compromised/degraded material where RNA samples (up to 18) are ligated with individual 3' barcoded adapters and then pooled together for subsequent enzymatic and biochemical preparations prior to analysis. All purifications are performed by polyacrylamide gel electrophoresis (PAGE), which allows size-specific selections and enrichments of barcoded small RNA species. This cDNA library preparation is well adapted to minute RNA inputs, as a pilot polymerase chain reaction (PCR) allows determination of a specific amplification cycle to produce optimal amounts of material for next-generation sequencing (NGS). This approach was optimized for the use of degraded FFPE RNA from specimens archived for up to 35 years and provides highly reproducible NGS data.
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Affiliation(s)
- Olivier Loudig
- Department of Research, Hackensack University Medical Center; Department of Medical Sciences, Seton Hall University; Department of Epidemiology and Population Health, Albert Einstein College of Medicine;
| | - Christina Liu
- Department of Research, Hackensack University Medical Center; Department of Medical Sciences, Seton Hall University
| | - Thomas Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine
| | - Iddo Z Ben-Dov
- Department of Nephrology and Hypertension, Hadassah - Hebrew University Medical Center
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27
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Nunes S, Silva IB, Ampuero MR, de Noronha ALL, de Souza LCL, Correia TC, Khouri R, Boaventura VS, Barral A, Ramos PIP, Brodskyn C, Oliveira PRS, Tavares NM. Integrated Analysis Reveals That miR-193b, miR-671, and TREM-1 Correlate With a Good Response to Treatment of Human Localized Cutaneous Leishmaniasis Caused by Leishmania braziliensis. Front Immunol 2018; 9:640. [PMID: 29670621 PMCID: PMC5893808 DOI: 10.3389/fimmu.2018.00640] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/14/2018] [Indexed: 12/15/2022] Open
Abstract
Localized cutaneous leishmaniasis (LCL) is a chronic disease characterized by ulcerated skin lesion(s) and uncontrolled inflammation. The mechanisms underlying the pathogenesis of LCL are not completely understood, and little is known about posttranscriptional regulation during LCL. MicroRNAs (miRNAs) are non-coding small RNAs that regulate gene expression and can be implicated in the pathogenesis of LCL. We investigated the involvement of miRNAs and their targets genes in human LCL using publicly available transcriptome data sets followed by ex vivo validation. Initial analysis highlighted that miRNA expression is altered during LCL, as patients clustered separately from controls. Joint analysis identified eight high confidence miRNAs that had altered expression (−1.5 ≤ fold change ≥ 1.5; p < 0.05) between cutaneous ulcers and uninfected skin. We found that the expression of miR-193b and miR-671 are greatly associated with their target genes, CD40 and TNFR, indicating the important role of these miRNAs in the expression of genes related to the inflammatory response observed in LCL. In addition, network analysis revealed that miR-193b, miR-671, and TREM1 correlate only in patients who show faster wound healing (up to 59 days) and not in patients who require longer cure times (more than 60 days). Given that these miRNAs are associated with control of inflammation and healing time, our findings reveal that they might influence the pathogenesis and prognosis of LCL.
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Affiliation(s)
- Sara Nunes
- Oswaldo Cruz Foundation, Gonçalo Moniz Institute, FIOCRUZ, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Icaro Bonyek Silva
- Oswaldo Cruz Foundation, Gonçalo Moniz Institute, FIOCRUZ, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Mariana Rosa Ampuero
- Oswaldo Cruz Foundation, Gonçalo Moniz Institute, FIOCRUZ, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | | | | | | | - Ricardo Khouri
- Oswaldo Cruz Foundation, Gonçalo Moniz Institute, FIOCRUZ, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Viviane Sampaio Boaventura
- Oswaldo Cruz Foundation, Gonçalo Moniz Institute, FIOCRUZ, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Aldina Barral
- Oswaldo Cruz Foundation, Gonçalo Moniz Institute, FIOCRUZ, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Pablo Ivan Pereira Ramos
- Oswaldo Cruz Foundation, Gonçalo Moniz Institute, FIOCRUZ, Salvador, Brazil.,Centre for Data and Knowledge Integration for Health (CIDACS), FIOCRUZ, Salvador, Brazil
| | - Cláudia Brodskyn
- Oswaldo Cruz Foundation, Gonçalo Moniz Institute, FIOCRUZ, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Pablo Rafael Silveira Oliveira
- Federal University of Bahia, Salvador, Brazil.,Centre for Data and Knowledge Integration for Health (CIDACS), FIOCRUZ, Salvador, Brazil
| | - Natalia Machado Tavares
- Oswaldo Cruz Foundation, Gonçalo Moniz Institute, FIOCRUZ, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
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28
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Drewry MD, Challa P, Kuchtey JG, Navarro I, Helwa I, Hu Y, Mu H, Stamer WD, Kuchtey RW, Liu Y. Differentially expressed microRNAs in the aqueous humor of patients with exfoliation glaucoma or primary open-angle glaucoma. Hum Mol Genet 2018; 27:1263-1275. [PMID: 29401312 PMCID: PMC6048986 DOI: 10.1093/hmg/ddy040] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/27/2017] [Accepted: 01/16/2018] [Indexed: 12/16/2022] Open
Abstract
Both exfoliation glaucoma (XFG) and primary open-angle glaucoma (POAG) have been linked to decreased conventional outflow of aqueous humor (AH). To better understand the molecular changes in the AH content under such conditions, we analyzed the miRNA profiles of AH samples from patients with POAG and XFG compared to non-glaucoma controls. Individual AH samples (n = 76) were collected from POAG and XFG patients and age-matched controls during surgical procedure. After RNA extraction, the miRNA profiles were individually determined in 12 POAG, 12 XFG and 11 control samples. We identified 205, 295 and 195 miRNAs in the POAG, XFG and control samples, respectively. Our differential expression analysis identified three miRNAs (miR-125b-5p, miR-302d-3p and miR-451a) significantly different between POAG and controls, five miRNAs (miR-122-5p, miR-3144-3p, miR-320a, miR-320e and miR-630) between XFG and controls and one miRNA (miR-302d-3p) between POAG and XFG. While none of these miRNAs have been previously linked to glaucoma, miR-122-5p may target three glaucoma-associated genes: OPTN, TMCO1 and TGF-ß1. Pathway analysis revealed that these miRNAs are involved in potential glaucoma pathways, including focal adhesion, tight junctions, and TGF-ß signaling. Comparison of the miRNA profile in AH to unrelated human serum (n = 12) exposed potential relationships between these two fluids, although they were not significantly correlated. In summary, we have successfully profiled the miRNA expression without amplification in individual human AH samples and identified several POAG or XFG-associated miRNAs. These miRNAs may play a role in pathways previously implicated in glaucoma and act as biomarkers for disease pathogenesis.
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Affiliation(s)
- Michelle D Drewry
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta, GA, USA
| | - Pratap Challa
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - John G Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Iris Navarro
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - Inas Helwa
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta, GA, USA
| | - Yanzhong Hu
- Department of Cell Biology and Genetics, Henan University School of Medicine, Kaifeng, Henan, China
| | - Hongmei Mu
- Kaifeng Key Lab of Cataract and Myopia, Institute of Eye Diseases, Kaifeng Centre Hospital, Kaifeng, Henan, China
| | - W Daniel Stamer
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - Rachel W Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta, GA, USA
- James and Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, USA
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA, USA
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29
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Van Laar R, Lincoln M, Van Laar B. Development and validation of a plasma-based melanoma biomarker suitable for clinical use. Br J Cancer 2018; 118:857-866. [PMID: 29360813 PMCID: PMC5886119 DOI: 10.1038/bjc.2017.477] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 02/07/2023] Open
Abstract
This corrects the article DOI: 10.1038/bjc.2017.85.
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Affiliation(s)
- Ryan Van Laar
- Geneseq Biosciences Pty Ltd, PO Box 309, Balaclava, VIC 3183, Victoria, Australia
| | - Mitchel Lincoln
- Geneseq Biosciences Pty Ltd, PO Box 309, Balaclava, VIC 3183, Victoria, Australia
| | - Barton Van Laar
- Geneseq Biosciences Pty Ltd, PO Box 309, Balaclava, VIC 3183, Victoria, Australia
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30
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Strauss P, Marti HP, Beisland C, Scherer A, Lysne V, Leh S, Flatberg A, Koch E, Beisvag V, Landolt L, Skogstrand T, Eikrem Ø. Expanding the Utilization of Formalin-Fixed, Paraffin-Embedded Archives: Feasibility of miR-Seq for Disease Exploration and Biomarker Development from Biopsies with Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2018. [PMID: 29534467 PMCID: PMC5877664 DOI: 10.3390/ijms19030803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Novel predictive tools for clear cell renal cell carcinoma (ccRCC) are urgently needed. MicroRNAs (miRNAs) have been increasingly investigated for their predictive value, and formalin-fixed paraffin-embedded biopsy archives may potentially be a valuable source of miRNA sequencing material, as they remain an underused resource. Core biopsies of both cancerous and adjacent normal tissues were obtained from patients (n = 12) undergoing nephrectomy. After small RNA-seq, several analyses were performed, including classifier evaluation, obesity-related inquiries, survival analysis using publicly available datasets, comparisons to the current literature and ingenuity pathway analyses. In a comparison of tumour vs. normal, 182 miRNAs were found with significant differential expression; miR-155 was of particular interest as it classified all ccRCC samples correctly and correlated well with tumour size (R² = 0.83); miR-155 also predicted poor survival with hazard ratios of 2.58 and 1.81 in two different TCGA (The Cancer Genome Atlas) datasets in a univariate model. However, in a multivariate Cox regression analysis including age, sex, cancer stage and histological grade, miR-155 was not a statistically significant survival predictor. In conclusion, formalin-fixed paraffin-embedded biopsy tissues are a viable source of miRNA-sequencing material. Our results further support a role for miR-155 as a promising cancer classifier and potentially as a therapeutic target in ccRCC that merits further investigation.
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Affiliation(s)
- Philipp Strauss
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Christian Beisland
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Urology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Andreas Scherer
- Spheromics, 81100 Kontiolahti, Finland;
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00100 Helsinki, Finland
| | - Vegard Lysne
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
| | - Sabine Leh
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Pathology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Arnar Flatberg
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; (A.F.); (V.B.)
| | - Even Koch
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
| | - Vidar Beisvag
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; (A.F.); (V.B.)
| | - Lea Landolt
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
| | - Trude Skogstrand
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway;
| | - Øystein Eikrem
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Correspondence: ; Tel.: +47-4544-6008
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31
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Ivanov MK, Titov SE, Glushkov SA, Dzyubenko VV, Malek AV, Arkhangelskaya PA, Samsonov RB, Mikhetko AA, Bakhidze EV, Berlev IV, Kolesnikov NN. Detection of high-grade neoplasia in air-dried cervical PAP smears by a microRNA-based classifier. Oncol Rep 2018; 39:1099-1111. [PMID: 29328473 PMCID: PMC5802032 DOI: 10.3892/or.2018.6214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/29/2017] [Indexed: 01/17/2023] Open
Abstract
Recent studies have shown that changes in the expression levels of certain microRNAs correlate with the degree of severity of cervical lesions. The aim of the present study was to develop a microRNA-based classifier for the detection of high-grade cervical intraepithelial neoplasia (CIN ≥2) in cytological samples from patients with different high-risk human papillomavirus (HR-HPV) viral loads. For this purpose, raw RT-qPCR data for 25 candidate microRNAs, U6 snRNA and human DNA in air-dried PAP smears from 174 women with different cervical cytological diagnoses, 144 of which were HR-HPV-positive [40 negative for intraepithelial lesion or malignancy (NILM), 34 low-grade squamous intraepithelial lesions (L-SIL), 57 high-grade squamous intraepithelial lesions (H-SIL), 43 invasive cancers], were statistically processed. The expression level changes of various individual microRNAs were found to be significantly correlated with the cytological diagnosis but the statistical significance of this correlation was critically dependent on the normalization strategy. We developed a linear classifier based on the paired ratios of 8 microRNA concentrations and cellular DNA content. The classifier determines the dimensionless coefficient (DF value), which increases with the severity of cervical lesion. The high- and low-grade CINs were better distinguished by the microRNA classifier than by the measurement of individual microRNA levels with the use of traditional normalization methods. The diagnostic sensitivity of detecting high-grade lesions (CIN ≥2) with the developed microRNA classifier was 83.4%, diagnostic specificity 81.2%, ROC AUC=0.913. The analysis can be performed with the same nucleic acid preparation as used for HPV testing. No statistically significant correlation of the DF value and HR-HPV DNA load was found. The DF value and the HR HPV presence and viral DNA load may be regarded as independent criteria that can complement each other in molecular screening for high-grade cervical intraepithelial neoplasia. Although it has several limitations, the present study showed that the small-scale analysis of microRNA signatures performed by simple PCR-based methods may be useful for improving the diagnostic/prognostic value of cervical screening.
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Affiliation(s)
| | | | | | | | - Anastasia V Malek
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | | | - Roman B Samsonov
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Andrey A Mikhetko
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Elena V Bakhidze
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Igor V Berlev
- N.N. Petrov Research Institute of Oncology, 197758 Saint Petersburg, Russia
| | - Nikolay N Kolesnikov
- Institute of Molecular and Cellular Biology, Siberian Branch of The Russian Academy of Sciences, 630090 Novosibirsk, Russia
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32
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Block I, Burton M, Sørensen KP, Andersen L, Larsen MJ, Bak M, Cold S, Thomassen M, Tan Q, Kruse TA. Association of miR-548c-5p, miR-7-5p, miR-210-3p, miR-128-3p with recurrence in systemically untreated breast cancer. Oncotarget 2018; 9:9030-9042. [PMID: 29507672 PMCID: PMC5823652 DOI: 10.18632/oncotarget.24088] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 01/02/2018] [Indexed: 01/10/2023] Open
Abstract
Current prognostic markers allocate the majority of lymph node (LN) negative and estrogen receptor (ER) positive breast cancer patients into the high-risk group. Accordingly, most patients receive systemic treatments although approximately 40% of these patients may have been cured by surgery and radiotherapy alone. Two studies identified seven prognostic microRNAs in systemically untreated, LN negative and ER positive breast cancer patients which may allow more precise patient classification. However, six of the seven microRNAs were analyzed in both studies but only found to be prognostic in one study. To validate their prognostic potential, we analyzed microRNA expression in an independent cohort (n = 110) using a pair-matched study design minimizing dependence of classical markers. The expression of hsa-miR-548c-5p was significantly associated with abridged disease-free survival (hazard ratio [HR]:1.96, p = 0.027). Contradicting published results, high hsa-miR-516-3p expression was associated with favorable outcome (HR:0.29, p = 0.0068). The association is probably time-dependent indicating later relapse. Additionally, re-analysis of previously published expression data of two matching cohorts (n = 100, n = 255) supports an association of hsa-miR-128-3p with shortened disease-free survival (HR:2.48, p = 0.0033) and an upregulation of miR-7-5p (p = 0.0038; p = 0.039) and miR-210-3p (p = 0.031) in primary tumors of patients who experienced metastases. Further analysis may verify the prognostic potential of these microRNAs.
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Affiliation(s)
- Ines Block
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Mark Burton
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Kristina P Sørensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Lars Andersen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Martin Bak
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Søren Cold
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Epidemiology, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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Abstract
Prostate cancer still represents a major health problem for men worldwide. Due to the specific limitation of the currently used clinical biomarkers for prostate cancer, there is a need to identify new and more accurate prostate-specific biomarkers, both for diagnosis and prediction. Small noncoding species of RNAs called microRNAs (miRNAs) have emerged as possible biomarkers in cancer tissues as well as biological fluids, including for prostate cancer. Moreover, it has been shown that miRNAs could be used as therapeutic targets in different cancer types, including prostate cancer, playing an important role in improving diagnosis and prognosis; and miRNAs have the potential to be clinically useful as predictors of response to personalized cancer therapy and as predictors of prognosis. The analysis of miRNAs in prostate tissue is rather straightforward and has been routinely done on fresh tissue. In addition, due to the more stable nature of miRNAs, they are amenable to be analyzed in archived formalin fixed paraffin embedded tissue as well, and also in serum, plasma and urine, using various analytical platforms including microarrays, next generation sequencing and real time PCR. Moreover, although the existence or prostasomes (microvesicles secreted by prostate cells including prostate cancer cells) has been known for years and they were studied as a source of biomarkers for prostate cancer, only recently it has been described that these vesicles also contain miRNAs that could be used as biomarkers in prostate cancer. This chapter underscores the feasibility of current technologies for miRNA analysis and their importance in prostate cancer biology. Moreover, elucidating the specific alteration of miRNA expression and how to modulate it in prostate tissue will open new avenues for developing therapeutic strategies for prostate cancer treatment.
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Affiliation(s)
- Ovidiu Balacescu
- Department of Functional Genomics, Proteomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Cluj-Napoca, Romania
| | | | - Catalin Marian
- Department of Biochemistry and Pharmacology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania.
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34
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Lai X, Gupta SK, Schmitz U, Marquardt S, Knoll S, Spitschak A, Wolkenhauer O, Pützer BM, Vera J. MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance. Theranostics 2018; 8:1106-1120. [PMID: 29464002 PMCID: PMC5817113 DOI: 10.7150/thno.19904] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 11/14/2017] [Indexed: 01/05/2023] Open
Abstract
High rates of lethal outcome in tumour metastasis are associated with the acquisition of invasiveness and chemoresistance. Several clinical studies indicate that E2F1 overexpression across high-grade tumours culminates in unfavourable prognosis and chemoresistance in patients. Thus, fine-tuning the expression of E2F1 could be a promising approach for treating patients showing chemoresistance. Methods: We integrated bioinformatics, structural and kinetic modelling, and experiments to study cooperative regulation of E2F1 by microRNA (miRNA) pairs in the context of anticancer chemotherapy resistance. Results: We showed that an enhanced E2F1 repression efficiency can be achieved in chemoresistant tumour cells through two cooperating miRNAs. Sequence and structural information were used to identify potential miRNA pairs that can form tertiary structures with E2F1 mRNA. We then employed molecular dynamics simulations to show that among the identified triplexes, miR-205-5p and miR-342-3p can form the most stable triplex with E2F1 mRNA. A mathematical model simulating the E2F1 regulation by the cooperative miRNAs predicted enhanced E2F1 repression, a feature that was verified by in vitro experiments. Finally, we integrated this cooperative miRNA regulation into a more comprehensive network to account for E2F1-related chemoresistance in tumour cells. The network model simulations and experimental data indicate the ability of enhanced expression of both miR-205-5p and miR-342-3p to decrease tumour chemoresistance by cooperatively repressing E2F1. Conclusions: Our results suggest that pairs of cooperating miRNAs could be used as potential RNA therapeutics to reduce E2F1-related chemoresistance.
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Dong H, Gao Q, Peng X, Sun Y, Han T, Zhao B, Liu Y, Wang C, Song X, Wu J, Yang L. Circulating MicroRNAs As Potential Biomarkers for Veterinary Infectious Diseases. Front Vet Sci 2017; 4:186. [PMID: 29209619 PMCID: PMC5701639 DOI: 10.3389/fvets.2017.00186] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/17/2017] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are a kind of small non-coding RNA molecules that could regulate multiple biological pathways at posttranscriptional level. Over 2,000 miRNAs have so far been discovered in humans, and many of them are found to be linked to various kinds of diseases. Thus, miRNAs are being considered as clinical diagnostic and therapeutic targets. With the discovery of high stability of circulating miRNAs in various kinds of mammalian body fluids, the potential of circulating miRNAs as diagnostic/prognostic biomarkers of infectious diseases aroused great interest among researchers. As far as human diseases are concerned, some biomarkers based on circulating miRNAs have been progressed to clinical application. In veterinary fields, however, this concept is only beginning to come into view. In this review, we summarize an update of preclinical studies on using circulating miRNAs as diagnostic biomarkers to combat infectious diseases that affect domestic animals.
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Affiliation(s)
- Hao Dong
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Qiang Gao
- Department of Inspection Technology Research, China Institute of Veterinary Drug Control, Beijing, China
| | - Xiaowei Peng
- Department of Inspection Technology Research, China Institute of Veterinary Drug Control, Beijing, China
| | - Yu Sun
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Tao Han
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Bolin Zhao
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Yufu Liu
- South China Agricultural University, Guangzhou, China
| | - Chuanbin Wang
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Xiaohui Song
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Jiajun Wu
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
| | - Lin Yang
- National Veterinarian Diagnostic Center, China Animal Disease Control Center, Beijing, China
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Patnaik SK, Kannisto ED, Mallick R, Vachani A, Yendamuri S. Whole blood microRNA expression may not be useful for screening non-small cell lung cancer. PLoS One 2017; 12:e0181926. [PMID: 28742859 PMCID: PMC5526508 DOI: 10.1371/journal.pone.0181926] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/28/2017] [Indexed: 12/17/2022] Open
Abstract
At least seven studies have suggested that microRNA levels in whole blood can be diagnostic for lung cancer. We conducted a large bi-institutional study to validate this. Qiagen® PAXgene™ Blood miRNA System was used to collect blood and extract RNA from it for 85 pathologic stage I-IV non-small cell lung cancer (NSCLC) cases and 76 clinically-relevant controls who had a benign pulmonary mass, or a high risk of developing lung cancer because of a history of cigarette smoking or age >60 years. Cases and controls were similar for age, gender, race, and blood hemoglobin and leukocyte but not platelet levels (0.23 and 0.26 million/μl, respectively; t test P = 0.01). Exiqon® MiRCURY™ microarrays were used to quantify microRNAs in RNA isolates. Quantification was also performed using Taqman™ microRNA reverse transcription (RT)-PCR assays for five microRNAs whose lung cancer-diagnostic potential had been suggested in seven published studies. Of the 1,941 human mature microRNAs detectable with the microarray platform, 598 (31%) were identified as expressed and reliably quantified among the study's subjects. However, none of the microRNAs was differentially expressed between cases and controls (P >0.05 at false discovery rate <5% in test using empirical Bayes-moderated t statistics). In classification analyses with leave-one-out internal cross-validation, cases and controls could be identified by microRNA expression with 47% and 50% accuracy with support vector machines and top-scoring pair methods, respectively. Cases and controls did not differ for RT-PCR-based measurements of any of the five microRNAs whose biomarker potential had been suggested by seven previous studies. Additionally, no difference for microRNA expression was noticed in microarray-based microRNA profiles of whole blood of 12 stage IA-IIIB NSCLC cases before and three-four weeks after tumor resection. These findings show that whole blood microRNA expression profiles lack diagnostic value for high-risk screening of NSCLC, though such value may exist for selective sub-groups of NSCLC and control populations.
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Affiliation(s)
- Santosh K. Patnaik
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- Department of Surgery, State University of New York, Buffalo, New York, United States of America
- * E-mail: (SY); (SP)
| | - Eric D. Kannisto
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Reema Mallick
- Department of Surgery, University of Minnesota, Minneapolis, United States of America
| | - Anil Vachani
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sai Yendamuri
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- Department of Surgery, State University of New York, Buffalo, New York, United States of America
- * E-mail: (SY); (SP)
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Millan MJ. Linking deregulation of non-coding RNA to the core pathophysiology of Alzheimer's disease: An integrative review. Prog Neurobiol 2017; 156:1-68. [PMID: 28322921 DOI: 10.1016/j.pneurobio.2017.03.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 02/06/2023]
Abstract
The human genome encodes a vast repertoire of protein non-coding RNAs (ncRNA), some specific to the brain. MicroRNAs, which interfere with the translation of target mRNAs, are of particular interest since their deregulation has been implicated in neurodegenerative disorders like Alzheimer's disease (AD). However, it remains challenging to link the complex body of observations on miRNAs and AD into a coherent framework. Using extensive graphical support, this article discusses how a diverse panoply of miRNAs convergently and divergently impact (and are impacted by) core pathophysiological processes underlying AD: neuroinflammation and oxidative stress; aberrant generation of β-amyloid-42 (Aβ42); anomalies in the production, cleavage and post-translational marking of Tau; impaired clearance of Aβ42 and Tau; perturbation of axonal organisation; disruption of synaptic plasticity; endoplasmic reticulum stress and the unfolded protein response; mitochondrial dysfunction; aberrant induction of cell cycle re-entry; and apoptotic loss of neurons. Intriguingly, some classes of miRNA provoke these cellular anomalies, whereas others act in a counter-regulatory, protective mode. Moreover, changes in levels of certain species of miRNA are a consequence of the above-mentioned anomalies. In addition to miRNAs, circular RNAs, piRNAs, long non-coding RNAs and other types of ncRNA are being increasingly implicated in AD. Overall, a complex mesh of deregulated and multi-tasking ncRNAs reciprocally interacts with core pathophysiological mechanisms underlying AD. Alterations in ncRNAs can be detected in CSF and the circulation as well as the brain and are showing promise as biomarkers, with the ultimate goal clinical exploitation as targets for novel modes of symptomatic and course-altering therapy.
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Affiliation(s)
- Mark J Millan
- Centre for Therapeutic Innovation in Neuropsychiatry, institut de recherche Servier, 125 chemin de ronde, 78290 Croissy sur Seine, France.
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38
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Loudig O, Wang T, Ye K, Lin J, Wang Y, Ramnauth A, Liu C, Stark A, Chitale D, Greenlee R, Multerer D, Honda S, Daida Y, Spencer Feigelson H, Glass A, Couch FJ, Rohan T, Ben-Dov IZ. Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens. Int J Mol Sci 2017; 18:ijms18030627. [PMID: 28335433 PMCID: PMC5372640 DOI: 10.3390/ijms18030627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 01/30/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens.
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Affiliation(s)
- Olivier Loudig
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Juan Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Yihong Wang
- Department of Pathology, Rhode Island Hospital, Providence, RI 02903, USA.
| | - Andrew Ramnauth
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Christina Liu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Azadeh Stark
- Department of Pathology and Breast Oncology Program, Henry Ford Health System, Detroit, MI 48202, USA.
| | - Dhananjay Chitale
- Department of Pathology and Breast Oncology Program, Henry Ford Health System, Detroit, MI 48202, USA.
| | - Robert Greenlee
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA.
| | - Deborah Multerer
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA.
| | - Stacey Honda
- Department of Pathology, Center for Health Research, Kaiser Permanente, 3288 Moanalua Road, Honolulu, HI 96819, USA.
| | - Yihe Daida
- Department of Pathology, Center for Health Research, Kaiser Permanente, 3288 Moanalua Road, Honolulu, HI 96819, USA.
| | | | - Andrew Glass
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR 97227, USA.
| | - Fergus J Couch
- Health Sciences Research, Mayo Clinic, Rochester, NY 55902, USA.
| | - Thomas Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
- Montefiore Medical Center, Bronx, NY 10467, USA.
| | - Iddo Z Ben-Dov
- Laboratory of Medical Transcriptomics, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel.
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Correia CN, Nalpas NC, McLoughlin KE, Browne JA, Gordon SV, MacHugh DE, Shaughnessy RG. Circulating microRNAs as Potential Biomarkers of Infectious Disease. Front Immunol 2017; 8:118. [PMID: 28261201 PMCID: PMC5311051 DOI: 10.3389/fimmu.2017.00118] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/25/2017] [Indexed: 12/12/2022] Open
Abstract
microRNAs (miRNAs) are a class of small non-coding endogenous RNA molecules that regulate a wide range of biological processes by post-transcriptionally regulating gene expression. Thousands of these molecules have been discovered to date, and multiple miRNAs have been shown to coordinately fine-tune cellular processes key to organismal development, homeostasis, neurobiology, immunobiology, and control of infection. The fundamental regulatory role of miRNAs in a variety of biological processes suggests that differential expression of these transcripts may be exploited as a novel source of molecular biomarkers for many different disease pathologies or abnormalities. This has been emphasized by the recent discovery of remarkably stable miRNAs in mammalian biofluids, which may originate from intracellular processes elsewhere in the body. The potential of circulating miRNAs as biomarkers of disease has mainly been demonstrated for various types of cancer. More recently, however, attention has focused on the use of circulating miRNAs as diagnostic/prognostic biomarkers of infectious disease; for example, human tuberculosis caused by infection with Mycobacterium tuberculosis, sepsis caused by multiple infectious agents, and viral hepatitis. Here, we review these developments and discuss prospects and challenges for translating circulating miRNA into novel diagnostics for infectious disease.
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Affiliation(s)
- Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Kirsten E McLoughlin
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland; University College Dublin, UCD Conway Institute of Biomolecular and Biomedical Research, Dublin, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland; University College Dublin, UCD Conway Institute of Biomolecular and Biomedical Research, Dublin, Ireland
| | - Ronan G Shaughnessy
- UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland
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40
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The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Int J Genomics 2017; 2017:1926304. [PMID: 28246590 PMCID: PMC5299160 DOI: 10.1155/2017/1926304] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023] Open
Abstract
High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.
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41
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Mansfield JR. Phenotyping Multiple Subsets of Immune Cells In Situ in FFPE Tissue Sections: An Overview of Methodologies. Methods Mol Biol 2017; 1546:75-99. [PMID: 27896758 DOI: 10.1007/978-1-4939-6730-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The recent clinical success of new cancer immunotherapy agents and methods is driving the need to understand the role of immune cells in solid tissues, especially tumors. Immune cell phenotyping via flow cytometry, while a cornerstone of immunology, is not spatially resolved and cannot analyze immune cell subsets in situ in clinical biopsy sections or to determine their interrelationships. To address this problem, a number of methodologies have been developed in attempts to phenotype immune and other cells in images acquired from tissue sections and to assess their organization in the tumor and its microenvironment. This chapter review the staining and multiplex image analysis methods that have been developed for phenotyping immune and other cells in formalin-fixed, paraffin-embedded (FFPE) tissue sections.
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42
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Fiammengo R. Can nanotechnology improve cancer diagnosis through miRNA detection? Biomark Med 2017; 11:69-86. [DOI: 10.2217/bmm-2016-0195] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
miRNAs are key regulators of gene expression, and alterations in their expression levels correlate with the onset and progression of cancer. Although miRNAs have been proposed as biomarkers for cancer diagnosis, their application in routine clinical praxis is yet to come. Current quantification strategies have limitation, and there is a great interest in developing innovative ones. Since a few years, nanotechnology-based approaches for miRNA quantification are emerging at fast pace but there is urgent need to go beyond the proof-of-concept stage. Nanotechnology will have a strong impact on cancer diagnosis through miRNA detection only if it is demonstrated that the newly developed approaches are indeed working on ‘real-world’ samples under standardized conditions.
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Affiliation(s)
- Roberto Fiammengo
- Center for Biomolecular Nanotechnologies@UniLe – Istituto Italiano di Tecnologia (IIT), Via Barsanti, 73010 Arnesano, Lecce, Italy
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43
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Mukhopadhyay CS, Verma R, Singh J. Extraction and qPCR-Based Detection of miRNAs from Cultured PBMCs of Bubaline Origin. Methods Mol Biol 2017; 1656:89-102. [PMID: 28808963 DOI: 10.1007/978-1-4939-7237-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2025]
Abstract
MicroRNAs are small noncoding but functionally important RNA molecules that are involved in regulating diverse cellular, metabolic, and immune processes. Their small size necessitates modification in traditional acid phenol-chloroform based RNA isolation procedures to get highly enriched fraction of small RNA that includes miRNAs and siRNAs . Further, of the different methods available, real-time PCR is a powerful tool for precise and specific detection and quantification of miRNA. Moreover, real-time PCR is used to validate the screening or expression of miRNAs that are discovered during high-throughput sequencing, or microarray analysis. We demonstrate here the method of extraction of miRNAs from cultured PBMCs of bubaline origin followed by the qPCR-based (both SYBR green and TaqMan -based chemistries) identification of miRNAs expressed in response to TLR ligand stimulation.
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Affiliation(s)
- Chandra S Mukhopadhyay
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India.
| | - Ramneek Verma
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India
| | - Jasdeep Singh
- Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, Punjab, 160012, India
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Dell'Aversana C, Giorgio C, Altucci L. MicroRNA Expression Profiling Using Agilent One-Color Microarray. Methods Mol Biol 2017; 1509:169-183. [PMID: 27826927 DOI: 10.1007/978-1-4939-6524-3_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
MicroRNA (miRNA) expression profiling is an important tool to identify miRNA regulation in physiological or pathological states. This technique has a large number of molecular diagnostic applications, including in cancer, cardiovascular and autoimmune diseases, and forensics. To date, a multitude of high-throughput genomic approaches have been developed. Here, we focus on miRNA expression profiling by microarray using SurePrint technology, providing a description of both the workflow and methods for expression profiling by Agilent One-Color Microarray.
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Affiliation(s)
- Carmela Dell'Aversana
- Institute of Genetics and Biophysics, CNR, 80131, Naples, Italy.
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via Antonio Vivaldi, 43, 80138, Naples, Italy.
| | - Cristina Giorgio
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via Antonio Vivaldi, 43, 80138, Naples, Italy
| | - Lucia Altucci
- Institute of Genetics and Biophysics, CNR, 80131, Naples, Italy
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via Antonio Vivaldi, 43, 80138, Naples, Italy
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Tsang HF, Xue VW, Koh SP, Chiu YM, Ng LPW, Wong SCC. NanoString, a novel digital color-coded barcode technology: current and future applications in molecular diagnostics. Expert Rev Mol Diagn 2016; 17:95-103. [DOI: 10.1080/14737159.2017.1268533] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Hin-Fung Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Vivian Weiwen Xue
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Su-Pin Koh
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Ya-Ming Chiu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Lawrence Po-Wah Ng
- Department of Pathology, Queen Elizabeth Hospital, Hospital Authority, Hong Kong Special Administrative Region, China
| | - Sze-Chuen Cesar Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
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46
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Nassar FJ, Nasr R, Talhouk R. MicroRNAs as biomarkers for early breast cancer diagnosis, prognosis and therapy prediction. Pharmacol Ther 2016; 172:34-49. [PMID: 27916656 DOI: 10.1016/j.pharmthera.2016.11.012] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Breast cancer is a major health problem that affects one in eight women worldwide. As such, detecting breast cancer at an early stage anticipates better disease outcome and prolonged patient survival. Extensive research has shown that microRNA (miRNA) are dysregulated at all stages of breast cancer. miRNA are a class of small noncoding RNA molecules that can modulate gene expression and are easily accessible and quantifiable. This review highlights miRNA as diagnostic, prognostic and therapy predictive biomarkers for early breast cancer with an emphasis on the latter. It also examines the challenges that lie ahead in their use as biomarkers. Noteworthy, this review addresses miRNAs reported in patients with early breast cancer prior to chemotherapy, radiotherapy, surgical procedures or distant metastasis (unless indicated otherwise). In this context, miRNA that are mentioned in this review were significantly modulated using more than one statistical test and/or validated by at least two studies. A standardized protocol for miRNA assessment is proposed starting from sample collection to data analysis that ensures comparative analysis of data and reproducibility of results.
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Affiliation(s)
- Farah J Nassar
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
| | - Rabih Talhouk
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon.
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47
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Pichler S, Gu W, Hartl D, Gasparoni G, Leidinger P, Keller A, Meese E, Mayhaus M, Hampel H, Riemenschneider M. The miRNome of Alzheimer's disease: consistent downregulation of the miR-132/212 cluster. Neurobiol Aging 2016; 50:167.e1-167.e10. [PMID: 27816213 DOI: 10.1016/j.neurobiolaging.2016.09.019] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 09/07/2016] [Accepted: 09/24/2016] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules, with essential functions in RNA silencing and post-transcriptional regulation of gene expression. miRNAs appear to regulate the development and function of the nervous system. Alterations of miRNA expression have been associated with Alzheimer's disease (AD). To characterize the AD miRNA signature, we examined genome-wide miRNA and mRNA expression patterns in the temporal cortex of AD and control samples. We validated our miRNA results by semiquantitative real-time polymerase chain reaction (PCR) in independent prefrontal cortex. Furthermore, we separated gray and white matter brain sections to identify the cellular origin of the altered miRNA expression. We observed genome-wide downregulation of hsa-miR-132-3p and hsa-miR-212-3p in AD with a stronger decrease in gray matter AD samples. We further identified 10 differently expressed transcripts achieving genome-wide levels of significance. Significantly deregulated miRNAs and mRNAs were correlated and examined for potential binding sites (in silico). This miRNome-wide study in AD provides supportive evidence and corroborates an important contribution of miR-132/212 and corresponding target mRNAs to the pathogenesis of AD.
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Affiliation(s)
- Sabrina Pichler
- Department of Psychiatry and Psychotherapy, Neurobiological Laboratory, Saarland University, Homburg, Germany.
| | - Wei Gu
- Department of Psychiatry and Psychotherapy, Neurobiological Laboratory, Saarland University, Homburg, Germany; Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Esch-Belval, Luxembourg
| | - Daniela Hartl
- Department of Psychiatry and Psychotherapy, Neurobiological Laboratory, Saarland University, Homburg, Germany
| | - Gilles Gasparoni
- Department of Psychiatry and Psychotherapy, Neurobiological Laboratory, Saarland University, Homburg, Germany
| | - Petra Leidinger
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Manuel Mayhaus
- Department of Psychiatry and Psychotherapy, Neurobiological Laboratory, Saarland University, Homburg, Germany
| | - Harald Hampel
- AXA Research Fund & UPMC Chair, Paris, France; Sorbonne Universités, Université Pierre et Marie Curie, Paris 06, Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A) & Institut du Cerveau et de la Moelle épinière (ICM), Département de Neurologie, Hôpital de la Pitié-Salpétrière, Paris, France
| | - Matthias Riemenschneider
- Department of Psychiatry and Psychotherapy, Neurobiological Laboratory, Saarland University, Homburg, Germany; Department of Psychiatry and Psychotherapy, Saarland University Hospital, Homburg, Germany
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Kichukova TM, Popov NT, Ivanov HY, Vachev TI. Circulating microRNAs as a Novel Class of Potential Diagnostic Biomarkers in Neuropsychiatric Disorders. Folia Med (Plovdiv) 2016; 57:159-72. [DOI: 10.1515/folmed-2015-0035] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 12/28/2015] [Indexed: 02/06/2023] Open
Abstract
AbstractNeuropsychiatric diseases, such as schizophrenia, bipolar disorder (BD), major depressive disorder (MDD) and autism spectrum disorder (ASD), are a huge burden on society, impairing the health of those affected, as well as their ability to learn and work. Biomarkers that reflect the dysregulations linked to neuropsychiatric diseases may potentially assist the diagnosis of these disorders. Most of these biomarkers are found in the brain tissue, which is not easily accessible. This is the challenge for the search of novel biomarkers that are present in various body fluids, including serum or plasma. As a group of important endogenous small noncoding RNAs that regulate gene expression at post-transcriptional level, microRNAs (miRNAs) play a crucial role in many physiological and pathological processes. Previously, researchers discovered that miRNAs contribute to the neurodevelopment and maturation, including neurite outgrowth, dendritogenesis and dendritic spine formation. These developments underline the significance of miRNAs as potential biomarkers for diagnosing and prognosing central nervous system diseases. Accumulated evidence indicates that there are considerable differences between the cell-free miRNA expression profiles of healthy subjects and those of patients. Therefore, circulating miRNAs are likely to become a new class of noninvasive, sensitive biomarkers. Despite the fact that little is known about the origin and functions of circulating miRNAs, their essential roles in the clinical diagnosis and prognosis of neuropsychiatric diseases make them attractive biomarkers. In this review we cover the increasing amounts of dataset that have accumulated in the last years on the use of circulating miRNAs and their values as potential biomarkers in most areas of neuropsychiatric diseases.
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Extensible Multiplex Real-time PCR of MicroRNA Using Microparticles. Sci Rep 2016; 6:22975. [PMID: 26964639 PMCID: PMC4786821 DOI: 10.1038/srep22975] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/23/2016] [Indexed: 01/08/2023] Open
Abstract
Multiplex quantitative real-time PCR (qPCR), which measures multiple DNAs in a given sample, has received significant attention as a mean of verifying the rapidly increasing genetic targets of interest in single phenotype. Here we suggest a readily extensible qPCR for the expression analysis of multiple microRNA (miRNA) targets using microparticles of primer-immobilized networks as discrete reactors. Individual particles, 200~500 μm in diameter, are identified by two-dimensional codes engraved into the particles and the non-fluorescent encoding allows high-fidelity acquisition of signal in real-time PCR. During the course of PCR, the amplicons accumulate in the volume of the particles with high reliability and amplification efficiency over 95%. In a quick assay comprising of tens of particles holding different primers, each particle brings the independent real-time amplification curve representing the quantitative information of each target. Limited amount of sample was analyzed simultaneously in single chamber through this highly multiplexed qPCR; 10 kinds of miRNAs from purified extracellular vesicles (EVs).
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Titov SE, Ivanov MK, Karpinskaya EV, Tsivlikova EV, Shevchenko SP, Veryaskina YA, Akhmerova LG, Poloz TL, Klimova OA, Gulyaeva LF, Zhimulev IF, Kolesnikov NN. miRNA profiling, detection of BRAF V600E mutation and RET-PTC1 translocation in patients from Novosibirsk oblast (Russia) with different types of thyroid tumors. BMC Cancer 2016; 16:201. [PMID: 26960768 PMCID: PMC4784369 DOI: 10.1186/s12885-016-2240-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 03/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The postoperative typing of thyroid lesions, which is instrumental in adequate patient treatment, is currently based on histologic examination. However, it depends on pathologist's qualification and can be difficult in some cases. Numerous studies have shown that molecular markers such as microRNAs and somatic mutations may be useful to assist in these cases, but no consensus exists on the set of markers that is optimal for that purpose. The aim of the study was to discriminate between different thyroid neoplasms by RT-PCR, using a limited set of microRNAs selected from literature. METHODS By RT-PCR we evaluated the relative levels of 15 microRNAs (miR-221, -222, -146b, -181b, -21, -187, -199b, -144, -192, -200a, -200b, -205, -141, -31, -375) and the presence of BRAF(V600E) mutation and RET-PTC1 translocation in surgically resected lesions from 208 patients from Novosibirsk oblast (Russia) with different types of thyroid neoplasms. Expression of each microRNA was normalized to adjacent non-tumor tissue. Three pieces of lesion tissue from each patient (39 goiters, 41 follicular adenomas, 16 follicular thyroid cancers, 108 papillary thyroid cancers, 4 medullary thyroid cancers) were analyzed independently to take into account method variation. RESULTS The diagnostic classifier based on profiling of 13 microRNAs was proposed, with total estimated accuracy varying from 82.7 to 99% for different nodule types. Relative expression of six microRNAs (miR-146b, -21, -221, -222, 375, -199b) appeared significantly different in BRAF(V600E)-positive samples (all classified as papillary thyroid carcinomas) compared to BRAF(V600E)-negative papillary carcinoma samples. CONCLUSIONS The results confirm practical feasibility of using molecular markers for typing of thyroid neoplasms and clarification of controversial cases.
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Affiliation(s)
- Sergei E Titov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia. .,JSC "Vector-Best", Koltsovo, Russia.
| | | | - Elena V Karpinskaya
- Novosibirsk Municipal Budgetary Healthcare Institution "Municipal Clinical Hospital #1", Novosibirsk, Russia
| | | | - Sergei P Shevchenko
- Novosibirsk Municipal Budgetary Healthcare Institution "Municipal Clinical Hospital #1", Novosibirsk, Russia
| | - Yulia A Veryaskina
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
| | - Larisa G Akhmerova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
| | - Tatiana L Poloz
- Non-governmental Healthcare Institution «Railroad Clinical Hospital on the Station Novosibirsk-Glavny", JSC Russian Railways, Novosibirsk, Russia
| | - Olesya A Klimova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia.,JSC "Vector-Best", Koltsovo, Russia
| | | | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
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