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Babion I, Miok V, Jaspers A, Huseinovic A, Steenbergen RDM, van Wieringen WN, Wilting SM. Identification of Deregulated Pathways, Key Regulators, and Novel miRNA-mRNA Interactions in HPV-Mediated Transformation. Cancers (Basel) 2020; 12:E700. [PMID: 32188026 PMCID: PMC7140059 DOI: 10.3390/cancers12030700] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 12/20/2022] Open
Abstract
Next to a persistent infection with high-risk human papillomavirus (HPV), molecular changes are required for the development of cervical cancer. To identify which molecular alterations drive carcinogenesis, we performed a comprehensive and longitudinal molecular characterization of HPV-transformed keratinocyte cell lines. Comparative genomic hybridization, mRNA, and miRNA expression analysis of four HPV-containing keratinocyte cell lines at eight different time points was performed. Data was analyzed using unsupervised hierarchical clustering, integrated longitudinal expression analysis, and pathway enrichment analysis. Biological relevance of identified key regulatory genes was evaluated in vitro and dual-luciferase assays were used to confirm predicted miRNA-mRNA interactions. We show that the acquisition of anchorage independence of HPV-containing keratinocyte cell lines is particularly associated with copy number alterations. Approximately one third of differentially expressed mRNAs and miRNAs was directly attributable to copy number alterations. Focal adhesion, TGF-beta signaling, and mTOR signaling pathways were enriched among these genes. PITX2 was identified as key regulator of TGF-beta signaling and inhibited cell growth in vitro, most likely by inducing cell cycle arrest and apoptosis. Predicted miRNA-mRNA interactions miR-221-3p_BRWD3, miR-221-3p_FOS, and miR-138-5p_PLXNB2 were confirmed in vitro. Integrated longitudinal analysis of our HPV-induced carcinogenesis model pinpointed relevant interconnected molecular changes and crucial signaling pathways in HPV-mediated transformation.
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Affiliation(s)
- Iris Babion
- Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (I.B.); (V.M.); (A.J.); (A.H.)
| | - Viktorian Miok
- Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (I.B.); (V.M.); (A.J.); (A.H.)
- Epidemiology & Biostatistics, Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
- Department of Functional Sciences, Faculty of Medicine, Victor Babeş University of Medicine and Pharmacy of Timişoara, 300041 Timişoara, Romania
| | - Annelieke Jaspers
- Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (I.B.); (V.M.); (A.J.); (A.H.)
| | - Angelina Huseinovic
- Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (I.B.); (V.M.); (A.J.); (A.H.)
| | - Renske D. M. Steenbergen
- Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (I.B.); (V.M.); (A.J.); (A.H.)
| | - Wessel N. van Wieringen
- Epidemiology & Biostatistics, Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
- Department of Mathematics, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Saskia M. Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands;
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Babion I, Jaspers A, van Splunter AP, van der Hoorn IA, Wilting SM, Steenbergen RD. miR-9-5p Exerts a Dual Role in Cervical Cancer and Targets Transcription Factor TWIST1. Cells 2019; 9:E65. [PMID: 31888045 PMCID: PMC7017350 DOI: 10.3390/cells9010065] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/19/2019] [Accepted: 12/24/2019] [Indexed: 12/19/2022] Open
Abstract
Squamous cell carcinoma (SCC) and adenocarcinoma (AC) represent the major cervical cancer histotypes. Both histotypes are caused by infection with high-risk HPV (hrHPV) and are associated with deregulated microRNA expression. Histotype-dependent expression has been observed for miR-9-5p, showing increased expression in SCC and low expression in AC. Here, we studied the regulation and functionality of miR-9-5p in cervical SCCs and ACs using cervical tissue samples and hrHPV-containing cell lines. Expression and methylation analysis of cervical tissues revealed that low levels of miR-9-5p in ACs are linked to methylation of its precursor genes, particularly miR-9-1. Stratification of tissue samples and hrHPV-containing cell lines suggested that miR-9-5p depends on both histotype and hrHPV type, with higher expression in SCCs and HPV16-positive cells. MiR-9-5p promoted cell viability and anchorage independence in cervical cancer cell lines SiHa (SCC, HPV16) and CaSki (metastasized SCC, HPV16), while it played a tumor suppressive role in HeLa (AC, HPV18). TWIST1, a transcription factor involved in epithelial-to-mesenchymal transition (EMT), was established as a novel miR-9-5p target. Our results show that miR-9-5p plays a dual role in cervical cancer in a histotype- and hrHPV type-dependent manner. MiR-9-5p mediated silencing of TWIST1 suggests two distinct mechanisms towards EMT in cervical cancer.
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Affiliation(s)
- Iris Babion
- Cancer Center Amsterdam, Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Annelieke Jaspers
- Cancer Center Amsterdam, Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Annina P. van Splunter
- Cancer Center Amsterdam, Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Iris A.E. van der Hoorn
- Cancer Center Amsterdam, Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Saskia M. Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Renske D.M. Steenbergen
- Cancer Center Amsterdam, Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
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Snoek BC, Babion I, Koppers-Lalic D, Pegtel DM, Steenbergen RD. Altered microRNA processing proteins in HPV-induced cancers. Curr Opin Virol 2019; 39:23-32. [PMID: 31408800 DOI: 10.1016/j.coviro.2019.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/15/2022]
Abstract
High-risk human papilloma virus (hrHPV) infections are associated with the development of anogenital cancers, in particular cervical cancer, and a subset of head and neck cancers. Previous studies have shown that microRNAs (miRNAs) contribute to the development and progression of HPV-induced malignancies. miRNAs are small non-coding RNAs that exist as multiple length and sequence variants, termed isomiRs. Efficient processing of miRNAs and generation of isomiRs is accomplished by several processing proteins. Deregulation of Drosha, AGO2, and TENT2, among others, has been observed in HPV-induced cancers and was even found at the precancerous stage. This suggests that miRNA processing proteins may be involved during early cancer development and that the generated isomiRs could provide promising biomarkers for early cancer diagnosis.
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Affiliation(s)
- Barbara C Snoek
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Iris Babion
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Danijela Koppers-Lalic
- Amsterdam UMC, Vrije Universiteit Amsterdam, Neurosurgery, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Dirk M Pegtel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Renske Dm Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands.
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Babion I, De Strooper LMA, Luttmer R, Bleeker MCG, Meijer CJLM, Heideman DAM, Wilting SM, Steenbergen RDM. Complementarity between miRNA expression analysis and DNA methylation analysis in hrHPV-positive cervical scrapes for the detection of cervical disease. Epigenetics 2019; 14:558-567. [PMID: 30955437 PMCID: PMC6557605 DOI: 10.1080/15592294.2019.1600390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cervical screening by high-risk HPV (hrHPV) testing requires additional risk stratification (triage), as most infections are transient and only a subset of hrHPV-positive women harbours clinically relevant disease. Molecular triage markers such as microRNAs (miRNAs) and DNA methylation markers are particularly promising, as they can be objectively tested directly on hrHPV-positive scrapes and cervicovaginal self-samples. Here, we evaluated the marker potential of 10 candidate miRNAs in 209 hrHPV-positive scrapes of women with underlying precancer (cervical intraepithelial neoplasia, grade 2–3 (CIN2-3)), cancer, or without disease (CIN0/1). A predictive miRNA classifier for CIN3 detection was built using logistic regression, which was compared to and combined with DNA methylation marker FAM19A4. Markers were correlated to histology parameters and hrHPV genotype. A miRNA classifier consisting of miR-149, miR-20a, and miR-93 achieved an area under the curve (AUC) of 0.834 for CIN3 detection, which was not significantly different to that of FAM19A4 methylation (AUC: 0.862, p = 0.591). Combining miRNA and methylation analysis demonstrated complementarity between both marker types (AUC: 0.939). While the miRNA classifier seemed more predictive for CIN2, FAM19A4 methylation was particularly high in HPV16-positive and histologically advanced CIN3, i.e. CIN3 with high lesion volume. The miRNA classifier, FAM19A4 methylation, and the miRNA/methylation combination were highest in cancer-associated scrapes. In conclusion, a panel of three miRNAs is discriminatory for CIN3 in hrHPV-positive scrapes and can complement DNA methylation analysis for the efficient detection of cervical disease. Combined analysis of the two marker types warrants further evaluation as triage strategy in hrHPV-based screening.
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Affiliation(s)
- Iris Babion
- a Pathology, Cancer Center Amsterdam , Amsterdam UMC, Vrije Universiteit Amsterdam , Amsterdam , The Netherlands
| | - Lise M A De Strooper
- a Pathology, Cancer Center Amsterdam , Amsterdam UMC, Vrije Universiteit Amsterdam , Amsterdam , The Netherlands
| | - Roosmarijn Luttmer
- a Pathology, Cancer Center Amsterdam , Amsterdam UMC, Vrije Universiteit Amsterdam , Amsterdam , The Netherlands
| | - Maaike C G Bleeker
- a Pathology, Cancer Center Amsterdam , Amsterdam UMC, Vrije Universiteit Amsterdam , Amsterdam , The Netherlands
| | - Chris J L M Meijer
- a Pathology, Cancer Center Amsterdam , Amsterdam UMC, Vrije Universiteit Amsterdam , Amsterdam , The Netherlands
| | - Daniëlle A M Heideman
- a Pathology, Cancer Center Amsterdam , Amsterdam UMC, Vrije Universiteit Amsterdam , Amsterdam , The Netherlands
| | - Saskia M Wilting
- b Department of Medical Oncology, Erasmus MC Cancer Institute , Erasmus University Medical Center , Rotterdam , The Netherlands
| | - Renske D M Steenbergen
- a Pathology, Cancer Center Amsterdam , Amsterdam UMC, Vrije Universiteit Amsterdam , Amsterdam , The Netherlands
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Snoek BC, Verlaat W, Babion I, Novianti PW, van de Wiel MA, Wilting SM, van Trommel NE, Bleeker MCG, Massuger LFAG, Melchers WJG, Sie D, Heideman DAM, Snijders PJF, Meijer CJLM, Steenbergen RDM. Genome-wide microRNA analysis of HPV-positive self-samples yields novel triage markers for early detection of cervical cancer. Int J Cancer 2018; 144:372-379. [PMID: 30192375 PMCID: PMC6518875 DOI: 10.1002/ijc.31855] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/20/2018] [Accepted: 07/30/2018] [Indexed: 02/06/2023]
Abstract
Offering self‐sampling for HPV testing improves the effectiveness of current cervical screening programs by increasing population coverage. Molecular markers directly applicable on self‐samples are needed to stratify HPV‐positive women at risk of cervical cancer (so‐called triage) and to avoid over‐referral and overtreatment. Deregulated microRNAs (miRNAs) have been implicated in the development of cervical cancer, and represent potential triage markers. However, it is unknown whether deregulated miRNA expression is reflected in self‐samples. Our study is the first to establish genome‐wide miRNA profiles in HPV‐positive self‐samples to identify miRNAs that can predict the presence of CIN3 and cervical cancer in self‐samples. Small RNA sequencing (sRNA‐Seq) was conducted to determine genome‐wide miRNA expression profiles in 74 HPV‐positive self‐samples of women with and without cervical precancer (CIN3). The optimal miRNA marker panel for CIN3 detection was determined by GRridge, a penalized method on logistic regression. Six miRNAs were validated by qPCR in 191 independent HPV‐positive self‐samples. Classification of sRNA‐Seq data yielded a 9‐miRNA marker panel with a combined area under the curve (AUC) of 0.89 for CIN3 detection. Validation by qPCR resulted in a combined AUC of 0.78 for CIN3+ detection. Our study shows that deregulated miRNA expression associated with CIN3 and cervical cancer development can be detected by sRNA‐Seq in HPV‐positive self‐samples. Validation by qPCR indicates that miRNA expression analysis offers a promising novel molecular triage strategy for CIN3 and cervical cancer detection applicable to self‐samples. What's new? MicroRNAs (miRNAs) are suspected of playing a role in cervical cancer development. They are also potential markers for the identification of human papillomavirus (HPV)‐infected women who are at risk of cervical cancer. Here, using small RNA sequencing of HPV‐positive self‐samples from women with and without cervical precancer (CIN3), the authors identify a miRNA signature consisting of multiple miRNAs that is strongly predictive of CIN3. Validation of this signature by qPCR revealed a good clinical performance for CIN3+ detection. The findings suggest that miRNA analysis is an effective means of CIN3+ prediction in HPV‐positive self‐samples obtained for cervical cancer screening.
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Affiliation(s)
- Barbara C Snoek
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Wina Verlaat
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Iris Babion
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Putri W Novianti
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands.,Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology and Biostatistics, Amsterdam, Netherlands
| | - Mark A van de Wiel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology and Biostatistics, Amsterdam, Netherlands.,Amsterdam UMC, Vrije Universiteit Amsterdam, Mathematics, Amsterdam, Netherlands
| | - Saskia M Wilting
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands.,Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Nienke E van Trommel
- Department of Gynecology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Maaike C G Bleeker
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Leon F A G Massuger
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Daoud Sie
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Daniëlle A M Heideman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Peter J F Snijders
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Chris J L M Meijer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands
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Babion I, Miok V, Jaspers A, Wieringen WNV, Steenbergen RD, Wilting SM. Abstract 5059: Comprehensive molecular profiling of HPV-induced transformation over time. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Although persistent infection with high-risk human papillomavirus (HPV) is generally acknowledged as necessary cause for cervical cancer, additional molecular changes are required for the development of cancer. Those changes include chromosomal aberrations that result in deregulated expression of coding and non-coding RNAs. In this study we performed a comprehensive and longitudinal molecular characterization of HPV-transformed keratinocyte cell lines, to identify the sequential order and relevance of these molecular alterations for HPV-induced transformation. Genome-wide chromosomal, mRNA and miRNA expression profiles were generated from 4 HPV-transformed keratinocyte cell lines at 8 different passages representing progressive stages of transformation. Unsupervised hierarchical clustering of DNA copy number, mRNA and miRNA profiles revealed that in all 4 cell lines most pronounced changes were associated with the acquisition of anchorage independence, a hallmark of transformation. Approximately one third of differentially expressed mRNAs and miRNAs was directly attributable to DNA copy number alterations. Focal adhesion, TGF-β signalling and mTOR signalling pathways were enriched among these genes. In addition, longitudinal analysis identified more than 600 potential miRNA-mRNA interactions that were negatively correlated during passaging. Four interactions were also predicted by 3 independent prediction algorithms, and have in part already been functionally validated, thereby demonstrating the validity of our approach. In conclusion, integrated longitudinal analysis of our HPV-induced transformation model enabled us to pinpoint relevant interconnected molecular changes and affected signalling pathways. Increased understanding of the interplay between different molecular alterations and affected pathways will be of importance for the clinical management of patients diagnosed with HPV-induced (pre)cancerous lesions.
Citation Format: Iris Babion, Viktorian Miok, Annelieke Jaspers, Wessel N. van Wieringen, Renske D. Steenbergen, Saskia M. Wilting. Comprehensive molecular profiling of HPV-induced transformation over time [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5059.
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Affiliation(s)
- Iris Babion
- VU University Medical Center, Amsterdam, Netherlands
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Babion I, Snoek BC, Novianti PW, Jaspers A, van Trommel N, Heideman DAM, Meijer CJLM, Snijders PJF, Steenbergen RDM, Wilting SM. Triage of high-risk HPV-positive women in population-based screening by miRNA expression analysis in cervical scrapes; a feasibility study. Clin Epigenetics 2018; 10:76. [PMID: 29930741 PMCID: PMC5992707 DOI: 10.1186/s13148-018-0509-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 05/29/2018] [Indexed: 01/17/2023] Open
Abstract
Background Primary testing for high-risk HPV (hrHPV) is increasingly implemented in cervical cancer screening programs. Many hrHPV-positive women, however, harbor clinically irrelevant infections, demanding additional disease markers to prevent over-referral and over-treatment. Most promising biomarkers reflect molecular events relevant to the disease process that can be measured objectively in small amounts of clinical material, such as miRNAs. We previously identified eight miRNAs with altered expression in cervical precancer and cancer due to either methylation-mediated silencing or chromosomal alterations. In this study, we evaluated the clinical value of these eight miRNAs on cervical scrapes to triage hrHPV-positive women in cervical screening. Results Expression levels of the eight candidate miRNAs in cervical tissue samples (n = 58) and hrHPV-positive cervical scrapes from a screening population (n = 187) and cancer patients (n = 38) were verified by quantitative RT-PCR. In tissue samples, all miRNAs were significantly differentially expressed (p < 0.05) between normal, high-grade precancerous lesions (CIN3), and/or cancer. Expression patterns detected in cervical tissue samples were reflected in cervical scrapes, with five miRNAs showing significantly differential expression between controls and women with CIN3 and cancer. Using logistic regression analysis, a miRNA classifier was built for optimal detection of CIN3 in hrHPV-positive cervical scrapes from the screening population and its performance was evaluated using leave-one-out cross-validation. This miRNA classifier consisted of miR-15b-5p and miR-375 and detected a major subset of CIN3 as well as all carcinomas at a specificity of 70%. The CIN3 detection rate was further improved by combining the two miRNAs with HPV16/18 genotyping. Interestingly, both miRNAs affected the viability of cervical cancer cells in vitro. Conclusions This study shows that miRNA expression analysis in cervical scrapes is feasible and enables the early detection of cervical cancer, thus underlining the potential of miRNA expression analysis for triage of hrHPV-positive women in cervical cancer screening. Electronic supplementary material The online version of this article (10.1186/s13148-018-0509-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Iris Babion
- 1Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Barbara C Snoek
- 1Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Putri W Novianti
- 1Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,2Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - Annelieke Jaspers
- 1Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Nienke van Trommel
- 3Center for Gynaecological Oncology, Antoni van Leeuwenhoek Hospital/Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniëlle A M Heideman
- 1Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Chris J L M Meijer
- 1Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Peter J F Snijders
- 1Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- 1Cancer Center Amsterdam, Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Saskia M Wilting
- 4Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
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Babion I, Snoek BC, van de Wiel MA, Wilting SM, Steenbergen RDM. A Strategy to Find Suitable Reference Genes for miRNA Quantitative PCR Analysis and Its Application to Cervical Specimens. J Mol Diagn 2018; 19:625-637. [PMID: 28826607 DOI: 10.1016/j.jmoldx.2017.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/11/2017] [Accepted: 04/27/2017] [Indexed: 12/21/2022] Open
Abstract
miRNAs represent an emerging class of promising biomarkers for cancer diagnostics. To perform reliable miRNA expression analysis using quantitative PCR, adequate data normalization is essential to remove nonbiological, technical variations. Ideal reference genes should be biologically stable and reduce technical variability of miRNA expression analysis. Herein is a new strategy for the identification and evaluation of reference genes that can be applied for miRNA-based diagnostic tests without entailing excessive additional experiments. We analyzed the expression of 11 carefully selected candidate reference genes in different types of cervical specimens [ie, tissues, scrapes, and self-collected cervicovaginal specimens (self-samples)]. To identify the biologically most stable reference genes, three commonly used algorithms (GeNorm, NormFinder, and BestKeeper) were combined. Signal-to-noise ratios and P values between control and disease groups were calculated to validate the reduction in technical variability on expression analysis of two marker miRNAs. miR-423 was identified as a suitable reference gene for all sample types, to be used in combination with RNU24 in cervical tissues, RNU43 in scrapes, and miR-30b in self-samples. These findings demonstrate that the choice of reference genes may differ between different types of specimens, even when originating from the same anatomical source. More important, it is shown that adequate normalization increases the signal-to-noise ratio, which is not observed when normalizing to commonly used reference genes.
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Affiliation(s)
- Iris Babion
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Barbara C Snoek
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Mark A van de Wiel
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, the Netherlands; Department of Mathematics, VU University Amsterdam, Amsterdam, the Netherlands
| | - Saskia M Wilting
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
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Sauer E, Babion I, Madea B, Courts C. An evidence based strategy for normalization of quantitative PCR data from miRNA expression analysis in forensic organ tissue identification. Forensic Sci Int Genet 2014; 13:217-23. [PMID: 25203915 DOI: 10.1016/j.fsigen.2014.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/01/2014] [Accepted: 08/06/2014] [Indexed: 01/09/2023]
Abstract
Messenger-RNA (mRNA)-based analysis of organ tissues and their differentiation in complex crime stains has recently been introduced as a potential and powerful tool to forensic genetics. Given the notoriously low quality of many forensic samples it seems advisable, though, to substitute mRNA with micro-RNA (miRNA) which is much less susceptible to degradation. However, reliable miRNA detection and quantification using quantitative PCR requires a solid and forensically relevant normalization strategy. In our study we evaluated a panel of 15 carefully selected reference genes for their suitability as endogenous controls in miRNA qPCR normalization in forensically relevant settings. We analyzed assay performances and expression variances in 35 individual samples and mixtures thereof integrating highly standardized protocols with contemporary methodologies and included several well-established computational algorithms. Based on these empirical results, we recommend SNORD48, SNORD24, and RNU6-2 as endogenous references since these exhibit the most stable expression levels and the least expected variation among the evaluated candidate reference genes in the given set of forensically relevant organ tissues including skin. To account for the lack of consensus on how best to perform and interpret quantitative PCR experiments, our study's documentation is according to MIQE guidelines, defining the "minimum information for publication of quantitative real-time PCR experiments".
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Affiliation(s)
- Eva Sauer
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Iris Babion
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Burkhard Madea
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Cornelius Courts
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany.
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