1
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Schreiberhuber L, Barrett JE, Wang J, Redl E, Herzog C, Vavourakis CD, Sundström K, Dillner J, Widschwendter M. Cervical cancer screening using DNA methylation triage in a real-world population. Nat Med 2024:10.1038/s41591-024-03014-6. [PMID: 38834848 DOI: 10.1038/s41591-024-03014-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/23/2024] [Indexed: 06/06/2024]
Abstract
Cervical cancer (CC) screening in women comprises human papillomavirus (HPV) testing followed by cytology triage of positive cases. Drawbacks, including cytology's low reproducibility and requirement for short screening intervals, raise the need for alternative triage methods. Here we used an innovative triage technique, the WID-qCIN test, to assess the DNA methylation of human genes DPP6, RALYL and GSX1 in a real-life cohort of 28,017 women aged ≥30 years who attended CC screening in Stockholm between January and March 2017. In the analysis of all 2,377 HPV-positive samples, a combination of WID-qCIN (with a predefined threshold) and HPV16 and/or HPV18 (HPV16/18) detected 93.4% of cervical intraepithelial neoplasia grade 3 and 100% of invasive CCs. The WID-qCIN/HPV16/18 combination predicted 69.4% of incident cervical intraepithelial neoplasia grade 2 or worse compared with 18.2% predicted by cytology. Cytology or WID-qCIN/HPV16/18 triage would require 4.1 and 2.4 colposcopy referrals to detect one cervical intraepithelial neoplasia grade 2 or worse, respectively, during the 6 year period. These findings support the use of WID-qCIN/HPV16/18 as an improved triage strategy for HPV-positive women.
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Affiliation(s)
- Lena Schreiberhuber
- European Translational Oncology Prevention and Screening Institute, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
| | - James E Barrett
- European Translational Oncology Prevention and Screening Institute, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
| | - Jiangrong Wang
- Center for Cervical Cancer Elimination, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Elisa Redl
- European Translational Oncology Prevention and Screening Institute, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening Institute, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
| | - Charlotte D Vavourakis
- European Translational Oncology Prevention and Screening Institute, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
| | - Karin Sundström
- Center for Cervical Cancer Elimination, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Dillner
- Center for Cervical Cancer Elimination, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening Institute, Hall in Tirol, Austria.
- Research Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria.
- General Hospital Hall, Tirol Kliniken, Hall in Tirol, Austria.
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK.
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
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2
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Herzog C, Vavourakis CD, Barrett JE, Karbon G, Villunger A, Wang J, Sundström K, Dillner J, Widschwendter M. HPV-induced host epigenetic reprogramming is lost upon progression to high-grade cervical intraepithelial neoplasia. Int J Cancer 2023; 152:2321-2330. [PMID: 36810770 DOI: 10.1002/ijc.34477] [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: 11/16/2022] [Revised: 01/11/2023] [Accepted: 02/07/2023] [Indexed: 02/23/2023]
Abstract
The impact of a pathogen on host disease can only be studied in samples covering the entire spectrum of pathogenesis. Persistent oncogenic human papilloma virus (HPV) infection is the most common cause for cervical cancer. Here, we investigate HPV-induced host epigenome-wide changes prior to development of cytological abnormalities. Using cervical sample methylation array data from disease-free women with or without an oncogenic HPV infection, we develop the WID (Women's cancer risk identification)-HPV, a signature reflective of changes in the healthy host epigenome related to high-risk HPV strains (AUC = 0.78, 95% CI: 0.72-0.85, in nondiseased women). Looking at HPV-associated changes across disease development, HPV-infected women with minor cytological alterations (cervical intraepithelial neoplasia grade 1/2, CIN1/2), but surprisingly not those with precancerous changes or invasive cervical cancer (CIN3+), show an increased WID-HPV index, indicating the WID-HPV may reflect a successful viral clearance response absent in progression to cancer. Further investigation revealed the WID-HPV is positively associated with apoptosis (ρ = 0.48; P < .001) and negatively associated with epigenetic replicative age (ρ = -0.43; P < .001). Taken together, our data suggest the WID-HPV captures a clearance response associated with apoptosis of HPV-infected cells. This response may be dampened or lost with increased underlying replicative age of infected cells, resulting in progression to cancer.
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Affiliation(s)
- Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Hall in Tirol, Tirol, Austria.,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Tirol, Austria
| | - Charlotte D Vavourakis
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Hall in Tirol, Tirol, Austria.,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Tirol, Austria
| | - James E Barrett
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Hall in Tirol, Tirol, Austria.,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Tirol, Austria
| | - Gerlinde Karbon
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Villunger
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Jiangrong Wang
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Karin Sundström
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Joakim Dillner
- Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Hall in Tirol, Tirol, Austria.,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Tirol, Austria.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, UK
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3
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Chitra B, Kumar SS. An optimized deep learning model using Mutation-based Atom Search Optimization algorithm for cervical cancer detection. Soft comput 2021. [DOI: 10.1007/s00500-021-06138-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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4
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Huang J, Gao H, Tan HZ. SOX1 Promoter Hypermethylation as a Potential Biomarker for High-Grade Squamous Intraepithelial Neoplasia Lesion and Cervical Carcinoma: A Meta-Analysis With Trial Sequential Analysis. Front Genet 2020; 11:633. [PMID: 32849763 PMCID: PMC7411256 DOI: 10.3389/fgene.2020.00633] [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: 07/23/2019] [Accepted: 05/26/2020] [Indexed: 12/17/2022] Open
Abstract
Background: DNA methylation has been widely assessed as a potential biomarker for the early detection of cervical cancer (CC). Herein, we assessed the associations of SOX1 promoter hypermethylation with squamous intraepithelial lesion and CC. Methods: Published studies and genome-wide methylation datasets were searched from electronic databases (up to April 2019). The associations of SOX1 hypermethylation with high-grade squamous intraepithelial lesion (HSIL) and CC risks were evaluated by odds ratios (ORs) and 95% confidence intervals (CIs). The summary receiver operator characteristic test was used to assess the diagnostic value of the SOX1 promoter hypermethylation of CC and intraepithelial neoplasia type III or worse (CIN3+). Trial sequential analysis (TSA) was performed to evaluate the stability of results and estimate the required information size (RIS). Results: In this meta-analysis of 17 published studies, the SOX1 methylation rates increased among low-grade SIL (LSIL, 27.27%), HSIL (40.75%), and CC (84.56%) specimens. Compared with control specimens, SOX1 promoter hypermethylation progressively increased the risk of HSIL by 4.20-fold (p < 0.001) and CC by 41.26-fold (p < 0.001). The pooled sensitivity of SOX1 methylation was estimated to be 0.85 (95% CI: 0.81–0.88) in differentiating patients with CC, corresponding to a specificity of 0.72 (95% CI: 0.69–0.75) and an area under the curve (AUC) of 0.93. Furthermore, the pooled sensitivity of SOX1 methylation was estimated to be 0.75 (95% CI: 0.72–0.78) in differentiating patients with CIN3+, corresponding to a specificity of 0.71 (95% CI: 0.69–0.73) and an AUC of 0.84. The pooled results of TCGA and GEO datasets showed that all CpG sites in SOX1 were associated with CC and 16 of 19 CpG sites were associated with HSIL. The results of TSA illustrated that the size was sufficient and significant associations were observed. Conclusion: This meta-analysis indicated that SOX1 promoter hypermethylation might have a potential value in the clinical diagnosis of CC and CIN3+.
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Affiliation(s)
- Jin Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Central South University, Changsha, China
| | - Hong Gao
- Department of Epidemiology and Health Statistics, School of Public Health, Central South University, Changsha, China.,School of Nursing, University of South China, Hengyang, China
| | - Hong-Zhuan Tan
- Department of Epidemiology and Health Statistics, School of Public Health, Central South University, Changsha, China
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5
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Singh A, Gupta S, Badarukhiya JA, Sachan M. Detection of aberrant methylation of HOXA9 and HIC1 through multiplex MethyLight assay in serum DNA for the early detection of epithelial ovarian cancer. Int J Cancer 2020; 147:1740-1752. [PMID: 32191343 DOI: 10.1002/ijc.32984] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/22/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
Accumulated evidence revealed that aberrant CpG island hypermethylation plays an important role in carcinogenesis which can serve as a promising target for molecular detection in body fluids. Despite a myriad of attempts to diagnose ovarian cancer (OC) at an early stage, this clinical aim remains a major challenge. To date, no single biomarker is able to accurately detect early OC in either tissue or body fluid. Aberrant DNA methylation patterns in circulating DNA provide highly specific cancer signals. In our study, we establish a novel panel of methylation-specific genes for the development of a TaqMan based qPCR assay to quantify methylation levels. We analyzed promoter methylation of homeobox A9 (HOXA9) and hypermethylated in cancer 1 (HIC1) quantitatively in 120 tissue samples and in 70 matched serum cell-free DNA (CFDNA) of cancerous and noncancerous samples by MethyLight assay. HOXA9 and HIC1 methylation occurred in 82.3 and 80.0% of OC tissue samples in singleplex assay, thereby confirming that methylation was highly cancer-specific. When either or both gene promoter showed methylation, the sensitivity was 88.2% with a specificity of 88.6% in tissue samples. The combined sensitivity for this novel marker panel in serum CFDNA was 88.9% (area under the curve [AUC] = 0.95). In contrast, no hypermethylation was observed in serum from matched cancer-free control women. Our results confirm the elevated performance of novel epigenetic marker panel (HOXA9 and HIC1) when analyzed in tissue and matched serum samples. Our findings reveal the potential of this biomarker panel as a suitable diagnostic serum biomarker for early screening of OC.
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Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | | | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
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6
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Zhang Y, Yuan Y, Li Y, Zhang P, Chen P, Sun S. An inverse interaction between HOXA11 and HOXA11-AS is associated with cisplatin resistance in lung adenocarcinoma. Epigenetics 2019; 14:949-960. [PMID: 31144606 DOI: 10.1080/15592294.2019.1625673] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
HOXA11, which is a member of the homeobox (HOX) gene family, and its natural antisense transcript (NAT) HOXA11-AS have been reported to be closely related to the development of lung cancer. We aimed to investigate their specific roles in cisplatin (DDP) resistance in lung adenocarcinoma (LUAD). First, we found that HOXA11 is hypermethylated and significantly downregulated in a DDP-resistant A549 cell line (A549/DDP) and LUAD tissues, while the HOXA11-AS expression level is elevated. Although HOXA11 and HOXA11-AS mRNA overlap in the 5'-untranslated region (5' UTR) and share two CpG islands, DNA methylation only regulates the expression of HOXA11. Then, we found that HOXA11 and HOXA11-AS have an inverse interaction by transfecting their siRNAs and overexpression vectors into A549 and A549/DDP cells. A dual-luciferase reporter assay further confirmed that the overlapping 5'UTR is essential for the bidirectional regulation between HOXA11 and HOXA11-AS. Functional analysis showed that knockdown of HOXA11 expression in A549 cells induced DDP resistance and activated Akt/β-catenin signaling, while overexpression of HOXA11 in A549/DDP cells increased DDP sensitivity and inhibited Akt/β-catenin signaling. Moreover, HOXA11-AS knockdown in A549 cells increased DDP sensitivity and inhibited Akt/β-catenin signaling, while the overexpression of HOXA11-AS in A549/DDP cells induced DDP resistance and activated Akt/β-catenin signaling. In conclusion, our study demonstrates that the inverse interaction between HOXA11 and HOXA11-AS promotes DDP resistance in LUAD.
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Affiliation(s)
- Youwei Zhang
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Yuan Yuan
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Yang Li
- b Department of Molecular Laboratory, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Peiying Zhang
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Pingsheng Chen
- c Department of Pathology, School of Basic Medical Sciences, Southeast University , Nanjing , China
| | - Sanyuan Sun
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
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7
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Kim HJ, Eoh KJ, Kim LK, Nam EJ, Yoon SO, Kim KH, Lee JK, Kim SW, Kim YT. The long noncoding RNA HOXA11 antisense induces tumor progression and stemness maintenance in cervical cancer. Oncotarget 2018; 7:83001-83016. [PMID: 27792998 PMCID: PMC5347748 DOI: 10.18632/oncotarget.12863] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/14/2016] [Indexed: 01/08/2023] Open
Abstract
Recent research has focused on the impact of long noncoding RNA (lncRNA) in cervical carcinogenesis. However, whether HOXA11 antisense (HOXA11-AS) is involved in cervical cancer remains to be elucidated. In the present study, we examined HOXA11-AS expression levels in cervical cancer patients and determined the relationships between HOXA11-AS expression and clinicopathological factors. We also investigated the bio-functional consequences of HOXA11-AS overexpression both in vitro and in vivo. HOXA11-AS expression was significantly greater in tissues from patients with cervical cancer than in control patients (P<0.001). Multivariate analysis showed that high HOXA11-AS was an independent prognosticator of overall survival (Hazard ratio=2.450, P=0.032). HOXA11-AS overexpression enhanced cell proliferation, migration, and tumor invasion in vitro, whereas HOXA11-AS knockdown inhibited these biologic aggressive features. These adverse changes were accompanied by characteristics of epithelial-mesenchymal transition (EMT). In vivo xenograft experiments using the siHOXA11-AS-transfected HeLa cells revealed that HOXA11-AS strongly induced tumor growth. Furthermore, we found that HOXA11-AS knockdown decreased cancer stemness and triggered the EMT program. In conclusion, HOXA11-AS overexpression correlated with poor survival in patients with cervical cancer. Thus, HOXA11-AS may be a pivotal target for exploring novel cervical cancer therapeutics.
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Affiliation(s)
- Hee Jung Kim
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung Jin Eoh
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea.,Department of Obstetrics and Gynecology, Yonsei University Graduate School, Seoul, Korea
| | - Lee Kyung Kim
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Ji Nam
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Sun Och Yoon
- Department of Pathology, Gangnam Severance Cancer Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kun-Hong Kim
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Kwan Lee
- Department of Obstetrics and Gynecology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Sang Wun Kim
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
| | - Young Tae Kim
- Institute of Women's Life Medical Science, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
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8
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Han YD, Wang XB, Cui NH, Zhang S, Wang C, Zheng F. Associations of P16INK4a promoter hypermethylation with squamous intra-epithelial lesion, cervical cancer and their clinicopathological features: a meta-analysis. Oncotarget 2018; 8:1871-1883. [PMID: 27669738 PMCID: PMC5352104 DOI: 10.18632/oncotarget.12202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 09/16/2016] [Indexed: 12/25/2022] Open
Abstract
To assess the associations of P16INK4a methylation status with low-grade squamous intra-epithelial lesion (LSIL), high-grade squamous intra-epithelial lesion (HSIL), cervical cancer (CC) and their clinicopathological features, a meta-analysis with 29 eligible studies was conducted. Pooled odds ratios (ORs) with their 95% confidence intervals (CIs) were estimated to assess the strength of the associations. Heterogeneity, sensitivity of pooled results and publication bias were also evaluated. Overall, there was an increasing trend of P16INK4a hypermethylation rates among LSIL (21.4%), HSIL (30.9%) and CC (35.0%) specimens. P16INK4a hypermethylation was significantly associated with the increased risk of LSIL, HSIL and CC, with the pooled ORs of 3.26 (95% CI: 1.86-5.71), 5.80 (95% CI: 3.80-8.84) and 12.17 (95% CI: 5.86-25.27), respectively. A significant association was also found between P16INK4a hypermethylation and smoking habit (OR = 3.88, 95% CI: 2.13-7.08). Taken together, meta-analysis results support P16INK4a hypermethylation as an epigenetic marker for the progression of cervical carcinogenesis.
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Affiliation(s)
- Ya-di Han
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xue-Bin Wang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ning-Hua Cui
- Department of Clinical Laboratory, Children's Hospital of Zhengzhou, Zhengzhou, Henan, China
| | - Shuai Zhang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Chen Wang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Fang Zheng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
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9
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Zhao G, Liu Z, Tian Y, Zhu M, Wang S, Wang H, Gao S, Ma Y, Zheng M. Stability, integrity, and recovery rate of cellular nucleic acids preserved in a new liquid-based cytology medium. Diagn Cytopathol 2018; 46:213-220. [PMID: 29341505 DOI: 10.1002/dc.23888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 12/11/2017] [Accepted: 12/20/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND Liquid-based cytology (LBC) has replaced the conventional Papanicolaou test in cervical cancer screening. The cervical swab specimens collected in LBC media can also be used for additional analyses including high-risk HPV (HR-HPV) test, DNA methylation analysis, and HPV E6/E7 mRNA test. METHODS The stability, integrity, and recovery rate of cellular DNA and RNA after storage at different conditions were evaluated by a quantitative real-time PCR (qPCR) based HR-HPV test, reverse transcription qPCR (RT-qPCR), and agarose gel electrophoresis. Cervical swab specimens collected in a newly developed LBC medium, VersaMedium, and ThinPrep PreservCyt medium were processed on Hologic ThinPrep 5000 instrument. RESULTS Cervical exfoliative cells fixed by VersaMedium exhibited good cellular morphology with intact membranes and delineated chromatin structures. Cellular DNA preserved in VersaMedium exhibited high level of stability at both room temperature and 4°C, and remained mostly intact at 4°C for up to 28 days. Cellular RNA preserved in VersaMedium maintained higher level of stability and integrity at 4°C than at room temperature. VersaMedium also showed no apparent adverse effect on the recovery rate of nucleic acids. CONCLUSION In addition to maintaining cellular morphology, when stored at 4°C, VersaMedium preserves cellular nucleic acids and PreservCyt medium without noticeable adverse effects on the recovery rate during purification. Therefore, VersaMedium is an appropriate LBC medium for the collection and preservation of cervical swab specimens. And VersaMedium preserved cellular nucleic acids are of such high quality that they are suitable for HR-HPV qPCR test and RT-qPCR analyses.
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Affiliation(s)
- Guodong Zhao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Zhaocheng Liu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Yaping Tian
- The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Minsheng Zhu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Shouli Wang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Hui Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.,School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Shen Gao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Yong Ma
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Minxue Zheng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
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10
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Ahmad A, Strohbuecker S, Tufarelli C, Sottile V. Expression of a SOX1 overlapping transcript in neural differentiation and cancer models. Cell Mol Life Sci 2017; 74:4245-4258. [PMID: 28674729 PMCID: PMC5641280 DOI: 10.1007/s00018-017-2580-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 06/04/2017] [Accepted: 06/26/2017] [Indexed: 12/28/2022]
Abstract
SOX1 is a member of the SOXB1 subgroup of transcription factors involved in early embryogenesis, CNS development and maintenance of neural stem cells. The structure and regulation of the human SOX1 locus has been less studied than that of SOX2, another member of the SOXB1 subgroup for which an overlapping transcript has been reported. Here we report that the SOX1 locus harbours a SOX1 overlapping transcript (SOX1-OT), and describe expression, splicing variants and detection of SOX1-OT in different stem and cancer cells. RT-PCR and RACE experiments were performed to detect and characterise the structure of SOX1-OT in neuroprogenitor cultures and across different cancer cell lines. SOX1-OT was found to present a complex structure including several unannotated exons, different transcript variants and at least two potential transcription start sites. SOX1-OT was found to be highly expressed in differentiated neural stem cells across different time points of differentiation, and its expression correlated with SOX1 gene expression. Concomitant expression of SOX1 and SOX1-OT was further observed in several cancer cell models. While the function of this transcript is unknown, the regulatory role reported for other lncRNAs strongly suggests a possible role for SOX1-OT in regulating SOX1 expression, as previously observed for SOX2. The elucidation of the genetic and regulatory context governing SOX1 expression will contribute to clarifying its role in stem cell differentiation and tumorigenesis.
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Affiliation(s)
- Azaz Ahmad
- Wolfson STEM Centre, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Stephanie Strohbuecker
- Wolfson STEM Centre, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Cristina Tufarelli
- Division of Graduate Entry Medicine & Health, School of Medicine, University of Nottingham, Derby, UK.
| | - Virginie Sottile
- Wolfson STEM Centre, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK.
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11
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Wang L, Cui Y, Sheng J, Yang Y, Kuang G, Fan Y, Jin J, Zhang Q. Epigenetic inactivation of HOXA11, a novel functional tumor suppressor for renal cell carcinoma, is associated with RCC TNM classification. Oncotarget 2017; 8:21861-21870. [PMID: 28423531 PMCID: PMC5400629 DOI: 10.18632/oncotarget.15668] [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: 08/08/2016] [Accepted: 01/16/2017] [Indexed: 11/25/2022] Open
Abstract
Epigenetic inactivation of HOXA11, a putative tumor suppressor, is frequently observed in a number of solid tumors, but has not been described in RCC (renal cell carcinoma). In this study, we investigated the expression, epigenetic changes and the function of HOXA11 in human renal cell carcinoma (RCC). HOXA11 was silenced or down-regulated in RCC cell lines and tissues. Methylation specific PCR (MSP) and bisulfite genomic sequencing (BGS) revealed that the HOXA11 promoter was hypermethylated in 5/6 RCC cell lines. Demethylation treatment resulted in demethylation of the promoter and increased HOXA11 expression in these cell lines. HOXA11 methylation was also detected in 68/95 (70.5%) primary RCC tumors, but only rare adjacent non-malignant renal tissues (13%, 3/23) showed hypermethylation of promoter. We also found that the methylation of HOXA11 was associated with higher TNM classification of RCC (p<0.05). Ectopic expression of HOXA11 led to significant inhibition of proliferation, colony formation, migration and invasion abilities and induced RCC cells apoptosis. Moreover, HOXA11 was found to inhibit Wnt signaling. Thus, our study demonstrated that HOXA11 function as a tumor suppressor in RCC, while it is frequently silenced by promoter methylation in RCC.
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Affiliation(s)
- Lu Wang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China.,Department of Urology, National Urological Cancer Center, Peking University First Hospital, Beijing 100034, China
| | - Yun Cui
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Jindong Sheng
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Yang Yang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Guanyu Kuang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Yu Fan
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China.,Department of Urology, National Research Center for Genitourinary Oncology, Peking University First Hospital, Beijing 100034, China
| | - Jie Jin
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
| | - Qian Zhang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing 100034, China
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12
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Clarke MA, Luhn P, Gage JC, Bodelon C, Dunn ST, Walker J, Zuna R, Hewitt S, Killian JK, Yan L, Miller A, Schiffman M, Wentzensen N. Discovery and validation of candidate host DNA methylation markers for detection of cervical precancer and cancer. Int J Cancer 2017; 141:701-710. [PMID: 28500655 DOI: 10.1002/ijc.30781] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/13/2017] [Indexed: 01/03/2023]
Abstract
Human papillomavirus (HPV) testing has been recently introduced as an alternative to cytology for cervical cancer screening. However, since most HPV infections clear without causing clinically relevant lesions, additional triage tests are required to identify women who are at high risk of developing cancer. We performed DNA methylation profiling on formalin-fixed, paraffin-embedded tissue specimens from women with benign HPV16 infection and histologically confirmed cervical intraepithelial neoplasia grade 3, and cancer using a bead-based microarray covering 1,500 CpG sites in over 800 genes. Methylation levels in individual CpG sites were compared using a t-test, and results were summarized by computing p-values. A total of 12 candidate genes (ADCYAP1, ASCL1, ATP10, CADM1, DCC, DBC1, HS3ST2, MOS, MYOD1, SOX1, SOX17 and TMEFF2) identified by DNA methylation profiling, plus an additional three genes identified from the literature (EPB41L3, MAL and miR-124) were chosen for validation in an independent set of 167 liquid-based cytology specimens using pyrosequencing and targeted, next-generation bisulfite sequencing. Of the 15 candidate gene markers, 10 had an area under the curve (AUC) of ≥ 0.75 for discrimination of high grade squamous intraepithelial lesions or worse (HSIL+) from <HSIL cytology using at least one assay. Overall, SOX1, DCC, and EPB41L3 showed the best discrimination with AUC values of ≥0.80, irrespective of methylation detection assay. In addition to verifying candidate markers from the literature (e.g., SOX1 and EPB41L3), we identified novel markers that may be considered for detection of cervical precancer and cancer and warrant further validation in prospective studies.
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Affiliation(s)
- Megan A Clarke
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Julia C Gage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - S Terence Dunn
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Joan Walker
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Rosemary Zuna
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Stephen Hewitt
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - J Keith Killian
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | | | | | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
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13
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Tong R, Yang Q, Wang C, Bi F, Jiang B. OVCA1 expression and its correlation with the expression levels of cyclin D1 and p16 in cervical cancer and intraepithelial neoplasia. Oncol Lett 2017; 13:2929-2936. [PMID: 28521400 PMCID: PMC5431343 DOI: 10.3892/ol.2017.5848] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/02/2016] [Indexed: 11/08/2022] Open
Abstract
The present study aimed to examine the associations between the protein and mRNA expression levels of ovarian cancer gene 1 (OVCA1), cyclin D1 and p16 and high-risk human papillomavirus (HR-HPV) infection in cervical lesions. The protein expression levels of OVCA1, cyclin D1 and p16 in 66 cases of cervical cancer, 64 cases of cervical intraepithelial neoplasia (CIN) and 34 normal cervix tissues were detected using immunohistochemistry. The mRNA expression levels of OVCA1, cyclin D1 and p16 in cervical cancer and normal cervix cells were detected using real-time polymerase chain reaction. The results revealed that the protein expression levels of OVCA1 increased gradually, whereas its mRNA expression levels decreased gradually, in the progression from normal cervix tissue to CIN and cervical cancer (P<0.01). In addition, significant differences in the protein expression levels of OVCA1 between low-and high-level CIN, as well as between the early and advanced stages of cervical cancer, were observed (P<0.05). No significant associations were detected between the protein and mRNA expression levels of OVCA1 and the pathological type of cervical cancer or the presence of lymph node metastasis (P>0.05). The expression levels of OVCA1 mRNA and protein were positively correlated with the levels of p16 expression (P<0.01). Significant differences were also observed in the OVCA1 protein and mRNA expression levels between the HR-HPV (+) and HR-HPV (−) groups (P<0.05). Therefore, aberrant expression of OVCA1 protein and mRNA may be important during the development of cervical lesions, particularly in the early stages. In addition, the mechanisms underlying the effects of OVCA1 during cervical cancer development may involve p16 and HPV, as the levels of OVCA1 in cervical lesions were correlated with abnormal expression of p16 and HR-HPV infection.
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Affiliation(s)
- Rui Tong
- Ward One of Minimally Invasive Gynecology, Nanhu Branch of Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China.,Ward Four of Tumor Gynecology, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Qing Yang
- Ward One of Minimally Invasive Gynecology, Nanhu Branch of Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Chunyan Wang
- Ward Four of Tumor Gynecology, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Fangfang Bi
- Ward One of Minimally Invasive Gynecology, Nanhu Branch of Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Bing Jiang
- Pathology Department, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
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14
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Verma M. The Role of Epigenomics in the Study of Cancer Biomarkers and in the Development of Diagnostic Tools. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 867:59-80. [PMID: 26530360 DOI: 10.1007/978-94-017-7215-0_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetics plays a key role in cancer development. Genetics alone cannot explain sporadic cancer and cancer development in individuals with no family history or a weak family history of cancer. Epigenetics provides a mechanism to explain the development of cancer in such situations. Alterations in epigenetic profiling may provide important insights into the etiology and natural history of cancer. Because several epigenetic changes occur before histopathological changes, they can serve as biomarkers for cancer diagnosis and risk assessment. Many cancers may remain asymptomatic until relatively late stages; in managing the disease, efforts should be focused on early detection, accurate prediction of disease progression, and frequent monitoring. This chapter describes epigenetic biomarkers as they are expressed during cancer development and their potential use in cancer diagnosis and prognosis. Based on epigenomic information, biomarkers have been identified that may serve as diagnostic tools; some such biomarkers also may be useful in identifying individuals who will respond to therapy and survive longer. The importance of analytical and clinical validation of biomarkers is discussed, along with challenges and opportunities in this field.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute (NCI), National Institutes of Health (NIH), Suite# 4E102. 9609 Medical Center Drive, MSC 9763, Bethesda, MD, 20892-9726, USA.
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15
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Bhat S, Kabekkodu SP, Noronha A, Satyamoorthy K. Biological implications and therapeutic significance of DNA methylation regulated genes in cervical cancer. Biochimie 2015; 121:298-311. [PMID: 26743075 DOI: 10.1016/j.biochi.2015.12.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/28/2015] [Indexed: 12/12/2022]
Abstract
Cervical cancer is the second most common cancer among women worldwide. About 528,000 women are diagnosed with cervical cancer contributing to around 266,000 deaths, across the globe every year. Out of these, the burden of 226,000 (85%) deaths occurs in the developing countries, who are less resource intensive to manage the disease. This is despite the fact that cervical cancer is amenable for early detection due to its long and relatively well-known natural history prior to its culmination as invasive disease. Infection with high risk human papillomavirus (hrHPVs) is essential but not sufficient to cause cervical cancer. Although it was thought that genetic mutations alone was sufficient to cause cervical cancer, the current epidemiological and molecular studies have shown that HPV infection along with genetic and epigenetic changes are frequently associated and essential for initiation, development and progression of the disease. Moreover, aberrant DNA methylation in host and HPV genome can be utilized not only as biomarkers for early detection, disease progression, diagnosis and prognosis of cervical cancer but also to design effective therapeutic strategies. In this review, we focus on recent studies on DNA methylation changes in cervical cancer and their potential role as biomarkers for early diagnosis, prognosis and targeted therapy.
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Affiliation(s)
- Samatha Bhat
- Department of Biotechnology, School of Life Sciences, Manipal University, Karnataka 576104, India
| | - Shama Prasada Kabekkodu
- Department of Biotechnology, School of Life Sciences, Manipal University, Karnataka 576104, India
| | - Ashish Noronha
- Department of Biotechnology, School of Life Sciences, Manipal University, Karnataka 576104, India
| | - Kapaettu Satyamoorthy
- Department of Biotechnology, School of Life Sciences, Manipal University, Karnataka 576104, India.
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16
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Chen J, Fu Z, Ji C, Gu P, Xu P, Yu N, Kan Y, Wu X, Shen R, Shen Y. Systematic gene microarray analysis of the lncRNA expression profiles in human uterine cervix carcinoma. Biomed Pharmacother 2015; 72:83-90. [PMID: 26054679 DOI: 10.1016/j.biopha.2015.04.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/06/2015] [Indexed: 10/23/2022] Open
Abstract
The human uterine cervix carcinoma is one of the most well-known malignancy reproductive system cancers, which threatens women health globally. However, the mechanisms of the oncogenesis and development process of cervix carcinoma are not yet fully understood. Long non-coding RNAs (lncRNAs) have been proved to play key roles in various biological processes, especially development of cancer. The function and mechanism of lncRNAs on cervix carcinoma is still rarely reported. We selected 3 cervix cancer and normal cervix tissues separately, then performed lncRNA microarray to detect the differentially expressed lncRNAs. Subsequently, we explored the potential function of these dysregulated lncRNAs through online bioinformatics databases. Finally, quantity real-time PCR was carried out to confirm the expression levels of these dysregulated lncRNAs in cervix cancer and normal tissues. We uncovered the profiles of differentially expressed lncRNAs between normal and cervix carcinoma tissues by using the microarray techniques, and found 1622 upregulated and 3026 downregulated lncRNAs (fold-change>2.0) in cervix carcinoma compared to the normal cervical tissue. Furthermore, we found HOXA11-AS might participate in cervix carcinogenesis by regulating HOXA11, which is involved in regulating biological processes of cervix cancer. This study afforded expression profiles of lncRNAs between cervix carcinoma tissue and normal cervical tissue, which could provide database for further research about the function and mechanism of key-lncRNAs in cervix carcinoma, and might be helpful to explore potential diagnosis factors and therapeutic targets for cervix carcinoma.
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Affiliation(s)
- Jie Chen
- Cervical Branch, Affiliated Nanjing Maternal and Child Health Hospital, Nanjing Medical University, Nanjing 210004, China
| | - Ziyi Fu
- Nanjing Maternal and Child Health Medical Institute, Affiliated Nanjing Maternal and Child Health Hospital, Nanjing Medical University, Nanjing 210004, China
| | - Chenbo Ji
- Nanjing Maternal and Child Health Medical Institute, Affiliated Nanjing Maternal and Child Health Hospital, Nanjing Medical University, Nanjing 210004, China
| | - Pingqing Gu
- Department of Clinical laboratory, Affiliated Nanjing Maternal and Child Health Hospital, Nanjing Medical University, Nanjing 210004, China
| | - Pengfei Xu
- Nanjing Maternal and Child Health Medical Institute, Affiliated Nanjing Maternal and Child Health Hospital, Nanjing Medical University, Nanjing 210004, China
| | - Ningzhu Yu
- Cervical Branch, Affiliated Nanjing Maternal and Child Health Hospital, Nanjing Medical University, Nanjing 210004, China
| | - Yansheng Kan
- Cervical Branch, Affiliated Nanjing Maternal and Child Health Hospital, Nanjing Medical University, Nanjing 210004, China
| | - Xiaowei Wu
- Department of Pharmacology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, China
| | - Rong Shen
- Cervical Branch, Affiliated Nanjing Maternal and Child Health Hospital, Nanjing Medical University, Nanjing 210004, China
| | - Yan Shen
- Cervical Branch, Affiliated Nanjing Maternal and Child Health Hospital, Nanjing Medical University, Nanjing 210004, China.
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17
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Tian X, Chen D, Zhang R, Zhou J, Peng X, Yang X, Zhang X, Zheng Z. Quantitative survey of multiple CpGs from 5 genes identifies CpG methylation panel discriminating between high- and low-grade cervical intraepithelial neoplasia. Clin Epigenetics 2015; 7:4. [PMID: 25699113 PMCID: PMC4334603 DOI: 10.1186/s13148-014-0037-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/16/2014] [Indexed: 12/14/2022] Open
Abstract
Background Studies of methylation biomarkers for cervical cancer often involved only few randomly selected CpGs per candidate gene analyzed by methylation-specific PCR-based methods, with often inconsistent results from different laboratories. We evaluated the role of different CpGs from multiple genes as methylation biomarkers for high-grade cervical intraepithelial neoplasia (CIN). Results We applied a mass spectrometry-based platform to survey the quantitative methylation levels of 34 CpG units from SOX1, PAX1, NKX6-1, LMX1A, and ONECUT1 genes in 100 cervical formalin-fixed paraffin-embedded (FFPE) tissues. We then used nonparametric statistics and Random Forest algorithm to rank significant CpG methylations and support vector machine with 10-fold cross validation and 200 times bootstrap resampling to build a predictive model separating CIN II/III from CIN I/normal subjects. We found only select CpG units showed significant differences in methylation between CIN II/III and CIN I/normal groups, while mean methylation levels per gene were similar between the two groups for each gene except PAX1. An optimal classification model involving five CpG units from SOX1, PAX1, NKX6-1, and LMX1A achieved 81.2% specificity, 80.4% sensitivity, and 80.8% accuracy. Conclusions Our study suggested that during CIN development, the methylation of CpGs within CpG islands is not uniform, with varying degrees of significance as biomarkers. Our study emphasizes the importance of not only methylated marker genes but also specific CpGs for identifying high-grade CINs. The 5-CpG classification model provides a promising biomarker panel for the early detection of cervical cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13148-014-0037-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoyi Tian
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
| | - Di Chen
- Department of Pathology, Aerospace Central Hospital, No. 15 Yuquan Road, Beijing, 100049 China
| | - Ran Zhang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
| | - Jun Zhou
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
| | - Xiaozhong Peng
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
| | - Xiaolin Yang
- Department of Biomedical Engineering, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
| | - Xiuru Zhang
- Department of Pathology, Beijing Tiantan Hospital Affiliated with Capital Medical University, No. 6 Tiantan Xili, Beijing, 100050 China
| | - Zhi Zheng
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, No. 5 Dong Dan San Tiao, Beijing, 100005 China
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18
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Cui Y, Gao D, Linghu E, Zhan Q, Chen R, Brock MV, Herman JG, Guo M. Epigenetic changes and functional study of HOXA11 in human gastric cancer. Epigenomics 2015; 7:201-13. [PMID: 25590359 DOI: 10.2217/epi.14.92] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
AIM To examine epigenetic changes and the function of HOXA11 in human gastric cancer (GC). MATERIALS & METHODS Seven GC cell lines, five cases of normal gastric mucosa and 112 cases primary GC samples were used in this study. RESULTS Expression of HOXA11 and lack of promoter region methylation were found in NCI-N87, MKN45, BGC823 and HGC27 cells. Loss of expression and complete methylation were found in AGS gastric cancer cells. Reduced expression and partial methylation were found in MGC803 and SGC7901 cells. Restoration of HOXA11 expression was induced by 5-aza-2'-deoxycytidine. HOXA11 was methylated in 81.25% (91/112) of primary GCs. The presence of methylation was associated with male gender, tumor size, tumor differentiation and lymph node metastasis (all p < 0.05). Restoration of HOXA11 expression reduced cell proliferation, invasion, migration and induced apoptosis and G2/M phase arrest. HOXA11 was found to inhibit Wnt signaling by upregulating NKD1 expression. CONCLUSION Epigenetic silencing of HOXA11 promotes GC proliferation, migration and invasion through activation of Wnt signaling.
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Affiliation(s)
- Yingying Cui
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
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19
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Hwang JA, Lee BB, Kim Y, Park SE, Heo K, Hong SH, Kim YH, Han J, Shim YM, Lee YS, Kim DH. HOXA11 hypermethylation is associated with progression of non-small cell lung cancer. Oncotarget 2014; 4:2317-25. [PMID: 24259349 PMCID: PMC3926829 DOI: 10.18632/oncotarget.1464] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This study was aimed at understanding the functional significance of HOXA11 hypermethylation in non-small cell lung cancer (NSCLC). HOXA11 hypermethylation was characterized in six lung cancer cell lines, and its clinical significance was analyzed using formalin-fixed paraffin-embedded tissues from 317 NSCLC patients, and Ki-67 expression was analyzed using immunohistochemistry. The promoter region of HOXA11 was highly methylated in six lung cancer cell lines, but not in normal bronchial epithelial cells. The loss of expression was restored by treatment of the cells with a demethylating agent, 5-aza-2'-deoxycytidine (5-Aza-dC). Transient transfection of HOXA11 into H23 lung cancer cells resulted in the inhibition of cell migration and proliferation. HOXA11 hypermethylation was found in 218 (69%) of 317 primary NSCLCs. HOXA11 hypermethylation was found at a higher prevalence in squamous cell carcinoma than in adenocarcinoma (74% vs. 63%, respectively). HOXA11 hypermethylation was associated with Ki-67 proliferation index (P = 0.03) and pT stage (P = 0.002), but not with patient survival. Patients with pT2 and pT3 stages were 1.85 times (95% confidence interval [CI] = 1.04-3.29; P = 0.04) and 5.47 times (95% CI = 1.18-25.50; P = 0.01), respectively, more likely to show HOXA11 hypermethylation than those with pT1 stage, after adjusting for age, sex, and histology. In conclusion, the present study suggests that HOXA11 hypermethylation may contribute to the progression of NSCLC by promoting cell proliferation or migration.
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Affiliation(s)
- Jung-Ah Hwang
- Cancer Genomics Branch, Research Institute, National Cancer Center, Goyang-si, Korea
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20
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Sun Z, Meng C, Wang S, Zhou N, Guan M, Bai C, Lu S, Han Q, Zhao RC. MicroRNA-1246 enhances migration and invasion through CADM1 in hepatocellular carcinoma. BMC Cancer 2014; 14:616. [PMID: 25159494 PMCID: PMC4150976 DOI: 10.1186/1471-2407-14-616] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 08/20/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The aberrant expression of microRNAs has been demonstrated to play a crucial role in the initiation and progression of hepatocarcinoma. miR-1246 expression in High invasive ability cell line than significantly higher than that in low invasive ability cell line. METHODS Transwell chambers (8-uM pore size; Costar) were used in the in vitro migration and invison anssay. Dual luciferase reporter gene construct and Dual luciferase reporter assay to identify the target of miR-1246. CADM1 expression was evaluated by immunohistochemistric staining. The clinical manifestations, treatments and survival were collected for statistical analysis. RESULTS Inhibition of miR-1246 effectively reduced migration and invasion of hepatocellular carcinoma cell lines. Bioinformatics and luciferase reporter assay revealed that miR-1246 specifically targeted the 3'-UTR of Cell adhesion molecule 1 and regulated its expression. Down-regulation of CADM1 enhanced migration and invasion of HCC cell lines. Furthermore, in tumor tissues obtained from liver cancer patients, the expression of miR-1246 was negatively correlated with CADM1 and the high expression of miR-1246 combined with low expression of CADM1 might serve as a risk factor for stage1 liver cancer patients. CONCLUSIONS Our study showed that miR-1246, by down-regulation CADM1, enhances migration and invasion in HCC cells.
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Affiliation(s)
| | | | | | | | | | | | | | - Qin Han
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, People's Republic of China.
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Bai Y, Fang N, Gu T, Kang Y, Wu J, Yang D, Zhang H, Suo Z, Ji S. HOXA11 gene is hypermethylation and aberrant expression in gastric cancer. Cancer Cell Int 2014; 14:79. [PMID: 25788862 PMCID: PMC4364045 DOI: 10.1186/s12935-014-0079-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/29/2014] [Indexed: 12/11/2022] Open
Abstract
Background Aberrant DNA methylation is an acquired epigenetic alteration that serves as an alternative to genetic defects in the inactivation of tumor suppressor genes and other genes in diverse human cancers. Gastric carcinoma is one of the tumors with a high frequency of aberrant methylation in promoter region. Hence we investigated the promoter methylation status and expression level of HOXA11 gene which may involve in GC development. Methods Thirty-two surgical excised gastric cancer specimens, twelve paired adjacent non-cancerous specimens and seven normal gastric mucosas were examined. The methylation status and expression level of HOXA11 gene were determined by bisulfite sequencing polymerase chain reaction (BSP), real-time polymerase chain reaction (RT-PCR) and immunohistochemistry (IHC) respectively. HOXA11 expression was knocked-down with siRNA to mimic HOXA11 gene hypermethylation and ability of cell proliferation and migration was determinate. In addition, we analyzed and correlated the findings with clinicopathological features. Results The methylation level of HOXA11 gene in gastric cancer tissues and adjacent non-cancerous tissues were higher than those in normal gastric mucosa (P < 0.05). The methylation level was higher in TNM III and IV patients of GC than those in TNM I and II patients (P < 0.05). The expression of HOXA11 mRNA and protein decreased in normal gastric mucosa, peri-cancer tissue and GC (P < 0.05). HOXA11 expression was inversely correlated with DNA methylation (P < 0.05). Knocked-down of HOXA11 expression with siRNA in BGC-823 cells enhanced cell proliferation compared with control, but no significant different was observed in migration ability. Conclusion Hypermethylation and decreased expression of HOXA11 gene may be involved in the carcinogenesis and development of GC and may provide useful information for the prediction of the malignant behaviors of GC. And the expression of HOXA11 is impaired by DNA methylation. However, repression of HOXA11 expression promoted BGC-823 cell proliferation.
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Affiliation(s)
- Yinguo Bai
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China ; Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
| | - Na Fang
- Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
| | - Tingxun Gu
- Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
| | - Yuhua Kang
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Jiang Wu
- Department of pathology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Desheng Yang
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Hui Zhang
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Zhimin Suo
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng 475000, Henan Province, China
| | - Shaoping Ji
- Department of Biochemistry and Molecular Biology, Medical School of Henan University, Kaifeng 475004, Henan Province, China
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Li T, Tang L, Bian D, Jia Y, Huang X, Zhang X. Detection of hTERC and c-MYC genes in cervical epithelial exfoliated cells for cervical cancer screening. Int J Mol Med 2014; 33:1289-97. [PMID: 24626956 DOI: 10.3892/ijmm.2014.1699] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/28/2014] [Indexed: 11/05/2022] Open
Abstract
Cervical cancer is the principal cause of mortality due to cancer in women worldwide. New predictive markers may increase survival rates by improving the treatment of patients at a high risk for cancer. This study was carried out to investigate the amplification of human telomerase RNA component (hTERC) or/and c-MYC in cervical epithelial exfoliated cells for cervical carcinoma screening. We collected 171 specimens. including speciments from normal cervix, benign lesions, cervical intraepithelial neoplasia (CIN)1, CIN2 and CIN3, or carcinoma in situ, as well as invasive cervical squamous cell carcinoma. Fluorescence in situ hybridization (FISH) was performed to detect alterations in hTERC and c-MYC expression. We analyzed the area under the receiver operating characteristic (ROC) curve (AUC), as well as the sensitivity and specificity of single screening and conjoined screening. There was a trend toward an increasing amplification of 2 genes with the increasing severity of cervical lesions. ROC curve analysis demonstrated that the AUC values of the hTERC gene for the screening of different cervical lesions were >0.8. Compared with the hTERC gene, the AUC of the c-MYC gene for the screening of ≥CIN3 was >0.8 and the AUC for the screening of other cervical lesions was >0.7. For the screening of cervical lesions above the grade of benign lesions, cytological diagnosis was superior to the gene detection with significant differences. For the screening of cervical lesions >CIN1, there were no statistically significant differences (P>0.05) between the hTERC gene and cytological diagnosis, whereas the screening results of c-MYC detection and cytological diagnosis differed significantly (P<0.05). For the screening of cervical lesions >CIN2 or >CIN3, the detection of hTERC and c-MYC genes and cytological diagnosis had similar screening results with no statistically significant differences (P>0.05). In conclusion, using FISH to detect the amplification of hTERC or/and c-MYC on cervical epithelial exfoliated cells may be a useful and specific screening method for precancerous lesions.
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Affiliation(s)
- Tian Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Liangdan Tang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Duhong Bian
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Ying Jia
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xin Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xinhua Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing 400016, P.R. China
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Imura J, Abe K, Uchida Y, Shibata M, Tsunematsu K, Sathoh M, Miwa S, Nakajima T, Nomoto K, Hayashi S, Tsuneyama K. Introduction and utility of liquid-based cytology on aspiration biopsy of peripheral nodular lesions of the lung. Oncol Lett 2014; 7:669-673. [PMID: 24520290 PMCID: PMC3919952 DOI: 10.3892/ol.2013.1763] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 11/06/2013] [Indexed: 01/31/2023] Open
Abstract
In the present study, aspiration biopsy cytology (ABC) was used for the diagnosis of peripheral nodular lesions in the lung (PNLL), and liquid-based cytology (LBC) was carried out on the material collected to evaluate it in comparison with the conventional method (CM). The subjects comprised 130 cases that underwent computed tomography (CT)-guided ABC for PNLL. A total of 73 cases received a tumor resection, with a diagnosis based on the pathology, while 57 cases were followed up, as the tumor showed no change on the radiological examinations. Biopsy samples from these patients and lavage fluid from the aspiration needles were used for analysis. Cellular material was obtained by centrifugation of the lavage fluid, and samples were prepared by two methods, direct smearing and LBC according to the ThinPrep method. The samples were categorized into three diagnoses: i) Benign, ii) suspicion of malignancy and iii) malignant. Appropriate samples were collected in 72% of cases by LBC, but only in 36% of cases by the CM. There was no marked difference in cellular images between the two methods, with the exception of a few specific cases. LBC on its own provided sensitivity at 68%, specificity at 61% and accuracy at 65%, while a combination of LBC and biopsy markedly improved these figures to 94, 81 and 84%, respectively. The introduction of LBC is considered useful for the cytopathological diagnosis of PNLL by CT-guided ABC. LBC enables the examination of appropriate samples rich in cellular components and supports a biopsy-based diagnosis. A combination of these two methods provides even higher diagnostic accuracy, and LBC is considered an excellent method to evaluate these pathological samples.
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Affiliation(s)
- Johji Imura
- Department of Diagnostic Pathology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Kaori Abe
- Department of Pathology, Ibaraki Prefectural Central Hospital, Kasama 309-1793, Japan
| | - Yoshiaki Uchida
- Department of Pathology, Ibaraki Prefectural Central Hospital, Kasama 309-1793, Japan
| | - Masaharu Shibata
- Department of Pathology, Ibaraki Prefectural Central Hospital, Kasama 309-1793, Japan
| | - Kazue Tsunematsu
- Department of Pathology, Ibaraki Prefectural Central Hospital, Kasama 309-1793, Japan
| | - Motohiro Sathoh
- Department of Radiology, Ibaraki Prefectural Central Hospital, Kasama 309-1793, Japan
| | - Shigeharu Miwa
- Department of Diagnostic Pathology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Takahiko Nakajima
- Department of Diagnostic Pathology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Kazuhiro Nomoto
- Department of Diagnostic Pathology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Shinichi Hayashi
- Department of Diagnostic Pathology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Koichi Tsuneyama
- Department of Diagnostic Pathology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
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Washiya K, Nakamura M, Mizuki Y, Motoi M, Kobayashi T, Yoshioka H, Watanabe J. Discriminating analysis of atypical squamous cells of undetermined significance of the uterine cervix using nuclear three-dimensional analysis. Acta Cytol 2013; 58:96-102. [PMID: 24247299 DOI: 10.1159/000355922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/20/2013] [Indexed: 11/19/2022]
Abstract
OBJECTIVE The Bethesda System (TBS) of uterine cervical cytology is a classification method that can improve accuracy in management and it includes descriptions on adequate specimens, human papillomavirus (HPV) involvement and estimated lesions. However, the judgment of atypical squamous cells of undetermined significance (ASC-US) using TBS features complicated diagnostic criteria and poor reproducibility due to the definition of ASC-US. Of patients diagnosed with ASC-US in the initial cytology, cervical intraepithelial neoplasia (CIN)1-2 cases positive for high-risk HPV (CIN+) and benign cases in histology negative for high-risk HPV (B-) were selected for discriminant analysis based on Mahalanobis distance, in order to improve the accuracy of the ASC-US diagnosis. STUDY DESIGN ASC-US cases featuring koilocytosis with little nuclear atypia (koilocytosis) and squamous epithelial cells with nuclear atypia (SC with atypia), morphologically diagnosed with liquid-based cytology specimens prepared using ThinPrep were included. The nuclei of koilocytosis cases (CIN+, 8 cases, and B-, 10 cases) and SC with atypia (CIN+, 19 cases, and B-, 15 cases) were three-dimensionally analyzed to conduct a discriminant analysis based on Mahalanobis distance. RESULTS Discrimination rates were 78.9% for CIN+ and 66.7% for B- in koilocytosis, and 50.7% for CIN+ and 72.1% for B- in SC with atypia. CONCLUSION The present method allows the objective analysis of nuclear chromatin, providing effective cytology regarding CIN+ in koilocytosis and B- in SC with atypia of ASC-US cases.
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Affiliation(s)
- Kiyotada Washiya
- Department of Medical Life Sciences, Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
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Brebi P, Maldonado L, Noordhuis MG, Ili C, Leal P, Garcia P, Brait M, Ribas J, Michailidi C, Perez J, Soudry E, Tapia O, Guzman P, Muñoz S, Van Neste L, Van Criekinge W, Irizarry R, Sidransky D, Roa JC, Guerrero-Preston R. Genome-wide methylation profiling reveals Zinc finger protein 516 (ZNF516) and FK-506-binding protein 6 (FKBP6) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population. Epigenetics 2013; 9:308-17. [PMID: 24241165 DOI: 10.4161/epi.27120] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cervical cancer is a major health concern among women in Latin America due to its high incidence and mortality. Therefore, the discovery of molecular markers for cervical cancer screening and triage is imperative. The aim of this study was to use a genome wide DNA methylation approach to identify novel methylation biomarkers in cervical cancer. DNA from normal cervical mucosa and cervical cancer tissue samples from Chile was enriched with Methylated DNA Immunoprecipitation (MeDIP), hybridized to oligonucleotide methylation microarrays and analyzed with a stringent bioinformatics pipeline to identify differentially methylated regions (DMRs) as candidate biomarkers. Quantitative Methylation Specific PCR (qMSP) was used to study promoter methylation of candidate DMRs in clinical samples from two independent cohorts. HPV detection and genotyping were performed by Reverse Line Blot analysis. Bioinformatics analysis revealed GGTLA4, FKBP6, ZNF516, SAP130, and INTS1 to be differentially methylated in cancer and normal tissues in the Discovery cohort. In the Validation cohort FKBP6 promoter methylation had 73% sensitivity and 80% specificity (AUC = 0.80). ZNF516 promoter methylation was the best biomarker, with both sensitivity and specificity of 90% (AUC = 0.92), results subsequently corroborated in a Prevalence cohort. Together, ZNF516 and FKBP6 exhibited a sensitivity of 84% and specificity of 81%, when considering both cohorts. Our genome wide DNA methylation assessment approach (MeDIP-chip) successfully identified novel biomarkers that differentiate between cervical cancer and normal samples, after adjusting for age and HPV status. These biomarkers need to be further explored in case-control and prospective cohorts to validate them as cervical cancer biomarkers.
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Affiliation(s)
- Priscilla Brebi
- Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA; School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile
| | - Leonel Maldonado
- Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Maartje G Noordhuis
- Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA; Department of Gynecologic Oncology; University Medical Center Groningen; Groningen, the Netherlands
| | - Carmen Ili
- Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA; School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile
| | - Pamela Leal
- Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA; School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile
| | - Patricia Garcia
- School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile
| | - Mariana Brait
- Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA; Clinical Research Coordination; Instituto Nacional de Câncer; Rio de Janeiro, Brazil
| | - Judit Ribas
- Pharmacology Unit; Department of Experimental Medicine; University of Lleida; Lleida, Spain
| | - Christina Michailidi
- Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Jimena Perez
- Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Ethan Soudry
- Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Oscar Tapia
- School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile
| | - Pablo Guzman
- School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile
| | - Sergio Muñoz
- School of Medicine; Department of Public Health; Universidad de La Frontera; Temuco, Chile
| | | | - Wim Van Criekinge
- MDxHealth PharmacoDx; Ghent, Belgium; BIOBIX; Department of Bioscience Engineering; Ghent University; Ghent Belgium
| | - Rafael Irizarry
- Bloomberg School of Public Health; Biostatistics Department; The Johns Hopkins University; Baltimore, MD USA
| | - David Sidransky
- Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Juan C Roa
- School of Medicine; Department of Pathology; Molecular Pathology Laboratory; Universidad de La Frontera; BIOREN-CEGIN; Temuco, Chile; School of Medicine; Department of Pathology; Pontificia Universidad Católica de Chile; Santiago, Chile
| | - Rafael Guerrero-Preston
- Otolaryngology Department; Head and Neck Cancer Research Division; The Johns Hopkins University School of Medicine; Baltimore, MD USA
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DNA methylation of PAX1 as a biomarker for oral squamous cell carcinoma. Clin Oral Investig 2013; 18:801-8. [PMID: 23907469 DOI: 10.1007/s00784-013-1048-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/03/2013] [Indexed: 12/25/2022]
Abstract
OBJECTIVES DNA methylation has been shown to be a promising cancer biomarker. The aim of this study was to evaluate DNA methylation of three transcription factors, sex-determining region Y-box 1 (SOX1), paired box gene 1 (PAX1), and zinc-finger 582 (ZNF582), in detecting oral squamous cell carcinoma (OSCC). MATERIALS AND METHODS A case-control study was conducted at Taipei Medical University Hospital in Taiwan with 31 cases of various oral cavity squamous cell carcinomas and 40 controls. Questionnaire data assessing environmental exposure, such as alcohol consumption, cigarette smoking, and betel nut chewing, were obtained from each participant. DNA from oral swabs were analyzed for methylation using quantitative methylation polymerase chain reaction with TaqMan probes. Methylation status was determined using a methylation index. RESULTS Methylation levels of SOX1, PAX1, and ZNF582 were significantly higher in cancer patients (p = 0.02, p = 0.02, and p = 0.03, respectively). Patients with highly methylated SOX1, PAX1, and ZNF582 had an increased cancer risk with odds ratios (ORs) of 16.50 (95 % CI = 2.85-96.65), 60.57 (95 % CI = 5.85-629.94), and 5.07 (95 % CI = 1.08-23.76), respectively. Area under the curve (AUC) values were 0.85, 0.78, and 0.78 for PAX1, SOX1, and ZNF582, respectively. When stratified based on environmental exposure, the AUC of PAX1 methylation (PAX1 (m) ) was 0.94 in environmental exposure-naïve subjects and 0.85 for SOX1 methylation in subjects who chewed betel nut. In general, the sensitivity and specificity of PAX1 (m) were 87 and 80 % for OSCC detection. The sensitivity of PAX1 (m) in subjects who chewed betel nut was 83 %, with a specificity of 75 %. CONCLUSIONS Testing PAX1 DNA methylation using oral swabs is a promising method for oral cancer detection. Combined assessments regarding betel nut consumption and DNA methylation can improve OSCC screening. CLINICAL RELEVANCE The double E (environmental and epigenetic) assessment is a potential strategy in OSCC screening.
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Bierkens M, Hesselink AT, Meijer CJLM, Heideman DAM, Wisman GBA, van der Zee AGJ, Snijders PJF, Steenbergen RDM. CADM1 and MAL promoter methylation levels in hrHPV-positive cervical scrapes increase proportional to degree and duration of underlying cervical disease. Int J Cancer 2013; 133:1293-9. [PMID: 23456988 DOI: 10.1002/ijc.28138] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 02/07/2013] [Indexed: 11/10/2022]
Abstract
Combined detection of cell adhesion molecule 1 (CADM1) and T-lymphocyte maturation-associated protein (MAL) promoter methylation in cervical scrapes is a promising triage strategy for high-risk human papillomavirus (hrHPV)-positive women. Here, CADM1 and MAL DNA methylation levels were analysed in cervical scrapes of hrHPV-positive women with no underlying high-grade disease, high-grade cervical intraepithelial neoplasia (CIN) and cervical cancer. CADM1 and MAL methylation levels in scrapes were first related to CIN-grade of the corresponding biopsy and second to CIN-grade stratified by the presence of 'normal' or 'abnormal' cytology as present in the accompanying scrape preceding the cervical biopsy. The scrapes included 167 women with ≤ CIN1, 54 with CIN2/3 and 44 with carcinoma. In a separate series of hrHPV-positive scrapes of women with CIN2/3 (n = 48), methylation levels were related to duration of preceding hrHPV infection (PHI; <5 and ≥ 5 years). Methylation levels were determined by quantitative methylation-specific PCR and normal cytology scrapes of hrHPV-positive women with histologically ≤ CIN1 served as reference. CADM1 and MAL methylation levels increased proportional to severity of the underlying lesion, showing an increase of 5.3- and 6.2-fold in CIN2/3, respectively, and 143.5- and 454.9-fold in carcinomas, respectively, compared to the reference. Methylation levels were also elevated in CIN2/3 with a longer duration of PHI (i.e. 11.5- and 13.6-fold, respectively). Moreover, per histological category, methylation levels were higher in accompanying scrapes with abnormal cytology than in scrapes with normal cytology. Concluding, CADM1 and MAL promoter methylation levels in hrHPV-positive cervical scrapes are related to the degree and duration of underlying cervical disease and markedly increased in cervical cancer.
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Affiliation(s)
- Mariska Bierkens
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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Chang L, He X, Yu G, Wu Y. Effectiveness of HPV 16 viral load and the E2/E6 ratio for the prediction of cervical cancer risk among Chinese women. J Med Virol 2013; 85:646-54. [PMID: 23364617 DOI: 10.1002/jmv.23490] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2012] [Indexed: 11/10/2022]
Abstract
The effectiveness of the E2/E6 ratio, the state of viral genome integration and the viral load of human papillomavirus 16 (HPV 16) in predicting the risk of cervical cancer among Chinese women was investigated. Quantitative PCRs for the E2/E6 ratio and the viral load were performed on 85 cervical cancer samples and 55 HPV 16 positive healthy controls. The integrated form of the viral genome was found in 10.9% control samples and in 26.4% cervical cancer samples (P = 0.02). The majority of the cervical cancer (63.2%) and control samples (60%) were mixed forms. The E2/E6 ratio was associated with a high risk of cervical cancer (OR = 7.29, P = 9.55E-6). The integrated form (OR = 6.54, P = 0.005) and mixed form (OR = 2.93, P = 0.042) increased the risk of cervical cancer. The mean viral load in cervical cancer samples (37,371 ± 227,135) was higher than that in the controls (4,619 ± 27,079; P = 0.011). Additionally, the viral load increased along with the cervical cancer progression from the International Federation of Gynecology and Obstetrics (FIGO) stage I (12,337 ± 25,604) to stage II (67,453 ± 319,821). Compared with the state of viral genome integration (area under the receiver operating characteristic curve (AUC) = 0.743) or the viral load (AUC = 0.694), the E2/E6 ratio improved the effectiveness of the risk prediction of cervical cancer (AUC = 0.777), with the sensitivity (specificity) 81.2% (71.7%). The state of viral genome integration and the viral load of HPV 16 were important factors for the risk prediction of cervical cancer among Chinese women, and the E2/E6 ratio had a better cervical cancer risk prediction with age adjustment.
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Affiliation(s)
- Lihong Chang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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Epigenetics makes its mark on women-specific cancers—an opportunity to redefine oncological approaches? Gynecol Oncol 2013; 128:134-143. [DOI: 10.1016/j.ygyno.2012.09.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/21/2012] [Accepted: 09/22/2012] [Indexed: 01/21/2023]
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WU JIANHONG, LIANG XUEAI, WU YUMEI, LI FENGSHUANG, DAI YINMEI. Identification of DNA methylation of SOX9 in cervical cancer using methylated-CpG island recovery assay. Oncol Rep 2012; 29:125-32. [DOI: 10.3892/or.2012.2077] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 09/06/2012] [Indexed: 11/05/2022] Open
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Lendvai Á, Johannes F, Grimm C, Eijsink JJH, Wardenaar R, Volders HH, Klip HG, Hollema H, Jansen RC, Schuuring E, Wisman GBA, van der Zee AGJ. Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia. Epigenetics 2012; 7:1268-78. [PMID: 23018867 DOI: 10.4161/epi.22301] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Epigenetic modifications, such as aberrant DNA promoter methylation, are frequently observed in cervical cancer. Identification of hypermethylated regions allowing discrimination between normal cervical epithelium and high-grade cervical intraepithelial neoplasia (CIN2/3), or worse, may improve current cervical cancer population-based screening programs. In this study, the DNA methylome of high-grade CIN lesions was studied using genome-wide DNA methylation screening to identify potential biomarkers for early diagnosis of cervical neoplasia. Methylated DNA Immunoprecipitation (MeDIP) combined with DNA microarray was used to compare DNA methylation profiles of epithelial cells derived from high-grade CIN lesions with normal cervical epithelium. Hypermethylated differentially methylated regions (DMRs) were identified. Validation of nine selected DMRs using BSP and MSP in cervical tissue revealed methylation in 63.2-94.7% high-grade CIN and in 59.3-100% cervical carcinomas. QMSP for the two most significant high-grade CIN-specific methylation markers was conducted exploring test performance in a large series of cervical scrapings. Frequency and relative level of methylation were significantly different between normal and cancer samples. Clinical validation of both markers in cervical scrapings from patients with an abnormal cervical smear confirmed that frequency and relative level of methylation were related with increasing severity of the underlying CIN lesion and that ROC analysis was discriminative. These markers represent the COL25A1 and KATNAL2 and their observed increased methylation upon progression could intimate the regulatory role in carcinogenesis. In conclusion, our newly identified hypermethylated DMRs represent specific DNA methylation patterns in high-grade CIN lesions and are candidate biomarkers for early detection.
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Affiliation(s)
- Ágnes Lendvai
- Department of Gynaecological Oncology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
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Patel DA, Rozek LS, Colacino JA, Van Zomeren-Dohm A, Ruffin MT, Unger ER, Dolinoy DC, Swan DC, Onyekwuluje J, DeGraffinreid CR, Paskett ED. Patterns of cellular and HPV 16 methylation as biomarkers for cervical neoplasia. J Virol Methods 2012; 184:84-92. [PMID: 22664184 PMCID: PMC3396790 DOI: 10.1016/j.jviromet.2012.05.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 05/21/2012] [Accepted: 05/24/2012] [Indexed: 11/21/2022]
Abstract
Aberrant promoter methylation of biologically relevant genes in cervical cancer and uneven CpG distribution within the human papillomavirus 16 (HPV 16) enhancer region have been reported. Cervical samples and questionnaires from 151 women screened for cervical cancer in Appalachian Ohio were analyzed. Methylation was measured by bisulfite sequencing in candidate gene sites in ESR1, DCC, p16, and LINE1 elements. Among 89 HPV 16-positive women, CpG sites in the E6 promoter and enhancer regions and the L1 region of the HPV 16 genome were measured. Methylation levels were compared by cervical cytology and HPV 16 status. HPV methylation was low regardless of cytology status, however E6 methylation was significantly higher in women with normal cytology. ESR1 and DCC methylation were significantly higher in HPV 16-positive women. Increased methylation at sites in the E6 promoter region was associated with lower odds of abnormal cytology. Increased methylation in candidate genes was associated with higher odds of abnormal cytology, particularly DCC region 2.4, DCC region 2.6, ESR1 region 3.2, and LINE1 site 1.2. HPV 16 genome CpG methylation was low except for the L1 region. In general, lower HPV 16 methylation and higher candidate gene methylation levels were associated with higher odds of abnormal cytology.
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Affiliation(s)
- Divya A. Patel
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University, FMB 307, 330 Cedar Street, New Haven, Connecticut 06520, U.S.A
| | - Laura S. Rozek
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 109 S. Observatory, 6630 Tower, Ann Arbor, Michigan 48109-2029, U.S.A
| | - Justin A. Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 109 S. Observatory, 6630 Tower, Ann Arbor, Michigan 48109-2029, U.S.A
| | - Adrienne Van Zomeren-Dohm
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 109 S. Observatory, 6630 Tower, Ann Arbor, Michigan 48109-2029, U.S.A
| | - Mack T. Ruffin
- Department of Family Medicine, University of Michigan, 1018 Fuller St., Ann Arbor, Michigan 48104-1213, U.S.A
| | - Elizabeth R. Unger
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Mail Stop G-41, Atlanta, Georgia 30333, U.S.A
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 109 S. Observatory Street, 6638 SPH I Tower, Ann Arbor, Michigan 48109-2029, U.S.A
| | - David C. Swan
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Mail Stop G-41, Atlanta, Georgia 30333, U.S.A
| | - Juanita Onyekwuluje
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Mail Stop G-41, Atlanta, Georgia 30333, U.S.A
| | - Cecilia R. DeGraffinreid
- Comprehensive Cancer Center, Ohio State University, 525 Gateway Building C, 1590 N. High Street, Columbus, Ohio 43201, U.S.A
| | - Electra D. Paskett
- Department of Internal Medicine, College of Medicine, Ohio State University, Suite 525, 1590 High Street, Columbus, Ohio, U.S.A
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Nelson HH, Marsit CJ, Christensen BC, Houseman EA, Kontic M, Wiemels JL, Karagas MR, Wrensch MR, Zheng S, Wiencke JK, Kelsey KT. Key epigenetic changes associated with lung cancer development: results from dense methylation array profiling. Epigenetics 2012; 7:559-66. [PMID: 22522909 DOI: 10.4161/epi.20219] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Epigenetic alterations are a common event in lung cancer and their identification can serve to inform on the carcinogenic process and provide clinically relevant biomarkers. Using paired tumor and non-tumor lung tissues from 146 individuals from three independent populations we sought to identify common changes in DNA methylation associated with the development of non-small cell lung cancer. Pathologically normal lung tissue taken at the time of cancer resection was matched to tumorous lung tissue and together were probed for methylation using Illumina GoldenGate arrays in the discovery set (n = 47 pairs) followed by bisulfite pyrosequencing for validation sets (n = 99 pairs). For each matched pair the change in methylation at each CpG was calculated (the odds ratio), and these ratios were averaged across individuals and ranked by magnitude to identify the CpGs with the greatest change in methylation associated with tumor development. We identified the top gene-loci representing an increase in methylation (HOXA9, 10.3-fold and SOX1, 5.9-fold) and decrease in methylation (DDR1, 8.1-fold). In replication testing sets, methylation was higher in tumors for HOXA9 (p < 2.2 × 10 (-16) ) and SOX1 (p < 2.2 × 10 (-16) ) and lower for DDR1 (p < 2.2 × 10 (-16) ). The magnitude and strength of these changes were consistent across squamous cell and adenocarcinoma tumors. Our data indicate that the identified genes consistently have altered methylation in lung tumors. Our identified genes should be included in translational studies that aim to develop screening for early disease detection.
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Affiliation(s)
- Heather H Nelson
- Masonic Cancer Center, Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA.
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Leonard SM, Wei W, Collins SI, Pereira M, Diyaf A, Constandinou-Williams C, Young LS, Roberts S, Woodman CB. Oncogenic human papillomavirus imposes an instructive pattern of DNA methylation changes which parallel the natural history of cervical HPV infection in young women. Carcinogenesis 2012; 33:1286-93. [DOI: 10.1093/carcin/bgs157] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Jones A, Lechner M, Fourkala EO, Kristeleit R, Widschwendter M. Emerging promise of epigenetics and DNA methylation for the diagnosis and management of women's cancers. Epigenomics 2012; 2:9-38. [PMID: 22122746 DOI: 10.2217/epi.09.47] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Over the last two decades, survival rates from women's cancers (breast, ovarian, endometrial and cervical cancer) have all but modestly improved despite huge efforts from both research and clinical communities. In parallel with this, the field of epigenetics has grown from its infancy into a promising scientific discipline. In particular, DNA methylation analysis has been adopted by oncologists in an attempt to better understand and manage cancer. Now that the epigenetic technological base has caught up, the potential of methylation markers in cancer research is finally being realized. In this review, we present the current status of epigenetic research into women's cancers with a main focus on DNA methylation analysis. We provide an overview of technological development, current markers of risk prediction, early detection, diagnosis, prognosis and response to treatment, and highlight the progression of epigenetic therapies. Finally, we comment on the potential impact of epigenetic analyses on the future of women's health.
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Affiliation(s)
- Allison Jones
- Department of Gynecological Oncology, Institute for Women's Health, University College London, 149 Tottenham Court Road, London, UK
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Teschendorff AE, Jones A, Fiegl H, Sargent A, Zhuang JJ, Kitchener HC, Widschwendter M. Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation. Genome Med 2012; 4:24. [PMID: 22453031 PMCID: PMC3446274 DOI: 10.1186/gm323] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/13/2012] [Accepted: 03/27/2012] [Indexed: 12/13/2022] Open
Abstract
Background Recently, it has been proposed that epigenetic variation may contribute to the risk of complex genetic diseases like cancer. We aimed to demonstrate that epigenetic changes in normal cells, collected years in advance of the first signs of morphological transformation, can predict the risk of such transformation. Methods We analyzed DNA methylation (DNAm) profiles of over 27,000 CpGs in cytologically normal cells of the uterine cervix from 152 women in a prospective nested case-control study. We used statistics based on differential variability to identify CpGs associated with the risk of transformation and a novel statistical algorithm called EVORA (Epigenetic Variable Outliers for Risk prediction Analysis) to make predictions. Results We observed many CpGs that were differentially variable between women who developed a non-invasive cervical neoplasia within 3 years of sample collection and those that remained disease-free. These CpGs exhibited heterogeneous outlier methylation profiles and overlapped strongly with CpGs undergoing age-associated DNA methylation changes in normal tissue. Using EVORA, we demonstrate that the risk of cervical neoplasia can be predicted in blind test sets (AUC = 0.66 (0.58 to 0.75)), and that assessment of DNAm variability allows more reliable identification of risk-associated CpGs than statistics based on differences in mean methylation levels. In independent data, EVORA showed high sensitivity and specificity to detect pre-invasive neoplasia and cervical cancer (AUC = 0.93 (0.86 to 1) and AUC = 1, respectively). Conclusions We demonstrate that the risk of neoplastic transformation can be predicted from DNA methylation profiles in the morphologically normal cell of origin of an epithelial cancer. Having profiled only 0.1% of CpGs in the human genome, studies of wider coverage are likely to yield improved predictive and diagnostic models with the accuracy needed for clinical application. Trial registration The ARTISTIC trial is registered with the International Standard Randomised Controlled Trial Number ISRCTN25417821.
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Affiliation(s)
- Andrew E Teschendorff
- Statistical Genomics Group, Paul O'Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK.
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Zhuang J, Jones A, Lee SH, Ng E, Fiegl H, Zikan M, Cibula D, Sargent A, Salvesen HB, Jacobs IJ, Kitchener HC, Teschendorff AE, Widschwendter M. The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer. PLoS Genet 2012; 8:e1002517. [PMID: 22346766 PMCID: PMC3276553 DOI: 10.1371/journal.pgen.1002517] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/15/2011] [Indexed: 12/19/2022] Open
Abstract
Aberrant DNA methylation is an important cancer hallmark, yet the dynamics of DNA methylation changes in human carcinogenesis remain largely unexplored. Moreover, the role of DNA methylation for prediction of clinical outcome is still uncertain and confined to specific cancers. Here we perform the most comprehensive study of DNA methylation changes throughout human carcinogenesis, analysing 27,578 CpGs in each of 1,475 samples, ranging from normal cells in advance of non-invasive neoplastic transformation to non-invasive and invasive cancers and metastatic tissue. We demonstrate that hypermethylation at stem cell PolyComb Group Target genes (PCGTs) occurs in cytologically normal cells three years in advance of the first morphological neoplastic changes, while hypomethylation occurs preferentially at CpGs which are heavily Methylated in Embryonic Stem Cells (MESCs) and increases significantly with cancer invasion in both the epithelial and stromal tumour compartments. In contrast to PCGT hypermethylation, MESC hypomethylation progresses significantly from primary to metastatic cancer and defines a poor prognostic signature in four different gynaecological cancers. Finally, we associate expression of TET enzymes, which are involved in active DNA demethylation, to MESC hypomethylation in cancer. These findings have major implications for cancer and embryonic stem cell biology and establish the importance of systemic DNA hypomethylation for predicting prognosis in a wide range of different cancers.
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Affiliation(s)
- Joanna Zhuang
- Department of Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, London, United Kingdom
- Statistical Genomics Group, University College London Cancer Institute, London, United Kingdom
| | - Allison Jones
- Department of Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, London, United Kingdom
| | - Shih-Han Lee
- Department of Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, London, United Kingdom
| | - Esther Ng
- Statistical Genomics Group, University College London Cancer Institute, London, United Kingdom
| | - Heidi Fiegl
- Department of Gynaecology and Obstetrics, Innsbruck Medical University, Innsbruck, Austria
| | - Michal Zikan
- Oncogynecologic Center, Department of Obstetrics and Gynaecology, Charles University Prague–First Faculty of Medicine and General Faculty Hospital, Prague, Czech Republic
| | - David Cibula
- Oncogynecologic Center, Department of Obstetrics and Gynaecology, Charles University Prague–First Faculty of Medicine and General Faculty Hospital, Prague, Czech Republic
| | - Alexandra Sargent
- School of Cancer and Imaging Science, Manchester Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Helga B. Salvesen
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Ian J. Jacobs
- Department of Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, London, United Kingdom
- School of Cancer and Imaging Science, Manchester Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Henry C. Kitchener
- School of Cancer and Imaging Science, Manchester Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Andrew E. Teschendorff
- Statistical Genomics Group, University College London Cancer Institute, London, United Kingdom
- * E-mail: (MW); (AET)
| | - Martin Widschwendter
- Department of Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, London, United Kingdom
- * E-mail: (MW); (AET)
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Dina R, Gudi M, Kocjan G, Schmitt F, Vielh P. The danger to cytopathology of over-specialization and its relevance for histopathology. Cytopathology 2011; 22:139-40. [PMID: 22142428 DOI: 10.1111/j.1365-2303.2011.00865.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sahasrabuddhe VV, Luhn P, Wentzensen N. Human papillomavirus and cervical cancer: biomarkers for improved prevention efforts. Future Microbiol 2011; 6:1083-98. [PMID: 21958146 PMCID: PMC3809085 DOI: 10.2217/fmb.11.87] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
While organized screening programs in industrialized countries have significantly reduced cervical cancer incidence, cytology-based screening has several limitations. Equivocal or mildly abnormal Pap tests require costly retesting or diagnostic work-up by colposcopy and biopsy. In low-resource countries, it has been difficult to establish and sustain cytology-based programs. Advances in understanding human papillomavirus biology and the natural history of human papillomavirus-related precancers and cancers have led to the discovery of a range of novel biomarkers in the past decade. In this article, we will discuss the potential role of new biomarkers for primary screening, triage and diagnosis in high-resource countries and their promise for prevention efforts in resource constrained settings.
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Affiliation(s)
- Vikrant V Sahasrabuddhe
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, 6120 Executive Blvd EPS 5024, Rockville MD 20852, USA
| | - Patricia Luhn
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, 6120 Executive Blvd EPS 5024, Rockville MD 20852, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, 6120 Executive Blvd EPS 5024, Rockville MD 20852, USA
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Hesselink AT, Heideman DAM, Steenbergen RDM, Coupé VMH, Overmeer RM, Rijkaart D, Berkhof J, Meijer CJLM, Snijders PJF. Combined promoter methylation analysis of CADM1 and MAL: an objective triage tool for high-risk human papillomavirus DNA-positive women. Clin Cancer Res 2011; 17:2459-65. [PMID: 21389098 DOI: 10.1158/1078-0432.ccr-10-2548] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Screening women for high-grade cervical intraepithelial neoplasia or cervical cancer (CIN3(+)) by high-risk human papillomavirus (hrHPV) testing has as side-effect the detection of hrHPV-positive women without clinically relevant lesions. Here, we developed an objective assay assessing the methylation status of the promoter regions of CADM1 and MAL to triage hrHPV-positive women for CIN3(+). EXPERIMENTAL DESIGN In a training set (51 women with CIN3(+) and 224 without CIN2(+)), panels consisting of one to four quantitative methylation-specific PCR (qMSP) assays (CADM1-m12,CADM1-m18,MAL-m1,MAL-m2) were analyzed. Cross-validated receiver-operating characteristics (ROC) curves were constructed and the panel with highest partial cross-validated area under the curve (AUC) was used for validation in an independent set of 236 consecutive hrHPV-positive women from a screening cohort. In the validation set, the ROC curve of the panel was compared with CIN3(+) sensitivity and specificity of cytology and of cytology combined with HPV16/18 genotyping. RESULTS In the training set, CADM1-m18 combined with MAL-m1 was the best panel (cross-validated partial AUC = 0.719). In the validation set, this panel revealed CIN3(+) sensitivities ranging from 100% (95% CI: 92.4-100) to 60.5% (95% CI: 47.1-74.6), with corresponding specificities ranging from 22.7% (95% CI: 20.2-25.2) to 83.3% (95% CI: 78.4-87.4). For cytology these were 65.8% (95% CI: 52.3-79.0) and 78.8% (95% CI: 73.7-83.1) and for cytology/HPV16/18, these were 84.2% (95% CI: 72.0-92.7) and 54.0% (95% CI: 49.2-58.7), respectively. The point estimates of both cytology and cytology/HPV16/18 were equal to the values of the ROC curve of CADM1-m18/MAL-m1. CONCLUSIONS We developed an objective methylation marker panel that was equally discriminatory for CIN3(+) as cytology or cytology with HPV16/18 genotyping in hrHPV-positive women. This opens the possibility for complete cervical screening by objective, nonmorphological molecular methods.
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Affiliation(s)
- Albertus T Hesselink
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
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Abstract
Ovarian cancer is the leading cause of death among gynecological cancers. It is now recognized that in addition to genetic alterations, epigenetic mechanisms, such as DNA methylation, histone modifications and nucleosome remodeling, play an important role in the development and progression of ovarian cancer by modulating chromatin structure, and gene and miRNA expression. Furthermore, epigenetic alterations have been recognized as useful tools for the development of novel biomarkers for diagnosis, prognosis, therapeutic prediction and monitoring of diseases. Moreover, new epigenetic therapies, such as DNA methyltransferase inhibitors and histone deacetylase inhibitors, have been found to be a potential therapeutic option, especially when used in combination with other agents. Here we discuss current developments in ovarian carcinoma epigenome research, the importance of the ovarian carcinoma epigenome for development of diagnostic and prognostic biomarkers, and the current epigenetic therapies used in ovarian cancer.
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Affiliation(s)
- Leonel Maldonado
- Department of Otolaryngology & Head & Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, USA
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Lai HC, Lin YW, Huang RL, Chung MT, Wang HC, Liao YP, Su PH, Liu YL, Yu MH. Quantitative DNA methylation analysis detects cervical intraepithelial neoplasms type 3 and worse. Cancer 2010; 116:4266-74. [PMID: 20564139 DOI: 10.1002/cncr.25252] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND DNA methylation may be used a potential biomarker for detecting cervical cancer. The authors of this report used quantitative methylation analysis of 4 genes in a full spectrum of cervical lesions to test its potential clinical application. METHODS This hospital-based, retrospective, case-control study was conducted in 185 patients and included patients who had a normal uterine cervix (n = 53), cervical intraepithelial neoplasm type 1 (CIN1) (n = 37), CIN2 (n = 22), CIN3 (n = 24), carcinoma in situ (CIS) (n = 22), squamous cell carcinoma (SCC, n = 20), and adenocarcinoma (AC) (n = 7). Methylation levels of the genes sex-determining region Y, box 1 (SOX1); paired box gene 1 (PAX1); LIM homeobox transcription factor 1α (LMX1A), and NK6 transcription factor-related locus 1 (NKX6-1) were determined by using real-time methylation-specific polymerase chain reaction (PCR) amplification. Cutoff values of the percentage of methylation reference (PMR) for different diagnoses were determined to test the sensitivity and specificity and to generate receiver operating characteristic (ROC) curves. Two-sided Mann-Whitney U tests were used to test differences in PMR between groups. RESULTS The PMRs of the 4 genes were significantly higher in CIN3 and worse (CIN3+) lesions than the PMRs in specimens of normal cervix and CIN1 or CIN2 (P < .001). ROC curve analysis demonstrated that the sensitivity, specificity, and accuracy for detecting CIN3+ lesions were 0.88, 0.82, and 0.95, respectively, for SOX1; 0.78, 0.91, and 0.89, respectively, for PAX1; 0.77, 0.88, and 0.90, respectively, for LMX1A; and 0.93, 0.97, and 0.97, respectively, for NKX6-1. CONCLUSIONS The current results indicated that quantitative PCR-based testing for DNA methylation of 4 genes holds great promise for cervical cancer screening and warrants further population-based studies using standardized DNA methylation testing.
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Affiliation(s)
- Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan, Republic of China.
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Kim JH, Choi YD, Lee JS, Lee JH, Nam JH, Choi C, Kweon SS, Fackler MJ, Sukumar S. Quantitative assessment of DNA methylation for the detection of cervical neoplasia in liquid-based cytology specimens. Virchows Arch 2010; 457:35-42. [PMID: 20496080 DOI: 10.1007/s00428-010-0936-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 04/29/2010] [Accepted: 05/11/2010] [Indexed: 01/04/2023]
Abstract
Previously, we have shown that methylation-specific PCR (MSP) analysis of a key panel of genes may be useful as an ancillary tool for diagnosing squamous cell carcinomas (SCC) and high-grade squamous intraepithelial lesions (HSIL) in cervical scrapings. Because quantitative MSP (QMSP) is more suitable as a screening tool than conventional MSP, we investigated the diagnostic role of QMSP for the detection of SCC and HSIL in cervical scrapings. A quantitative multiplex-MSP approach was used to examine promoter methylation of five genes (APC, HIN-1, RAR-beta, RASSF1A, and Twist) in biopsy-confirmed SCC (n = 63), HSIL (n = 45), low-grade SIL (LSIL, n = 26), and negative (n = 28) liquid-based cytology samples. For four genes (HIN-1, RAR-beta, RASSF1A, and Twist), the methylation levels among four groups were significantly different (p < 0.001 for each). Methylation levels of HIN-1, RAR-beta, RASSF1A, and Twist were increased in HSIL and SCC samples, compared with either negative or LSIL samples. However, methylation levels were not significantly different between SCC and HSIL, with the exception of RASSF1A. Receiver-operating characteristic analysis demonstrated that HIN-1, RAR-beta, RASSF1A, and Twist had the ability to distinguish HSIL/SCC from LSIL/negative samples. The two-gene combination (RASSF1A/Twist) showed the best performance in distinguishing HSIL/SCC from LSIL/negative samples. The estimated specificity of this two-gene panel for detecting HSIL/SCC was 90.7%, and its sensitivity was 74.1%. These results suggest that quantitative detection of aberrant DNA methylation in cervical scrapings may be a promising high-throughput approach for the diagnosis of HSIL/SCC.
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Affiliation(s)
- Jo-Heon Kim
- Department of Pathology, School of Medicine, Jeju National University, Jejusi, Republic of Korea
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