1
|
Letafati A, Taghiabadi Z, Zafarian N, Tajdini R, Mondeali M, Aboofazeli A, Chichiarelli S, Saso L, Jazayeri SM. Emerging paradigms: unmasking the role of oxidative stress in HPV-induced carcinogenesis. Infect Agent Cancer 2024; 19:30. [PMID: 38956668 PMCID: PMC11218399 DOI: 10.1186/s13027-024-00581-8] [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: 02/27/2024] [Accepted: 04/17/2024] [Indexed: 07/04/2024] Open
Abstract
The contribution of the human papillomavirus (HPV) to cancer is significant but not exclusive, as carcinogenesis involves complex mechanisms, notably oxidative stress. Oxidative stress and HPV can independently cause genome instability and DNA damage, contributing to tumorigenesis. Oxidative stress-induced DNA damage, especially double-strand breaks, aids in the integration of HPV into the host genome and promotes the overexpression of two viral proteins, E6 and E7. Lifestyle factors, including diet, smoking, alcohol, and psychological stress, along with genetic and epigenetic modifications, and viral oncoproteins may influence oxidative stress, impacting the progression of HPV-related cancers. This review highlights various mechanisms in oxidative-induced HPV-mediated carcinogenesis, including altered mitochondrial morphology and function leading to elevated ROS levels, modulation of antioxidant enzymes like Superoxide Dismutase (SOD), Glutathione (GSH), and Glutathione Peroxidase (GPx), induction of chronic inflammatory environments, and activation of specific cell signaling pathways like the Phosphoinositide 3-kinase, Protein kinase B, Mammalian target of rapamycin (PI3K/AKT/mTOR) and the Extracellular signal-regulated kinase (ERK) signaling pathway. The study highlights the significance of comprehending and controlling oxidative stress in preventing and treating cancer. We suggested that incorporating dietary antioxidants and targeting cancer cells through mechanisms involving ROS could be potential interventions to mitigate the impact of oxidative stress on HPV-related malignancies.
Collapse
Affiliation(s)
- Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran
| | - Zahra Taghiabadi
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran
| | - Negar Zafarian
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran
| | - Roxana Tajdini
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran
| | - Mozhgan Mondeali
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran
| | - Amir Aboofazeli
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran
| | - Silvia Chichiarelli
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, 00185, Rome, Italy
| | - Luciano Saso
- Department of Physiology and Pharmacology, Vittorio Erspamer", Sapienza University, Rome, Italy.
| | - Seyed Mohammad Jazayeri
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran.
| |
Collapse
|
2
|
Rozemeijer K, Dias Gonçalves Lima F, Ter Braak TJ, Hesselink AT, Prins JM, de Vries HJC, Steenbergen RDM. Analytical validation and diagnostic performance of the ASCL1/ZNF582 methylation test for detection of high-grade anal intraepithelial neoplasia and anal cancer. Tumour Virus Res 2024; 17:200275. [PMID: 38160718 PMCID: PMC10821616 DOI: 10.1016/j.tvr.2023.200275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024] Open
Abstract
DNA methylation testing on biopsies can detect high-grade anal intraepithelial neoplasia (HGAIN) in need of treatment and anal cancer. This study aimed to analytically validate and determine the diagnostic performance of a newly developed multiplex quantitative methylation-specific PCR, PreCursor-M AnoGYN (RUO), combining ASCL1, ZNF582 and a reference (ACTB) in one assay. Analytical validation was performed on two qPCR devices using predefined quality criteria. Diagnostic performance was determined on a cross-sectional series of 111 anal biopsies covering all stages of anal disease. Differences in methylation levels were assessed using the Kruskal-Wallis test. Area under the curve was determined using logistic regression analysis. Detection rates were calculated at predefined specificities for the cross-sectional and an additional longitudinal series of 23 HGAIN biopsies preceding anal cancer (i.e., progressive HGAIN). For both devices analytical quality criteria were met. ASCL1 and ZNF582 methylation levels increased with increasing severity of disease (p < 6*10-8). Diagnostic performance for AIN3+ was 0.81. All cancers and virtually all progressive HGAIN were detected at 70% and 80% specificity. In conclusion, the ASCL1/ZNF582 methylation test (PreCursor-M AnoGYN (RUO)) was demonstrated to be highly robust and reproducible. Moreover, it had excellent diagnostic accuracy to detect AIN3+ and can potentially be used to guide HGAIN management.
Collapse
Affiliation(s)
- Kirsten Rozemeijer
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Fernando Dias Gonçalves Lima
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands; Amsterdam UMC, Location AMC, Department of Dermatology, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Timo J Ter Braak
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | | | - Jan M Prins
- Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Amsterdam UMC, Location AMC, Department of Internal Medicine, Division of Infectious Diseases, Amsterdam, the Netherlands
| | - Henry J C de Vries
- Amsterdam UMC, Location AMC, Department of Dermatology, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Public Health Service Amsterdam, Cluster Infectious Diseases, Department of Research, Amsterdam, the Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands.
| |
Collapse
|
3
|
Kushwah AS, Masood S, Mishra R, Banerjee M. Genetic and epigenetic alterations in DNA repair genes and treatment outcome of chemoradiotherapy in cervical cancer. Crit Rev Oncol Hematol 2024; 194:104240. [PMID: 38122918 DOI: 10.1016/j.critrevonc.2023.104240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/06/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Cervical cancer (CaCx) is the deadliest malignancy among women which is caused by human papillomavirus (HPV) and anthro-demographical/clinicopathological factors. HPV oncoproteins E6 and E7 target p53 and RB (retinoblastoma) protein degradation, Ataxia telangiectasia mutated (ATM), ATM-RAD3-related (ATR) inactivation and subsequent impairment of non-homologous end joining (NHEJ), homologous recombination, and base excision repair pathways. There is also an accumulation of genetic and epigenetic alterations in Tumor Growth Suppressors (TGS), oncogenes, and DNA repair genes leading to increased genome instability and CaCx development. These alterations might be responsible for differential clinical response to Cisplatin-based chemoradiotherapy (CRT) in patients. This review explores HPV-mediated DNA damage as a risk factor in CaCx development, the mechanistic role of genetic and epigenetic alterations in DNA repair genes and their association with CRT and outcome, It also explores new possibilities for the development of genetic and epigenetic-based biomarkers for diagnostic, prognostic, and molecular therapeutic interventions.
Collapse
Affiliation(s)
- Atar Singh Kushwah
- Department of Urology and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York 10029, NY, USA; Molecular & Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India; Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Shireen Masood
- Molecular & Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Rajnikant Mishra
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Monisha Banerjee
- Molecular & Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India.
| |
Collapse
|
4
|
García-Vielma C, Cortés-Gutiérrez EI, Fernández JL, Dávila-Rodríguez MI, Gosálvez J. DBD-FISH Using Specific Chromosomal Region Probes for the Study of Cervical Carcinoma Progression. Methods Mol Biol 2024; 2784:271-284. [PMID: 38502492 DOI: 10.1007/978-1-0716-3766-1_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Genomic instability is an important biomarker in the progression of cervical carcinoma. DBD-FISH (DNA breakage detection-fluorescence in situ hybridization) is a sensitive method that detects strand breaks, alkali-labile sites, and incomplete DNA excision repair in cells of the cervical epithelium. This technique integrates the microgel immersion of cells from a vaginal lesion scraping and the DNA unwinding treatment with the capacity of FISH integrated into digital image analysis. Cells captured within an agarose matrix are lysed and submerged in an alkaline unwinding solution that generates single-stranded DNA motifs at the ends of internal DNA strand breaks. After neutralization, the microgel is dehydrated and the cells are incubated with DNA-labeled probes. The quantity of a hybridized probe at a target sequence corresponds to the measure of the single-stranded DNA produced during the unwinding step, which is equivalent to the degree of local DNA breakage. DNA damage does not show uniformly throughout the entire DNA of a cell; rather, it is confined to specific chromosomal sites. In this chapter, an overview of the technique is supplied, focusing on its ability for assessing the association between DNA damage in specific sequences and in the progressive stages of cervical carcinoma.
Collapse
Affiliation(s)
- Catalina García-Vielma
- Department of Genetics, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social (IMSS), Monterrey, Nuevo León, Mexico
| | | | - José L Fernández
- Genetics Unit, INIBIC, Complejo Hospitalario Universitario A Coruña, La Coruña, Spain
- Laboratorio de Genética Molecular y Radiobiología Centro Oncológico de Galicia, La Coruña, Spain
| | | | - Jaime Gosálvez
- Unit of Genetics, Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| |
Collapse
|
5
|
Zhang F, Zhang X, Zhang H, Lin D, Fan H, Guo S, An F, Zhao Y, Li J, Schrodi SJ, Zhang D. Pan-precancer and cancer DNA methylation profiles revealed significant tissue specificity of interrupted biological processes in tumorigenesis. Epigenetics 2023; 18:2231222. [PMID: 37393582 DOI: 10.1080/15592294.2023.2231222] [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: 03/03/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
DNA methylation (DNAme) alterations are known to initiate from the precancerous stage of tumorigenesis. Herein, we investigated the global and local patterns of DNAme perturbations in tumorigenesis by analysing the genome-wide DNAme profiles of the cervix, colorectum, stomach, prostate, and liver at precancerous and cancer stages. We observed global hypomethylation in tissues of both two stages, except for the cervix, whose global DNAme level in normal tissue was lower than that of the other four tumour types. For alterations shared by both stages, there were common hyper-methylation (sHyperMethyl) and hypo-methylation (sHypoMethyl) changes, of which the latter type was more frequently identified in all tissues. Biological pathways interrupted by sHyperMethyl and sHypoMethyl alterations demonstrated significant tissue specificity. DNAme bidirectional chaos indicated by the enrichment of both sHyperMethyl and sHypoMethyl changes in the same pathway was observed in most tissues and was a common phenomenon, particularly in liver lesions. Moreover, for the same enriched pathways, different tissues may be affected by distinct DNAme types. For the PI3K-Akt signalling pathway, sHyperMethyl enrichment was observed in the prostate dataset, but sHypoMethyl enrichment was observed in the colorectum and liver datasets. Nevertheless, they did not show an increased possibility in survival prediction of patients in comparison with other DNAme types. Additionally, our study demonstrated that gene-body DNAme changes of tumour suppressor genes and oncogenes may persist from precancerous lesions to the tumour. Overall, we demonstrate the tissue specificity and commonality of cross-stage alterations in DNA methylation profiles in multi-tissue tumorigenesis.
Collapse
Affiliation(s)
- Feifan Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Xin Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Haikun Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Dongdong Lin
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Hailang Fan
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Shicheng Guo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Fang An
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Yaqian Zhao
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Jun Li
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Steven J Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Dake Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| |
Collapse
|
6
|
Liu Y, Chen Y, Xiong J, Zhu P, An Y, Li S, Chen P, Li Q. Performance of DNA methylation analysis in the detection of high-grade cervical intraepithelial neoplasia or worse (CIN3+): a cross-sectional study. Infect Agent Cancer 2023; 18:77. [PMID: 38031140 PMCID: PMC10687787 DOI: 10.1186/s13027-023-00555-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
It is commonly accepted that host genes show high methylation in cervical intraepithelial neoplasia 3 (CIN3) or worse (CIN3+). However, study quality varies, as does the clinical performance of markers in different populations. We aimed to validate candidate gene DNA methylation with standardized testing methods in the same batch of samples. We first compared the performance of 16 DNA methylation markers for detecting CIN3+ in the 82-sample training set, including 24 subjects with ≤ CIN1, 10 subjects with CIN2, 23 subjects with CIN3, and 25 subjects with cervical cancer (CC). Then five methylation markers were selected and subsequently validated among an independent set of 74 subjects, including 47 subjects with ≤ CIN1, 13 subjects with CIN2, 6 subjects with CIN3, and 8 subjects with CC. The results in the validation set revealed that methylation analysis of the SOX1 (SOX1m) showed a superior level of clinical performance (AUC = 0.879; sensitivity = 85.7%; specificity = 90.0%). SOX1m had better accuracy than cytology, with a reduced referral rate (23.0% vs. 31.4%) and a lower number of overtreatment (5 vs. 13) cases among high-risk human papillomavirus (hrHPV)-positive women. Importantly, among hrHPV-positive and SOX1m-negative women, only 1 CIN3 patient was at risk for follow-up after 1 year, whereas 1 CIN3 patient and 1 CC patient were at risk among hrHPV-positive and cytology-negative women. In this investigation, we screened 16 reported methylation markers to provide a basis for future studies related to potential precancerous lesion/cancer methylation markers in the Chinese population. The study also revealed that SOX1m has optimal CIN3+ detection performance, suggesting that it may be a promising biomarker for detecting CIN3+ in the Chinese population.
Collapse
Affiliation(s)
- Yuxiang Liu
- Department of Gynaecology and Obstetrics, The Second Xiangya Hospital, Central South University, 139 Renmin Road, Changsha, 410011, People's Republic of China
| | - Yan Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, People's Republic of China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China
- Xiangya Medical Laboratory, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China
| | - Jing Xiong
- Department of Gynaecology and Obstetrics, The Second Xiangya Hospital, Central South University, 139 Renmin Road, Changsha, 410011, People's Republic of China
| | - Peng Zhu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, People's Republic of China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China
| | - Yuhang An
- Xiangya Medical Laboratory, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China
| | - Shu Li
- Xiangya Medical Laboratory, Central South University, 110 Xiangya Road, Changsha, 410078, People's Republic of China
| | - Puxiang Chen
- Department of Gynaecology and Obstetrics, The Second Xiangya Hospital, Central South University, 139 Renmin Road, Changsha, 410011, People's Republic of China.
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, People's Republic of China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, People's Republic of China.
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.
| |
Collapse
|
7
|
Han X, Fang F, Cui W, Liu Y, Liu Y. Effect of Ethanol-Induced Methyl Donors Consumption on the State of Hypomethylation in Cervical Cancer. Int J Mol Sci 2023; 24:ijms24097729. [PMID: 37175434 PMCID: PMC10178338 DOI: 10.3390/ijms24097729] [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: 03/20/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Cervical cancer causes malignant tumors in females and threatens the physical and mental health of women. Current research shows that persistent infection of high-risk HPV is the main cause of cervical cancer. However, not all cervical cancer is caused by HPV infection, which may also be related to other factors, such as nutritional status and lifestyle. This study focuses on the effect of alcohol consumption on the methylation status of cervical cancer from the perspective of methyl donors. We established a mouse tumor-bearing model with cervical cancer SiHa cells, and at the same time, we cultured SiHa cells in vitro. Different concentrations of ethanol were administered to the model mice and SiHa cells. Then, we detected the levels of the methyl-donor folate and methionine and their metabolite homocysteine levels in mice serum, tumor tissues, and SiHa cells. Furthermore, we determined the expression of the members of the DNA methyltransferase family (DNMT1, DNMT3a, and DNMT3b) in tumor tissue by immunohistochemistry. qRT-PCR and Western blotting analysis were used to detect the mRNA and protein levels of members of the DNA methyltransferase family in cervical cancer SiHa cells. Our results show that the levels of the methyl donor (folate and methionine) decreased with the increase of ethanol concentration (p < 0.05), and the homocysteine level increased significantly (p < 0.05). In SiHa cells, the mRNA and protein levels of the DNMT family members and their receptors were significantly higher than those in the control group (p < 0.05). Collectively, these results suggest that ethanol could influence DNMT expression by inducing methyl donor consumption, thereby causing cervical cancer cells to exhibit genome-wide hypomethylation.
Collapse
Affiliation(s)
- Xiao Han
- Department of Nutrition and Food Safety, School of Public Health, Jilin University, 1163 Xin Min Street, Changchun 130021, China
| | - Fang Fang
- Department of Nutrition and Food Safety, School of Public Health, Jilin University, 1163 Xin Min Street, Changchun 130021, China
| | - Weiwei Cui
- Department of Nutrition and Food Safety, School of Public Health, Jilin University, 1163 Xin Min Street, Changchun 130021, China
| | - Ya Liu
- Department of Nutrition and Food Safety, School of Public Health, Jilin University, 1163 Xin Min Street, Changchun 130021, China
| | - Yuxin Liu
- Department of Nutrition and Food Safety, School of Public Health, Jilin University, 1163 Xin Min Street, Changchun 130021, China
| |
Collapse
|
8
|
Vink FJ, Meijer CJLM, Lissenberg-Witte BI, Visser C, Duin S, Snyman LC, Richter KL, van der Merwe FH, Botha MH, Steenbergen RDM, Dreyer G. Validation of ASCL1 and LHX8 Methylation Analysis as Primary Cervical Cancer Screening Strategy in South African Women with Human Immunodeficiency Virus. Clin Infect Dis 2022; 76:416-423. [PMID: 36366827 PMCID: PMC9907555 DOI: 10.1093/cid/ciac801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Compared with women who are human immunodeficiency virus (HIV) negative, women with human immunodeficiency virus (WWH) have a higher human papillomavirus (HPV) prevalence and increased cervical cancer risk, emphasizing the need for effective cervical cancer screening in this population. The present study aimed to validate methylation markers ASCL1 and LHX8 for primary screening in a South African cohort of WWH. METHODS In this post hoc analysis within the DIAgnosis in Vaccine And Cervical Cancer Screen (DiaVACCS) study, a South African observational multicenter cohort study, cervical scrape samples from 411 HIV-positive women were analyzed for hypermethylation of ASCL1 and LHX8 genes, HPV DNA, and cytology. Sensitivities, specificities, and positive and negative predictive values of primary methylation-based, HPV-based and cytology-based screening were calculated for the detection of cervical intraepithelial neoplasia of grade 3 or higher. RESULTS Single markers ASCL1 and LHX8 resulted in a good performance for the detection of cervical intraepithelial neoplasia of grade 3 or higher, with sensitivities of 85.9% (95% confidence interval [CI], 78.2%-93.6%) and 89.7% (83.0%-96.5%), respectively, and specificities of 72.9% (67.3%-78.5%) and 75.0% (69.5%-80.5%). Combining markers ASCL1 and LHX8 resulted in a lower sensitivity compared with HPV testing (84.6% vs 93.6%, respectively; ratio, 0.90 [95% CI, .82-.99]) and a higher specificity (86.7% vs 78.3%; ratio 1.11 [1.02-1.20]) and reduced the referral rate from 46.8% to 33.4%. ASCL1/LHX8 methylation had a significantly higher sensitivity than cytology (threshold, high-grade intraepithelial squamous lesion or worse), (84.6% vs 74.0%, respectively; ratio, 1.16 [95% CI, 1.01-1.32]) and similar specificity (86.7% vs 91.0%; ratio, 0.95 [.90-1.003]). CONCLUSIONS Our results validate the accuracy of ASCL1/LHX8 methylation analysis for primary screening in WWH, which offers a full-molecular alternative to cytology- or HPV-based screening, without the need for additional triage testing.
Collapse
Affiliation(s)
- Frederique J Vink
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands,Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Chris J L M Meijer
- Correspondence: C. J. L. M. Meijer, Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands ()
| | - Birgit I Lissenberg-Witte
- Department of Epidemiology and Data Science, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Cathy Visser
- Gynaecologic Oncology Unit, Department of Obstetrics & Gynaecology, University of Pretoria Faculty of Health Sciences, Pretoria, South Africa
| | - Sylvia Duin
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands,Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Leon C Snyman
- Gynaecologic Oncology Unit, Department of Obstetrics & Gynaecology, University of Pretoria Faculty of Health Sciences, Pretoria, South Africa
| | - Karin L Richter
- Department of Medical Virology, University of Pretoria Faculty of Health Sciences, Pretoria, South Africa
| | - Frederick H van der Merwe
- Gynaecologic Oncology Unit, Department of Obstetrics & Gynaecology, Stellenbosch University Faculty of Health Sciences, Stellenbosch, South Africa
| | - Matthys H Botha
- Gynaecologic Oncology Unit, Department of Obstetrics & Gynaecology, Stellenbosch University Faculty of Health Sciences, Stellenbosch, South Africa
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands,Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | |
Collapse
|
9
|
Yang X, Chen Y, Li M, Zhu W. ERBB3 methylation and immune infiltration in tumor microenvironment of cervical cancer. Sci Rep 2022; 12:8112. [PMID: 35581263 PMCID: PMC9114106 DOI: 10.1038/s41598-022-11415-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
ERBB3, a member of the ERBB family of receptor tyrosine kinases, plays an important role in cancer, despite its lack of intrinsic carcinogenic mechanism of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC). Research on bioinformatics methods through multi-omics, this work proves that ERBB3 gene mutation, methylation modification have extensive regulatory mechanisms on the CESC microenvironment. We found that ERBB3 is involved in carcinogenesis of cervical cancer and is not associated with its prognosis. The carcinogenic mechanism is mainly related to the suppression of the immune system between tumor infiltrating lymphocytes (TILs) and the methylation of the RNA level. Our study indicated ERBB3 is more likely to be a carcinogenic factor than a key prognostic factor for cervical cancer. Methylation of ERBB3 may work as a checkpoint immunotherapy target in CESC, DNA methylation modification of the 4480 base pair downstream of ERBB3 transcription initiation site was the highest.
Collapse
Affiliation(s)
- Xiaoyue Yang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Jiangsu University, Jiefang Road 438, Zhenjiang, 212001, Jiangsu, China.,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Sanxiang Road 1055, Suzhou, 215000, Jiangsu, China
| | - Ying Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Sanxiang Road 1055, Suzhou, 215000, Jiangsu, China
| | - Mei Li
- Department of Pathology, Affiliated Hospital of Jiangsu University, Jiefang Road 438, Zhenjiang, 212001, Jiangsu, China.
| | - Weipei Zhu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Sanxiang Road 1055, Suzhou, 215000, Jiangsu, China.
| |
Collapse
|
10
|
Age-Related DNA Methylation in Normal Kidney Tissue Identifies Epigenetic Cancer Risk Susceptibility Loci in the ANKRD34B and ZIC1 Genes. Int J Mol Sci 2022; 23:ijms23105327. [PMID: 35628134 PMCID: PMC9141100 DOI: 10.3390/ijms23105327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/01/2023] Open
Abstract
Both age-dependent and age-independent alteration of DNA methylation in human tissues are functionally associated with the development of many malignant and non-malignant human diseases. TCGA-KIRC data were biometrically analyzed to identify new loci with age-dependent DNA methylation that may contribute to tumor risk in normal kidney tissue. ANKRD34B and ZIC1 were evaluated as candidate genes by pyrosequencing of 539 tissues, including 239 normal autopsy, 157 histopathologically tumor-adjacent normal, and 143 paired tumor kidney samples. All candidate CpG loci demonstrated a strong correlation between relative methylation levels and age (R = 0.70−0.88, p < 2 × 10−16) and seven out of 10 loci were capable of predicting chronological age in normal kidney tissues, explaining 84% of the variance (R = 0.92). Moreover, significantly increased age-independent methylation was found for 9 out of 10 CpG loci in tumor-adjacent tissues, compared to normal autopsy tissues (p = 0.001−0.028). Comparing tumor and paired tumor-adjacent tissues revealed two patient clusters showing hypermethylation, one cluster without significant changes in methylation, and a smaller cluster demonstrating hypomethylation in the tumors (p < 1 × 10−10). Taken together, our results show the presence of additional methylation risk factors besides age for renal cancer in normal kidney tissue. Concurrent tumor-specific hypermethylation suggests a subset of these loci are candidates for epigenetic renal cancer susceptibility.
Collapse
|
11
|
Zhang L, Tan W, Yang H, Zhang S, Dai Y. Detection of Host Cell Gene/HPV DNA Methylation Markers: A Promising Triage Approach for Cervical Cancer. Front Oncol 2022; 12:831949. [PMID: 35402283 PMCID: PMC8990922 DOI: 10.3389/fonc.2022.831949] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 02/05/2023] Open
Abstract
Cervical cancer is the most prevalent gynecologic malignancy, especially in women of low- and middle-income countries (LMICs). With a better understanding of the etiology and pathogenesis of cervical cancer, it has been well accepted that this type of cancer can be prevented and treated via early screening. Due to its higher sensitivity than cytology to identify precursor lesions of cervical cancer, detection of high-risk human papillomavirus (HR-HPV) DNA has been implemented as the primary screening approach. However, a high referral rate for colposcopy after HR-HPV DNA detection due to its low specificity in HR-HPV screening often leads to overtreatment and thus increases the healthcare burden. Emerging evidence has demonstrated that detection of host cell gene and/or HPV DNA methylation represents a promising approach for the early triage of cervical cancer in HR-HPV-positive women owing to its convenience and comparable performance to cytology, particularly in LMICs with limited healthcare resources. While numerous potential markers involving DNA methylation of host cell genes and the HPV genome have been identified thus far, it is crucial to define which genes or panels involving host and/or HPV are feasible and appropriate for large-scale screening and triage. An ideal approach for screening and triage of CIN/ICC requires high sensitivity and adequate specificity and is suitable for self-sampling and inexpensive to allow population-based screening, particularly in LMICs. In this review, we summarize the markers of host cell gene/HR-HPV DNA methylation and discuss their triage performance and feasibility for high-grade precancerous cervical intraepithelial neoplasia or worse (CIN2+ and CIN3+) in HR-HPV-positive women.
Collapse
Affiliation(s)
- Lingyi Zhang
- Laboratory of Cancer Precision Medicine, The First Hospital of Jilin University, Changchun, China.,Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun, China
| | - Wenxi Tan
- Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun, China
| | - Hongmei Yang
- Laboratory of Cancer Precision Medicine, The First Hospital of Jilin University, Changchun, China.,Department of Critical Care Medicine, The First Hospital of Jilin University, Changchun, China
| | - Songling Zhang
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, China
| | - Yun Dai
- Laboratory of Cancer Precision Medicine, The First Hospital of Jilin University, Changchun, China
| |
Collapse
|
12
|
van den Helder R, Steenbergen RDM, van Splunter AP, Mom CH, Tjiong MY, Martin I, Rosier-van Dunné FMF, van der Avoort IAM, Bleeker MCG, van Trommel NE. HPV AND DNA METHYLATION TESTING IN URINE FOR CERVICAL INTRAEPITHELIAL NEOPLASIA AND CERVICAL CANCER DETECTION. Clin Cancer Res 2022; 28:2061-2068. [PMID: 35266975 DOI: 10.1158/1078-0432.ccr-21-3710] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/28/2021] [Accepted: 03/08/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Biomarker detection in urine offers a potential solution to increase effectiveness of cervical cancer screening programs by attracting non-responders. In this prospective study, the presence of high-risk human papillomavirus (hrHPV DNA) and the performance of DNA methylation analysis was determined for the detection of cervical cancer and high-grade cervical intraepithelial neoplasia (CIN2/3) in urine, and compared to paired cervicovaginal self-samples and clinician-taken cervical scrapes. METHODS A total of 587 samples were included from 113 women with cervical cancer, 92 women with CIN2/3, and 64 controls. Samples were tested for hrHPV DNA and five methylation markers. Univariate and multivariate logistic regression and leave-one-out cross-validation were used to determine the methylation marker performance for CIN3 and cervical cancer (CIN3+) detection in urine. Agreement between samples was determined using Cohen's kappa statistics and the Spearman correlation coefficients. RESULTS HrHPV presence was high in all sample types, 79% to 92%. Methylation levels of all markers in urine significantly increased with increasing severity of disease. The optimal marker panel (ASCL1/LHX8) resulted in an AUC of 0.84 for CIN3+ detection in urine, corresponding to an 86% sensitivity at a 70% predefined specificity. At this threshold 96%(109/113) of cervical cancers, 68%(46/64) of CIN3 and 58%(14/24) of CIN2 were detected. Between paired samples, a strong agreement for HPV16/18 genotyping and a fair to strong correlation for methylation was found. CONCLUSION HrHPV DNA and DNA methylation testing in urine offers a promising solution to detect cervical cancer and CIN2/3 lesions, especially for women currently unreached by conventional screening methods.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Nienke E van Trommel
- Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, Noord-Holland, Netherlands
| |
Collapse
|
13
|
Hentschel AE, Beijert IJ, Bosschieter J, Kauer PC, Vis AN, Lissenberg-Witte BI, van Moorselaar RJA, Steenbergen RDM, Nieuwenhuijzen JA. Bladder cancer detection in urine using DNA methylation markers: a technical and prospective preclinical validation. Clin Epigenetics 2022; 14:19. [PMID: 35123558 PMCID: PMC8818199 DOI: 10.1186/s13148-022-01240-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/26/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The development of accurate urinary biomarkers for non-invasive and cost-effective detection of primary and recurrent bladder tumours is recognized as one of the major clinical needs in bladder cancer diagnostics. The purposes of this study were (1) to validate the results of a previous technical comparison by determining the diagnostic performance of nine methylation markers in urine pellet compared to full void urine, and (2) to validate the diagnostic performance of the optimal marker panel GHSR/MAL from a previous exploratory study in a preclinical setting.
Methods
Urine samples of 108 patients with bladder cancer and 100 age- and gender-matched controls were prospectively collected for methylation analysis. Urinary methylation levels of the markers FAM19A4, GHSR, MAL, miR-129, miR-935, PHACTR3, PRDM14, SST and ZIC1 were determined with quantitative methylation-specific PCR in urine pellet. Area under the curves (AUCs) were determined for individual markers and the marker panel GHSR/MAL. The diagnostic performance of the marker panel GHSR/MAL was evaluated in the total study population and in different subgroups of patients with bladder cancer using the Chi-square test. The diagnostic accuracy was assessed by leave-one-out cross-validation.
Results
All nine urinary methylation markers (FAM19A4, GHSR, MAL, miR-129, miR-935, PHACTR3, PRDM14, SST and ZIC1) showed significantly higher methylation levels in bladder cancer patients than in controls (p < 0.001). Area under the curves (AUCs) of the nine methylation markers tested in urine pellet were similar to AUCs in full void urine of an independent previous cohort. GHSR/MAL reached an AUC of 0.89 (95% confidence interval [CI] 0.84–0.94), at 80% sensitivity and 93% specificity. Sensitivity of GHSR/MAL increased with higher tumour grades, higher tumour stages, in primary vs. recurrent tumours, and in males vs. females.
Conclusions
This technical validation supports the robustness of DNA methylation analysis in urine pellet and full void urine for the non-invasive detection of bladder cancer. Subsequent preclinical validation confirmed the diagnostic potential of GHSR/MAL. These findings underline the diagnostic potential of the marker panel GHSR/MAL for future bladder cancer diagnostics.
Collapse
|
14
|
Regauer S, Reich O, Kashofer K. HPV-negative Squamous Cell Carcinomas of the Cervix With Special Focus on Intraepithelial Precursor Lesions. Am J Surg Pathol 2022; 46:147-158. [PMID: 34387215 DOI: 10.1097/pas.0000000000001778] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Recently, the World Health Organization (WHO) recognized human papilloma virus (HPV)-independent invasive cervical squamous cell carcinoma (SCC) without recognizing the existence of precursor lesions. This is a detailed characterization of 3 preinvasive lesions and 6 invasive SCC negative for HPV-DNA (32 genotypes), HPV-mRNA (14 genotypes) and genomic HPV sequencing. We evaluated histologic features, expression of p16ink4a, p53, CK7, and CK17, aberrations in 50 cancer genes and chromosomal copy number variations. HPV-negative preinvasive lesions were extensive basaloid or highly differentiated keratinizing intraepithelial proliferations of 3 to 20 cell layers thickness, partly with prominent cervical gland involvement. Overall, 2/3 intraepithelial lesions and the in situ component of 1/6 SCC showed p16ink4a block staining, while 1/6 in situ component revealed heterogenous p16ink4a staining. All invasive components of keratinizing SCC were p16ink4a-negative. Preinvasive and invasive SCC showed inconsistent CK7 and CK17 staining. Nuclear p53 overexpression was restricted to the TP53 gene mutated SCC. The highly vascularized peritumoral stroma showed a dense inflammatory infiltrate including plasma cells and intratumoral and peritumoral eosinophilic granulocytes. Inconsistent somatic gene mutations (PIK3CA, STK11, TP53, SMARC2B, and GNAS) occurred predominantly in nonhotspot locations at low mutational frequency in 3/6 SCC. Consistent aberrations included the pathogenic (angiogenic) germline polymorphism Q472H in the KDR gene (7/9 patients), and chromosome 3q gains (4/9 patients). In conclusion, HPV-negative intraepithelial cervical precancerous lesions exist, either as highly differentiated keratinized intraepithelial proliferations reminiscent of differentiated vulvar intraepithelial neoplasia, or undifferentiated basaloid intraepithelial lesions with occasional p16ink4a block staining resembling high-grade squamous intraepithelial lesion. Gains of chromosome 3q, angiogenic germline variants the inflammatory infiltrate may contribute to progression of HPV-negative cervical carcinogenesis.
Collapse
Affiliation(s)
| | - Olaf Reich
- Department of Obstetrics and Gynecology, Medical University Graz, Graz, Austria
| | | |
Collapse
|
15
|
Kashofer K, Regauer S, Reich O, Petru E, Winter E. Driver gene mutations in micro-invasive cervical squamous cancers have no prognostic significance. Gynecol Oncol 2022; 165:121-128. [PMID: 35101299 DOI: 10.1016/j.ygyno.2022.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To evaluate the prevalence of somatic gene mutations in different stages of cervical carcinogenesis placing special emphasis on micro-invasive pT1a cervical squamous cell cancers (SCC). METHODS Micro-dissected samples of 32 micro-invasive pT1a and 55 ≥ pT1b SCC were evaluated by next generation sequencing of 50 cancer genes (cancer hot spot panel). RESULTS At primary diagnosis, 8/32 (25%) pT1a SCC, 10/28 (36%) pT1b SCC and 15/27 (56%) pT2/3 SCC carried somatic gene mutations. The most commonly affected gene was the PIK3CA gene in hot spot regions E545K and E453K in 5/8 (62%) pT1a SCC, 7/15 (70%) pT1b SCC and 10/15 (66%) pT2/3 SCC followed by FBXW7 (n = 4), KRAS and RB1 (n = 2 each). ERBB2, APC, ATM, MLP gene mutations occurred only once. Solitary activating oncogenic somatic mutations dominated over tumor suppressor mutation in 88% pT1a, 80% pT1b and 60% pT2/3 SCC. Concomitant mutations involved typically an activating oncogenic mutation and an inactivating tumor-suppressor gene mutation. All patients with pT1a SCC are alive without evidence of disease after surgical treatment, independent of mutational status or lympho-vascular space invasion. CONCLUSIONS Activating oncogenic gene mutations, in particular in the PIK3CA gene, occur early in cervical carcinogenesis. Although driver gene mutations bestow tumor cells with a growth advantage, early detection and complete removal of all cancer cells - with or without somatic gene mutations - are essential for cure. In contrast to advanced inoperable SCC, where PIK3CA driver gene mutations carry an adverse prognosis, the mutational status in surgically treated micro-invasive SCC is prognostically irrelevant.
Collapse
Affiliation(s)
- Karl Kashofer
- Diagnostic- and Research Institute of Pathology, Medical University Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Sigrid Regauer
- Diagnostic- and Research Institute of Pathology, Medical University Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria.
| | - Olaf Reich
- Department of Gynecology and Obstetrics, Medical University Graz, Auenbruggerplatz 14, 8036 Graz, Austria
| | - Edgar Petru
- Department of Gynecology and Obstetrics, Medical University Graz, Auenbruggerplatz 14, 8036 Graz, Austria
| | - Elke Winter
- Diagnostic- and Research Institute of Pathology, Medical University Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| |
Collapse
|
16
|
Siegel EM, Ajidahun A, Berglund A, Guerrero W, Eschrich S, Putney RM, Magliocco A, Riggs B, Winter K, Simko JP, Ajani JA, Guha C, Okawara GS, Abdalla I, Becker MJ, Pizzolato JF, Crane CH, Brown KD, Shibata D. Genome-wide host methylation profiling of anal and cervical carcinoma. PLoS One 2021; 16:e0260857. [PMID: 34882728 PMCID: PMC8659695 DOI: 10.1371/journal.pone.0260857] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
HPV infection results in changes in host gene methylation which, in turn, are thought to contribute to the neoplastic progression of HPV-associated cancers. The objective of this study was to identify joint and disease-specific genome-wide methylation changes in anal and cervical cancer as well as changes in high-grade pre-neoplastic lesions. Formalin-fixed paraffin-embedded (FFPE) anal tissues (n = 143; 99% HPV+) and fresh frozen cervical tissues (n = 28; 100% HPV+) underwent microdissection, DNA extraction, HPV genotyping, bisulfite modification, DNA restoration (FFPE) and analysis by the Illumina HumanMethylation450 Array. Differentially methylated regions (DMR; t test q<0.01, 3 consecutive significant CpG probes and mean Δβ methylation value>0.3) were compared between normal and cancer specimens in partial least squares (PLS) models and then used to classify anal or cervical intraepithelial neoplasia-3 (AIN3/CIN3). In AC, an 84-gene PLS signature (355 significant probes) differentiated normal anal mucosa (NM; n = 9) from AC (n = 121) while a 36-gene PLS signature (173 significant probes) differentiated normal cervical epithelium (n = 10) from CC (n = 9). The CC progression signature was validated using three independent publicly available datasets (n = 424 cases). The AC and CC progression PLS signatures were interchangeable in segregating normal, AIN3/CIN3 and AC and CC and were found to include 17 common overlapping hypermethylated genes. Moreover, these signatures segregated AIN3/CIN3 lesions similarly into cancer-like and normal-like categories. Distinct methylation changes occur across the genome during the progression of AC and CC with overall similar profiles and add to the evidence suggesting that HPV-driven oncogenesis may result in similar non-random methylomic events. Our findings may lead to identification of potential epigenetic drivers of HPV-associated cancers and also, of potential markers to identify higher risk pre-cancerous lesions.
Collapse
Affiliation(s)
- Erin M. Siegel
- Departments of Cancer Epidemiology, Tampa, FL, United States of America
| | - Abidemi Ajidahun
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Anders Berglund
- Biostatistics and Bioinformatics, Tampa, FL, United States of America
| | - Whitney Guerrero
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Steven Eschrich
- Biostatistics and Bioinformatics, Tampa, FL, United States of America
| | - Ryan M. Putney
- Biostatistics and Bioinformatics, Tampa, FL, United States of America
| | - Anthony Magliocco
- Anatomic Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States of America
| | - Bridget Riggs
- Departments of Cancer Epidemiology, Tampa, FL, United States of America
| | - Kathryn Winter
- NRG Oncology Statistics and Data Management Center–ACR, Philadelphia, PA, United States of America
| | - Jeff P. Simko
- UCSF Medical Center-Mount Zion, San Francisco, CA, United States of America
| | - Jaffer A. Ajani
- M D Anderson Cancer Center, Houston, TX, United States of America
| | - Chandan Guha
- Montefiore Medical Center, New York, NY, United States of America
| | - Gordon S. Okawara
- Juravinski Cancer Centre at Hamilton Health Sciences, Hamilton, ON, United States of America
| | - Ibrahim Abdalla
- Cancer Research for the Ozarks CCOP, Springfield, MO, United States of America
| | - Mark J. Becker
- Columbus Community Clinical Oncology Program, Columbus, OH, United States of America
| | - Joseph F. Pizzolato
- Mount Sinai Comprehensive Cancer Center CCOP, Miami, FL, United States of America
| | | | - Kevin D. Brown
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, United States of America
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, United States of America
| |
Collapse
|
17
|
Human Papillomaviruses-Associated Cancers: An Update of Current Knowledge. Viruses 2021; 13:v13112234. [PMID: 34835040 PMCID: PMC8623401 DOI: 10.3390/v13112234] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/21/2022] Open
Abstract
Human papillomaviruses (HPVs), which are small, double-stranded, circular DNA viruses infecting human epithelial cells, are associated with various benign and malignant lesions of mucosa and skin. Intensive research on the oncogenic potential of HPVs started in the 1970s and spread across Europe, including Croatia, and worldwide. Nowadays, the causative role of a subset of oncogenic or high-risk (HR) HPV types, led by HPV-16 and HPV-18, of different anogenital and head and neck cancers is well accepted. Two major viral oncoproteins, E6 and E7, are directly involved in the development of HPV-related malignancies by targeting synergistically various cellular pathways involved in the regulation of cell cycle control, apoptosis, and cell polarity control networks as well as host immune response. This review is aimed at describing the key elements in HPV-related carcinogenesis and the advances in cancer prevention with reference to past and on-going research in Croatia.
Collapse
|
18
|
Tegshee B, Kondo K, Soejima S, Muguruma K, Tsuboi M, Kajiura K, Kawakami Y, Kawakita N, Toba H, Yoshida M, Takizawa H, Tangoku A. GHSR methylation-dependent expression of a variant ligand and receptor of the ghrelin system induces thymoma tumorigenesis. Oncol Lett 2021; 22:793. [PMID: 34630704 PMCID: PMC8477069 DOI: 10.3892/ol.2021.13054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 08/19/2021] [Indexed: 12/17/2022] Open
Abstract
Our previous study reported that the DNA methylation of growth hormone secretagogue receptor (GHSR) was significantly higher in thymoma or thymic carcinoma (TC) than in normal thymic tissue samples. Thymic epithelial tumors (TETs) with higher GHSR DNA methylation were associated with significantly worse prognosis than those with lower levels of DNA methylation. Diversified components of the ghrelin-GHSR axis may exert opposing effects in cancer progression, depending on the cancer type in question. However, the precise function of the axis remains unclear. In the present study, the mRNA expression of five key components of the ghrelin system [native ligand ghrelin, variant ligand In-1 ghrelin, native receptor GHSR1a, variant receptor GHSR1b and acylation enzyme ghrelin O-acyltransferase (GOAT)] were examined in 58 TET samples by reverse transcription-quantitative PCR, and protein expression of GHSR1a and GHSR1b was assessed in 20 TETs using immunohistochemistry. The results revealed that In-1 ghrelin, GHSR1b (variant forms) and GOAT were more strongly expressed in thymoma compared with thymic-adjacent tissue. By contrast, no significant differences were observed in the expression of ghrelin and GHSR1a (native forms) between thymoma and thymic tissue. The mRNA expression of In-1 ghrelin and GHSR1b (variant forms) was positively associated with GHSR methylation in thymoma tissue samples. However, a relationship was not found between ghrelin, GHSR1a or GOAT expression (native forms) and GHSR methylation in thymoma. Immunohistochemical analysis revealed that mRNA expression of GHSR1a and GHSR1b generally correlated with expression of the corresponding protein, and that the expression of GHSR1b was increased in advanced-stage TETs. These results indicate that the DNA methylation of GHSR is associated with a shift from native expression (ghrelin and GHSR1a) to variant expression (In-1 ghrelin and GHSR1b), which induces the tumorigenesis of thymoma, but not TC.
Collapse
Affiliation(s)
- Bilguun Tegshee
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Tokushima 770-8509, Japan
| | - Kazuya Kondo
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Tokushima 770-8509, Japan
| | - Shiho Soejima
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Tokushima 770-8509, Japan
| | - Kyoka Muguruma
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Tokushima 770-8509, Japan
| | - Mitsuhiro Tsuboi
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Koichiro Kajiura
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Yukikiyo Kawakami
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Naoya Kawakita
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Hiroaki Toba
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Mitsuteru Yoshida
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Hiromitsu Takizawa
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Akira Tangoku
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University, Kuramoto-cho, Tokushima 770-8503, Japan
| |
Collapse
|
19
|
Verhoef L, Bleeker MCG, Polman N, Steenbergen RDM, Meijer CJLM, Melchers WJG, Bekkers RL, Molijn AC, Quint WG, van Kemenade FJ, Berkhof J, Heideman DAM. Performance of DNA methylation analysis of ASCL1, LHX8, ST6GALNAC5, GHSR, ZIC1 and SST for the triage of HPV-positive women: Results from a Dutch primary HPV-based screening cohort. Int J Cancer 2021; 150:440-449. [PMID: 34558659 PMCID: PMC9293097 DOI: 10.1002/ijc.33820] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/17/2021] [Accepted: 08/31/2021] [Indexed: 01/12/2023]
Abstract
Methylation of host‐cell deoxyribonucleic acid (DNA) has been proposed as a promising biomarker for triage of high‐risk (hr) human papillomavirus (HPV) positive women at screening. Our study aims to validate recently identified host‐cell DNA methylation markers for triage in an hrHPV‐positive cohort derived from primary HPV‐based cervical screening in The Netherlands. Methylation markers ASCL1, LHX8, ST6GALNAC5, GHSR, ZIC1 and SST were evaluated relative to the ACTB reference gene by multiplex quantitative methylation‐specific PCR (qMSP) in clinician‐collected cervical samples (n = 715) from hrHPV‐positive women (age 29‐60 years), who were enrolled in the Dutch IMPROVE screening trial (NTR5078). Primary clinical end‐point was cervical intraepithelial neoplasia grade 3 (CIN3) or cancer (CIN3+). The single‐marker and bi‐marker methylation classifiers developed for CIN3 detection in a previous series of hrHPV‐positive clinician‐collected cervical samples were applied. The diagnostic accuracy was visualised using receiver operating characteristic (ROC) curves and assessed through area under the ROC curve (AUC). The performance of the methylation markers to detect CIN3+ was determined using the predefined threshold calibrated at 70% clinical specificity. Individual methylation makers showed good performance for CIN3+ detection, with highest AUC for ASCL1 (0.844) and LHX8 (0.830). Combined as a bi‐marker panel with predefined threshold, ASCL1/LHX8 yielded a CIN3+ sensitivity of 76.9% (70/91; 95% CI 68.3‐85.6%) at a specificity of 74.5% (465/624; 95% CI 71.1‐77.9%). In conclusion, our study shows that the individual host‐cell DNA methylation classifiers and the bi‐marker panel ASCL1/LHX8 have clinical utility for the detection of CIN3+ in hrHPV‐positive women invited for routine screening.
Collapse
Affiliation(s)
- Lisanne Verhoef
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Maaike C G Bleeker
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Nicole Polman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Chris J L M Meijer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Willem J G Melchers
- Radboud University Medical Center, Medical Microbiology, Nijmegen, The Netherlands
| | - Ruud L Bekkers
- GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands.,Department of Obstetrics and Gynaecology, Catharina Hospital, Eindhoven, The Netherlands
| | - Anco C Molijn
- DDL Diagnostic Laboratory, NMDL-LCPL, Rijswijk, The Netherlands
| | - Wim G Quint
- DDL Diagnostic Laboratory, NMDL-LCPL, Rijswijk, The Netherlands
| | | | - Johannes Berkhof
- Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, The Netherlands
| | - Daniëlle A M Heideman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
20
|
Exploring Differentially Methylated Genes in Vulvar Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13143580. [PMID: 34298793 PMCID: PMC8306700 DOI: 10.3390/cancers13143580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Vulvar squamous cell carcinoma (VSCC) is the most common form of vulvar malignancy, and its incidence has increased in recent years. For better diagnosis and prognostication, and to expand available treatment options, molecular characterization of VSCC is crucial. We sought to identify aberrations in DNA methylation in VSCC, as this has been implicated in the development of several cancers. To this end, we performed genome-wide methylation sequencing on a set of VSCC and normal vulvar tissue using the Infinium MethylationEPIC BeadChip array. We detected 199 genes to be differentially methylated in VSCC compared to normal vulvar tissue. Of these, 194 genes were hyper-methylated, which leads to a loss of function of the genes. As most of these genes are involved in transcription regulator activity, our results suggest that disruption of this process plays an important role in VSCC development. Abstract DNA methylation is the most widely studied mechanism of epigenetic modification, which can influence gene expression without alterations in DNA sequences. Aberrations in DNA methylation are known to play a role in carcinogenesis, and methylation profiling has enabled the identification of biomarkers of potential clinical interest for several cancers. For vulvar squamous cell carcinoma (VSCC), however, methylation profiling remains an under-studied area. We sought to identify differentially methylated genes (DMGs) in VSCC, by performing Infinium MethylationEPIC BeadChip (Illumina) array sequencing, on a set of primary VSCC (n = 18), and normal vulvar tissue from women with no history of vulvar (pre)malignancies (n = 6). Using a false-discovery rate of 0.05, beta-difference (Δβ) of ±0.5, and CpG-island probes as cut-offs, 199 DMGs (195 hyper-methylated, 4 hypo-methylated) were identified for VSCC. Most of the hyper-methylated genes were found to be involved in transcription regulator activity, indicating that disruption of this process plays a vital role in VSCC development. The majority of VSCCs harbored amplifications of chromosomes 3, 8, and 9. We identified a set of DMGs in this exploratory, hypothesis-generating study, which we hope will facilitate epigenetic profiling of VSCCs. Prognostic relevance of these DMGs deserves further exploration in larger cohorts of VSCC and its precursor lesions.
Collapse
|
21
|
van der Zee RP, Richel O, van Noesel CJM, Ciocănea-Teodorescu I, van Splunter AP, Ter Braak TJ, Nathan M, Cuming T, Sheaff M, Kreuter A, Meijer CJLM, Quint WGV, de Vries HJC, Prins JM, Steenbergen RDM. Cancer Risk Stratification of Anal Intraepithelial Neoplasia in Human Immunodeficiency Virus-Positive Men by Validated Methylation Markers Associated With Progression to Cancer. Clin Infect Dis 2021; 72:2154-2163. [PMID: 32266940 PMCID: PMC8204787 DOI: 10.1093/cid/ciaa397] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/07/2020] [Indexed: 12/16/2022] Open
Abstract
Background High-grade anal intraepithelial neoplasia (HGAIN; AIN2–3) is highly prevalent in HIV+ men, but only a minority of these lesions progress towards cancer. Currently, cancer progression risk cannot be established; therefore, no consensus exists on whether HGAIN should be treated. This study aimed to validate previously identified host cell DNA methylation markers for detection and cancer risk stratification of HGAIN. Methods A large independent cross-sectional series of 345 anal cancer, AIN3, AIN2, AIN1, and normal control biopsies of HIV+ men was tested for DNA methylation of 6 genes using quantitative methylation-specific PCR. We determined accuracy for detection of AIN3 and cancer (AIN3+) by univariable and multivariable logistic regression analysis, followed by leave-one-out cross-validation. Methylation levels were assessed in a series of 10 anal cancer cases with preceding HGAIN at similar anatomic locations, and compared with the cross-sectional series. Results Methylation levels of all genes increased with increasing severity of disease (P < .05). HGAIN revealed a heterogeneous methylation pattern, with a subset resembling cancer. ZNF582 showed highest accuracy (AUC = 0.88) for AIN3+ detection, slightly improved by addition of ASCL1 and SST (AUC = 0.89), forming a marker panel. In the longitudinal series, HGAIN preceding cancer displayed high methylation levels similar to cancers. Conclusions We validated the accuracy of 5 methylation markers for the detection of anal (pre-) cancer. High methylation levels in HGAIN were associated with progression to cancer. These markers provide a promising tool to identify HGAIN in need of treatment, preventing overtreatment of HGAIN with a low cancer progression risk.
Collapse
Affiliation(s)
- Ramon P van der Zee
- Department of Pathology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Department of Internal Medicine, Division of Infectious Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AI&II), Amsterdam, The Netherlands.,Department of Dermatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Olivier Richel
- Department of Internal Medicine, Division of Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam University Medical Centers, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Iuliana Ciocănea-Teodorescu
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Annina P van Splunter
- Department of Pathology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Timo J Ter Braak
- Department of Pathology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Mayura Nathan
- Homerton Anal Neoplasia Service, Homerton University Hospital, London, United Kingdom
| | - Tamzin Cuming
- Homerton Anal Neoplasia Service, Homerton University Hospital, London, United Kingdom
| | - Michael Sheaff
- Department of Cellular Pathology, Barts Health National Health Service (NHS) Trust, London, United Kingdom
| | - Alexander Kreuter
- Department of Dermatology, Venerology, and Allergology, Helios St Elisabeth Hospital Oberhausen, University Witten/Herdecke, Oberhausen, Germany
| | - Chris J L M Meijer
- Department of Pathology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Wim G V Quint
- DDL Diagnostic Laboratory, Rijswijk, The Netherlands
| | - Henry J C de Vries
- Department of Dermatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Sexually Transmitted Infections Outpatient Clinic, Department of Infectious Diseases, Public Health Service of Amsterdam (GGD Amsterdam), Amsterdam, The Netherlands
| | - Jan M Prins
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AI&II), Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
22
|
Thuijs NB, Berkhof J, Özer M, Duin S, van Splunter AP, Snoek BC, Heideman DAM, van Beurden M, Steenbergen RDM, Bleeker MCG. DNA methylation markers for cancer risk prediction of vulvar intraepithelial neoplasia. Int J Cancer 2021; 148:2481-2488. [PMID: 33426639 PMCID: PMC8048962 DOI: 10.1002/ijc.33459] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/01/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022]
Abstract
Current clinical and histological classifications are unable to determine the risk of vulvar squamous cell carcinoma (VSCC) in high-grade vulvar intraepithelial neoplasia (VIN), making prognostic biomarkers highly needed. We studied host-cell DNA methylation markers in high-grade squamous intraepithelial lesion (HSIL) and differentiated VIN (dVIN) without VSCC, in HSIL and dVIN adjacent to VSCC and in human papillomavirus (HPV) positive and negative VSCC, relative to control vulvar tissues. A series of 192 formalin-fixed paraffin-embedded vulvar samples, including VSCC (n = 58), VIN adjacent to VSCC (n = 30), VIN without VSCC during follow-up (n = 41) and normal vulvar tissues (n = 63), were tested for 12 DNA methylation markers with quantitative multiplex methylation-specific PCR (qMSP). HPV status was determined by p16INK4A immunohistochemistry and high-risk HPV PCR analysis. Logistic regression analyses were used to determine methylation patterns and methylation marker performance for VIN and VSCC detection. Methylation markers showed significantly higher methylation levels with increasing severity of disease. VIN adjacent to VSCC showed a similar methylation-high pattern as VSCC, while VIN without VSCC displayed a heterogeneous methylation pattern. Vulvar carcinogenesis is associated with increased DNA methylation. Higher DNA methylation levels in VIN seem to reflect higher cancer risk, emphasizing the high potential of DNA methylation biomarkers in the diagnostic workup of VIN. As a next step, longitudinal studies are needed to verify the prognostic value of methylation biomarkers as a clinical tool for stratification of cancer risk in women with VIN.
Collapse
Affiliation(s)
- Nikki B. Thuijs
- Pathology, Cancer Center AmsterdamAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Johannes Berkhof
- Epidemiology and Data ScienceAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Müjde Özer
- Plastic, Reconstructive and Hand SurgeryAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Sylvia Duin
- Pathology, Cancer Center AmsterdamAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Annina P. van Splunter
- Pathology, Cancer Center AmsterdamAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Barbara C. Snoek
- Pathology, Cancer Center AmsterdamAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Daniëlle A. M. Heideman
- Pathology, Cancer Center AmsterdamAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Marc van Beurden
- Department of GynecologyAntoni van Leeuwenhoek hospitalAmsterdamThe Netherlands
| | - Renske D. M. Steenbergen
- Pathology, Cancer Center AmsterdamAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Maaike C. G. Bleeker
- Pathology, Cancer Center AmsterdamAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| |
Collapse
|
23
|
Vink FJ, Dick S, Heideman DAM, De Strooper LMA, Steenbergen RDM, Lissenberg-Witte BI, Floore A, Bonde JH, Oštrbenk Valenčak A, Poljak M, Petry KU, Hillemanns P, van Trommel NE, Berkhof J, Bleeker MCG, Meijer CJLM. Classification of high-grade cervical intraepithelial neoplasia by p16 ink4a , Ki-67, HPV E4 and FAM19A4/miR124-2 methylation status demonstrates considerable heterogeneity with potential consequences for management. Int J Cancer 2021; 149:707-716. [PMID: 33729551 PMCID: PMC8252755 DOI: 10.1002/ijc.33566] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 01/08/2023]
Abstract
High‐grade cervical intraepithelial neoplasia (CIN2 and CIN3) represents a heterogeneous disease with varying cancer progression risks. Biomarkers indicative for a productive human papillomavirus (HPV) infection (HPV E4) and a transforming HPV infection (p16ink4a, Ki‐67 and host‐cell DNA methylation) could provide guidance for clinical management in women with high‐grade CIN. This study evaluates the cumulative score of immunohistochemical expression of p16ink4a (Scores 0‐3) and Ki‐67 (Scores 0‐3), referred to as the “immunoscore” (IS), in 262 CIN2 and 235 CIN3 lesions derived from five European cohorts in relation to immunohistochemical HPV E4 expression and FAM19A4/miR124‐2 methylation in the corresponding cervical scrape. The immunoscore classification resulted in 30 lesions within IS group 0‐2 (6.0%), 151 lesions within IS group 3‐4 (30.4%) and 316 lesions within IS group 5‐6 (63.6%). E4 expression decreased significantly from CIN2 to CIN3 (P < .001) and with increasing immunoscore group (Ptrend < .001). Methylation positivity increased significantly from CIN2 to CIN3 (P < .001) and with increasing immunoscore group (Ptrend < .001). E4 expression was present in 9.8% of CIN3 (23/235) and in 12.0% of IS group 5‐6 (38/316). Notably, in a minority (43/497, 8.7%) of high‐grade lesions, characteristics of both transforming HPV infection (DNA hypermethylation) and productive HPV infection (E4 expression) were found simultaneously. Next, we stratified all high‐grade CIN lesions, based on the presumed cancer progression risk of the biomarkers used, into biomarker profiles. These biomarker profiles, including immunoscore and methylation status, could help the clinician in the decision for immediate treatment or a “wait and see” policy to reduce overtreatment of high‐grade CIN lesions.
What's new?
Treating all high‐grade cervical intraepithelial neoplasia (CIN2/3) with excisional therapy leads to overtreatment, as these lesions have varying cancer progression risks. Here, the authors evaluated expression patterns of p16ink4a, Ki‐67 and the HPV E4 protein, and methylation of FAM19A4/miR124‐2 in high‐grade CIN. The biomarker expression patterns revealed the high degree of heterogeneity among CIN2/3 lesions. Biomarker profiles based on the presumed cancer progression risks were established and could guide clinicians in choosing whether to treat immediately or wait and see.
Collapse
Affiliation(s)
- Frederique J Vink
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Stèfanie Dick
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Daniëlle A M Heideman
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Lise M A De Strooper
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Birgit I Lissenberg-Witte
- Department of Epidemiology and Data Science, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Arno Floore
- Self-screen B.V., Amsterdam, The Netherlands
| | - Jesper H Bonde
- Molecular Pathology Laboratory, Department of Pathology, Hvidovre Hospital, Hvidovre, Denmark
| | - Anja Oštrbenk Valenčak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Karl U Petry
- Department of Gynecologic Oncology, Klinikum Wolfsburg, Wolfsburg, Germany
| | - Peter Hillemanns
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Nienke E van Trommel
- Antoni van Leeuwenhoek, Netherlands Cancer Institute, Department of Gynecologic Oncology, Centre of Gynecologic Oncology Amsterdam, Amsterdam, The Netherlands
| | - Johannes Berkhof
- Department of Epidemiology and Data Science, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Maaike C G Bleeker
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Chris J L M Meijer
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
24
|
Van Keer S, van Splunter AP, Pattyn J, De Smet A, Herzog SA, Van Ostade X, Tjalma WAA, Ieven M, Van Damme P, Steenbergen RDM, Vorsters A. Triage of human papillomavirus infected women by methylation analysis in first-void urine. Sci Rep 2021; 11:7862. [PMID: 33846517 PMCID: PMC8042010 DOI: 10.1038/s41598-021-87329-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/26/2021] [Indexed: 11/28/2022] Open
Abstract
Host cell DNA methylation analysis in urine provides promising triage markers for women diagnosed with a high-risk (HR) human papillomavirus (HPV) infection. In this study, we have investigated a panel of six host cell methylation markers (GHSR, SST, ZIC1, ASCL1, LHX8, ST6GALNAC5) in cervicovaginal secretions collected within the first part of the urine void (FVU) from a referral population. Cytology, histology, and HPV DNA genotyping results on paired FVU and cervical samples were available. Urinary median methylation levels from HR-HPV (n = 93) positive women were found to increase for all markers with severity of underlying disease. Significantly elevated levels were observed for GHSR and LHX8 in relation to high-grade cervical intraepithelial neoplasia (CIN2 +; n = 33), with area under de curve values of 0.80 (95% Confidence Interval (CI) 0.59–0.92) and 0.76 (95% CI 0.58–0.89), respectively. These findings are the first to support the assertion that methylation analysis of host cell genes is feasible in FVU and holds promise as molecular, triage strategy to discern low- from high-grade cervical disease in HR-HPV positive women. Molecular testing on FVU may serve to increase cervical cancer screening attendance in hard-to-reach populations whilst reducing loss to follow-up and await further optimization and validation studies.
Collapse
Affiliation(s)
- Severien Van Keer
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Campus Drie Eiken, Building S2, Universiteitsplein 1, 2610, Wilrijk, Belgium.
| | - Annina P van Splunter
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Jade Pattyn
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Campus Drie Eiken, Building S2, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Annemie De Smet
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Campus Drie Eiken, Building S2, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Sereina A Herzog
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Xaveer Van Ostade
- Laboratory of Proteinscience, Proteomics & Epigenetic Signalling (PPES), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Wiebren A A Tjalma
- Multidisciplinary Breast Clinic, Unit Gynaecologic Oncology, Department of Obstetrics and Gynaecology, Antwerp University Hospital (UZA), Wilrijkstraat 10, 2650, Edegem, Belgium.,Molecular Imaging, Pathology, Radiotherapy, Oncology (MIPRO), Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Margareta Ieven
- Laboratory of Medical Microbiology (LMM), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Campus Drie Eiken, Building S2, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Renske D M Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Alex Vorsters
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Campus Drie Eiken, Building S2, Universiteitsplein 1, 2610, Wilrijk, Belgium
| |
Collapse
|
25
|
Impact of Collection Volume and DNA Extraction Method on the Detection of Biomarkers and HPV DNA in First-Void Urine. Molecules 2021; 26:molecules26071989. [PMID: 33915837 PMCID: PMC8036936 DOI: 10.3390/molecules26071989] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 12/22/2022] Open
Abstract
The potential of first-void (FV) urine as a non-invasive liquid biopsy for detection of human papillomavirus (HPV) DNA and other biomarkers has been increasingly recognized over the past decade. In this study, we investigated whether the volume of this initial urine stream has an impact on the analytical performance of biomarkers. In parallel, we evaluated different DNA extraction protocols and introduced an internal control in the urine preservative. Twenty-five women, diagnosed with high-risk HPV, provided three home-collected FV urine samples using three FV urine collection devices (Colli-Pee) with collector tubes that differ in volume (4, 10, 20 mL). Each collector tube was prefilled with Urine Conservation Medium spiked with phocine herpesvirus 1 (PhHV-1) DNA as internal control. Five different DNA extraction protocols were compared, followed by PCR for GAPDH and PhHV-1 (qPCR), HPV DNA, and HBB (HPV-Risk Assay), and ACTB (methylation-specific qPCR). Results showed limited effects of collection volume on human and HPV DNA endpoints. In contrast, significant variations in yield for human endpoints were observed for different DNA extraction methods (p < 0.05). Additionally, the potential of PhHV-1 as internal control to monitor FV urine collection, storage, and processing was demonstrated.
Collapse
|
26
|
Canberk S, Lima AR, Pinto M, Máximo V. Translational Potential of Epigenetic-Based Markers on Fine-Needle Aspiration Thyroid Specimens. Front Med (Lausanne) 2021; 8:640460. [PMID: 33834032 PMCID: PMC8021713 DOI: 10.3389/fmed.2021.640460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/03/2021] [Indexed: 12/31/2022] Open
Abstract
The awareness of epigenetic alterations leading to neoplasia attracted the attention of researchers toward its potential use in the management of cancer, from diagnosis to prognosis and prediction of response to therapies. Our group has focused its attention on the epigenomics of thyroid neoplasms. Although most of the epigenetic studies have been applied on histological samples, the fact is that cytology, through fine-needle aspiration, is a primary diagnostic method for many pathologies, of which thyroid nodules are one of the most paradigmatic examples. This has led to an increasing literature report of epigenetic studies using these biological samples over the past decade. In this review, our group aimed to document recent research of epigenetic alterations and its associated assessment techniques, based on cytology material. Our review covers the main epigenetic categories—DNA methylation, histone modification, and RNA-silencing—whose evidence in thyroid cytology samples may represent solid soil for future prospectively designed studies aiming at validating patterns of epigenetic alterations and their potential use in the clinical management of thyroid neoplasms.
Collapse
Affiliation(s)
- Sule Canberk
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal.,Cancer Signalling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal.,Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Ana Rita Lima
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal.,Cancer Signalling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal.,Faculty of Medicine of the University of Porto (FMUP), Alameda Prof. Hernâni Monteiro, Porto, Portugal
| | - Mafalda Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal.,Cancer Signalling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
| | - Valdemar Máximo
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal.,Cancer Signalling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal.,Faculty of Medicine of the University of Porto (FMUP), Alameda Prof. Hernâni Monteiro, Porto, Portugal.,Department of Pathology, Faculty of Medicine of the University of Porto (FMUP), Alameda Prof. Hernâni Monteiro, Porto, Portugal
| |
Collapse
|
27
|
Xu Y, Luo H, Hu Q, Zhu H. Identification of Potential Driver Genes Based on Multi-Genomic Data in Cervical Cancer. Front Genet 2021; 12:598304. [PMID: 33664766 PMCID: PMC7921803 DOI: 10.3389/fgene.2021.598304] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/07/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Cervical cancer became the third most common cancer among women, and genome characterization of cervical cancer patients has revealed the extensive complexity of molecular alterations. However, identifying driver mutation and depicting molecular classification in cervical cancer remain a challenge. Methods: We performed an integrative multi-platform analysis of a cervical cancer cohort from The Cancer Genome Atlas (TCGA) based on 284 clinical cases and identified the driver genes and possible molecular classification of cervical cancer. Results: Multi-platform integration showed that cervical cancer exhibited a wide range of mutation. The top 10 mutated genes were TTN, PIK3CA, MUC4, KMT2C, MUC16, KMT2D, SYNE1, FLG, DST, and EP300, with a mutation rate from 12 to 33%. Applying GISTIC to detect copy number variation (CNV), the most frequent chromosome arm-level CNVs included losses in 4p, 11p, and 11q and gains in 20q, 3q, and 1q. Then, we performed unsupervised consensus clustering of tumor CNV profiles and methylation profiles and detected four statistically significant expression subtypes. Finally, by combining the multidimensional datasets, we identified 10 potential driver genes, including GPR107, CHRNA5, ZBTB20, Rb1, NCAPH2, SCA1, SLC25A5, RBPMS, DDX3X, and H2BFM. Conclusions: This comprehensive analysis described the genetic characteristic of cervical cancer and identified novel driver genes in cervical cancer. These results provide insight into developing precision treatment in cervical cancer.
Collapse
Affiliation(s)
- Yuexun Xu
- Department of Gynecology and Obstetrics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Luo
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qunchao Hu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Haiyan Zhu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
28
|
The Origin of Tumor DNA in Urine of Urogenital Cancer Patients: Local Shedding and Transrenal Excretion. Cancers (Basel) 2021; 13:cancers13030535. [PMID: 33572525 PMCID: PMC7866784 DOI: 10.3390/cancers13030535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/26/2021] [Indexed: 01/07/2023] Open
Abstract
In urogenital cancers, urine as a liquid biopsy for non-invasive cancer detection holds great promise for future clinical application. Their anatomical position allows for the local shedding of tumor DNA, but recent data indicate that tumor DNA in urine might also result from transrenal excretion. This study aims to assess the origin of tumor-associated DNA in the urine of 5 bladder and 25 cervical cancer patients. Besides natural voided urine, paired urine samples were collected in which contact with the local tumor was circumvented to bypass local shedding. The latter concerned nephrostomy urine in bladder cancer patients, and catheter urine in cervical cancer patients. Methylation levels of GHSR, SST, and ZIC1 were determined using paired bladder tumor tissues and cervical scrapes as a reference. Urinary methylation levels were compared to natural voided urine of matched controls. To support methylation results, mutation analysis was performed in urine and tissue samples of bladder cancer patients. Increased methylation levels were not only found in natural voided urine from bladder and cervical cancer patients, but also in the corresponding nephrostomy and catheter urine. DNA mutations detected in bladder tumor tissues were also detectable in all paired natural voided urine as well as in a subset of nephrostomy urine. These results provide the first evidence that the suitability of urine as a liquid biopsy for urogenital cancers relies both on the local shedding of tumor cells and cell fragments, as well as the transrenal excretion of tumor DNA into the urine.
Collapse
|
29
|
Diefenbach D, Greten HJ, Efferth T. Genomic landscape analyses in cervical carcinoma and consequences for treatment. Curr Opin Pharmacol 2020; 54:142-157. [PMID: 33166910 DOI: 10.1016/j.coph.2020.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 11/28/2022]
Abstract
Where we are on the road to 'tailor-made' precision medicine for drug-resistant cervical carcinoma? We explored studies about analyses of viral and human genomes, epigenomes and transcriptomes, DNA mutation analyses, their importance in detecting HPV sequences, mechanisms of drug resistance to established and targeted therapies with small molecule or therapeutic antibodies, to radiosensitivity and to chemoradiotherapy. The value of repurposing of old drugs initially approved for other disease indications and now considered for cervix cancer therapy is also discussed. The microbiome influences drug response and survival too. HPV genomic integration sites were less significant. Nomograms (Lee et al., 2013) even outperformed FIGO staging regarding prediction of five-year overall survival times. We conclude that there are still many loose threads to be followed up, before coherent conclusions for individualized therapy of drug-resistant cervical carcinoma can be drawn.
Collapse
Affiliation(s)
- Dominik Diefenbach
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | | | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany.
| |
Collapse
|
30
|
van den Helder R, Wever BMM, van Trommel NE, van Splunter AP, Mom CH, Kasius JC, Bleeker MCG, Steenbergen RDM. Non-invasive detection of endometrial cancer by DNA methylation analysis in urine. Clin Epigenetics 2020; 12:165. [PMID: 33143739 PMCID: PMC7640380 DOI: 10.1186/s13148-020-00958-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
Background The incidence of endometrial cancer is rising, and current diagnostics often require invasive biopsy procedures. Urine may offer an alternative sample type, which is easily accessible and allows repetitive self-sampling at home. Here, we set out to investigate the feasibility of endometrial cancer detection in urine using DNA methylation analysis. Results Urine samples of endometrial cancer patients (n = 42) and healthy controls (n = 46) were separated into three fractions (full void urine, urine sediment, and urine supernatant) and tested for three DNA methylation markers (GHSR, SST, ZIC1). Strong to very strong correlations (r = 0.77–0.92) were found amongst the different urine fractions. All DNA methylation markers showed increased methylation levels in patients as compared to controls, in all urine fractions. The highest diagnostic potential for endometrial cancer detection in urine was found in full void urine, with area under the receiver operating characteristic curve values ranging from 0.86 to 0.95. Conclusions This feasibility study demonstrates, for the first time, that DNA methylation analysis in urine could provide a non-invasive alternative for the detection of endometrial cancer. Further investigation is warranted to validate its clinical usefulness. Potential applications of this diagnostic approach include the screening of asymptomatic women, triaging women with postmenopausal bleeding symptoms, and monitoring women with increased endometrial cancer risk.
Collapse
Affiliation(s)
- Rianne van den Helder
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands.,Antoni van Leeuwenhoek/Netherlands Cancer Institute, Center of Gynecologic Oncology Amsterdam, Department of Gynecologic Oncology, Amsterdam, The Netherlands
| | - Birgit M M Wever
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Nienke E van Trommel
- Antoni van Leeuwenhoek/Netherlands Cancer Institute, Center of Gynecologic Oncology Amsterdam, Department of Gynecologic Oncology, Amsterdam, The Netherlands
| | - Annina P van Splunter
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Constantijne H Mom
- Amsterdam UMC, University of Amsterdam, Center of Gynecologic Oncology Amsterdam, Department of Gynecologic Oncology, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Jenneke C Kasius
- Amsterdam UMC, University of Amsterdam, Center of Gynecologic Oncology Amsterdam, Department of Gynecologic Oncology, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Maaike C G Bleeker
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands.
| |
Collapse
|
31
|
Kremer WW, Vink FJ, van Zummeren M, Dreyer G, Rozendaal L, Doorbar J, Bleeker MCG, Meijer CJLM. Characterization of cervical biopsies of women with HIV and HPV co-infection using p16 ink4a, ki-67 and HPV E4 immunohistochemistry and DNA methylation. Mod Pathol 2020; 33:1968-1978. [PMID: 32249820 DOI: 10.1038/s41379-020-0528-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/11/2020] [Accepted: 03/11/2020] [Indexed: 12/23/2022]
Abstract
This study aims to characterize cervical intraepithelial neoplasia (CIN) in women living with HIV using biomarkers. Immunohistochemical (IHC) staining for human papillomavirus (HPV) E4 protein indicates CIN with productive HPV infection, whereas Ki-67 and p16ink4a indicate CIN with transforming characteristics, which may be further characterized using DNA hypermethylation, indicative for advanced transforming CIN. Cervical biopsies (n = 175) from 102 HPV positive women living with HIV were independently reviewed by three expert pathologists. The consensus CIN grade was used as reference standard. IHC staining patterns were scored for Ki-67 (0-3), p16ink4a (0-3), and E4 (0-2) and correlated to methylation levels of four cellular genes in corresponding cervical scrapes. Reference standards and immunoscores were obtained from 165 biopsies:15 no dysplasia, 91 CIN1, 31 CIN2, and 28 CIN3. Ki-67 and p16ink4a scores increased with increasing CIN grade, while E4 positivity was highest in CIN1 and CIN2 lesions. E4 positive CIN1 lesions had higher Ki-67 and p16ink4a scores and higher methylation levels compared with E4 negative CIN1 lesions. E4 positive biopsies with low cumulative Ki-67/p16 ink4a immunoscores (0-3) had significantly higher methylation levels compared with E4 negative biopsies. No significant differences in Ki-67 and p16ink4a scores and methylation levels were observed between E4 negative and positive CIN2 or CIN3 lesions. The presence of high methylation levels in scrapes of CIN lesions with IHC characteristics of both productive (E4 positive) and transforming infections (increased Ki-67/p16ink4a expression) in women living with HIV might indicate a rapid aggressive course of HPV infections towards cancer in these women.
Collapse
Affiliation(s)
- Wieke W Kremer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, de Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Frederique J Vink
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, de Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Marjolein van Zummeren
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, de Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Greta Dreyer
- Department of Obstetrics and Gynecology, University of Pretoria, Pretoria, South Africa
| | - Lawrence Rozendaal
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, de Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - John Doorbar
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Maaike C G Bleeker
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, de Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Chris J L M Meijer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, de Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
| |
Collapse
|
32
|
Muse ME, Titus AJ, Salas LA, Wilkins OM, Mullen C, Gregory KJ, Schneider SS, Crisi GM, Jawale RM, Otis CN, Christensen BC, Arcaro KF. Enrichment of CpG island shore region hypermethylation in epigenetic breast field cancerization. Epigenetics 2020; 15:1093-1106. [PMID: 32255732 PMCID: PMC7518670 DOI: 10.1080/15592294.2020.1747748] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/14/2020] [Accepted: 03/05/2020] [Indexed: 12/31/2022] Open
Abstract
While changes in DNA methylation are known to occur early in breast carcinogenesis and the landscape of breast tumour DNA methylation is profoundly altered compared with normal tissue, there have been limited efforts to identify DNA methylation field cancerization effects in histologically normal breast tissue adjacent to tumour. Matched tumour, histologically normal tissue of the ipsilateral breast (ipsilateral-normal), and histologically normal tissue of the contralateral breast (contralateral-normal) were obtained from nine women undergoing bilateral mastectomy. Laser capture microdissection was used to select epithelial cells from normal tissue, and neoplastic cells from tumour for genome-scale measures of DNA methylation with the Illumina HumanMethylationEPIC array. We identified substantially more CpG loci that were differentially methylated between contralateral-normal and tumour (63,271 CpG loci q < 0.01), than between ipsilateral-normal and tumour (38,346 CpG loci q < 0.01). We identified differential methylation in ipsilateral-normal relative to contralateral-normal tissue (9,562 CpG loci p < 0.01). In this comparison, hypomethylated loci were significantly enriched for breast cancer-relevant transcription factor binding sites including those for ESR1, FoxA1, and GATA3 and hypermethylated loci were significantly enriched for CpG island shore regions. In addition, progression of shore hypermethylation was observed in tumours compared to matched ipsilateral normal tissue, and these alterations tracked to several well-established tumour suppressor genes. Our results indicate an epigenetic field effect in surrounding histologically normal tissue. This work offers an opportunity to focus investigations of early DNA methylation alterations in breast carcinogenesis and potentially develop epigenetic biomarkers of disease risk. ABBREVIATIONS DCIS: ductal carcinoma in situ; GO: gene ontology; OR: odds ratio; CI: confidence interval; TFBS: transcription factor binding site; LOLA: Locus Overlap Analysis.
Collapse
Affiliation(s)
- Meghan E. Muse
- Department of Epidemiology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Alexander J. Titus
- Department of Epidemiology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Lucas A. Salas
- Department of Epidemiology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Owen M. Wilkins
- Department of Epidemiology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Chelsey Mullen
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Kelly J. Gregory
- Pioneer Valley Life Sciences Institute, Baystate Medical Center, Springfield, MA, USA
| | - Sallie S. Schneider
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
- Pioneer Valley Life Sciences Institute, Baystate Medical Center, Springfield, MA, USA
| | - Giovanna M. Crisi
- Department of Pathology, University of Massachusetts Medical School-Baystate Health, Springfield, MA, USA
| | - Rahul M. Jawale
- Department of Pathology, University of Massachusetts Medical School-Baystate Health, Springfield, MA, USA
| | - Christopher N. Otis
- Department of Pathology, University of Massachusetts Medical School-Baystate Health, Springfield, MA, USA
| | - Brock C. Christensen
- Department of Epidemiology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
- Department of Molecular & Systems Biology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
- Department of Community & Family Medicine, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Kathleen F. Arcaro
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| |
Collapse
|
33
|
Dick S, Verhoef L, De Strooper LM, Ciocănea-Teodorescu I, Wisman GBA, Meijer CJ, Bleeker MC, Steenbergen RD, Heideman DA. Evaluation of six methylation markers derived from genome-wide screens for detection of cervical precancer and cancer. Epigenomics 2020; 12:1569-1578. [PMID: 32938193 DOI: 10.2217/epi-2019-0331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Aim: To evaluate the triage performance of six host-cell DNA methylation markers derived from two genome-wide discovery screens for detection of cervical precancer (cervical intraepithelial neoplasia 3 [CIN]) and cancer. Materials & methods: Human papillomavirus-positive cervical scrapes of controls (≤CIN1; n = 352) and women diagnosed with CIN3 (n = 175) or cervical cancer (n = 50) were analyzed for methylation of ASCL1, LHX8, ST6GALNAC5, GHSR, SST and ZIC1. Results: Methylation levels increased significantly with disease severity (all markers p < 0.001). Three markers (ASCL1, LHX8, ZIC1) showed receiver operating characteristic curves with area under the curve >0.800 after leave-one-out cross-validation. Bi-marker panel ASCL1/LHX8 had highest area under the curve (0.882), and detected 83.4% of CIN3 and all cervical cancers at specificity of 82.4%. Conclusion: All six methylation markers showed an equivalent, high performance for the triage of human papillomavirus-positive women using cervical scrapes with complementarity between markers.
Collapse
Affiliation(s)
- Stèfanie Dick
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Lisanne Verhoef
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Lise Ma De Strooper
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Iuliana Ciocănea-Teodorescu
- Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology & Biostatistics, De Boelelaan 1117, Amsterdam, The Netherlands
| | - G Bea A Wisman
- University of Groningen, University Medical Centre Groningen, Gynaecologic Oncology, Cancer Research Center Groningen, Groningen, The Netherlands
| | - Chris Jlm Meijer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Maaike Cg Bleeker
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Renske Dm Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Daniëlle Am Heideman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| |
Collapse
|
34
|
Coppedè F, Stoccoro A, Nicolì V, Gallo R, De Rosa A, Guida M, Maestri M, Lucchi M, Ricciardi R, Migliore L. Investigation of GHSR methylation levels in thymomas from patients with Myasthenia Gravis. Gene 2020; 752:144774. [PMID: 32442579 DOI: 10.1016/j.gene.2020.144774] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 04/21/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Hypermethylation of the growth hormone secretagogue receptor gene (GHSR) is increasingly observed in human cancers, suggesting that it could represent a pan-cancer biomarker of clinical interest. However, little is still known concerning GHSR methylation levels in thymic epithelial tumors, and particularly in thymomas from patients with Myasthenia Gravis (TAMG). MATERIAL AND METHODS In the present study we collected DNA samples from circulating lymphocytes and surgically resected tumor tissues of 65 TAMG patients, and from the adjacent healthy thymic tissue available from 43 of them. We then investigated GHSR methylation levels in the collected tissues searching for correlation with the clinical characteristics of the samples. RESULTS GHSR hypermethylation was observed in 18 thymoma samples (28%) compared to the healthy thymic tissues (P < 1 × 10-4), and those samples were particularly enriched in advanced disease stages than stage I (94% were in stage II or higher). GHSR was demethylated in the remaining 47 thymomas, as well as in all the investigated healthy thymic samples and in circulating lymphocytes. CONCLUSIONS GHSR hypermethylation is not a pan-cancer marker or an early event in TAMG, but occurs in almost 1/4 of them and mainly from stage II onward. Subsequent studies are required to clarify the molecular pathways leading to GHSR hypermethylation in TAMG tissues and their relevance to disease progression.
Collapse
Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, Lab. of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, Lab. of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy
| | - Vanessa Nicolì
- Department of Translational Research and of New Surgical and Medical Technologies, Lab. of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy
| | - Roberta Gallo
- Department of Translational Research and of New Surgical and Medical Technologies, Lab. of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy
| | - Anna De Rosa
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Pisa, Italy
| | - Melania Guida
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Pisa, Italy
| | - Michelangelo Maestri
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Pisa, Italy
| | - Marco Lucchi
- Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, Pisa University Hospital, Pisa, Italy; Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Pisa, Italy
| | - Roberta Ricciardi
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Pisa, Italy; Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, Pisa University Hospital, Pisa, Italy
| | - Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, Lab. of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy; Department of Laboratory Medicine, Pisa University Hospital, Pisa, Italy
| |
Collapse
|
35
|
van der Zee RP, Richel O, van Noesel CJM, Novianti PW, Ciocanea-Teodorescu I, van Splunter AP, Duin S, van den Berk GEL, Meijer CJLM, Quint WGV, de Vries HJC, Prins JM, Steenbergen RDM. Host Cell Deoxyribonucleic Acid Methylation Markers for the Detection of High-grade Anal Intraepithelial Neoplasia and Anal Cancer. Clin Infect Dis 2020; 68:1110-1117. [PMID: 30060049 PMCID: PMC6424081 DOI: 10.1093/cid/ciy601] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/26/2018] [Indexed: 01/10/2023] Open
Abstract
Background High-grade anal intraepithelial neoplasia (AIN2/3; HGAIN) is highly prevalent in human immunodeficiency virus positive (HIV+) men who have sex with men (MSM), but only a minority will eventually progress to cancer. Currently, the cancer risk cannot be established, and therefore all HGAIN is treated, resulting in overtreatment. We assessed host cell deoxyribonucleic acid (DNA) methylation markers for detecting HGAIN and anal cancer. Methods Tissue samples of HIV+ men with anal cancer (n = 26), AIN3 (n = 24), AIN2 (n = 42), AIN1 (n = 22) and HIV+ male controls (n = 34) were analyzed for methylation of 9 genes using quantitative methylation-specific polymerase chain reaction. Univariable and least absolute shrinkage and selection operator logistic regression, followed by leave-one-out cross-validation, were used to determine the performance for AIN3 and cancer detection. Results Methylation of all genes increased significantly with increasing severity of disease (P < 2 × 10-6). HGAIN samples revealed heterogeneous methylation patterns, with a subset resembling cancer. Four genes (ASCL1, SST, ZIC1,ZNF582) showed remarkable performance for AIN3 and anal cancer detection (area under the curve [AUC] > 0.85). ZNF582 (AUC = 0.89), detected all cancers and 54% of AIN3 at 93% specificity. Slightly better performance (AUC = 0.90) was obtained using a 5-marker panel. Conclusions DNA methylation is associated with anal carcinogenesis. A marker panel that includes ZNF582 identifies anal cancer and HGAIN with a cancer-like methylation pattern, warrantingvalidation studies to verify its potential for screening and management of HIV+ MSM at risk for anal cancer.
Collapse
Affiliation(s)
- Ramon P van der Zee
- Department of Pathology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Division of Infectious Diseases, Department of Internal Medicine, Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Dermatology, Amsterdam University Medical Centers, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Olivier Richel
- Division of Infectious Diseases, Department of Internal Medicine, Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Putri W Novianti
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Centers, VU University Medical Center, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Iuliana Ciocanea-Teodorescu
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Centers, VU University Medical Center, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Annina P van Splunter
- Department of Pathology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Sylvia Duin
- Department of Pathology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Guido E L van den Berk
- Department of Internal Medicine, Onze Lieve Vrouwe Gasthuis (OLVG), Amsterdam, The Netherlands
| | - Chris J L M Meijer
- Department of Pathology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Wim G V Quint
- Delft Diagnostic Laboratory (DDL), Rijswijk, The Netherlands
| | - Henry J C de Vries
- Department of Dermatology, Amsterdam University Medical Centers, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, The Netherlands.,Department of Infectious Diseases, Sexually Transmitted Infections Outpatient Clinic, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Jan M Prins
- Division of Infectious Diseases, Department of Internal Medicine, Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
36
|
Comparative Analysis of Urine Fractions for Optimal Bladder Cancer Detection Using DNA Methylation Markers. Cancers (Basel) 2020; 12:cancers12040859. [PMID: 32252299 PMCID: PMC7226114 DOI: 10.3390/cancers12040859] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/25/2020] [Accepted: 03/31/2020] [Indexed: 12/15/2022] Open
Abstract
DNA methylation analysis of full void urine and urine pellet seems promising for bladder cancer (BC) detection and surveillance. Urinary cell-free DNA from urine supernatant is now gaining interest for other molecular tests in BC. This study aims to evaluate which urine fraction is preferred for BC diagnosis using methylation markers: full void urine, urine pellet or supernatant. Methylation levels of nine markers were determined in the three urine fractions and correlated with their respective tumor tissues in BC patients and compared to controls. For all markers and marker panel GHSR/MAL, diagnostic performance was determined by calculating the area under the curve (AUC) of the respective receiver operating characteristic curves. For most of the markers, there was a significant correlation between the methylation levels in each of the urine fractions and the matched tumor tissues. Urine pellet was the most representative fraction. Generally, AUCs for BC diagnosis were comparable among the fractions. The highest AUC was obtained for GHSR/MAL in urine pellet: AUC 0.87 (95% confidence interval: 0.73-1.00), corresponding to a sensitivity of 78.6% and a specificity of 91.7%. Our results demonstrate that cellular and cell-free DNA in urine can be used for BC diagnosis by urinary methylation analysis. Based on our comparative analysis and for practical reasons, we recommend the use of urine pellet.
Collapse
|
37
|
Methylation analysis in urine fractions for optimal CIN3 and cervical cancer detection. PAPILLOMAVIRUS RESEARCH 2020; 9:100193. [PMID: 32171935 PMCID: PMC7082622 DOI: 10.1016/j.pvr.2020.100193] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/31/2020] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Urine sampling is an interesting solution for CIN3 and cervical cancer detection. Urine can be separated in different fractions: full void urine, urine sediment and urine supernatant. We aimed to determine which urine fraction is most competent for CIN3 and cervical cancer detection by methylation analysis. METHODS Urine samples (27 controls, 30 CIN3 and 17 cervical cancer) were processed into 3 fractions and tested for 5 methylation markers (ASCL1, GHSR, LHX8, SST, ZIC1). We determined Spearman correlation coefficients between fractions, compared methylation levels and calculated AUCs for CIN3 and cancer detection. RESULTS In general strong correlations (r > 0.60) were found between urine fractions. Methylation levels increased significantly with severity of underlying disease in all urine fractions. CIN3 and controls differed significantly for 2 markers in full void urine, 4 markers in urine sediment and 1 marker in urine supernatant, with AUCs of 0.55-0.79. Comparison of cancer to controls was highly significant for all markers in all fractions, yielding AUCs of 0.87-0.99. CONCLUSION Methylation analysis performs excellent in all urine fractions for cervical cancer detection. Our results indicate the potential of CIN3 detection by urinary methylation analysis, and demonstrate that urine sediment performs best to detect CIN3.
Collapse
|
38
|
Neuropeptide receptor genes GHSR and NMUR1 are candidate epigenetic biomarkers and predictors for surgically treated patients with oropharyngeal cancer. Sci Rep 2020; 10:1007. [PMID: 31974445 PMCID: PMC6978330 DOI: 10.1038/s41598-020-57920-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/08/2020] [Indexed: 12/20/2022] Open
Abstract
Pathological staging and histological grading systems are useful, but imperfect, predictors of recurrence in head and neck squamous cell carcinoma (HNSCC). Aberrant promoter methylation is the main type of epigenetic modification that plays a role in the inactivation of tumor suppressor genes. To identify new potential prognostic markers, we investigated the promoter methylation status of five neuropeptide receptor genes. The methylation status of the target genes was compared with clinical characteristics in 278 cases; 72 hypopharyngeal cancers, 54 laryngeal cancers, 75 oropharyngeal cancers, and 77 oral cavity cancers were studied. We found that the NTSR1, NTSR2, GHSR, MLNR, and NMUR1 promoters were methylated in 47.8%, 46.8%, 54.3%, 39.2%, and 43.5% of the samples, respectively. GHSR and NMUR1 promoter methylation independently predicted recurrence in HNSCC. In patients with oropharyngeal cancer (n = 75), GHSR and NMUR1 promoter methylation significantly correlates with survival in surgically treated patients. We classified our patients as having a low, intermediate, or high-risk of death based on three factors: HPV status, and GHSR and NMUR1 promoter methylation. The disease-free survival (DFS) rates were 87.1%, 42.7%, and 17.0%, respectively. Combined data analysis of the methylation status of ten-eleven translocation (TET) family genes indicated a trend toward greater methylation indices as the number of TET methylation events increased. In the current study, we presented the relationship between the methylation status of the GHSR and NMUR1 genes and recurrence in HNSCC, specifically in risk classification of oropharyngeal carcinomas cases with HPV status.
Collapse
|
39
|
Xu W, Xu M, Wang L, Zhou W, Xiang R, Shi Y, Zhang Y, Piao Y. Integrative analysis of DNA methylation and gene expression identified cervical cancer-specific diagnostic biomarkers. Signal Transduct Target Ther 2019; 4:55. [PMID: 31871774 PMCID: PMC6908647 DOI: 10.1038/s41392-019-0081-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/25/2019] [Accepted: 05/10/2019] [Indexed: 12/24/2022] Open
Abstract
Cervical cancer is the leading cause of death among women with cancer worldwide. Here, we performed an integrative analysis of Illumina HumanMethylation450K and RNA-seq data from TCGA to identify cervical cancer-specific DNA methylation markers. We first identified differentially methylated and expressed genes and examined the correlation between DNA methylation and gene expression. The DNA methylation profiles of 12 types of cancers, including cervical cancer, were used to generate a candidate set, and machine-learning techniques were adopted to define the final cervical cancer-specific markers in the candidate set. Then, we assessed the protein levels of marker genes by immunohistochemistry by using tissue arrays containing 93 human cervical squamous cell carcinoma samples and cancer-adjacent normal tissues. Promoter methylation was negatively correlated with the local regulation of gene expression. In the distant regulation of gene expression, the methylation of hypermethylated genes was more likely to be negatively correlated with gene expression, while the methylation of hypomethylated genes was more likely to be positively correlated with gene expression. Moreover, we identified four cervical cancer-specific methylation markers, cg07211381 (RAB3C), cg12205729 (GABRA2), cg20708961 (ZNF257), and cg26490054 (SLC5A8), with 96.2% sensitivity and 95.2% specificity by using the tenfold cross-validation of TCGA data. The four markers could distinguish tumors from normal tissues with a 94.2, 100, 100, and 100% AUC in four independent validation sets from the GEO database. Overall, our study demonstrates the potential use of methylation markers in cervical cancer diagnosis and may boost the development of new epigenetic therapies.
Collapse
Affiliation(s)
- Wanxue Xu
- School of Medicine, Nankai University, Tianjin, China
| | - Mengyao Xu
- School of Medicine, Nankai University, Tianjin, China
| | - Longlong Wang
- School of Medicine, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
| | - Wei Zhou
- School of Medicine, Nankai University, Tianjin, China
| | - Rong Xiang
- School of Medicine, Nankai University, Tianjin, China
| | - Yi Shi
- School of Medicine, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
| | - Yunshan Zhang
- Reproductive Medical Center, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
| | - Yongjun Piao
- School of Medicine, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China
| |
Collapse
|
40
|
Zinc finger of the cerebellum 5 promotes colorectal cancer cell proliferation and cell cycle progression through enhanced CDK1/CDC25c signaling. Arch Med Sci 2019; 17:449-461. [PMID: 33747280 PMCID: PMC7959057 DOI: 10.5114/aoms.2019.89677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 02/02/2019] [Indexed: 12/14/2022] Open
Abstract
Introduction Colorectal cancer (CRC), mostly caused by external or environmental factors, is the third most common and lethal cancer worldwide. Although a large number of investigations have been carried out to reveal the evolution of CRC, the underlying mechanisms of CRC remain unclear. Material and methods Expression of zinc finger of the cerebellum 5 (ZIC5) in CRC tissues and cell models was measured by qRT-PCR and IHC. Cell transfection was carried out for ZIC5 overexpression or knockdown. The MTT assay was applied to examine the capacity of glioma cell proliferation. Wound healing assay and tumor invasion assay were used to test the capacity of glioma cell migration and invasion respectively. Cell cycle analysis and western blot were used to verify the apoptosis rates of CRC cells upon ZIC5 overexpression or downregulation. A further tumor Xenograft study was used to examine the effects of ZIC5 on tumor malignancy in vivo. Results Cell models using HCT116 and SW620 cells were established to study the ZIC5 function upon ZIC5 overexpression of knockdown. Consistently, we discovered that ZIC5 also significantly increased in Chinese CRC patients. In addition, ZIC5 promoted CRC cell proliferation through increasing the proportion of cells maintained in the S phase. ZIC5 overexpression facilitated the capacity of CRC cell migration and invasion. Inhibition of ZIC5 mitigated such malignant effects. Conclusions Collectively, investigations of the ZIC5 in CRC provided a new insight into CRC diagnosis, treatment, prognosis and next-step translational therapeutic developments from bench to clinic.
Collapse
|
41
|
Gu X, Guo XK, Chen BH, Gao XJ, Chen F, Liu Q. Prognostic and clinicopathological value of ZIC1 in patients with cervical squamous cell carcinoma. Oncol Lett 2019; 18:6621-6627. [PMID: 31788119 PMCID: PMC6865731 DOI: 10.3892/ol.2019.11007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/30/2019] [Indexed: 01/05/2023] Open
Abstract
The aim of the present study was to analyze the differences in zinc finger of the cerebellum 1 (ZIC1) expression between cervical cancer tissue, precancer tissue and normal cervical tissue to determine its clinicopathological and prognostic value in cervical squamous cell carcinoma (CSCC). Reverse transcription-quantitative PCR was used to determine the mRNA expression levels of ZIC1 in 569 fresh-frozen biopsy tissues, and immunohistochemistry was performed to detect ZIC1 protein expression in 80 CSCC tissues and 320 cervical intraepithelial neoplasia (CIN) grade III samples. The association of ZIC1 expression with the clinicopathological characteristics of CSCC was then analyzed using Cox regression analysis, and Kaplan-Meier curves were used to analyze the prognostic value. The level of ZIC1 mRNA expression in CSCC was significantly lower compared with normal cervical tissues and CIN I–III tissues (P<0.001). There was a negative correlation between ZIC1 immunoreactivity score (IRS) in CSCC tissue and adjacent noncancerous tissue (R=−0.279; P=0.012); the mean IRS of ZIC1 in CSCC tissue was 5.36±3.48, which was significantly lower compared with the corresponding adjacent noncancerous tissues (11.31±5.68; P<0.001) and CIN III samples (10.42±1.54; P<0.001). In addition, expression of ZIC1 was negatively associated with International Federation of Gynecology and Obstetrics (FIGO) stage (P=0.027) and lymph node metastasis (P<0.001). In Cox regression analysis, ZIC1 expression [hazard ratio (HR), 0.61; 95% confidence interval (CI), 0.40–0.92; P=0.018), FIGO staging (HR, 3.55; 95% CI, 2.35–5.37; P<0.001) and lymph node metastasis (HR, 2.50; 95% CI, 1.62–3.86; P<0.001) were three independent prognostic factors of overall survival. Furthermore, ZIC1 expression was also associated with disease-free survival (P=0.003). These results suggest that ZIC1 expression in CSCC may be lower than in normal cervical tissues or CIN tissues, and high expression of ZIC1 may be negatively associated with FIGO stage and lymph node metastasis. Therefore, ZIC1 may be a promising biomarker for the prognosis of CSCC.
Collapse
Affiliation(s)
- Xing Gu
- Department of Gynecology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| | - Xue-Ke Guo
- Department of Gynecology, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Bi-Hui Chen
- Department of Gynecology, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, Jiangsu 215300, P.R. China
| | - Xiao-Jiao Gao
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| | - Fang Chen
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| | - Qin Liu
- Department of Gynecology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| |
Collapse
|
42
|
Zhang C, Ge S, Wang J, Jing X, Li H, Mei S, Zhang J, Liang K, Xu H, Zhang X, Zhang C. Epigenomic profiling of DNA methylation for hepatocellular carcinoma diagnosis and prognosis prediction. J Gastroenterol Hepatol 2019; 34:1869-1877. [PMID: 31038805 DOI: 10.1111/jgh.14694] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 03/31/2019] [Accepted: 04/23/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM DNA hypermethylation has emerged as a novel molecular biomarker for the diagnosis and prognosis prediction of many cancers. We aimed to identify clinically useful biomarkers regulated by DNA methylation in hepatocellular carcinoma (HCC). METHODS Genome-wide methylation analysis in HCCs and paired noncancerous tissues was performed using an Illumina Infinium HumanMethylation 450K BeadChip array. Methylation-specific polymerase chain reaction and pyrosequencing were used to validate the methylation status of selected genes in 100 paired HCCs and noncancerous samples. RESULTS A total of 97 027 (20.0%) out of 485 577 CpG sites significantly were differed between HCC and noncancerous tissues. Among all the significant CpG sites, 48.8% are hypermethylated and 51.2% are hypomethylated in HCCs. Multiple signaling pathways (AMP-activated protein kinase, estrogen, and adipocytokine) involved in gene methylation were identified in HCC. FES was selected for further analysis based on its high level of methylation confirmed by polymerase chain reaction and pyrosequencing. The result showed that FES hypermethylation was correlated with tumor size (0.001), serum alpha fetoprotein (0.023), and tumor differentiation (0.006). FES protein was significantly downregulated in 51/100 (51%) HCCs, and 94.12% (48/51) of them were due to promoter hypermethylation. Both FES hypermethylation and protein downregulation were associated with the progression-free survival and overall survival of HCC patients. Overexpressed and knockdown of FES confirmed its inhibitory effect on the proliferation and migration of HCC cells. CONCLUSIONS We identified many new differentially methylated CpGs in HCCs and demonstrate that FES functions as a tumor suppressor gene in HCC and its methylation status could be used as an indicator for prognosis of HCC.
Collapse
Affiliation(s)
- Cheng Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Shuang Ge
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Jun Wang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Xiaotong Jing
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | | | - Shuyu Mei
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Juan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Ke Liang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Hui Xu
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Xiaoying Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| |
Collapse
|
43
|
Cortés-Gutiérrez EI, García-Vielma C, Dávila-Rodríguez MI, Sánchez-Dávila H, Fernández JL, Gosálvez J. 1p36 is a chromosomal site of genomic instability in cervical intraepithelial neoplasia. Biotech Histochem 2019; 95:137-144. [DOI: 10.1080/10520295.2019.1652344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
| | - C. García-Vielma
- Department of Genetics, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social (IMSS), Monterrey, México
| | - M. I. Dávila-Rodríguez
- Department of Genetics, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social (IMSS), Monterrey, México
| | - H. Sánchez-Dávila
- High Specialty Medical Unit No. 23. Hospital of Obstetrics and Gynecology, Dr. Ignacio Morones Prieto of Instituto Mexicano del Seguro Social
| | - J. L. Fernández
- Genetics Unit, Complejo Hospitalario Universitario A Coruña-INIBIC, La Coruña, Spain
| | - J. Gosálvez
- Department of Biology, Genetic Unit, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| |
Collapse
|
44
|
Adcock R, Cuzick J, Hunt WC, McDonald RM, Wheeler CM. Role of HPV Genotype, Multiple Infections, and Viral Load on the Risk of High-Grade Cervical Neoplasia. Cancer Epidemiol Biomarkers Prev 2019; 28:1816-1824. [PMID: 31488417 DOI: 10.1158/1055-9965.epi-19-0239] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/08/2019] [Accepted: 08/28/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Human papillomavirus (HPV) testing provides a much more sensitive method of detection for high-grade lesions than cytology, but specificity is low. Here, we explore the extent to which full HPV genotyping, viral load, and multiplicity of types can be used to improve specificity. METHODS A population-based sample of 47,120 women undergoing cervical screening was tested for 13 high-risk HPV genotypes. Positive predictive values (PPV) for cervical intraepithelial neoplasia (CIN) grade 2 or worse (CIN2+; N = 3,449) and CIN3 or worse (CIN3+; N = 1,475) over 3 years of follow-up were estimated for HPV genotype and viral load. Weighted multivariate logistic regression models were used to estimate the odds of CIN2+ or CIN3+ according to genotype, multiplicity of types, and viral load. RESULTS High-risk HPV was detected in 15.4% of women. A hierarchy of HPV genotypes based on sequentially maximizing PPVs for CIN3+ found HPV16>33>31 to be the most predictive, followed sequentially by HPV18>35>58>45>52>59>51>39>56>68. After adjusting for higher ranked genotypes, the inclusion of multiple HPV infections added little to risk prediction. High viral loads for HPV18, 35, 52, and 58 carried more risk than low viral loads for HPV16, 31, and 33. High viral load for HPV16 was significantly more associated with CIN3+ than low viral load. CONCLUSIONS HPV genotype and viral load, but not multiplicity of HPV infections, are important predictors of CIN2+ and CIN3+. IMPACT The ability to identify women at higher risk of CIN2+ and CIN3+ based on both HPV genotype and viral load could be important for individualizing triage plans, particularly as HPV becomes the primary screening test.
Collapse
Affiliation(s)
- Rachael Adcock
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, United Kingdom
| | - Jack Cuzick
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, United Kingdom
| | - William C Hunt
- Center for HPV Prevention, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Ruth M McDonald
- Center for HPV Prevention, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | | | | |
Collapse
|
45
|
Amini M, Foroughi K, Talebi F, Aghagolzade Haji H, Kamali F, Jandaghi P, Hoheisel JD, Manoochehri M. GHSR DNA hypermethylation is a new epigenetic biomarker for gastric adenocarcinoma and beyond. J Cell Physiol 2019; 234:15320-15329. [PMID: 30677130 DOI: 10.1002/jcp.28179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Aberrations of DNA methylation are early events in the development of tumors. In this study, we investigated the DNA methylation status of growth hormone secretagogue receptor (GHSR), a promising pan-cancer biomarker, in gastric cancer (GC). Initially, data sets from DNA methylation and gene expression studies available at Gene Expression Omnibus (GEO) were analyzed. Confirmation was done on primary tumor specimens and adjacent normal stomach tissue samples. Both analyses showed significant hypermethylation of GHSR. For further validation, The Cancer Genome Atlas data on stomach cancer was used. A receiver operating characteristic curve analysis yielded an area under the curve value of 0.85, corroborating its usefulness as a diagnostic marker. A genome-wide comethylation analysis revealed several correlated genes. CREB1 was found to act as an upstream regulator of this gene network. Furthermore, GHSR methylation was found to be a biomarker in several other tumor entities, namely cancers of the bladder, endometrium, esophagus, head and neck, liver, thyroid, kidney, and ovary. Our findings along with previous reports on other types of cancer suggest a high potential of GHSR gene methylation as a pan-cancer biomarker, which could be considered for liquid biopsy applications.
Collapse
Affiliation(s)
- Mohammad Amini
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Kobra Foroughi
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Fatemeh Talebi
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Hemat Aghagolzade Haji
- Department of Biochemistry, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Fatemeh Kamali
- Iran National Tumor Bank, Cancer Institute of Iran, Tehran, Iran
| | - Pouria Jandaghi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis (B070), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mehdi Manoochehri
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran.,Molecular Genetics of Breast Cancer (B072), German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
46
|
Jiao X, Zhang S, Jiao J, Zhang T, Qu W, Muloye GM, Kong B, Zhang Q, Cui B. Promoter methylation of SEPT9 as a potential biomarker for early detection of cervical cancer and its overexpression predicts radioresistance. Clin Epigenetics 2019; 11:120. [PMID: 31426855 PMCID: PMC6700799 DOI: 10.1186/s13148-019-0719-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/30/2019] [Indexed: 01/22/2023] Open
Abstract
Background Cervical cancer screening by combined cytology and HPV test has reduced the incidence of cervical cancer, but cytological screening lacks a higher sensitivity while HPV testing possesses a lower specificity. Most patients with invasive cervical cancer are treated with radiotherapy. However, insensitivity to radiotherapy leads to poor efficacy. Methods Illumina Methylation EPIC 850k Beadchip was used for genomic screening. We detected methylation of SEPT9 and mRNA expression in different cervical tissues by using methylation-specific PCR and qRT-PCR. Then using CCK8, migration assay, and flow cytometry to detect the biological function and irradiation resistance of SEPT9 in vitro and in vivo. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and co-immunoprecipitation (CoIP) were used to find the interacting gene with SEPT9. Immunostaining of CD206 in cervical cancer and polarization of macrophages (M2) were evaluated by immunofluorescence and WB. The Cancer Genome Atlas (TCGA) database was used for screening the potential miRNAs induced by SEPT9. Results Hyper-methylation of SEPT9 detects cervical cancer and normal tissues, normal+CIN1 and CIN2+CIN3+cancer with high sensitivity and specificity (AUC = 0.854 and 0.797, respectively, P < 0.001). The mRNA and protein expression of SEPT9 was upregulated in cervical cancer tissues when compared to para-carcinoma tissues. SEPT9 promotes proliferation, invasion, migration, and influences the cell cycle of cervical cancer. SEPT9 interacted with HMGB1-RB axis increases irradiation resistance. Furthermore, SEPT9 mediated miR-375 via the tumor-associated macrophages (TAMs) polarization, affecting the resistance to radiotherapy in cervical cancer. Conclusions These findings give us the evidence that SEPT9 methylation could be a biomarker for cervical cancer diagnoses. It promotes tumorigenesis and radioresistance of cervical cancer by targeting HMGB1-RB axis and causes polarization of macrophages by mediating miR-375. We suggest SEPT9 could be a potential screening and therapeutic biomarker for cervical cancer. Electronic supplementary material The online version of this article (10.1186/s13148-019-0719-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xinlin Jiao
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 West Wenhua Road, Ji'nan, 250012, Shandong, People's Republic of China
| | - Siying Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 West Wenhua Road, Ji'nan, 250012, Shandong, People's Republic of China.,Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan, 250012, Shandong, People's Republic of China
| | - Jun Jiao
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 West Wenhua Road, Ji'nan, 250012, Shandong, People's Republic of China
| | - Teng Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 West Wenhua Road, Ji'nan, 250012, Shandong, People's Republic of China
| | - Wenjie Qu
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 West Wenhua Road, Ji'nan, 250012, Shandong, People's Republic of China
| | - Guy Mutangala Muloye
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 West Wenhua Road, Ji'nan, 250012, Shandong, People's Republic of China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 West Wenhua Road, Ji'nan, 250012, Shandong, People's Republic of China.,Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan, 250012, Shandong, People's Republic of China
| | - Qing Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 West Wenhua Road, Ji'nan, 250012, Shandong, People's Republic of China. .,Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan, 250012, Shandong, People's Republic of China.
| | - Baoxia Cui
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 West Wenhua Road, Ji'nan, 250012, Shandong, People's Republic of China.
| |
Collapse
|
47
|
Moreland BS, Oman KM, Bundschuh R. A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction. BMC Bioinformatics 2019; 20:431. [PMID: 31426747 PMCID: PMC6700779 DOI: 10.1186/s12859-019-3011-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 07/29/2019] [Indexed: 11/12/2022] Open
Abstract
Background Protein pulldown using Methyl-CpG binding domain (MBD) proteins followed by high-throughput sequencing is a common method to determine DNA methylation. Algorithms have been developed to estimate absolute methylation level from read coverage generated by affinity enrichment-based techniques, but the most accurate one for MBD-seq data requires additional data from an SssI-treated Control experiment. Results Using our previous characterizations of Methyl-CpG/MBD2 binding in the context of an MBD pulldown experiment, we build a model of expected MBD pulldown reads as drawn from SssI-treated DNA. We use the program BayMeth to evaluate the effectiveness of this model by substituting calculated SssI Control data for the observed SssI Control data. By comparing methylation predictions against those from an RRBS data set, we find that BayMeth run with our modeled SssI Control data performs better than BayMeth run with observed SssI Control data, on both 100 bp and 10 bp windows. Adapting the model to an external data set solely by changing the average fragment length, our calculated data still informs the BayMeth program to a similar level as observed data in predicting methylation state on a pulldown data set with matching WGBS estimates. Conclusion In both internal and external MBD pulldown data sets tested in this study, BayMeth used with our modeled pulldown coverage performs better than BayMeth run without the inclusion of any estimate of SssI Control pulldown, and is comparable to – and in some cases better than – using observed SssI Control data with the BayMeth program. Thus, our MBD pulldown alignment model can improve methylation predictions without the need to perform additional control experiments. Electronic supplementary material The online version of this article (10.1186/s12859-019-3011-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Blythe S Moreland
- Department of Physics, The Ohio State University, Columbus, OH, USA.,Present address: Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH,, USA
| | - Kenji M Oman
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ralf Bundschuh
- Department of Physics, The Ohio State University, Columbus, OH, USA. .,Department of Chemistry&Biochemistry, Division of Hematology, and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
48
|
Dick S, Kremer WW, De Strooper LM, Lissenberg-Witte BI, Steenbergen RD, Meijer CJ, Berkhof J, Heideman DA. Long-term CIN3+ risk of HPV positive women after triage with FAM19A4/miR124-2 methylation analysis. Gynecol Oncol 2019; 154:368-373. [DOI: 10.1016/j.ygyno.2019.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/30/2019] [Accepted: 06/02/2019] [Indexed: 01/02/2023]
|
49
|
Olusola P, Banerjee HN, Philley JV, Dasgupta S. Human Papilloma Virus-Associated Cervical Cancer and Health Disparities. Cells 2019; 8:cells8060622. [PMID: 31234354 PMCID: PMC6628030 DOI: 10.3390/cells8060622] [Citation(s) in RCA: 185] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/15/2019] [Accepted: 06/19/2019] [Indexed: 12/25/2022] Open
Abstract
Cervical cancer develops through persistent infection with high-risk human papilloma virus (hrHPV) and is a leading cause of death among women worldwide and in the United States. Periodic surveillance through hrHPV and Pap smear-based testing has remarkably reduced cervical cancer incidence worldwide and in the USA. However, considerable discordance in the occurrence and outcome of cervical cancer in various populations exists. Lack of adequate health insurance appears to act as a major socioeconomic burden for obtaining cervical cancer preventive screening in a timely manner, which results in disparate cervical cancer incidence. On the other hand, cervical cancer is aggressive and often detected in advanced stages, including African American and Hispanic/Latina women. In this context, our knowledge of the underlying molecular mechanism and genetic basis behind the disparate cervical cancer outcome is limited. In this review, we shed light on our current understanding and knowledge of racially disparate outcomes in cervical cancer.
Collapse
Affiliation(s)
- Patti Olusola
- Departments of Family Medicine, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA.
| | - Hirendra Nath Banerjee
- Natural, Pharmacy and Health Sciences, Elizabeth City State University, North Carolina, Elizabeth City, NC 27909, USA.
| | - Julie V Philley
- Medicine, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA.
| | - Santanu Dasgupta
- Medicine, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA.
| |
Collapse
|
50
|
Sendagorta-Cudós E, Burgos-Cibrián J, Rodríguez-Iglesias M. Infecciones genitales por el virus del papiloma humano. Enferm Infecc Microbiol Clin 2019; 37:324-334. [DOI: 10.1016/j.eimc.2019.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/22/2022]
|