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Peronace C, Cione E, Abrego-Guandique DM, Fazio MD, Panduri G, Caroleo MC, Cannataro R, Minchella P. FAM19A4 and hsa-miR124-2 Double Methylation as Screening for ASC-H- and CIN1 HPV-Positive Women. Pathogens 2024; 13:312. [PMID: 38668267 PMCID: PMC11054986 DOI: 10.3390/pathogens13040312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
The DNA methylation levels of host cell genes increase with the severity of the cervical intraepithelial neoplasia (CIN) grade and are very high in cervical cancer. Our study aims to evaluate FAM19A4 and hsa-miR124-2 methylation in Atypical Squamous cells with high-grade squamous intraepithelial lesions (ASC-H) and in CIN1, defined as low-grade squamous intraepithelial lesions (LSILs) by the Bethesda classification, as possible early warning biomarkers for managing women with high-risk HPV infections (hrHPV). FAM19A4 and hsa-miR124-2 methylation tests were conducted on fifty-six cervical screening samples from a subset of women aged 30-64 years old. Specimens were collected into ThinPrep PreservCyt Solution. Their HrHPV genotype and cytology diagnosis were known. A Qiasure (Qiagen) was used for FAM19A4 and hsa-miR124-2 methylation testing on bisulfite-converted DNA, according to the manufacturer's specifications. The reported results were hypermethylation-positive or -negative. We found that FAM194A4 and hsa-miR124-2 methylation was detected in 75% of ASC-H cases with a persistent infection of hrHPV. A total of 60% of CIN1 lesions were found to be positive for methylation, and 83.3% were when the cytology was CIN2/3. In addition, as a novelty of this pilot study, we found that combined FAM19A4 and hsa-miR124-2 methylation positivity rates (both methylated) were associated with the HPV genotypes 16, 18, and 59 and covered 22 and 25% of ASC-H and CIN1 cases, respectively. The methylation of these two genes, in combination with HPV genotyping, can be used as an early warning biomarker in the management and follow-up of women with ASC-H and CIN1 to avoid their progression to cervical cancer.
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Affiliation(s)
- Cinzia Peronace
- Unit of Microbiology and Virology, PO Pugliese, AOU Renato Dulbecco, 88100 Catanzaro, Italy; (M.D.F.); (G.P.); (P.M.)
| | - Erika Cione
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende (CS), Italy
- Galascreen Laboratories, University of Calabria, 87036 Rende (CS), Italy; (D.M.A.-G.); (M.C.C.); (R.C.)
| | - Diana Marisol Abrego-Guandique
- Galascreen Laboratories, University of Calabria, 87036 Rende (CS), Italy; (D.M.A.-G.); (M.C.C.); (R.C.)
- Department of Health Sciences, University of Magna Graecia, 88100 Catanzaro, Italy
| | - Marco De Fazio
- Unit of Microbiology and Virology, PO Pugliese, AOU Renato Dulbecco, 88100 Catanzaro, Italy; (M.D.F.); (G.P.); (P.M.)
| | - Giuseppina Panduri
- Unit of Microbiology and Virology, PO Pugliese, AOU Renato Dulbecco, 88100 Catanzaro, Italy; (M.D.F.); (G.P.); (P.M.)
| | - Maria Cristina Caroleo
- Galascreen Laboratories, University of Calabria, 87036 Rende (CS), Italy; (D.M.A.-G.); (M.C.C.); (R.C.)
- Department of Health Sciences, University of Magna Graecia, 88100 Catanzaro, Italy
| | - Roberto Cannataro
- Galascreen Laboratories, University of Calabria, 87036 Rende (CS), Italy; (D.M.A.-G.); (M.C.C.); (R.C.)
| | - Pasquale Minchella
- Unit of Microbiology and Virology, PO Pugliese, AOU Renato Dulbecco, 88100 Catanzaro, Italy; (M.D.F.); (G.P.); (P.M.)
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Huseinovic A, Xu M, Jaspers A, Bais B, Steenbergen RDM. miR-129-5p inhibits anchorage-independent growth through silencing of ACTN1 and the ELK4/c-FOS axis in HPV-transformed keratinocytes. J Med Virol 2024; 96:e29580. [PMID: 38566572 DOI: 10.1002/jmv.29580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/21/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
A persistent infection with human papillomavirus (HPV) can induce precancerous lesions of the cervix that may ultimately develop into cancer. Cervical cancer development has been linked to altered microRNA (miRNA) expression, with miRNAs regulating anchorage-independent growth being particularly important for the progression of precancerous lesions to cancer. In this study, we set out to identify and validate targets of miR-129-5p, a previously identified tumor suppressive miRNA involved in anchorage-independent growth and HPV-induced carcinogenesis. We predicted 26 potential miR-129-5p targets using online databases, followed by KEGG pathway enrichment analysis. RT-qPCR and luciferase assays confirmed that 3'UTR regions of six genes (ACTN1, BMPR2, CAMK4, ELK4, EP300, and GNAQ) were targeted by miR-129-5p. Expressions of ACTN1, CAMK4, and ELK4 were inversely correlated to miR-129-5p expression in HPV-transformed keratinocytes, and their silencing reduced anchorage-independent growth. Concordantly, miR-129-5p overexpression decreased protein levels of ACTN1, BMPR2, CAMK4 and ELK4 in anchorage-independent conditions. Additionally, c-FOS, a downstream target of ELK4, was downregulated upon miR-129-5p overexpression, suggesting regulation through the ELK4/c-FOS axis. ACTN1 and ELK4 expression was also upregulated in high-grade precancerous lesions and cervical cancers, supporting their clinical relevance. In conclusion, we identified six targets of miR-129-5p involved in the regulation of anchorage-independent growth, with ACTN1, BMPR2, ELK4, EP300, and GNAQ representing novel targets for miR-129-5p. For both ACTN1 and ELK4 functional and clinical relevance was confirmed, indicating that miR-129-5p-regulated ACTN1 and ELK4 expression contributes to HPV-induced carcinogenesis.
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Affiliation(s)
- Angelina Huseinovic
- Department of Pathology, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Mengfei Xu
- Department of Pathology, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Annelieke Jaspers
- Department of Pathology, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Brigitte Bais
- Department of Pathology, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam UMC, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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Nguyen TB, Do DN, Nguyen-Thi ML, Hoang-The H, Tran TT, Nguyen-Thanh T. Identification of potential crucial genes and key pathways shared in Inflammatory Bowel Disease and cervical cancer by machine learning and integrated bioinformatics. Comput Biol Med 2022; 149:105996. [DOI: 10.1016/j.compbiomed.2022.105996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/10/2022] [Accepted: 08/14/2022] [Indexed: 11/15/2022]
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Huseinovic A, Jaspers A, van Splunter AP, Sørgård H, Wilting SM, Swarts DRA, van der Meulen IH, van Beusechem VW, de Menezes RX, Steenbergen RDM. Functional Screen for microRNAs Suppressing Anchorage-Independent Growth in Human Cervical Cancer Cells. Int J Mol Sci 2022; 23:4791. [PMID: 35563182 DOI: 10.3390/ijms23094791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/21/2022] [Indexed: 02/04/2023] Open
Abstract
The progression of anchorage-dependent epithelial cells to anchorage-independent growth represents a critical hallmark of malignant transformation. Using an in vitro model of human papillomavirus (HPV)-induced transformation, we previously showed that acquisition of anchorage-independent growth is associated with marked (epi)genetic changes, including altered expression of microRNAs. However, the laborious nature of the conventional growth method in soft agar to measure this phenotype hampers a high-throughput analysis. We developed alternative functional screening methods using 96- and 384-well ultra-low attachment plates to systematically investigate microRNAs regulating anchorage-independent growth. SiHa cervical cancer cells were transfected with a microRNA mimic library (n = 2019) and evaluated for cell viability. We identified 84 microRNAs that consistently suppressed growth in three independent experiments. Further validation in three cell lines and comparison of growth in adherent and ultra-low attachment plates yielded 40 microRNAs that specifically reduced anchorage-independent growth. In conclusion, ultra-low attachment plates are a promising alternative for soft-agar assays to study anchorage-independent growth and are suitable for high-throughput functional screening. Anchorage independence suppressing microRNAs identified through our screen were successfully validated in three cell lines. These microRNAs may provide specific biomarkers for detecting and treating HPV-induced precancerous lesions progressing to invasive cancer, the most critical stage during cervical cancer development.
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Sadri Nahand J, Shojaie L, Akhlagh SA, Ebrahimi MS, Mirzaei HR, Bannazadeh Baghi H, Mahjoubin-Tehran M, Rezaei N, Hamblin MR, Tajiknia V, Rahimian N, Mirzaei H. Cell death pathways and viruses: Role of microRNAs. Mol Ther Nucleic Acids 2021; 24:487-511. [PMID: 33898103 DOI: 10.1016/j.omtn.2021.03.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Viral infections lead to the death of more than a million people each year around the world, both directly and indirectly. Viruses interfere with many cell functions, particularly critical pathways for cell death, by affecting various intracellular mediators. MicroRNAs (miRNAs) are a major example of these mediators because they are involved in many (if not most) cellular mechanisms. Virus-regulated miRNAs have been implicated in three cell death pathways, namely, apoptosis, autophagy, and anoikis. Several molecules (e.g., BECN1 and B cell lymphoma 2 [BCL2] family members) are involved in both apoptosis and autophagy, while activation of anoikis leads to cell death similar to apoptosis. These mechanistic similarities suggest that common regulators, including some miRNAs (e.g., miR-21 and miR-192), are involved in different cell death pathways. Because the balance between cell proliferation and cell death is pivotal to the homeostasis of the human body, miRNAs that regulate cell death pathways have drawn much attention from researchers. miR-21 is regulated by several viruses and can affect both apoptosis and anoikis via modulating various targets, such as PDCD4, PTEN, interleukin (IL)-12, Maspin, and Fas-L. miR-34 can be downregulated by viral infection and has different effects on apoptosis, depending on the type of virus and/or host cell. The present review summarizes the existing knowledge on virus-regulated miRNAs involved in the modulation of cell death pathways. Understanding the mechanisms for virus-mediated regulation of cell death pathways could provide valuable information to improve the diagnosis and treatment of many viral diseases.
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Kremer WW, Steenbergen R, Heideman D, Kenter GG, Meijer C. The use of host cell DNA methylation analysis in the detection and management of women with advanced cervical intraepithelial neoplasia: a review. BJOG 2020; 128:504-514. [PMID: 32619334 PMCID: PMC7818489 DOI: 10.1111/1471-0528.16395] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 12/24/2022]
Abstract
This paper briefly reviews the role of hypermethylation of host cell genes in cervical carcinogenesis and discusses potential clinical applications of methylation analysis in the management of high-risk HPV (hrHPV) -positive women. We argue that methylation assays can be used: 1. for primary triage of hrHPV-positive women to detect cervical cancer and advanced cervical intraepithelial neoplasia (CIN); 2. as secondary triage for women with minor cytological abnormalities to identify those with the highest risk of CIN3 or worse; 3. as exit test for women leaving the screening programme to identify cervical cancer and advanced CIN; and 4. to support management of CIN. TWEETABLE ABSTRACT: This paper discusses potential clinical applications of DNA methylation analysis in the management of women with a high-risk HPV infection.
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Affiliation(s)
- W W Kremer
- Department of Pathology, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rdm Steenbergen
- Department of Pathology, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dam Heideman
- Department of Pathology, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - G G Kenter
- Obstetrics and Gynaecology, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Centre for Gynaecological Oncology Amsterdam, Antoni van Leeuwenhoek-Netherlands Cancer Institute and Amsterdam UMC, Amsterdam, The Netherlands
| | - Cjlm Meijer
- Department of Pathology, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Hentschel AE, Nieuwenhuijzen JA, Bosschieter J, Splunter APV, Lissenberg-Witte BI, Voorn JPV, Segerink LI, Moorselaar RJAV, Steenbergen RDM. Comparative Analysis of Urine Fractions for Optimal Bladder Cancer Detection Using DNA Methylation Markers. Cancers (Basel) 2020; 12:E859. [PMID: 32252299 DOI: 10.3390/cancers12040859] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [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.
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Babion I, Miok V, Jaspers A, Huseinovic A, Steenbergen RDM, van Wieringen WN, Wilting SM. Identification of Deregulated Pathways, Key Regulators, and Novel miRNA-mRNA Interactions in HPV-Mediated Transformation. Cancers (Basel) 2020; 12:E700. [PMID: 32188026 PMCID: PMC7140059 DOI: 10.3390/cancers12030700] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 12/20/2022] Open
Abstract
Next to a persistent infection with high-risk human papillomavirus (HPV), molecular changes are required for the development of cervical cancer. To identify which molecular alterations drive carcinogenesis, we performed a comprehensive and longitudinal molecular characterization of HPV-transformed keratinocyte cell lines. Comparative genomic hybridization, mRNA, and miRNA expression analysis of four HPV-containing keratinocyte cell lines at eight different time points was performed. Data was analyzed using unsupervised hierarchical clustering, integrated longitudinal expression analysis, and pathway enrichment analysis. Biological relevance of identified key regulatory genes was evaluated in vitro and dual-luciferase assays were used to confirm predicted miRNA-mRNA interactions. We show that the acquisition of anchorage independence of HPV-containing keratinocyte cell lines is particularly associated with copy number alterations. Approximately one third of differentially expressed mRNAs and miRNAs was directly attributable to copy number alterations. Focal adhesion, TGF-beta signaling, and mTOR signaling pathways were enriched among these genes. PITX2 was identified as key regulator of TGF-beta signaling and inhibited cell growth in vitro, most likely by inducing cell cycle arrest and apoptosis. Predicted miRNA-mRNA interactions miR-221-3p_BRWD3, miR-221-3p_FOS, and miR-138-5p_PLXNB2 were confirmed in vitro. Integrated longitudinal analysis of our HPV-induced carcinogenesis model pinpointed relevant interconnected molecular changes and crucial signaling pathways in HPV-mediated transformation.
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Affiliation(s)
- Iris Babion
- Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (I.B.); (V.M.); (A.J.); (A.H.)
| | - Viktorian Miok
- Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (I.B.); (V.M.); (A.J.); (A.H.)
- Epidemiology & Biostatistics, Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
- Department of Functional Sciences, Faculty of Medicine, Victor Babeş University of Medicine and Pharmacy of Timişoara, 300041 Timişoara, Romania
| | - Annelieke Jaspers
- Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (I.B.); (V.M.); (A.J.); (A.H.)
| | - Angelina Huseinovic
- Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (I.B.); (V.M.); (A.J.); (A.H.)
| | - Renske D. M. Steenbergen
- Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (I.B.); (V.M.); (A.J.); (A.H.)
| | - Wessel N. van Wieringen
- Epidemiology & Biostatistics, Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
- Department of Mathematics, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Saskia M. Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands;
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Abstract
Over the last years, epigenetic changes, including DNA methylation and histone modifications detected in early tumorigenesis and cancer progression, have been proposed as biomarkers for cancer detection, tumor prognosis, and prediction to treatment response. Importantly for the clinical use of DNA methylation biomarkers, specific methylation signatures can be detected in many body fluids including serum/plasma samples. Several of these potential epigenetic biomarkers detected in women's cancers, colorectal cancers, prostate, pancreatic, gastric, and lung cancers are discussed. Studies conducted in breast cancer, for example, found that aberrant methylation detection of several genes in serum DNA and genome-wide epigenetic change could be used for early breast cancer diagnosis and prediction of breast cancer risk. In colorectal cancers, numerous studies have been conducted to identify specific methylation markers important for CRC detection and in fact clinical assays evaluating the methylation status of SEPT19 gene and vimentin, became commercially available. Furthermore, some epigenetic changes detected in gastric washes have been suggested as potential circulating noninvasive biomarkers for the early detection of gastric cancers. For the early detection of prostate cancer, few epigenetic markers have shown a better sensitivity and specificity than serum PSA, indicating that the inclusion of these markers together with current screening tools, could improve early diagnosis and may reduce unnecessary repeat biopsies. Similarly, in pancreatic cancers, abnormal DNA methylation of several genes including NPTX2, have been suggested as a diagnostic biomarker. Epigenetic dysregulation was also observed in several tumor suppressor genes and miRNAs in lung cancer patients, suggesting the important role of these changes in cancer initiation and progression. In conclusion, epigenetic changes detected in biological fluids could play an essential role in the early detection of several cancer types and this may have a great impact for the cancer precision medicine field.
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Bosschieter J, Nieuwenhuijzen JA, Hentschel A, van Splunter AP, Segerink LI, Vis AN, Wilting SM, Lissenberg-Witte BI, A van Moorselaar RJ, Steenbergen RD. A two-gene methylation signature for the diagnosis of bladder cancer in urine. Epigenomics 2019; 11:337-347. [PMID: 30706728 DOI: 10.2217/epi-2018-0094] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
AIM To analyze the potential of 14 cancer-associated genes, including six miRNAs, for bladder cancer (BC) diagnosis in urine. PATIENTS & METHODS DNA methylation levels of 14 genes were analyzed in urine of 72 BC patients and 75 healthy controls using quantitative methylation-specific PCR. Multivariate logistic regression analysis was used to determine an optimal marker panel. RESULTS Ten genes were significantly hypermethylated in BC patients. The GHSR/MAL combination showed the best diagnostic performance, reaching a sensitivity of 92% (95% CI: 86-99) and a specificity of 85% (95% CI: 76-94). CONCLUSION We identified a novel two-gene panel with a high diagnostic accuracy for BC that can be applied in a noninvasive, urine-based test.
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Affiliation(s)
- Judith Bosschieter
- Amsterdam UMC, Vrije Universiteit Amsterdam, Urology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Jakko A Nieuwenhuijzen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Urology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Anouk Hentschel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Urology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Annina P van Splunter
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Loes I Segerink
- BIOS Lab on a Chip group, MESA+ & MIRA institutes, University of Twente, Enschede, The Netherlands
| | - André N Vis
- Amsterdam UMC, Vrije Universiteit Amsterdam, Urology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Saskia M Wilting
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Birgit I Lissenberg-Witte
- Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology & Biostatistics, Amsterdam Public Health, Amsterdam, The Netherlands
| | - R Jeroen A van Moorselaar
- Amsterdam UMC, Vrije Universiteit Amsterdam, Urology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Renske Dm Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
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Bearer EL, Mulligan BS. Epigenetic Changes Associated with Early Life Experiences: Saliva, A Biospecimen for DNA Methylation Signatures. Curr Genomics 2018; 19:676-698. [PMID: 30532647 PMCID: PMC6225450 DOI: 10.2174/1389202919666180307150508] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/21/2017] [Accepted: 03/04/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Adverse Childhood Experiences (ACEs), which include traumatic injury, are associated with poor health outcomes in later life, yet the biological mechanisms mediating this association are unknown. Neurocircuitry, immune system and hormone regulation differ from normal in adults reporting ACEs. These systems could be affected by epigenetic changes, including methylation of cytosine (5mC) in genomic DNA, activated by ACEs. Since 5mC levels influence gene expression and can be long-lasting, altered 5mC status at specific sites or throughout the genome is hypothesized to influence mental and physical outcomes after ACE(s). Human and animal studies support this, with animal models allowing experiments for attributing causality. Here we provide a lengthy introduction and background on 5mC and the impact of early life adversity. OBJECTIVE Next we address the issue of a mixture of cell types in saliva, the most accessible biospecimen for 5mC analysis. Typical human bio-specimens for 5mC analysis include saliva or buccal swabs, whole blood or types of blood cells, tumors and post-mortem brain. In children saliva is the most accessible biospecimen, but contains a mixture of keratinocytes and white blood cells, as do buccal swabs. Even in saliva from the same individual at different time points, cell composition may differ widely. Similar issues affect analysis in blood, where nucleated cells represent a wide array of white blood cell types. Unless variations in ratios of these cells between each sample are included in the analysis, results can be unreliable. METHODS Several different biochemical assays are available to test for site-specific methylation levels genome-wide, each producing different information, with high-density arrays being the easiest to use, and bisulfite whole genome sequencing the most comprehensive. We compare results from different assays and use high-throughput computational processing to deconvolve cell composition in saliva samples. RESULTS Here we present examples demonstrating the critical importance of determining the relative contribution of blood cells versus keratinocytes to the 5mC profile found in saliva. We further describe a strategy to perform a reference-based computational correction for cell composition, and therefore to identify differential methylation patterns due to experience, or for the diagnosis of phenotypes that correlate between traits, such as hormone levels, trauma status and various mental health outcomes. CONCLUSION Specific sites that respond to adversity with altered methylation levels in either blood cells, keratinocytes or both can be identified by this rigorous approach, which will then be useful as diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Elaine L. Bearer
- Address correspondence to this author at the Department of Pathology MSC 08-4640, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, USA; Tel: 505-272-2404; Fax: 505-272-8084; E-mails: ;
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Abstract
Epigenetics is the study of heritable mechanisms that can modify gene activity and phenotype without modifying the genetic code. The basis for the concept of epigenetics originated more than 2,000 yr ago as a theory to explain organismal development. However, the definition of epigenetics continues to evolve as we identify more of the components that make up the epigenome and dissect the complex manner by which they regulate and are regulated by cellular functions. A substantial and growing body of research shows that nutrition plays a significant role in regulating the epigenome. Here, we critically assess this diverse body of evidence elucidating the role of nutrition in modulating the epigenome and summarize the impact such changes have on molecular and physiological outcomes with regards to human health.
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Affiliation(s)
- Folami Y Ideraabdullah
- Departments of Genetics and Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina; and Departments of Nutrition and Pediatrics, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
| | - Steven H Zeisel
- Departments of Genetics and Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina; and Departments of Nutrition and Pediatrics, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
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13
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Verlaat W, Van Leeuwen RW, Novianti PW, Schuuring E, Meijer CJLM, Van Der Zee AGJ, Snijders PJF, Heideman DAM, Steenbergen RDM, Wisman GBA. Host-cell DNA methylation patterns during high-risk HPV-induced carcinogenesis reveal a heterogeneous nature of cervical pre-cancer. Epigenetics 2018; 13:769-778. [PMID: 30079796 PMCID: PMC6224221 DOI: 10.1080/15592294.2018.1507197] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cervical cancer development following a persistent infection with high-risk human papillomavirus (hrHPV) is driven by additional host-cell changes, such as altered DNA methylation. In previous studies, we have identified 12 methylated host genes associated with cervical cancer and pre-cancer (CIN2/3). This study systematically analyzed the onset and DNA methylation pattern of these genes during hrHPV-induced carcinogenesis using a longitudinal in vitro model of hrHPV-transformed cell lines (n = 14) and hrHPV-positive cervical scrapings (n = 113) covering various stages of cervical carcinogenesis. DNA methylation analysis was performed by quantitative methylation-specific PCR (qMSP) and relative qMSP values were used to analyze the data. The majority of genes displayed a comparable DNA methylation pattern in both cell lines and clinical specimens. DNA methylation onset occurred at early or late immortal passage, and DNA methylation levels gradually increased towards tumorigenic cells. Subsequently, we defined a so-called cancer-like methylation-high pattern based on the DNA methylation levels observed in cervical scrapings from women with cervical cancer. This cancer-like methylation-high pattern was observed in 72% (38/53) of CIN3 and 55% (11/20) of CIN2, whereas it was virtually absent in hrHPV-positive controls (1/26). In conclusion, hrHPV-induced carcinogenesis is characterized by early onset of DNA methylation, typically occurring at the pre-tumorigenic stage and with highest DNA methylation levels at the cancer stage. Host-cell DNA methylation patterns in cervical scrapings from women with CIN2 and CIN3 are heterogeneous, with a subset displaying a cancer-like methylation-high pattern, suggestive for a higher cancer risk.
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Affiliation(s)
- Wina Verlaat
- a Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology , Cancer Center Amsterdam , Amsterdam , The Netherlands
| | - Robert W Van Leeuwen
- b Department of Gynecologic Oncology , University of Groningen, University Medical Center Groningen, Cancer Research Center Groningen , Groningen , The Netherlands
| | - Putri W Novianti
- a Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology , Cancer Center Amsterdam , Amsterdam , The Netherlands
| | - Ed Schuuring
- c Department of Pathology , University of Groningen, University Medical Center Groningen, Cancer Research Center Groningen , Groningen , The Netherlands
| | - Chris J L M Meijer
- a Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology , Cancer Center Amsterdam , Amsterdam , The Netherlands
| | - Ate G J Van Der Zee
- b Department of Gynecologic Oncology , University of Groningen, University Medical Center Groningen, Cancer Research Center Groningen , Groningen , The Netherlands
| | - Peter J F Snijders
- a Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology , Cancer Center Amsterdam , Amsterdam , The Netherlands
| | - Daniëlle A M Heideman
- a Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology , Cancer Center Amsterdam , Amsterdam , The Netherlands
| | - Renske D M Steenbergen
- a Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology , Cancer Center Amsterdam , Amsterdam , The Netherlands
| | - G Bea A Wisman
- b Department of Gynecologic Oncology , University of Groningen, University Medical Center Groningen, Cancer Research Center Groningen , Groningen , The Netherlands
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14
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Bosschieter J, Bach S, Bijnsdorp IV, Segerink LI, Rurup WF, van Splunter AP, Bahce I, Novianti PW, Kazemier G, van Moorselaar RJA, Steenbergen RDM, Nieuwenhuijzen JA. A protocol for urine collection and storage prior to DNA methylation analysis. PLoS One 2018; 13:e0200906. [PMID: 30142219 PMCID: PMC6108475 DOI: 10.1371/journal.pone.0200906] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 07/04/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Urine poses an attractive non-invasive means for obtaining liquid biopsies for oncological diagnostics. Especially molecular analysis on urinary DNA is a rapid growing field. However, optimal and practical storage conditions that result in preservation of urinary DNA, and in particular hypermethylated DNA (hmDNA), are yet to be determined. AIM To determine the most optimal and practical conditions for urine storage that result in adequate preservation of DNA for hmDNA analysis. METHODS DNA yield for use in methylation analysis was determined by quantitative methylation specific PCR (qMSP) targeting the ACTB and RASSF1A genes on bisulfite modified DNA. First, DNA yield (ACTB qMSP) was determined in a pilot study on urine samples of healthy volunteers using two preservatives (Ethylenediaminetetraacetic acid (EDTA) and Urine Conditioning Buffer, Zymo Research) at four different temperatures (room temperature (RT), 4°C, -20°C, -80°C) for four time periods (1, 2, 7, 28 days). Next, hmDNA levels (RASSF1A qMSP) in stored urine samples of patients suffering from bladder cancer (n = 10) or non-small cell lung cancer (NSCLC; n = 10) were measured at day 0 and 7 upon storage with and without the addition of 40mM EDTA and/or 20 μl/ml Penicillin Streptomycin (PenStrep) at RT and 4°C. RESULTS In the pilot study, DNA for methylation analysis was only maintained at RT upon addition of preserving agents. In urine stored at 4°C for a period of 7 days or more, the addition of either preserving agent yielded a slightly better preservation of DNA. When urine was stored at -20 °C or -80 °C for up to 28 days, DNA was retained irrespective of the addition of preserving agents. In bladder cancer and NSCLC samples stored at RT loss of DNA was significantly less if EDTA was added compared to no preserving agents (p<0.001). Addition of PenStrep did not affect DNA preservation (p>0.99). Upon storage at 4°C, no difference in DNA preservation was found after the addition of preserving agents (p = 0.18). The preservation of methylated DNA (RASSF1A) was strongly correlated to that of unmethylated DNA (ACTB) in most cases, except when PCR values became inaccurate. CONCLUSIONS Addition of EDTA offers an inexpensive preserving agent for urine storage at RT up to seven days allowing for reliable hmDNA analysis. To avoid bacterial overgrowth PenStrep can be added without negatively affecting DNA preservation.
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Affiliation(s)
- J. Bosschieter
- Cancer Center Amsterdam, Department of Urology, VU University Medical Centre, Amsterdam, the Netherlands
- * E-mail:
| | - S. Bach
- Cancer Center Amsterdam, Department of Surgery, VU University Medical Centre, Amsterdam, the Netherlands
| | - I. V. Bijnsdorp
- Cancer Center Amsterdam, Department of Urology, VU University Medical Centre, Amsterdam, the Netherlands
| | - L. I. Segerink
- BIOS Lab on a Chip group, University of Twente, Enschede, the Netherlands
| | - W. F. Rurup
- BIOS Lab on a Chip group, University of Twente, Enschede, the Netherlands
| | - A. P. van Splunter
- Cancer Center Amsterdam, Department of Pathology and Molecular Biology, VU University Medical Centre, Amsterdam, the Netherlands
| | - I. Bahce
- Cancer Center Amsterdam, Department of Pulmonology, VU University Medical Centre, Amsterdam, the Netherlands
| | - P. W. Novianti
- Cancer Center Amsterdam, Department of Pathology and Molecular Biology, VU University Medical Centre, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Department of Epidemiology and Biostatistics, VU University Medical Centre, Amsterdam, the Netherlands
| | - G. Kazemier
- Cancer Center Amsterdam, Department of Surgery, VU University Medical Centre, Amsterdam, the Netherlands
| | - R. J. A. van Moorselaar
- Cancer Center Amsterdam, Department of Urology, VU University Medical Centre, Amsterdam, the Netherlands
| | - R. D. M. Steenbergen
- Cancer Center Amsterdam, Department of Pathology and Molecular Biology, VU University Medical Centre, Amsterdam, the Netherlands
| | - J. A. Nieuwenhuijzen
- Cancer Center Amsterdam, Department of Urology, VU University Medical Centre, Amsterdam, the Netherlands
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15
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Di Domenico M, Giovane G, Kouidhi S, Iorio R, Romano M, De Francesco F, Feola A, Siciliano C, Califano L, Giordano A. HPV epigenetic mechanisms related to Oropharyngeal and Cervix cancers. Cancer Biol Ther 2018; 19:850-857. [PMID: 28362190 DOI: 10.1080/15384047.2017.1310349] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Human Papilloma Virus infection is very frequent in humans and is mainly transmitted sexually. The majority of infections are transient and asymptomatic, however, if the infection persists, it can occur with a variety of injuries to skin and mucous membranes, depending on the type of HPV involved. Some types of HPV are classified as high oncogenic risk as associated with the onset of cancer. The tumors most commonly associated with HPV are cervical and oropharyngeal cancer, epigenetic mechanisms related to HPV infection include methylation changes to host and viral DNA and chromatin modification in host species. This review is focused about epigenethic mechanism, such as MiRNAs expression, related to cervix and oral cancer. Specifically it discuss about molecular markers associated to a more aggressive phenotype. In this way we will analyze genes involved in meiotic sinaptonemal complex, transcriptional factors, of orthokeratins, sinaptogirin, they are all expressed in cancer in a way not more dependent on cell differentiation but HPV-dependent.
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Affiliation(s)
- Marina Di Domenico
- a Department of Biochemistry , Biophysics and General Pathology, University of Campania "Luigi Vanvitelli" , Italy.,b IRCCS Institute of Women's Health Malzoni Clinic , Avellino , Italy.,c Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University , Philadelphia , PA , USA
| | - Giancarlo Giovane
- d Department of Experimental Medicine , Section of Hygiene, Occupational Medicine and Forensic Medicine, University of Campania "Luigi Vanvitelli" , Italy
| | - Soumaya Kouidhi
- e Laboratory BVBGR, LR11ES31, ISBST, Higher Institute of Biotechnology of Sidi Thabet, University of Manouba , Tunis , Tunisia.,f Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University Tunis El Manar , Tunis
| | - Rosamaria Iorio
- a Department of Biochemistry , Biophysics and General Pathology, University of Campania "Luigi Vanvitelli" , Italy
| | - Maurizio Romano
- g Hepatobiliary and Liver Transplantation Unit, Azienda Ospedaliera , Padova , Italy.,h Department of Surgical , Gastrointestinal and Oncological Sciences (DiSCOG), University of Padova , Padova ( PD ), Italy
| | - Francesco De Francesco
- h Department of Surgical , Gastrointestinal and Oncological Sciences (DiSCOG), University of Padova , Padova ( PD ), Italy
| | - Antonia Feola
- a Department of Biochemistry , Biophysics and General Pathology, University of Campania "Luigi Vanvitelli" , Italy
| | - Camilla Siciliano
- a Department of Biochemistry , Biophysics and General Pathology, University of Campania "Luigi Vanvitelli" , Italy
| | - Luigi Califano
- i Department of Maxillofacial Surgery , University of Naples "Federico II" , Naples , Italy
| | - Antonio Giordano
- c Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University , Philadelphia , PA , USA.,j Department of Medicine , Surgery and Neuroscience, University of Siena , Siena , Italy
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Fu Y, Li J, Tang Q, Zou C, Shen L, Jin L, Li C, Fang C, Liu R, Li M, Zhao S, Li C. Integrated analysis of methylome, transcriptome and miRNAome of three pig breeds. Epigenomics 2018; 10:597-612. [PMID: 29692202 DOI: 10.2217/epi-2017-0087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AIM Integrated analysis of methylome and transcriptome may help understand the molecular basis of the different breeds with different traits of commercial interest. MATERIALS & METHODS We obtained the first genome-wide methylome with single-base resolution, miRNAome and transcriptome from three swine breeds. RESULTS We displayed the landscape of the three omics in the whole-genome level. Integrated outcomes of methylome with genetic selection, miRNAome and transcriptome are also provided. Finally, we identified 11 candidate differentially methylated genes associated with phenotype variance in pigs. CONCLUSION DNA methylation not only suppresses transcriptome but also miRNAome. The different -omics data have complicated interaction in directly or indirectly and exhibited close relations with the distinct phenotypic traits of growth, disease resistance and energy metabolism.
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Affiliation(s)
- Yuhua Fu
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Jingxuan Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Qianzi Tang
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Cheng Zou
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Linyuan Shen
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Long Jin
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Cencen Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Chengchi Fang
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Rui Liu
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Mingzhou Li
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Shuhong Zhao
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
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17
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Sannigrahi MK, Sharma R, Singh V, Panda NK, Rattan V, Khullar M. DNA methylation regulated microRNAs in HPV-16-induced head and neck squamous cell carcinoma (HNSCC). Mol Cell Biochem 2018; 448:321-33. [PMID: 29455435 DOI: 10.1007/s11010-018-3336-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/15/2018] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Epigenetic modifications have been reported to play an important role in regulating gene expression and these modifications become critical when they have a role in controlling another important layer of epigenetic regulation namely microRNAs. In the present study, we have identified the microRNAs that may be regulated by promoter DNA methylation and histone acetylation in Human papilloma virus-positive head and neck squamous cell carcinoma. METHODOLOGY HPV-negative cell line (UPCI:SCC-116) and HPV-16 +ve cell line (UPCI:SCC-090) were treated with methylation inhibitor (5-aza-2'-deoxycytidine, AZA) and acetylation inhibitor (Trichostatin-A, TSA), followed by micro-array analysis. The differentially expressed miRNAs were validated in control (n = 10), HPV-16 +ve (n = 30), and HPV -ve (n = 30) HNC, TCGA (n = 529) tissue samples, and two HPV -ve (SCC116 and Hacat) and two HPV +ve (SCC090 and SiHa) cell lines. Methylation-specific PCR (MSP) and chromatin immunoprecipitation assay (CHIP) were performed to validate their regulation. In silico and in vitro analyses of identified miRNAs were done to study putative pathways they target and their possible role in carcinogenesis. RESULTS Among 10 miRNAs specifically up-regulated in microarray analysis of AZA-treated SCC090 cells, we observed significantly decreased expression of hsa-miR-181c-5p, hsa-miR-132-5p, hsa-miR-658 in HPV +ve HNC cohort, TCGA tissue samples, and cell lines as compared to their HPV -ve counterpart, and their promoter region also possesses CpG islands. MSP and analysis of TCGA data (MethHC) revealed increased frequency of methylation at the promoter of hsa-miR-132-5p that is negatively correlated with its expression. In TSA-treated SCC090 cells, out of 7 miRNAs, two namely Hsa-miR-129-2-3p and Hsa-miR-449a were found to be up-regulated as compared to HPV -ve cells. However, the levels of enrichment by anti-acetyl-H3 and anti-acetyl-H4 were significantly low in cell lines compared to respective controls and both were up-regulated in HPV +ve compared to HPV -ve TCGA tissue samples. In silico analysis revealed hsa-miR-132-5p targeted canonical β-catenin/wnt pathway and modulation of down-stream genes of the pathway was observed on over-expression/inhibition of hsa-miR-132-5p. CONCLUSION This study suggests the role of epigenetic modifications in regulating expression of miRNAs in HPV +ve HNSCC.
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18
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Tao P, Wen H, Yang B, Zhang A, Wu X, Li Q. miR-144 inhibits growth and metastasis of cervical cancer cells by targeting VEGFA and VEGFC. Exp Ther Med 2017; 15:562-568. [PMID: 29387205 DOI: 10.3892/etm.2017.5392] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 07/11/2017] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRs) are aberrantly expressed in various cancer types and have critical roles in their genesis and progression. miR-144 has been identified to be involved in the development of hepatocellular carcinoma and rectal cancer. However, the roles of miR-144 in cervical cancer and the underlying molecular mechanisms have remained elusive. The present study identified that miR-144 was significantly decreased in cervical cancer tissues compared with that in matched normal cervical tissues as well as in metastatic vs. non-metastatic cervical cancer tissues. miR-144 downregulation was significantly associated with the International Federation of Gynecology and Obstetrics stage and lymph node metastasis. In a gain-of function study, miR-144 mimics were transfected into the Hela and C33A cervical cancer cell lines, which led to suppression of cell growth. In addition, overexpression of miR-144 inhibited the migration and invasion of Hela and C33A cells. Furthermore, a bioinformatics analysis identified vascular endothelial growth factor A (VEGFA) VEGFC as two novel target genes of miR-144. Of note, a dual luciferase reporter assay, reverse-transcription quantitative polymerase chain reaction analysis and western blot analysis demonstrated that miR-144 repressed the expression of VEGFA and VEGFC by directly targeting to their 3'-untranslated region. Taken together, the results suggested that miR-144 acts as a tumor suppressor in the proliferation and metastasis of cervical cancer cells by directly targeting VEGFA and VEGFC, suggesting that miR-144 may be a novel promising diagnostic and therapeutic biomarker for cervical cancer.
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Affiliation(s)
- Pingping Tao
- Department of Obstetrics and Gynecology, People's Hospital of Shanghai Pudong New Area, Shanghai 201299, P.R. China
| | - Hao Wen
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Binlie Yang
- Department of Obstetrics and Gynecology, People's Hospital of Shanghai Pudong New Area, Shanghai 201299, P.R. China
| | - Ai Zhang
- Department of Obstetrics and Gynecology, People's Hospital of Shanghai Pudong New Area, Shanghai 201299, P.R. China
| | - Xiaohua Wu
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Qing Li
- Department of Pathology, People's Hospital of Shanghai Pudong New Area, Shanghai 201299, P.R. China
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19
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Kakavandi E, Shahbahrami R, Goudarzi H, Eslami G, Faghihloo E. Anoikis resistance and oncoviruses. J Cell Biochem 2017; 119:2484-2491. [DOI: 10.1002/jcb.26363] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/15/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Ehsan Kakavandi
- Department of VirologySchool of Public HealthTehran University of Medical SciencesTehranIran
- Students’ Scientific Research CenterTehran University of Medical SciencesTehranIran
| | - Ramin Shahbahrami
- Department of VirologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | - Hossein Goudarzi
- Department of MicrobiologySchool of MedicineShahid Beheshti University of Medical SciencesTehranIran
| | - Gita Eslami
- Department of MicrobiologySchool of MedicineShahid Beheshti University of Medical SciencesTehranIran
| | - Ebrahim Faghihloo
- Department of MicrobiologySchool of MedicineShahid Beheshti University of Medical SciencesTehranIran
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