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Patel KB, Padhya TA, Huang J, Hernandez-Prera JC, Li T, Chung CH, Wang L, Wang X. Plasma cell-free DNA methylome profiling in pre- and post-surgery oral cavity squamous cell carcinoma. Mol Carcinog 2023; 62:493-502. [PMID: 36636912 PMCID: PMC10023468 DOI: 10.1002/mc.23501] [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: 09/28/2022] [Revised: 11/29/2022] [Accepted: 12/30/2022] [Indexed: 01/14/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC), a highly heterogeneous disease that involves multiple anatomic sites, is a leading cause of cancer-related mortality worldwide. Although the utility of noninvasive biomarkers based on circulating cell-free DNA (cfDNA) methylation profiling has been widely recognized, limited studies have been reported so far regarding the dynamics of cfDNA methylome in oral cavity squamous cell carcinoma (OCSCC). It is hypothesized in this study that comparison of methylation profiles in pre- and postsurgery plasma samples will reveal OCSCC-specific prognostic and diagnostic biomarkers. As a strategy to further prioritize tumor-specific targets, top differential methylated regions (DMRs) were called by reanalyzing methylation data from paired tumor and normal tissue collected in the the cancer genome atlas head-neck squamous cell carcinoma (TCGA) head and neck cancer cohort. Matched plasma samples from eight patients with OCSCC were collected at Moffitt Cancer Center before and after surgical resection. Plasma-derived cfDNA was analyzed by cfMBD-seq, which is a high-sensitive methylation profiling assay. Differential methylation analysis was then performed based on the matched samples profiled. In the top 200 HNSCC-specific DMRs detected based on the TCGA data set, a total of 23 regions reached significance in the plasma-based DMR test. The top five validated DMR regions (ranked by the significance in the plasma study) are located in the promoter regions of genes PENK, NXPH1, ZIK1, TBXT, and CDO1, respectively. The genome-wide cfDNA DMR analysis further highlighted candidate biomarkers located in genes SFRP4, SOX1, IRF4, and PCDH17. The prognostic relevance of candidate genes was confirmed by survival analysis using the TCGA data. This study supports the utility of cfDNA-based methylome profiling as a promising noninvasive biomarker source for OCSCC and HNSCC.
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Affiliation(s)
- Krupal B Patel
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Tapan A Padhya
- Otolaryngology - Head and Neck Surgery, University of South Florida Morsani College of Medicine, Tampa, USA
| | - Jinyong Huang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Juan C Hernandez-Prera
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Tingyi Li
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Moffitt Cancer Center Immuno-Oncology Program, Tampa, FL 33612, USA
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Macedo-Silva C, Constâncio V, Miranda-Gonçalves V, Leite-Silva P, Salta S, Lobo J, Guimarães R, Carvalho-Maia C, Gigliano D, Farinha M, Sousa O, Henrique R, Jerónimo C. DNA methylation biomarkers accurately detect esophageal cancer prior and post neoadjuvant chemoradiation. Cancer Med 2023; 12:8777-8788. [PMID: 36670548 PMCID: PMC10134363 DOI: 10.1002/cam4.5623] [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: 09/20/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Esophageal cancer (ECa) is associated with high mortality, mostly due to late diagnosis, precluding curativeintent surgery. Hence, neoadjuvant chemoradiation (ChRT) is recommended in most patients regardless of histological subtype. A proportion of these patients, however, achieve complete disease remission and might be spared of radical surgery. The lack of reliable, minimally invasive biomarkers able to detect post-ChRT disease persistence is, nonetheless, a major drawback. We have previously shown that miRNA promotor methylation enables accurate cancer detection in tissues and liquid biopsies but has been seldom explored in ECa patients. AIMS Herein, we sought to unveil and validate novel candidate biomarkers able to detect ECa prior and post ChRT. MATERIALS AND METHODS Promoter methylation of miR129-2, miR124-3 and ZNF569 was assessed, using quantitative methylation-specific PCR (qMSP), in tissue samples from normal esophagus, treatment-naïve and post-ChRT ECa, as well as in liquid biopsies from ECa patients. RESULTS All genes disclosed significantly different promoter methylation levels between ECa and normal esophagus, accurately detecting post-ChRT disease, especially for adenocarcinoma. Remarkably, miR129-2me /ZNF569me methylation panel identified ECa in liquid samples with 53% sensitivity and 87% specificity. DISCUSSION MiR129-2me , miR124-3me and ZNF569me accurately discriminate ECa, either pre- or post-ChRT, from normal tissue, enabling ECa detection. Furthermore, circulalting methylation-based biomarkers are promising minimally invasive tools to detect post-ChRT residual ECa. CONCLUSION Overall, our results encourage the use of miRNA methylation biomarkers as accurate ECa detection tools as a novel approach for ChRT response monitoring.
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Affiliation(s)
- Catarina Macedo-Silva
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Vera Constâncio
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Vera Miranda-Gonçalves
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Pedro Leite-Silva
- Cancer Epidemiology Group, Research Center & Department of Epidemiology of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Sofia Salta
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - João Lobo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rita Guimarães
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Carina Carvalho-Maia
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Davide Gigliano
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Mónica Farinha
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Olga Sousa
- Department of Radiation Oncology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
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Han YK, Park HY, Park SG, Hwang JJ, Park HR, Yi JM. Promoter Methylation of Cancer Stem Cell Surface Markers as an Epigenetic Biomarker for Prognosis of Oral Squamous Cell Carcinoma. Int J Mol Sci 2022; 23:ijms232314624. [PMID: 36498950 PMCID: PMC9737199 DOI: 10.3390/ijms232314624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Growing evidence suggests that genetic and epigenetic factors, including environmental factors, contribute to the development of oral squamous cell carcinoma (OSCC). Here, we investigated the transcriptional silencing of the CD24, CD44, CD133, and CD147 genes, which are well-known cancer stem cell surface markers in various cancer types, including OSCC. We first examined the correlation between the transcriptional expression level and reactivation by 5-aza-2′-deoxycytidine (5-aza-dC) and the promoter methylation levels of the four genes in several OSCC cell lines. We observed promoter hypermethylation for the CD24, CD133, and CD147 genes at 70%, 75%, and 70%, respectively, in OSCC cell lines compared to normal oral mucosa tissues (<53%), indicating that this methylation pattern is cancer-specific, which was confirmed by bisulfite sequencing analysis. More specifically, the expression and methylation profiles of CD133 and CD147 extracted from The Cancer Genome Atlas (TCGA) database were negatively correlated, supporting their epigenetic regulation in primary OSCC tumors. The methylation status of CD133 and CD147 was associated with poor survival in patients with OSCC using the TCGA database. Our findings provide additional insight into the abnormal DNA methylation of CD133 and that CD147 could be used for the diagnosis and therapeutic treatment of patients with OSCC.
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Affiliation(s)
- Yu Kyeong Han
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Republic of Korea
| | - Ha Young Park
- Department of Pathology, College of Medicine, Inje University, Busan 47392, Republic of Korea
| | - Sae-Gwang Park
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Republic of Korea
| | - Jae Joon Hwang
- Department of Oral and Maxillofacial Radiology, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
- Dental and Life Science Institute & Dental Research Institute, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
| | - Hae Ryoun Park
- Department of Oral Pathology, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
| | - Joo Mi Yi
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Republic of Korea
- Correspondence: ; Tel.: +82-51-890-6734
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Şeref C, Acar Ö, Kılıç M, Vural M, Sağlıcan Y, Saraç H, Coşkun B, İnce Ü, Esen T, Lack NA. Histologically benign PI-RADS 4 and 5 lesions contain cancer-associated epigenetic alterations. Prostate 2022; 82:145-153. [PMID: 34672371 DOI: 10.1002/pros.24255] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/31/2021] [Accepted: 09/29/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND The detection rate of clinically significant prostate cancer has improved with the use of multiparametric magnetic resonance imaging (mpMRI). Yet, even with MRI-guided biopsy 15%-35% of high-risk lesions (Prostate Imaging-Reporting and Data System [PI-RADS] 4 and 5) are histologically benign. It is unclear if these false positives are due to diagnostic/sampling errors or pathophysiological alterations. To better understand this, we tested histologically benign PI-RAD 4 and 5 lesions for common malignant epigenetic alterations. MATERIALS AND METHODS MRI-guided in-bore biopsy samples were collected from 45 patients with PI-RADS 4 (n = 31) or 5 (n = 14) lesions. Patients had a median clinical follow-up of 3.8 years. High-risk mpMRI patients were grouped based on their histology into biopsy positive for tumor (BPT; n = 28) or biopsy negative for tumor (BNT; n = 17). From these biopsy samples, DNA methylation of well-known tumor suppressor genes (APC, GSTP1, and RARβ2) was quantified. RESULTS Similar to previous work we observed high rates of promoter methylation at GSTP1 (92.7%), RARβ2 (57.3%), and APC (37.8%) in malignant BPT samples but no methylation in benign TURP chips. Interestingly, similar to the malignant samples the BNT biopsies also had increased methylation at the promoter of GSTP1 (78.8%) and RARβ2 (34.6%). However, despite these epigenetic alterations none of these BNT patients developed prostate cancer, and those who underwent repeat mpMRI (n = 8) demonstrated either radiological regression or stability. CONCLUSIONS Histologically benign PI-RADS 4 and 5 lesions harbor prostate cancer-associated epigenetic alterations.
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Affiliation(s)
- Ceren Şeref
- Department of Health Sciences, Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Ömer Acar
- Department of Urology, Koc University School of Medicine, Istanbul, Turkey
| | - Mert Kılıç
- Department of Urology, VKF American Hospital, Istanbul, Turkey
| | - Metin Vural
- Department of Radiology, VKF American Hospital, Istanbul, Turkey
| | - Yeşim Sağlıcan
- Department of Pathology, Acıbadem University School of Medicine, Istanbul, Turkey
| | - Hilal Saraç
- Department of Health Sciences, Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Bilgen Coşkun
- Department of Radiology, VKF American Hospital, Istanbul, Turkey
| | - Ümit İnce
- Department of Pathology, Acıbadem University School of Medicine, Istanbul, Turkey
| | - Tarık Esen
- Department of Urology, Koc University School of Medicine, Istanbul, Turkey
- Department of Urology, VKF American Hospital, Istanbul, Turkey
| | - Nathan A Lack
- Department of Health Sciences, Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
- Department of Medical Pharmacology, Koç University School of Medicine, Istanbul, Turkey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
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5
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Ghantous Y, Nashef A, Abu-Elnaaj I. Epigenetic Alterations Associated with the Overall Survival and Recurrence Free Survival among Oral Squamous Cell Carcinoma Patients. J Clin Med 2020; 9:E1035. [PMID: 32272578 PMCID: PMC7231254 DOI: 10.3390/jcm9041035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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] [Received: 03/01/2020] [Revised: 03/25/2020] [Accepted: 04/03/2020] [Indexed: 12/11/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a fatal disease caused by complex interactions between environmental, genomic, and epigenetic alterations. In the current study, we aimed to identify clusters of genes whose promoter methylation status correlated with various tested clinical features. Molecular datasets of genetic and methylation analysis based on whole-genome sequencing of 159 OSCC patients were obtained from the The Cancer Genome Atlas (TCGA) data portal. Genes were clustered based on their methylation status and were tested for their association with demographic, pathological, and clinical features of the patients. Overall, seven clusters of genes were revealed that showed a significant association with the overall survival/recurrence free survival of patients. The top ranked genes within cluster 4, which showed the worst prognosis, primarily acted as paraneoplastic genes, while the genes within cluster 6 primarily acted as anti-tumor genes. A significant difference was found regarding the mean age in the different clusters. No significant correlation was found between the tumor staging and the different clusters. In conclusion, our result provided a proof-of-principle for the existence of phenotypic diversity among the epigenetic clusters of OSCC and demonstrated the utility of the use epigenetics alterations in devolving new prognostic and therapeutics tools for OSCC patients.
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Affiliation(s)
- Yasmen Ghantous
- Department of Oral and Maxillofacial Surgery, Baruch Padeh medical center Poriya, The lower Galilee 15208, Israel;
| | - Aysar Nashef
- Department of Oral and Maxillofacial Surgery, Baruch Padeh medical center Poriya, The lower Galilee 15208, Israel;
| | - Imad Abu-Elnaaj
- Department of Oral and Maxillofacial Surgery, Baruch Padeh medical center Poriya, The lower Galilee 15208, Israel;
- The Azrieli Faculty of Medicine, Bar Illan University, Safed 1311502, Israel;
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Bhat S, Kabekkodu SP, Varghese VK, Chakrabarty S, Mallya SP, Rotti H, Pandey D, Kushtagi P, Satyamoorthy K. Aberrant gene-specific DNA methylation signature analysis in cervical cancer. Tumour Biol 2017; 39:1010428317694573. [PMID: 28351298 DOI: 10.1177/1010428317694573] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024] Open
Abstract
Multicomponent molecular modifications such as DNA methylation may offer sensitive and specific cervical intraepithelial neoplasia and cervical cancer biomarkers. In this study, we tested cervical tissues at various stages of tumor progression for 5-methylcytosine and 5-hydroxymethylcytosine levels and also DNA promoter methylation profile of a panel of genes for its diagnostic potential. In total, 5-methylcytosine, 5-hydroxymethylcytosine, and promoter methylation of 33 genes were evaluated by reversed-phase high-performance liquid chromatography, enzyme-linked immunosorbent assay based technique, and bisulfate-based next generation sequencing. The 5-methylcytosine and 5-hydroxymethylcytosine contents were significantly reduced in squamous cell carcinoma and receiver operating characteristic curve analysis showed a significant difference in (1) 5-methylcytosine between normal and squamous cell carcinoma tissues (area under the curve = 0.946) and (2) 5-hydroxymethylcytosine levels among normal, squamous intraepithelial lesions and squamous cell carcinoma. Analyses of our next generation sequencing results and data from five independent published studies consisting of 191 normal, 10 low-grade squamous intraepithelial lesions, 21 high-grade squamous intraepithelial lesions, and 335 malignant tissues identified a panel of nine genes ( ARHGAP6, DAPK1, HAND2, NKX2-2, NNAT, PCDH10, PROX1, PITX2, and RAB6C) which could effectively discriminate among the various groups with sensitivity and specificity of 80%-100% (p < 0.05). Furthermore, 12 gene promoters (ARHGAP6, HAND2, LHX9, HEY2, NKX2-2, PCDH10, PITX2, PROX1, TBX3, IKBKG, RAB6C, and DAPK1) were also methylated in one or more of the cervical cancer cell lines tested. The global and gene-specific methylation of the panel of genes identified in our study may serve as useful biomarkers for the early detection and clinical management of cervical cancer.
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Affiliation(s)
- Samatha Bhat
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Shama Prasada Kabekkodu
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Vinay Koshy Varghese
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Sanjiban Chakrabarty
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Sandeep P Mallya
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Harish Rotti
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Deeksha Pandey
- 2 Department of Obstetrics & Gynaecology, Kasturba Medical College, Manipal University, Manipal, India
| | - Pralhad Kushtagi
- 3 Department of Obstetrics & Gynaecology, Kasturba Medical College, Manipal University, Mangalore, India
| | - Kapaettu Satyamoorthy
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
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Huisman C, van der Wijst MGP, Falahi F, Overkamp J, Karsten G, Terpstra MM, Kok K, van der Zee AGJ, Schuuring E, Wisman GBA, Rots MG. Prolonged re-expression of the hypermethylated gene EPB41L3 using artificial transcription factors and epigenetic drugs. Epigenetics 2015; 10:384-96. [PMID: 25830725 DOI: 10.1080/15592294.2015.1034415] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Epigenetic silencing of tumor suppressor genes (TSGs) is considered a significant event in the progression of cancer. For example, EPB41L3, a potential biomarker in cervical cancer, is often silenced by cancer-specific promoter methylation. Artificial transcription factors (ATFs) are unique tools to re-express such silenced TSGs to functional levels; however, the induced effects are considered transient. Here, we aimed to improve the efficiency and sustainability of gene re-expression using engineered zinc fingers fused to VP64 (ZF-ATFs) or DNA methylation modifiers (ZF-Tet2 or ZF-TDG) and/or by co-treatment with epigenetic drugs [5-aza-2'-deoxycytidine or Trichostatin A (TSA)]. The EPB41L3-ZF effectively bound its methylated endogenous locus, as also confirmed by ChIP-seq. ZF-ATFs reactivated the epigenetically silenced target gene EPB41L3 (∼ 10-fold) in breast, ovarian, and cervical cancer cell lines. Prolonged high levels of EPB41L3 (∼ 150-fold) induction could be achieved by short-term co-treatment with epigenetic drugs. Interestingly, for otherwise ineffective ZF-Tet2 or ZF-TDG treatments, TSA facilitated re-expression of EPB41L3 up to twofold. ATF-mediated re-expression demonstrated a tumor suppressive role for EPB41L3 in cervical cancer cell lines. In conclusion, epigenetic reprogramming provides a novel way to improve sustainability of re-expression of epigenetically silenced promoters.
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