1
|
Yuan T, Wankhede D, Edelmann D, Kather JN, Tagscherer KE, Roth W, Bewerunge-Hudler M, Brobeil A, Kloor M, Bläker H, Brenner H, Hoffmeister M. Large-scale external validation and meta-analysis of gene methylation biomarkers in tumor tissue for colorectal cancer prognosis. EBioMedicine 2024; 105:105223. [PMID: 38917511 PMCID: PMC11255517 DOI: 10.1016/j.ebiom.2024.105223] [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: 02/15/2024] [Revised: 04/29/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND DNA methylation biomarkers in colorectal cancer (CRC) tissue hold potential as prognostic indicators. However, individual studies have yielded heterogeneous results, and external validation is largely absent. We conducted a comprehensive external validation and meta-analysis of previously suggested gene methylation biomarkers for CRC prognosis. METHODS We performed a systematic search to identify relevant studies investigating gene methylation biomarkers for CRC prognosis until March 2024. Our external validation cohort with long-term follow-up included 2303 patients with CRC from 22 hospitals in southwest Germany. We used Cox regression analyses to assess associations between previously suggested gene methylation biomarkers and prognosis, adjusting for clinical variables. We calculated pooled hazard ratios (HRs) and their 95% confidence intervals (CIs) using random-effects models. FINDINGS Of 151 single gene and 29 multiple gene methylation biomarkers identified from 121 studies, 37 single gene and seven multiple gene biomarkers were significantly associated with CRC prognosis after adjustment for clinical variables. Moreover, the directions of these associations with prognosis remained consistent between the original studies and our validation analyses. Seven single biomarkers and two multi-biomarker signatures were significantly associated with CRC prognosis in the meta-analysis, with a relatively strong level of evidence for CDKN2A, WNT5A, MLH1, and EVL. INTERPRETATION In a comprehensive evaluation of the so far identified gene methylation biomarkers for CRC prognosis, we identified candidates with potential clinical relevance for further investigation. FUNDING The German Research Council, the Interdisciplinary Research Program of the National Center for Tumor Diseases (NCT), Germany, the German Federal Ministry of Education and Research.
Collapse
Affiliation(s)
- Tanwei Yuan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Durgesh Wankhede
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany
| | | | - Wilfried Roth
- Institute of Pathology, University Medical Center Mainz, Mainz, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Alexander Brobeil
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthias Kloor
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hendrik Bläker
- Institute of Pathology, University of Leipzig Medical Center, Leipzig, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
2
|
Takasawa K, Asada K, Kaneko S, Shiraishi K, Machino H, Takahashi S, Shinkai N, Kouno N, Kobayashi K, Komatsu M, Mizuno T, Okubo Y, Mukai M, Yoshida T, Yoshida Y, Horinouchi H, Watanabe SI, Ohe Y, Yatabe Y, Kohno T, Hamamoto R. Advances in cancer DNA methylation analysis with methPLIER: use of non-negative matrix factorization and knowledge-based constraints to enhance biological interpretability. Exp Mol Med 2024; 56:646-655. [PMID: 38433247 PMCID: PMC10985003 DOI: 10.1038/s12276-024-01173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 03/05/2024] Open
Abstract
DNA methylation is an epigenetic modification that results in dynamic changes during ontogenesis and cell differentiation. DNA methylation patterns regulate gene expression and have been widely researched. While tools for DNA methylation analysis have been developed, most of them have focused on intergroup comparative analysis within a dataset; therefore, it is difficult to conduct cross-dataset studies, such as rare disease studies or cross-institutional studies. This study describes a novel method for DNA methylation analysis, namely, methPLIER, which enables interdataset comparative analyses. methPLIER combines Pathway Level Information Extractor (PLIER), which is a non-negative matrix factorization (NMF) method, with regularization by a knowledge matrix and transfer learning. methPLIER can be used to perform intersample and interdataset comparative analysis based on latent feature matrices, which are obtained via matrix factorization of large-scale data, and factor-loading matrices, which are obtained through matrix factorization of the data to be analyzed. We used methPLIER to analyze a lung cancer dataset and confirmed that the data decomposition reflected sample characteristics for recurrence-free survival. Moreover, methPLIER can analyze data obtained via different preprocessing methods, thereby reducing distributional bias among datasets due to preprocessing. Furthermore, methPLIER can be employed for comparative analyses of methylation data obtained from different platforms, thereby reducing bias in data distribution due to platform differences. methPLIER is expected to facilitate cross-sectional DNA methylation data analysis and enhance DNA methylation data resources.
Collapse
Affiliation(s)
- Ken Takasawa
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan.
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan.
| | - Ken Asada
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Syuzo Kaneko
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Hidenori Machino
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Satoshi Takahashi
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Norio Shinkai
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Nobuji Kouno
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Kazuma Kobayashi
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Masaaki Komatsu
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Takaaki Mizuno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Yu Okubo
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Masami Mukai
- Division of Medical Informatics, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Tatsuya Yoshida
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Yukihiro Yoshida
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Hidehito Horinouchi
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Yuichiro Ohe
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, 104-0045, Japan.
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan.
| |
Collapse
|
3
|
Brisset M, Mehlen P, Meurette O, Hollande F. Notch receptor/ligand diversity: contribution to colorectal cancer stem cell heterogeneity. Front Cell Dev Biol 2023; 11:1231416. [PMID: 37860822 PMCID: PMC10582728 DOI: 10.3389/fcell.2023.1231416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Cancer cell heterogeneity is a key contributor to therapeutic failure and post-treatment recurrence. Targeting cell subpopulations responsible for chemoresistance and recurrence seems to be an attractive approach to improve treatment outcome in cancer patients. However, this remains challenging due to the complexity and incomplete characterization of tumor cell subpopulations. The heterogeneity of cells exhibiting stemness-related features, such as self-renewal and chemoresistance, fuels this complexity. Notch signaling is a known regulator of cancer stem cell (CSC) features in colorectal cancer (CRC), though the effects of its heterogenous signaling on CRC cell stemness are only just emerging. In this review, we discuss how Notch ligand-receptor specificity contributes to regulating stemness, self-renewal, chemoresistance and cancer stem cells heterogeneity in CRC.
Collapse
Affiliation(s)
- Morgan Brisset
- Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Melbourne, VIC, Australia
- Centre for Cancer Research, The University of Melbourne, Melbourne, VIC, Australia
- Cancer Cell Death Laboratory, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Patrick Mehlen
- Cancer Cell Death Laboratory, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Olivier Meurette
- Cancer Cell Death Laboratory, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Frédéric Hollande
- Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, Melbourne, VIC, Australia
- Centre for Cancer Research, The University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
4
|
Yu Y, Xue W, Liu Z, Chen S, Wang J, Peng Q, Xu L, Liu X, Cui C, Fan JB. A novel DNA methylation marker to identify lymph node metastasis of colorectal cancer. Front Oncol 2022; 12:1000823. [PMID: 36313642 PMCID: PMC9614158 DOI: 10.3389/fonc.2022.1000823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Lymph node metastasis (LNM) of colorectal cancer (CRC) is an important factor for both prognosis and treatment. Given the deficiencies of conventional tests, we aim to discover novel DNA methylation markers to efficiently identify LNM status of CRC. In this study, genome-wide methylation sequencing was performed in a cohort (n=30) using fresh CRC tissue to discover differentially methylated markers. These markers were subsequently validated with fluorescence quantitative PCR in a cohort (n=221), and the optimal marker was compared to conventional diagnostic methods. Meanwhile, immunohistochemistry was used to verify the effectiveness of the antibody corresponding to this marker in a cohort (n=56). LBX2 achieved an AUC of 0.87, specificity of 87.3%, sensitivity of 75.7%, and accuracy of 81.9%, which outperformed conventional methods including imaging (CT, PET-CT) with an AUC of 0.52, CA199 with an AUC of 0.58, CEA with an AUC of 0.56. LBX2 was also superior to clinicopathological indicators including the depth of tumor invasion and lymphatic invasion with an AUC of 0.61and 0.63 respectively. Moreover, the AUC of LBX2 antibody was 0.84, which was also better than these conventional methods. In conclusion, A novel methylation marker LBX2 could be used as a simple, cost-effective, and reliable diagnostic method for LNM of CRC.
Collapse
Affiliation(s)
- Yingdian Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenyuan Xue
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zefeng Liu
- Department of General Surgery, Zhujiang Hosipital, Southern Medical University, Guangzhou, China
| | - Shang Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jun Wang
- AnchorDx Medical Co., Ltd., International Bio-Island, Guangzhou, China
| | - Quanzhou Peng
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Linhao Xu
- AnchorDx Medical Co., Ltd., International Bio-Island, Guangzhou, China
| | - Xin Liu
- AnchorDx Medical Co., Ltd., International Bio-Island, Guangzhou, China
| | - Chunhui Cui
- Department of General Surgery, Zhujiang Hosipital, Southern Medical University, Guangzhou, China
- *Correspondence: Jian-Bing Fan, ; Chunhui Cui,
| | - Jian-Bing Fan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- AnchorDx Medical Co., Ltd., International Bio-Island, Guangzhou, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Jian-Bing Fan, ; Chunhui Cui,
| |
Collapse
|
5
|
Zhang Q, Zhu Z, Guan J, Hu Y, Zhou W, Ye W, Lin B, Weng S, Chen Y, Zheng C. Hes1 Controls Proliferation and Apoptosis in Chronic Lymphoblastic Leukemia Cells by Modulating PTEN Expression. Mol Biotechnol 2022; 64:1419-1430. [PMID: 35704163 DOI: 10.1007/s12033-022-00476-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/02/2022] [Indexed: 12/26/2022]
Abstract
Hairy and enhancer of split homolog-1 (HES1), regulated by the Notch, has been reported to play important roles in the immune response and cancers, such as leukemia. In this study, we aim to explore the effect of HES1-mediated Notch1 signaling pathway in chronic lymphocytic leukemia (CLL). Reverse transcription quantitative polymerase chain reaction and Western blot assay were conducted to determine the expression of HES1, Notch1, and PTEN in B lymphocytes of peripheral blood samples of 60 CLL patients. We used lentivirus-mediated overexpression or silencing of HES1 and the Notch1 signaling pathway inhibitor, MW167, to detect the interaction among HES1, Notch1, and PTEN in CLL MEC1 and HG3 cells. MTT assay and flow cytometry were employed for detection of biological behaviors of CLL cells. HES1 and Notch1 showed high expression, but PTEN displayed low expression in B lymphocytes of peripheral blood samples of patients with CLL in association with poor prognosis. HES1 bound to the promoter region of PTEN and reduced PTEN expression. Overexpression of HES1 activated the Notch1 signaling pathway, thus promoting the proliferation of CLL cells, increasing the proportion of cells arrested at the S phase and limiting the apoptosis of CLL cells. Collectively, HES1 can promote activation of the Notch1 signaling pathway to cause PTEN transcription inhibition and the subsequent expression reduction, thereby promoting the proliferation and inhibiting the apoptosis of CLL cells.
Collapse
Affiliation(s)
- Qikai Zhang
- Wenzhou Medical University, Wenzhou, 325000, People's Republic of China
| | - Zongsi Zhu
- Wenzhou Medical University, Wenzhou, 325000, People's Republic of China
| | - Jiaqiang Guan
- Wenzhou Medical University, Wenzhou, 325000, People's Republic of China
| | - Yingying Hu
- Department of Haematology and Chemotherapy, Wenzhou Central Hospital, Theorem Clinical College of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Wenjin Zhou
- Department of Chemotherapy, Cancer Hospital of The University of Chinese Academy of Science, Wenzhou Campus, Wenzhou, 325000, People's Republic of China
| | - Wanchun Ye
- Department of Chemotherapy, Cancer Hospital of The University of Chinese Academy of Science, Wenzhou Campus, Wenzhou, 325000, People's Republic of China
| | - Bijing Lin
- Department of Haematology and Chemotherapy, Wenzhou Central Hospital, Theorem Clinical College of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Shanshan Weng
- Department of Haematology and Chemotherapy, Wenzhou Central Hospital, Theorem Clinical College of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Yuemiao Chen
- Department of Haematology and Chemotherapy, Wenzhou Central Hospital, Theorem Clinical College of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Cuiping Zheng
- Department of Haematology and Chemotherapy, Wenzhou Central Hospital, Theorem Clinical College of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China.
| |
Collapse
|
6
|
The effects of a mixture of Lactobacillus species on colorectal tumor cells activity through modulation of Hes1 pathway. PHARMANUTRITION 2020. [DOI: 10.1016/j.phanu.2020.100207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
7
|
Dzobo K, Senthebane DA, Ganz C, Thomford NE, Wonkam A, Dandara C. Advances in Therapeutic Targeting of Cancer Stem Cells within the Tumor Microenvironment: An Updated Review. Cells 2020; 9:E1896. [PMID: 32823711 PMCID: PMC7464860 DOI: 10.3390/cells9081896] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/04/2020] [Accepted: 08/11/2020] [Indexed: 12/24/2022] Open
Abstract
Despite great strides being achieved in improving cancer patients' outcomes through better therapies and combinatorial treatment, several hurdles still remain due to therapy resistance, cancer recurrence and metastasis. Drug resistance culminating in relapse continues to be associated with fatal disease. The cancer stem cell theory posits that tumors are driven by specialized cancer cells called cancer stem cells (CSCs). CSCs are a subpopulation of cancer cells known to be resistant to therapy and cause metastasis. Whilst the debate on whether CSCs are the origins of the primary tumor rages on, CSCs have been further characterized in many cancers with data illustrating that CSCs display great abilities to self-renew, resist therapies due to enhanced epithelial to mesenchymal (EMT) properties, enhanced expression of ATP-binding cassette (ABC) membrane transporters, activation of several survival signaling pathways and increased immune evasion as well as DNA repair mechanisms. CSCs also display great heterogeneity with the consequential lack of specific CSC markers presenting a great challenge to their targeting. In this updated review we revisit CSCs within the tumor microenvironment (TME) and present novel treatment strategies targeting CSCs. These promising strategies include targeting CSCs-specific properties using small molecule inhibitors, immunotherapy, microRNA mediated inhibitors, epigenetic methods as well as targeting CSC niche-microenvironmental factors and differentiation. Lastly, we present recent clinical trials undertaken to try to turn the tide against cancer by targeting CSC-associated drug resistance and metastasis.
Collapse
Affiliation(s)
- Kevin Dzobo
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), UCT Medical Campus, Anzio Road, Observatory, Cape Town 7925, South Africa; (D.A.S.); (C.G.)
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Dimakatso Alice Senthebane
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), UCT Medical Campus, Anzio Road, Observatory, Cape Town 7925, South Africa; (D.A.S.); (C.G.)
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Chelene Ganz
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), UCT Medical Campus, Anzio Road, Observatory, Cape Town 7925, South Africa; (D.A.S.); (C.G.)
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Nicholas Ekow Thomford
- Division of Human Genetics, Department of Pathology and Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; (N.E.T.); (A.W.); (C.D.)
- Department of Medical Biochemistry, School of Medical Sciences, College of Health Sciences, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology and Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; (N.E.T.); (A.W.); (C.D.)
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology and Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; (N.E.T.); (A.W.); (C.D.)
| |
Collapse
|
8
|
Romero-Garcia S, Prado-Garcia H, Carlos-Reyes A. Role of DNA Methylation in the Resistance to Therapy in Solid Tumors. Front Oncol 2020; 10:1152. [PMID: 32850327 PMCID: PMC7426728 DOI: 10.3389/fonc.2020.01152] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the recent advances in chemotherapeutic treatments against cancer, some types of highly aggressive and invasive cancer develop drug resistance against conventional therapies, which continues to be a major problem in the fight against cancer. In recent years, studies of alterations of DNA methylome have given us a better understanding of the role of DNA methylation in the development of tumors. DNA methylation (DNAm) is an epigenetic change that promotes the covalent transfer of methyl groups to DNA. This process suppresses gene expression through the modulation of the transcription machinery access to the chromatin or through the recruitment of methyl binding proteins. DNAm is regulated mainly by DNA methyltransferases. Aberrant DNAm contributes to tumor progression, metastasis, and resistance to current anti-tumoral therapies. Aberrant DNAm may occur through hypermethylation in the promoter regions of tumor suppressor genes, which leads to their silencing, while hypomethylation in the promoter regions of oncogenes can activate them. In this review, we discuss the impact of dysregulated methylation in certain genes, which impact signaling pathways associated with apoptosis avoidance, metastasis, and resistance to therapy. The analysis of methylome has revealed patterns of global methylation, which regulate important signaling pathways involved in therapy resistance in different cancer types, such as breast, colon, and lung cancer, among other solid tumors. This analysis has provided gene-expression signatures of methylated region-specific DNA that can be used to predict the treatment outcome in response to anti-cancer therapy. Additionally, changes in cancer methylome have been associated with the acquisition of drug resistance. We also review treatments with demethylating agents that, in combination with standard therapies, seem to be encouraging, as tumors that are in early stages can be successfully treated. On the other hand, tumors that are in advanced stages can be treated with these combination schemes, which could sensitize tumor cells that are resistant to the therapy. We propose that rational strategies, which combine specific demethylating agents with conventional treatment, may improve overall survival in cancer patients.
Collapse
Affiliation(s)
- Susana Romero-Garcia
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
| | - Heriberto Prado-Garcia
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
| | - Angeles Carlos-Reyes
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases "Ismael Cosío Villegas", Mexico City, Mexico
| |
Collapse
|
9
|
Hu H, Wang T, Pan R, Yang Y, Li B, Zhou C, Zhao J, Huang Y, Duan S. Hypermethylated Promoters of Secreted Frizzled-Related Protein Genes are Associated with Colorectal Cancer. Pathol Oncol Res 2018; 25:567-575. [PMID: 30368728 DOI: 10.1007/s12253-018-0505-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/15/2018] [Indexed: 12/17/2022]
Abstract
Colorectal cancer (CRC) is one of the leading causes of death worldwide. Aberrant DNA methylation has been recognized as one of the most common molecular alterations in CRC. The goal of this study was to investigate the diagnostic value of SFRP1 and SFRP2 methylation for CRC. A total of 80 pairs of CRC patients were recruited to test the association of SFRP1 and SFRP2 promotor methylation with CRC. Methylation assay was performed using quantitative methylation-specific polymerase chain reaction (qMSP) method. In this study, we found the methylation levels of SFRP1 and SFRP2 in CRC tumor tissues were significantly higher than those in the adjacent non-tumor tissues (SFRP1: P = 2E-5; SFRP2: P = 0.014). Further bioinformatics analysis of TCGA data confirmed the association of the two genes with CRC (SFRP1: P = 7E-21; SFRP2: P = 5E-24). Luciferase reporter gene assay showed that the recombinant plasmids with SFRP1 and SFRP2 fragments could significantly enhance promoter activity (SFRP1: P = 0.002; SFRP2: P = 0.004). In addition, SFRP1 and SFRP2 methylation were inversely correlated with the mRNA expression displayed by TCGA data mining (SFRP1: r = -0.432, P = 4E-11; SFRP2: r = -0.478, P = 1E-13). GEO data analysis indicated that SFRP1 and SFRP2 expression were increased in three CRC cell lines (COLO320, HCT116 and HT29) after 5'-AZA-deoxycytidine treatment, suggesting that DNA methylation played an important role in regulating gene expression of the two genes. Our results confirmed that promoter methylation of SFRP1 and SFRP2 contributed to the risk of CRC.
Collapse
Affiliation(s)
- Haochang Hu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Tiangong Wang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Ranran Pan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yong Yang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Bin Li
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Cong Zhou
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Jun Zhao
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yi Huang
- Department of Neurosurgery of Ningbo First Hospital, Ningbo University School of Medicine, Ningbo, Zhejiang, China.
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.
| |
Collapse
|