1
|
Orsini A, Diquigiovanni C, Bonora E. Omics Technologies Improving Breast Cancer Research and Diagnostics. Int J Mol Sci 2023; 24:12690. [PMID: 37628869 PMCID: PMC10454385 DOI: 10.3390/ijms241612690] [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: 06/12/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Breast cancer (BC) has yielded approximately 2.26 million new cases and has caused nearly 685,000 deaths worldwide in the last two years, making it the most common diagnosed cancer type in the world. BC is an intricate ecosystem formed by both the tumor microenvironment and malignant cells, and its heterogeneity impacts the response to treatment. Biomedical research has entered the era of massive omics data thanks to the high-throughput sequencing revolution, quick progress and widespread adoption. These technologies-liquid biopsy, transcriptomics, epigenomics, proteomics, metabolomics, pharmaco-omics and artificial intelligence imaging-could help researchers and clinicians to better understand the formation and evolution of BC. This review focuses on the findings of recent multi-omics-based research that has been applied to BC research, with an introduction to every omics technique and their applications for the different BC phenotypes, biomarkers, target therapies, diagnosis, treatment and prognosis, to provide a comprehensive overview of the possibilities of BC research.
Collapse
Affiliation(s)
| | - Chiara Diquigiovanni
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40131 Bologna, Italy; (A.O.); (E.B.)
| | | |
Collapse
|
2
|
Shoukat I, Mueller CR. Searching for DNA methylation in patients triple-negative breast cancer: a liquid biopsy approach. Expert Rev Mol Diagn 2023; 23:41-51. [PMID: 36715539 DOI: 10.1080/14737159.2023.2173579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Liquid biopsies are proving to have diagnostic and prognostic value in many different cancers, and in breast cancer they have the potential to improve outcomes by providing valuable information throughout a patient's cancer journey. However, patients with triple negative breast cancer (TNBC) have received little benefit from such liquid biopsies due to underlying limitations in the discovery and utility of robust biomarkers. Here, we examine the development of DNA methylation-based liquid biopsy assays for breast cancer and how they pertain to TNBC. AREAS COVERED We conducted a systematic review of liquid biopsy assays for breast cancer and analyzed their relevance in TNBC. We show that the utility of DNA mutation-based assays is poor for TNBC due to the low mutational frequencies across the genome in this subtype. We offer a detailed review of mDETECT - a liquid biopsy specifically designed for assessing tumor burden in TNBC patients. EXPERT OPINION DNA methylation are foundational and robust events that occur in cancer evolution and may differentiate almost all forms of cancer, including TNBC. Longitudinal patient monitoring using DNA methylation-based liquid biopsies offers great potential for improving the detection and management of TNBC.
Collapse
Affiliation(s)
- Irsa Shoukat
- Queen's Cancer Research Institute, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Christopher R Mueller
- Queen's Cancer Research Institute, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| |
Collapse
|
3
|
Rodems TS, Juang DS, Stahlfeld CN, Gilsdorf CS, Krueger TEG, Heninger E, Zhao SG, Sperger JM, Beebe DJ, Haffner MC, Lang JM. SEEMLIS: a flexible semi-automated method for enrichment of methylated DNA from low-input samples. Clin Epigenetics 2022; 14:37. [PMID: 35272673 PMCID: PMC8908705 DOI: 10.1186/s13148-022-01252-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/18/2022] [Indexed: 01/02/2023] Open
Abstract
Background DNA methylation alterations have emerged as hallmarks of cancer and have been proposed as screening, prognostic, and predictive biomarkers. Traditional approaches for methylation analysis have relied on bisulfite conversion of DNA, which can damage DNA and is not suitable for targeted gene analysis in low-input samples. Here, we have adapted methyl-CpG-binding domain protein 2 (MBD2)-based DNA enrichment for use on a semi-automated exclusion-based sample preparation (ESP) platform for robust and scalable enrichment of methylated DNA from low-input samples, called SEEMLIS. Results We show that combining methylation-sensitive enzyme digestion with ESP-based MBD2 enrichment allows for single gene analysis with high sensitivity for GSTP1 in highly impure, heterogenous samples. We also show that ESP-based MBD2 enrichment coupled with targeted pre-amplification allows for analysis of multiple genes with sensitivities approaching the single cell level in pure samples for GSTP1 and RASSF1 and sensitivity down to 14 cells for these genes in highly impure samples. Finally, we demonstrate the potential clinical utility of SEEMLIS by successful detection of methylated gene signatures in circulating tumor cells (CTCs) from patients with prostate cancer with varying CTC number and sample purity. Conclusions SEEMLIS is a robust assay for targeted DNA methylation analysis in low-input samples, with flexibility at multiple steps. We demonstrate the feasibility of this assay to analyze DNA methylation in prostate cancer cells using CTCs from patients with prostate cancer as a real-world example of a low-input analyte of clinical importance. In summary, this novel assay provides a platform for determining methylation signatures in rare cell populations with broad implications for research as well as clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01252-4.
Collapse
Affiliation(s)
- Tamara S Rodems
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Duane S Juang
- Department of Pathology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - Charlotte N Stahlfeld
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Cole S Gilsdorf
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Tim E G Krueger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Erika Heninger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Jamie M Sperger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - David J Beebe
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Pathology, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, N., Seattle, WA, 98109, USA.,Department of Pathology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA.,Department of Pathology, Johns Hopkins School of Medicine, 600 N Wolfe St., Baltimore, MD, 21287, USA
| | - Joshua M Lang
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA. .,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA. .,7151 WI Institutes for Medical Research, 1111 Highland Ave., Madison, WI, 53705, USA.
| |
Collapse
|
4
|
Tissue-Specific Methylation Biosignatures for Monitoring Diseases: An In Silico Approach. Int J Mol Sci 2022; 23:ijms23062959. [PMID: 35328380 PMCID: PMC8952417 DOI: 10.3390/ijms23062959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 02/06/2023] Open
Abstract
Tissue-specific gene methylation events are key to the pathogenesis of several diseases and can be utilized for diagnosis and monitoring. Here, we established an in silico pipeline to analyze high-throughput methylome datasets to identify specific methylation fingerprints in three pathological entities of major burden, i.e., breast cancer (BrCa), osteoarthritis (OA) and diabetes mellitus (DM). Differential methylation analysis was conducted to compare tissues/cells related to the pathology and different types of healthy tissues, revealing Differentially Methylated Genes (DMGs). Highly performing and low feature number biosignatures were built with automated machine learning, including: (1) a five-gene biosignature discriminating BrCa tissue from healthy tissues (AUC 0.987 and precision 0.987), (2) three equivalent OA cartilage-specific biosignatures containing four genes each (AUC 0.978 and precision 0.986) and (3) a four-gene pancreatic β-cell-specific biosignature (AUC 0.984 and precision 0.995). Next, the BrCa biosignature was validated using an independent ccfDNA dataset showing an AUC and precision of 1.000, verifying the biosignature’s applicability in liquid biopsy. Functional and protein interaction prediction analysis revealed that most DMGs identified are involved in pathways known to be related to the studied diseases or pointed to new ones. Overall, our data-driven approach contributes to the maximum exploitation of high-throughput methylome readings, helping to establish specific disease profiles to be applied in clinical practice and to understand human pathology.
Collapse
|
5
|
The potential of liquid biopsy in the management of cancer patients. Semin Cancer Biol 2022; 84:69-79. [DOI: 10.1016/j.semcancer.2022.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 03/06/2022] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
|
6
|
Cheng YJ, Wang CH, Hsu KF, Lee GB. Isolation and Quantification of Methylated Cell-Free DNA in Plasma on an Integrated Microfluidic System. Anal Chem 2022; 94:2134-2141. [DOI: 10.1021/acs.analchem.1c04471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yu-Jen Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Keng-Fu Hsu
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Gwo-Bin Lee
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
- Institute of NanoEngineering and MicroSystems, National Tsing Hua University, Hsinchu 30013, Taiwan
| |
Collapse
|
7
|
Tserpeli V, Stergiopoulou D, Londra D, Giannopoulou L, Buderath P, Balgkouranidou I, Xenidis N, Grech C, Obermayr E, Zeillinger R, Pavlakis K, Rampias T, Kakolyris S, Kasimir-Bauer S, Lianidou ES. Prognostic Significance of SLFN11 Methylation in Plasma Cell-Free DNA in Advanced High-Grade Serous Ovarian Cancer. Cancers (Basel) 2021; 14:cancers14010004. [PMID: 35008168 PMCID: PMC8750111 DOI: 10.3390/cancers14010004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Epigenetic alterations in ctDNA are highly promising as a source of novel potential liquid biopsy biomarkers and comprise a very promising liquid biopsy approach in ovarian cancer, for early diagnosis, prognosis and response to treatment. Methods: In the present study, we examined the methylation status of six gene promoters (BRCA1, CST6, MGMT, RASSF10, SLFN11 and USP44) in high-grade serous ovarian cancer (HGSOC). We evaluated the prognostic significance of DNA methylation of these six gene promoters in primary tumors (FFPEs) and plasma cfDNA samples from patients with early, advanced and metastatic HGSOC. Results: We report for the first time that the DNA methylation of SLFN11 in plasma cfDNA was significantly correlated with worse PFS (p = 0.045) in advanced stage HGSOC. Conclusions: Our results strongly indicate that SLFN11 epigenetic inactivation could be a predictor of resistance to platinum drugs in ovarian cancer. Our results should be further validated in studies based on a larger cohort of patients, in order to further explore whether the DNA methylation of SLFN11 promoter could serve as a potential prognostic DNA methylation biomarker and a predictor of resistance to platinum-based chemotherapy in ovarian cancer.
Collapse
Affiliation(s)
- Victoria Tserpeli
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Dimitra Stergiopoulou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Dora Londra
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Lydia Giannopoulou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
| | - Paul Buderath
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Hufelandstrasse 55, D-45122 Essen, Germany; (P.B.); (S.K.-B.)
| | - Ioanna Balgkouranidou
- Department of Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (I.B.); (N.X.); (S.K.)
| | - Nikolaos Xenidis
- Department of Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (I.B.); (N.X.); (S.K.)
| | - Christina Grech
- Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (C.G.); (E.O.); (R.Z.)
| | - Eva Obermayr
- Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (C.G.); (E.O.); (R.Z.)
| | - Robert Zeillinger
- Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (C.G.); (E.O.); (R.Z.)
| | - Kitty Pavlakis
- Pathology Department, IASO Women’s Hospital, 15123 Athens, Greece;
| | - Theodoros Rampias
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
| | - Stylianos Kakolyris
- Department of Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (I.B.); (N.X.); (S.K.)
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Hufelandstrasse 55, D-45122 Essen, Germany; (P.B.); (S.K.-B.)
| | - Evi S. Lianidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (V.T.); (D.S.); (D.L.); (L.G.)
- Correspondence: ; Tel.: +30-210-7274311
| |
Collapse
|
8
|
Vietri MT, D'Elia G, Benincasa G, Ferraro G, Caliendo G, Nicoletti GF, Napoli C. DNA methylation and breast cancer: A way forward (Review). Int J Oncol 2021; 59:98. [PMID: 34726251 DOI: 10.3892/ijo.2021.5278] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/01/2021] [Indexed: 11/05/2022] Open
Abstract
The current management of breast cancer (BC) lacks specific non‑invasive biomarkers able to provide an early diagnosis of the disease. Epigenetic‑sensitive signatures are influenced by environmental exposures and are mediated by direct molecular mechanisms, mainly guided by DNA methylation, which regulate the interplay between genetic and non‑genetic risk factors during cancerogenesis. The inactivation of tumor suppressor genes due to promoter hypermethylation is an early event in carcinogenesis. Of note, targeted tumor suppressor genes are frequently hypermethylated in patient‑derived BC tissues and peripheral blood biospecimens. In addition, epigenetic alterations in triple‑negative BC, as the most aggressive subtype, have been identified. Thus, detecting both targeted and genome‑wide DNA methylation changes through liquid‑based assays appears to be a useful clinical strategy for early detection, more accurate risk stratification and a personalized prediction of therapeutic response in patients with BC. Of note, the DNA methylation profile may be mapped by isolating the circulating tumor DNA from the plasma as a more accessible biospecimen. Furthermore, the sensitivity to treatment with chemotherapy, hormones and immunotherapy may be altered by gene‑specific DNA methylation, suggesting novel potential drug targets. Recently, the use of epigenetic drugs administered alone and/or with anticancer therapies has led to remarkable results, particularly in patients with BC resistant to anticancer treatment. The aim of the present review was to provide an update on DNA methylation changes that are potentially involved in BC development and their putative clinical utility in the fields of diagnosis, prognosis and therapy.
Collapse
Affiliation(s)
- Maria Teresa Vietri
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanna D'Elia
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuseppe Ferraro
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Gemma Caliendo
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanni Francesco Nicoletti
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| |
Collapse
|
9
|
Duque G, Manterola C, Otzen T, Arias C, Galindo B, Mora M, Guerrero E, García N. Clinical utility of liquid biopsy in breast cancer: A systematic review. Clin Genet 2021; 101:285-295. [PMID: 34687555 DOI: 10.1111/cge.14077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/18/2022]
Abstract
Advancements in genetic sequencing techniques along with the identification of specific mutations and structural changes in multiple cancer genes, make it possible to identify circulating tumor cells and cell free nucleic acids as blood-based biomarkers, serving as a liquid biopsy (LB) with great utility for the diagnosis, treatment and follow-up of patients with neoplasms. This systematic review focuses on the clinical utility of LB in patients with breast cancer (BC). Articles published between 1990 and 2021 were included. Databases searched: Trip Database, WoS, EMBASE, PubMed, SCOPUS, and Clinical Keys. Variables studied: Publication year, country, number of cases, primary study design, LB detection methods, genes found, overall survival, disease-free survival, stage, response to treatment, clinical utility, BC molecular type, systemic treatment and methodological quality of primary studies. Of 2619 articles, 74 were retained representing 12 658 patients, mainly cohort studies (66.2%), the majority were from China (15%) and Japan (12.2%). All primary studies described clinical stage and type of systemic treatment used. Most used biomarker detection method: DNA (52.7%) and type of analysis: quantification of total cfDNA (35.1%). PIK3CA mutation was most frequent (62.9%). Evidence suggests clinically useful applications of BC. Though heterogeneous, publications suggest that LB will constitute part of the standard diagnostic-therapeutic process of BC.
Collapse
Affiliation(s)
- Galo Duque
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile.,Faculty of Medicine, Universidad del Azuay, Cuenca, Ecuador
| | - Carlos Manterola
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile.,Center of Excellence in Morphological and Surgical Studies (CEMyQ), Universidad de La Frontera, Temuco, Chile
| | - Tamara Otzen
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile.,Center of Excellence in Morphological and Surgical Studies (CEMyQ), Universidad de La Frontera, Temuco, Chile
| | - Cristina Arias
- Faculty of Medicine, Universidad del Azuay, Cuenca, Ecuador
| | - Bryan Galindo
- Faculty of Medicine, Universidad del Azuay, Cuenca, Ecuador
| | - Miriann Mora
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile.,Faculty of Medicine, Universidad del Azuay, Cuenca, Ecuador
| | - Enmanuel Guerrero
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile.,Solca Cancer Institute, Sociedad de Lucha Contra el Cáncer, Cuenca, Ecuador
| | - Nayeli García
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile
| |
Collapse
|
10
|
Xu D, Ding S, Cao M, Yu X, Wang H, Qiu D, Xu Z, Bi X, Mu Z, Li K. A Pan-Cancer Analysis of Cystatin E/M Reveals Its Dual Functional Effects and Positive Regulation of Epithelial Cell in Human Tumors. Front Genet 2021; 12:733211. [PMID: 34603393 PMCID: PMC8484784 DOI: 10.3389/fgene.2021.733211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
Cystatin E/M (CST6), a representative cysteine protease inhibitor, plays both tumor-promoting and tumor-suppressing functions and is pursued as an epigenetically therapeutic target in special cancer types. However, a comprehensive and systematic analysis for CST6 in pan-cancer level is still lacking. In the present study, we explored the expression pattern of CST6 in multiple cancer types across ∼10,000 samples from TCGA (The Cancer Genome Atlas) and ∼8,000 samples from MMDs (Merged Microarray-acquired Datasets). We found that the dynamic expression alteration of CST6 was consistent with dual function in different types of cancer. In addition, we observed that the expression of CST6 was globally regulated by the DNA methylation in its promoter region. CST6 expression was positively correlated with the epithelial cell infiltration involved in epithelial-to-mesenchymal transition (EMT) and proliferation. The relationship between CST6 and tumor microenvironment was also explored. In particular, we found that CST6 serves a protective function in the process of melanoma metastasis. Finally, the clinical association analysis further revealed the dual function of CST6 in cancer, and a combination of the epithelial cell infiltration and CST6 expression could predict the prognosis for SKCM patients. In summary, this first CST6 pan-cancer study improves the understanding of the dual functional effects on CST6 in different types of human cancer.
Collapse
Affiliation(s)
- Dahua Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering and Cancer Institute of the First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Shun Ding
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Meng Cao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiaorong Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hong Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering and Cancer Institute of the First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Dongqin Qiu
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Zhengyang Xu
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Xiaoman Bi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering and Cancer Institute of the First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Zhonglin Mu
- Department of Otolaryngology, Head and Neck Surgery, The First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Kongning Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering and Cancer Institute of the First Affiliated Hospital, Hainan Medical University, Haikou, China.,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| |
Collapse
|
11
|
A DNA Methylation-Based Gene Signature Can Predict Triple-Negative Breast Cancer Diagnosis. Biomedicines 2021; 9:biomedicines9101394. [PMID: 34680511 PMCID: PMC8533184 DOI: 10.3390/biomedicines9101394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer (BC) subtype and lacks targeted treatment. It is diagnosed by the absence of immunohistochemical expression of several biomarkers, but this method still displays some interlaboratory variability. DNA methylome aberrations are common in BC, thereby methylation profiling could provide the identification of accurate TNBC diagnosis biomarkers. Here, we generated a signature of differentially methylated probes with class prediction ability between 5 non-neoplastic breast and 7 TNBC tissues (error rate = 0.083). The robustness of this signature was corroborated in larger cohorts of additional 58 non-neoplastic breast, 93 TNBC, and 150 BC samples from the Gene Expression Omnibus repository, where it yielded an error rate of 0.006. Furthermore, we validated by pyrosequencing the hypomethylation of three out of 34 selected probes (FLJ43663, PBX Homeobox 1 (PBX1), and RAS P21 protein activator 3 (RASA3) in 51 TNBC, even at early stages of the disease. Finally, we found significantly lower methylation levels of FLJ43663 in cell free-DNA from the plasma of six TNBC patients than in 15 healthy donors. In conclusion, we report a novel DNA methylation signature with potential predictive value for TNBC diagnosis.
Collapse
|
12
|
Palanca-Ballester C, Rodriguez-Casanova A, Torres S, Calabuig-Fariñas S, Exposito F, Serrano D, Redin E, Valencia K, Jantus-Lewintre E, Diaz-Lagares A, Montuenga L, Sandoval J, Calvo A. Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies. Cancers (Basel) 2021; 13:cancers13123016. [PMID: 34208598 PMCID: PMC8233712 DOI: 10.3390/cancers13123016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term "liquid biopsy" (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from "bench to bedside".
Collapse
Affiliation(s)
- Cora Palanca-Ballester
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Susana Torres
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Silvia Calabuig-Fariñas
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Francisco Exposito
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Diego Serrano
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Eloisa Jantus-Lewintre
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
| | - Luis Montuenga
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
- Correspondence: (J.S.); (A.C.)
| | - Alfonso Calvo
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Correspondence: (J.S.); (A.C.)
| |
Collapse
|
13
|
Guo Q, Hua Y. The assessment of circulating cell-free DNA as a diagnostic tool for breast cancer: an updated systematic review and meta-analysis of quantitative and qualitative ssays. Clin Chem Lab Med 2021; 59:1479-1500. [PMID: 33951758 DOI: 10.1515/cclm-2021-0193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES This updated meta-analysis aimed to assess the diagnostic accuracy of circulating cell-free DNA (cfDNA) in breast cancer (BC). CONTENT An extensive systematic search was performed in PubMed, Scopus, Embase, and Science Direct databases to retrieve all related literature. Various diagnostic estimates, including sensitivity (SE), specificity (SP), likelihood ratios (LRs), diagnostic odds ratio (DOR), and area under the curve (AUC) of summary receiver operating characteristic (sROC) curve, were also calculated using bivariate linear mixed models. SUMMARY In this meta-analysis, 57 unique articles (130 assays) on 4246 BC patients and 2,952 controls, were enrolled. For quantitative approaches, pooled SE, SP, PLR, NLR, DOR, and AUC were obtained as 0.80, 0.88, 6.7, 0.23, 29, and 0.91, respectively. Moreover, for qualitative approaches, pooled SE and SP for diagnostic performance were obtained as 0.36 and 0.98, respectively. In addition, PLR was 14.9 and NLR was 0.66. As well, the combined DOR was 23, and the AUC was 0.79. OUTLOOK Regardless of promising SE and SP, analysis of LRs suggested that quantitative assays are not robust enough neither for BC confirmation nor for its exclusion. On the other hand, qualitative assays showed satisfying performance only for confirming the diagnosis of BC, but not for its exclusion. Furthermore, qualitative cfDNA assays showed a better diagnostic performance in patients at the advanced stage of cancer, which represented no remarkable clinical significance as a biomarker for early detection.
Collapse
Affiliation(s)
- Qingfeng Guo
- Department of General Surgery, Affiliated Hospital of Jiangnan University (Original Area of Wuxi No. 3 People's Hospital), Wuxi, P.R. China
| | - Yuming Hua
- Department of General Surgery, Affiliated Hospital of Jiangnan University (Original Area of Wuxi No. 3 People's Hospital), Wuxi, P.R. China
| |
Collapse
|
14
|
Cystatin M/E (Cystatin 6): A Janus-Faced Cysteine Protease Inhibitor with Both Tumor-Suppressing and Tumor-Promoting Functions. Cancers (Basel) 2021; 13:cancers13081877. [PMID: 33919854 PMCID: PMC8070812 DOI: 10.3390/cancers13081877] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 01/08/2023] Open
Abstract
Alongside its contribution in maintaining skin homeostasis and its probable involvement in fetal and placental development, cystatin M/E (also known as cystatin 6) was first described as a tumor suppressor of breast cancer. This review aims to provide an update on cystatin M/E with particular attention paid to its role during tumorigenesis. Cystatin M/E, which is related to type 2 cystatins, displays the unique property of being a dual tight-binding inhibitor of both legumain (also known as asparagine endopeptidase) and cysteine cathepsins L, V and B, while its expression level is epigenetically regulated via the methylation of the CST6 promoter region. The tumor-suppressing role of cystatin M/E was further reported in melanoma, cervical, brain, prostate, gastric and renal cancers, and cystatin M/E was proposed as a biomarker of prognostic significance. Contrariwise, cystatin M/E could have an antagonistic function, acting as a tumor promoter (e.g., oral, pancreatic cancer, thyroid and hepatocellular carcinoma). Taking into account these apparently divergent functions, there is an urgent need to decipher the molecular and cellular regulatory mechanisms of the expression and activity of cystatin M/E associated with the safeguarding homeostasis of the proteolytic balance as well as its imbalance in cancer.
Collapse
|
15
|
Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13040728. [PMID: 33578793 PMCID: PMC7916622 DOI: 10.3390/cancers13040728] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed. Abstract Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.
Collapse
|
16
|
Rahat B, Ali T, Sapehia D, Mahajan A, Kaur J. Circulating Cell-Free Nucleic Acids as Epigenetic Biomarkers in Precision Medicine. Front Genet 2020; 11:844. [PMID: 32849827 PMCID: PMC7431953 DOI: 10.3389/fgene.2020.00844] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/13/2020] [Indexed: 12/20/2022] Open
Abstract
The circulating cell-free nucleic acids (ccfNAs) are a mixture of single- or double-stranded nucleic acids, released into the blood plasma/serum by different tissues via apoptosis, necrosis, and secretions. Under healthy conditions, ccfNAs originate from the hematopoietic system, whereas under various clinical scenarios, the concomitant tissues release ccfNAs into the bloodstream. These ccfNAs include DNA, RNA, microRNA (miRNA), long non-coding RNA (lncRNA), fetal DNA/RNA, and mitochondrial DNA/RNA, and act as potential biomarkers in various clinical conditions. These are associated with different epigenetic modifications, which show disease-related variations and so finding their role as epigenetic biomarkers in clinical settings. This field has recently emerged as the latest advance in precision medicine because of its clinical relevance in diagnostic, prognostic, and predictive values. DNA methylation detected in ccfDNA has been widely used in personalized clinical diagnosis; furthermore, there is also the emerging role of ccfRNAs like miRNA and lncRNA as epigenetic biomarkers. This review focuses on the novel approaches for exploring ccfNAs as epigenetic biomarkers in personalized clinical diagnosis and prognosis, their potential as therapeutic targets and disease progression monitors, and reveals the tremendous potential that epigenetic biomarkers present to improve precision medicine. We explore the latest techniques for both quantitative and qualitative detection of epigenetic modifications in ccfNAs. The data on epigenetic modifications on ccfNAs are complex and often milieu-specific posing challenges for its understanding. Artificial intelligence and deep networks are the novel approaches for decoding complex data and providing insight into the decision-making in precision medicine.
Collapse
Affiliation(s)
- Beenish Rahat
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Taqveema Ali
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Divika Sapehia
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Aatish Mahajan
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Jyotdeep Kaur
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
17
|
Delmonico L, Alves G, Bines J. Cell free DNA biology and its involvement in breast carcinogenesis. Adv Clin Chem 2020; 97:171-223. [PMID: 32448434 DOI: 10.1016/bs.acc.2019.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Liquid biopsy represents a procedure for minimally invasive analysis of non-solid tissue, blood and other body fluids. It comprises a set of analytes that includes circulating tumor cells (CTCs) and circulating free DNA (cfDNA), RNA, long noncoding RNA (lncRNA) and micro RNA (miRNA), as well as extracellular vesicles. These novel analytes represent an alternative tool to complement diagnosis and monitor and predict response to treatment of the tumoral process and may be used for other disease processes such viral and parasitic infection. This review focuses on the biologic and molecular characteristics of cfDNA in general and the molecular changes (mutational and epigenetic) proven useful in oncologic practice for diagnosis, monitoring and treatment of breast cancer specifically.
Collapse
Affiliation(s)
- Lucas Delmonico
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Gilda Alves
- Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - José Bines
- Instituto Nacional de Câncer (INCA-HCIII), Rio de Janeiro, Brazil
| |
Collapse
|
18
|
Stastny I, Zubor P, Kajo K, Kubatka P, Golubnitschaja O, Dankova Z. Aberrantly Methylated cfDNA in Body Fluids as a Promising Diagnostic Tool for Early Detection of Breast Cancer. Clin Breast Cancer 2020; 20:e711-e722. [PMID: 32792225 DOI: 10.1016/j.clbc.2020.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/29/2020] [Accepted: 05/11/2020] [Indexed: 12/24/2022]
Abstract
Breast malignancies are the leading type of cancer among women. Its prevention and early detection, particularly in young women, remains challenging. To this end, cell-free DNA (cfDNA) detected in body fluids demonstrates great potential for early detection of tissue transformation and altered molecular setup, such as epigenetic profiles. Aberrantly methylated cfDNA in body fluids could therefore serve as a potential diagnostic and prognostic tool in breast cancer management. Abnormal methylation may lead to both an activation of oncogenes via hypomethylation and an inactivation of tumor suppressor genes by hypermethylation. We update the state of the art in the area of aberrant cfDNA methylation analyses as a diagnostic and prognostic tool in breast cancer, report on the main technological challenges, and provide an outlook for advancing the overall management of breast malignancies based on cfDNA as a target for diagnosis and tailored therapies.
Collapse
Affiliation(s)
- Igor Stastny
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Obstetrics and Gynaecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
| | - Pavol Zubor
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Gynecologic Oncology, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Karol Kajo
- Department of Pathology, St Elizabeth Cancer Institute Hospital, Bratislava, Slovak Republic; Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kubatka
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Olga Golubnitschaja
- Radiological Hospital, Rheinische, Excellence University of Bonn, Bonn, Germany; Breast Cancer Research Centre, Rheinische, Excellence University of Bonn, Bonn, Germany; Centre for Integrated Oncology, Cologne-Bonn, Excellence University of Bonn, Bonn, Germany
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic
| |
Collapse
|
19
|
Constâncio V, Nunes SP, Henrique R, Jerónimo C. DNA Methylation-Based Testing in Liquid Biopsies as Detection and Prognostic Biomarkers for the Four Major Cancer Types. Cells 2020; 9:cells9030624. [PMID: 32150897 PMCID: PMC7140532 DOI: 10.3390/cells9030624] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022] Open
Abstract
Lung, breast, colorectal, and prostate cancers are the most incident worldwide. Optimal population-based cancer screening methods remain an unmet need, since cancer detection at early stages increases the prospects of successful and curative treatment, leading to a lower incidence of recurrences. Moreover, the current parameters for cancer patients’ stratification have been associated with divergent outcomes. Therefore, new biomarkers that could aid in cancer detection and prognosis, preferably detected by minimally invasive methods are of major importance. Aberrant DNA methylation is an early event in cancer development and may be detected in circulating cell-free DNA (ccfDNA), constituting a valuable cancer biomarker. Furthermore, DNA methylation is a stable alteration that can be easily and rapidly quantified by methylation-specific PCR methods. Thus, the main goal of this review is to provide an overview of the most important studies that report methylation biomarkers for the detection and prognosis of the four major cancers after a critical analysis of the available literature. DNA methylation-based biomarkers show promise for cancer detection and management, with some studies describing a “PanCancer” detection approach for the simultaneous detection of several cancer types. Nonetheless, DNA methylation biomarkers still lack large-scale validation, precluding implementation in clinical practice.
Collapse
Affiliation(s)
- Vera Constâncio
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Sandra P. Nunes
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
| | - Rui Henrique
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
- Correspondence: or ; Tel.: +351-225084000; Fax: + 351-225084047
| |
Collapse
|
20
|
Mendaza S, Ulazia-Garmendia A, Monreal-Santesteban I, Córdoba A, de Azúa YR, Aguiar B, Beloqui R, Armendáriz P, Arriola M, Martín-Sánchez E, Guerrero-Setas D. ADAM12 is A Potential Therapeutic Target Regulated by Hypomethylation in Triple-Negative Breast Cancer. Int J Mol Sci 2020; 21:ijms21030903. [PMID: 32019179 PMCID: PMC7036924 DOI: 10.3390/ijms21030903] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 02/08/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype and currently lacks any effective targeted therapy. Since epigenetic alterations are a common event in TNBC, DNA methylation profiling can be useful for identifying potential biomarkers and therapeutic targets. Here, genome-wide DNA methylation from eight TNBC and six non-neoplastic tissues was analysed using Illumina Human Methylation 450K BeadChip. Results were validated by pyrosequencing in an independent cohort of 50 TNBC and 24 non-neoplastic samples, where protein expression was also assessed by immunohistochemistry. The functional role of disintegrin and metalloproteinase domain-containing protein 12(ADAM12) in TNBC cell proliferation, migration and drug response was analysed by gene expression silencing with short hairpin RNA. Three genes (Von Willenbrand factor C and Epidermal Growth Factor domain-containing protein (VWCE), tetraspanin-9 (TSPAN9) and ADAM12) were found to be exclusively hypomethylated in TNBC. Furthermore, ADAM12 hypomethylation was associated with a worse outcome in TNBC tissues and was also found in adjacent-to-tumour tissue and, preliminarily, in plasma from TNBC patients. In addition, ADAM12 silencing decreased TNBC cell proliferation and migration and improved doxorubicin sensitivity in TNBC cells. Our results indicate that ADAM12 is a potential therapeutic target and its hypomethylation could be a poor outcome biomarker in TNBC.
Collapse
Affiliation(s)
- Saioa Mendaza
- Molecular Pathology of Cancer Group, Navarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain; (S.M.); (A.U.-G.); (D.G.-S.)
| | - Ane Ulazia-Garmendia
- Molecular Pathology of Cancer Group, Navarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain; (S.M.); (A.U.-G.); (D.G.-S.)
| | - Iñaki Monreal-Santesteban
- Molecular Pathology of Cancer Group, Navarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain; (S.M.); (A.U.-G.); (D.G.-S.)
| | - Alicia Córdoba
- Department of Pathology, ComplejoHospitalario de Navarra (CHN), Irunlarrea 3, 31008, Pamplona, Spain; (A.C.); (Y.R.d.A.); (B.A.); (R.B.); (M.A.)
| | - Yerani Ruiz de Azúa
- Department of Pathology, ComplejoHospitalario de Navarra (CHN), Irunlarrea 3, 31008, Pamplona, Spain; (A.C.); (Y.R.d.A.); (B.A.); (R.B.); (M.A.)
| | - Begoña Aguiar
- Department of Pathology, ComplejoHospitalario de Navarra (CHN), Irunlarrea 3, 31008, Pamplona, Spain; (A.C.); (Y.R.d.A.); (B.A.); (R.B.); (M.A.)
| | - Raquel Beloqui
- Department of Pathology, ComplejoHospitalario de Navarra (CHN), Irunlarrea 3, 31008, Pamplona, Spain; (A.C.); (Y.R.d.A.); (B.A.); (R.B.); (M.A.)
| | - Pedro Armendáriz
- Department of Surgery, ComplejoHospitalario de Navarra, (CHN), Irunlarrea 3, 31008, Pamplona, Spain;
| | - Marta Arriola
- Department of Pathology, ComplejoHospitalario de Navarra (CHN), Irunlarrea 3, 31008, Pamplona, Spain; (A.C.); (Y.R.d.A.); (B.A.); (R.B.); (M.A.)
| | - Esperanza Martín-Sánchez
- Molecular Pathology of Cancer Group, Navarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain; (S.M.); (A.U.-G.); (D.G.-S.)
- Correspondence: ; Tel.: +34-848-423319
| | - David Guerrero-Setas
- Molecular Pathology of Cancer Group, Navarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain; (S.M.); (A.U.-G.); (D.G.-S.)
- Department of Pathology, ComplejoHospitalario de Navarra (CHN), Irunlarrea 3, 31008, Pamplona, Spain; (A.C.); (Y.R.d.A.); (B.A.); (R.B.); (M.A.)
| |
Collapse
|
21
|
Abstract
Breast cancer is a highly heterogeneous and dynamic disease, exhibiting unique somatic alterations that lead to disease recurrence and resistance. Tumor biopsy and conventional imaging approaches are not able to provide sufficient information regarding the early detection of recurrence and real time monitoring through tracking sensitive or resistance mechanisms to treatment. Circulating tumor DNA (ctDNA) analysis has emerged as an attractive noninvasive methodology to detect cancer-specific genetic aberrations in plasma including DNA mutations and DNA methylation patterns. Numerous studies have reported on the potential of ctDNA analysis in the management of early and advanced stages of breast cancer. Advances in high-throughput technologies, especially next generation sequencing and PCR-based assays, were highly important for the successful application of ctDNA analysis. However, before being integrated into clinical practice, ctDNA analysis needs to be standardized and validated through the performance of multicenter prospective and well-designed clinical studies. This review is focused on the clinical utility of ctDNA analysis, especially at the DNA mutation and methylation level, in breast cancer patients, incorporating the latest advances in technological approaches and involving key studies in the early and metastatic setting.
Collapse
Affiliation(s)
- Eleni Tzanikou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
| | - Evi Lianidou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
| |
Collapse
|
22
|
Cystatins in cancer progression: More than just cathepsin inhibitors. Biochimie 2019; 166:233-250. [PMID: 31071357 DOI: 10.1016/j.biochi.2019.05.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/03/2019] [Indexed: 12/20/2022]
Abstract
Cystatins are endogenous and reversible inhibitors of cysteine peptidases that are important players in cancer progression. Besides their primary role as regulators of cysteine peptidase activity, cystatins are involved in cancer development and progression through proteolysis-independent mechanisms. Mechanistic studies of cystatin function revealed that they affect all stages of cancer progression including tumor growth, apoptosis, invasion, metastasis and angiogenesis. Recently, the involvement of cystatins in the antitumor immune responses was reported. In this review, we discuss molecular mechanisms and clinical aspects of cystatins in cancer. Altered expression of cystatins in cancer resulting in harmful excessive cysteine peptidase activity has been a subject of several studies in order to find correlations with clinical outcome and therapy response. However, involvement in anti-tumor immune response and signaling cascades leading to cancer progression designates cystatins as possible targets for development of new anti-tumor drugs.
Collapse
|
23
|
Yang C, Yu T, Liu Z, Ye X, Liao X, Wang X, Han C, Zhu G, Qin W, Peng T. Cystatin F as a key family 2 cystatin subunit and prognostic biomarker for early‑stage pancreatic ductal adenocarcinoma. Oncol Rep 2019; 42:79-90. [PMID: 31059105 PMCID: PMC6549077 DOI: 10.3892/or.2019.7135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/17/2019] [Indexed: 01/03/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies, and early diagnosis and assessment may enhance the quality of life and survival of patients. The prognostic value of key family 2 cystatins subunit in PDAC patients remains unknown. The potential molecular roles of family 2 cystatins and related pathways were investigated using bioinformatics analysis. The relationship of family 2 cystatin expression levels and clinical outcomes of 112 patients with early-stage PDAC were evaluated via univariate and combined survival analysis. A prognostic nomogram model was also constructed and gene set enrichment analysis was performed to investigate potential pathways in PDAC. The pathways, interaction networks, and Gene Ontology term analysis of the cystatin gene family were analyzed in the present study. Cystatin F (CST7) was identified as the key subunit of family 2 cystatins in survival analysis. PDAC patients who harbored a higher expression level of CST7 had a lower risk in overall survival (adjusted HROS=0.44, 95% CI=0.25-0.77, P=0.004) and a longer survival time in various subgroups. The prognostic nomogram indicated that the CST7 expression model effectively predicted the outcomes of patients with early-stage PDAC (predictive ability >0.75). In the gene set enrichment analysis, it was revealed that CST7 expression may be involved in immune regulation and be associated with cell adhesion. CST7 could be a useful biomarker for the prognostic prediction of early-stage PDAC after pancreaticoduodenectomy.
Collapse
Affiliation(s)
- Chengkun Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Tingdong Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Zhengqian Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xinping Ye
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xiangkun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Chuangye Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Wei Qin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| |
Collapse
|
24
|
Lee JH, Jeong H, Choi JW, Oh HE, Kim YS. Liquid biopsy prediction of axillary lymph node metastasis, cancer recurrence, and patient survival in breast cancer: A meta-analysis. Medicine (Baltimore) 2018; 97:e12862. [PMID: 30334995 PMCID: PMC6211877 DOI: 10.1097/md.0000000000012862] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Liquid biopsies using circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA) have been developed for early cancer detection and patient monitoring. To investigate the clinical usefulness of ctDNA aberrations and cfDNA levels in patients with breast cancer (BC), we conducted a meta-analysis of 69 published studies on 5736 patients with BC. METHODS The relevant publications were identified by searching PubMed and Embase databases. The effect sizes of outcome parameters were pooled using a random-effects model. RESULTS The ctDNA mutation rates of TP53, PIK3CA, and ESR1 were approximately 38%, 27%, and 32%, respectively. High levels of cfDNA were associated with BCs rather than with healthy controls. However, these detection rates were not satisfactory for BC screening. Although the precise mechanisms have been unknown, high cfDNA levels were significantly associated with axillary lymph node metastasis (odds ratio [OR] = 2.148, P = .030). The ctDNA mutations were significantly associated with cancer recurrence (OR = 3.793, P < .001), short disease-free survival (univariate hazard ratio [HR] = 5.180, P = .026; multivariate HR = 3.605, P = .001), and progression-free survival (HR = 1.311, P = .013) rates, and poor overall survival outcomes (HR = 2.425, P = .007). CONCLUSION This meta-analysis demonstrates that ctDNA mutation status predicts disease recurrence and unfavorable survival outcomes, while cfDNA levels can be predictive of axillary lymph node metastasis in patients with BC.
Collapse
|
25
|
Li D, Li P, Wu J, Yi J, Dou Y, Guo X, Yin Y, Wang D, Ma C, Qiu L. Methylation of NBPF1 as a novel marker for the detection of plasma cell-free DNA of breast cancer patients. Clin Chim Acta 2018; 484:81-86. [DOI: 10.1016/j.cca.2018.05.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/09/2018] [Accepted: 05/14/2018] [Indexed: 12/18/2022]
|
26
|
Giannopoulou L, Mastoraki S, Buderath P, Strati A, Pavlakis K, Kasimir-Bauer S, Lianidou ES. ESR1 methylation in primary tumors and paired circulating tumor DNA of patients with high-grade serous ovarian cancer. Gynecol Oncol 2018; 150:355-360. [PMID: 29807696 DOI: 10.1016/j.ygyno.2018.05.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/11/2018] [Accepted: 05/20/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Estrogen receptor, coded by the ESR1 gene, is highly expressed in epithelial ovarian cancer. ESR1 gene is frequently methylated in many types of gynecological malignancies. However, only a few studies attempted to investigate the role of ESR1 methylation and its clinical significance in ovarian cancer so far. The aim of our study was to examine ESR1 methylation status in primary tumors and corresponding circulating tumor DNA of patients with high-grade serous ovarian cancer (HGSC). METHODS ESR1 methylation was detected by a highly specific and sensitive real-time methylation-specific PCR assay. Two groups of HGSC samples were analyzed: group A (n = 66 primary tumors) and group B (n = 53 primary tumors and 50 corresponding plasma samples). RESULTS ESR1 was found methylated in both groups of primary tumors: in 32/66 (48.5%) of group A and in 15/53 (28.3%) of group B. 19/50 (38.0%) corresponding plasma samples of group B were also methylated for ESR1. A significant agreement for ESR1 methylation was observed between primary tumors and paired plasma ctDNA samples (P = 0.004). Interestingly, the presence of ESR1 methylation in primary tumor samples of group B was significantly correlated with a better overall survival (P = 0.027) and progression-free survival (P = 0.041). CONCLUSIONS We report for the first time the presence of ESR1 methylation in plasma ctDNA of patients with HGSC. The agreement between ESR1 methylation in primary tumors and paired ctDNA is statistically significant. Our results indicate a correlation between the presence of ESR1 methylation and a better clinical outcome in HGSC patients.
Collapse
Affiliation(s)
- Lydia Giannopoulou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens 15771, Greece
| | - Sophia Mastoraki
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens 15771, Greece
| | - Paul Buderath
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Hufelandstrasse 55, Essen D-45122, Germany
| | - Areti Strati
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens 15771, Greece
| | - Kitty Pavlakis
- Pathology Department, IASO women's hospital, 15123 Marousi, Athens, Greece
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Hufelandstrasse 55, Essen D-45122, Germany
| | - Evi S Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens 15771, Greece.
| |
Collapse
|
27
|
Abstract
Next year will mark 60 years since Dr. Leslie Foulds outlined his hypothesis that cancer is "a dynamic process advancing through stages that are qualitatively different," leading the way to our view of cancer progression as we know it today. Our understanding of the mechanisms of these stages has been continuously evolving this past half-century, and there has always been an active discussion of the roles of both genetic and epigenetic changes in directing this progression. In this review, we focus on the roles one particular epigenetic mark-DNA methylation-plays in these various "discontinuous" stages of cancer. Understanding these steps not only gives us a better picture of how this fascinating biological process operates, but also opens the doors to new prognostic biomarkers and therapies against these malignancies.
Collapse
|
28
|
Ward E, Varešlija D, Charmsaz S, Fagan A, Browne AL, Cosgrove N, Cocchiglia S, Purcell SP, Hudson L, Das S, O'Connor D, O'Halloran PJ, Sims AH, Hill AD, Young LS. Epigenome-wide SRC-1-Mediated Gene Silencing Represses Cellular Differentiation in Advanced Breast Cancer. Clin Cancer Res 2018; 24:3692-3703. [PMID: 29567811 DOI: 10.1158/1078-0432.ccr-17-2615] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 02/12/2018] [Accepted: 03/16/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Despite the clinical utility of endocrine therapies for estrogen receptor-positive (ER) breast cancer, up to 40% of patients eventually develop resistance, leading to disease progression. The molecular determinants that drive this adaptation to treatment remain poorly understood. Methylome aberrations drive cancer growth yet the functional role and mechanism of these epimutations in drug resistance are poorly elucidated.Experimental Design: Genome-wide multi-omics sequencing approach identified a differentially methylated hub of prodifferentiation genes in endocrine resistant breast cancer patients and cell models. Clinical relevance of the functionally validated methyl-targets was assessed in a cohort of endocrine-treated human breast cancers and patient-derived ex vivo metastatic tumors.Results: Enhanced global hypermethylation was observed in endocrine treatment resistant cells and patient metastasis relative to sensitive parent cells and matched primary breast tumor, respectively. Using paired methylation and transcriptional profiles, we found that SRC-1-dependent alterations in endocrine resistance lead to aberrant hypermethylation that resulted in reduced expression of a set of differentiation genes. Analysis of ER-positive endocrine-treated human breast tumors (n = 669) demonstrated that low expression of this prodifferentiation gene set significantly associated with poor clinical outcome (P = 0.00009). We demonstrate that the reactivation of these genes in vitro and ex vivo reverses the aggressive phenotype.Conclusions: Our work demonstrates that SRC-1-dependent epigenetic remodeling is a 'high level' regulator of the poorly differentiated state in ER-positive breast cancer. Collectively these data revealed an epigenetic reprograming pathway, whereby concerted differential DNA methylation is potentiated by SRC-1 in the endocrine resistant setting. Clin Cancer Res; 24(15); 3692-703. ©2018 AACR.
Collapse
Affiliation(s)
- Elspeth Ward
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Damir Varešlija
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sara Charmsaz
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ailis Fagan
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alacoque L Browne
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Nicola Cosgrove
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sinéad Cocchiglia
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Siobhan P Purcell
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Lance Hudson
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sudipto Das
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Darran O'Connor
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Philip J O'Halloran
- Department of Neurosurgery, National Neurosurgical Center, Beaumont Hospital, Dublin, Ireland
| | - Andrew H Sims
- Applied Bioinformatics of Cancer Group, University of Edinburgh Cancer Research UK Centre, MRC Institute of Genetics & Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Arnold D Hill
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leonie S Young
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland.
| |
Collapse
|
29
|
Kumar M, Choudhury Y, Ghosh SK, Mondal R. Application and optimization of minimally invasive cell-free DNA techniques in oncogenomics. Tumour Biol 2018; 40:1010428318760342. [PMID: 29484962 DOI: 10.1177/1010428318760342] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The conventional method of measuring biomarkers in malignant tissue samples has already given subversive growth in cancer diagnosis, prognosis, and therapy selection. However, the regression and heterogeneity associated with tumor tissue biopsy have urged for the development of an alternative approach. Considering the limitations, cell-free DNA has emerged as a surrogate alternative, facilitating preoperative chemoradiotherapy (p < 0.0001) treatment response in rectal cancer and detection of biomarker in lung cancer. This potential of cell-free DNA in several other cancers has yet to be explored based on clinical relevance by optimizing the preanalytical factors. This review has highlighted the crucial parameters from blood collection to cell-free DNA analysis that has a significant impact on the accuracy and reliability of clinical data. The quantity of cell-free DNA is also a limiting factor. Therefore, a proper preanalytical factor for blood collection, its stability, centrifugation speed, and plasma storage condition are to be optimized for developing cancer-specific biomarkers useful for clinical purpose. Liquid biopsy-based origin of cell-free DNA has revolutionized the area of cancer research. Lack of preanalytical and analytical procedures may be considered for identification of novel biomarkers through next-generation sequencing of tumor-originated cell-free DNA in contradiction to tissue biopsy for cancer-specific biomarkers.
Collapse
Affiliation(s)
- Manish Kumar
- 1 Department of Biotechnology, Assam University, Silchar, India
| | | | - Sankar Kumar Ghosh
- 1 Department of Biotechnology, Assam University, Silchar, India.,2 University of Kalyani, Kalyani, India
| | - Rosy Mondal
- 3 Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
| |
Collapse
|
30
|
Targeting the Epigenome as a Novel Therapeutic Approach for Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1026:287-313. [DOI: 10.1007/978-981-10-6020-5_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
31
|
Mastoraki S, Strati A, Tzanikou E, Chimonidou M, Politaki E, Voutsina A, Psyrri A, Georgoulias V, Lianidou E. ESR1 Methylation: A Liquid Biopsy-Based Epigenetic Assay for the Follow-up of Patients with Metastatic Breast Cancer Receiving Endocrine Treatment. Clin Cancer Res 2017; 24:1500-1510. [PMID: 29284708 DOI: 10.1158/1078-0432.ccr-17-1181] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/29/2017] [Accepted: 12/21/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Liquid biopsy provides real-time monitoring of tumor evolution and response to therapy through analysis of circulating tumor cells (CTCs) and plasma-circulating tumor DNA (ctDNA). ESR1 epigenetic silencing potentially affects response to endocrine treatment. We evaluated ESR1 methylation in CTCs and paired plasma ctDNA. We evaluated ESR1 methylation in CTCs and paired plasma ctDNA as a potential biomarker for response to everolimus/exemestane treatment.Experimental Design: A highly sensitive and specific real-time MSP assay for ESR1 methylation was developed and validated in (i) 65 primary breast tumors formalin-fixed paraffin-embedded (FFPE), (ii) EpCAM+ CTC fractions (122 patients and 30 healthy donors; HD), (iii) plasma ctDNA (108 patients and 30HD), and (iv) in CTCs (CellSearch) and in paired plasma ctDNA for 58 patients with breast cancer. ESR1 methylation status was investigated in CTCs isolated from serial peripheral blood samples of 19 patients with ER+/HER2- advanced breast cancer receiving everolimus/exemestane.Results:ESR1 methylation was detected in: (i) 25/65 (38.5%) FFPEs, (ii) EpCAM+ CTC fractions: 26/112 (23.3%) patients and 1/30 (3.3%) HD, and (iii) plasma ctDNA: 8/108 (7.4%) patients and 1/30 (3.3%) HD. ESR1 methylation was highly concordant in 58 paired DNA samples, isolated from CTCs (CellSearch) and corresponding plasma. In serial peripheral blood samples of patients treated with everolimus/exemestane, ESR1 methylation was observed in 10/36 (27.8%) CTC-positive samples, and was associated with lack of response to treatment (P = 0.023, Fisher exact test).Conclusions: We report for the first time the detection of ESR1 methylation in CTCs and a high concordance with paired plasma ctDNA. ESR1 methylation in CTCs was associated with lack of response to everolimus/exemestane regimen. ESR1 methylation should be further evaluated as a potential liquid biopsy-based biomarker. Clin Cancer Res; 24(6); 1500-10. ©2017 AACR.
Collapse
Affiliation(s)
- Sophia Mastoraki
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Areti Strati
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Eleni Tzanikou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Maria Chimonidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | | | | | - Amanda Psyrri
- Oncology Unit, 2nd Department of Internal Medicine-Propaedeutic, Attikon University Hospital, Haidari, Greece
| | | | - Evi Lianidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece.
| |
Collapse
|
32
|
Cree IA, Uttley L, Buckley Woods H, Kikuchi H, Reiman A, Harnan S, Whiteman BL, Philips ST, Messenger M, Cox A, Teare D, Sheils O, Shaw J. The evidence base for circulating tumour DNA blood-based biomarkers for the early detection of cancer: a systematic mapping review. BMC Cancer 2017; 17:697. [PMID: 29061138 PMCID: PMC5654013 DOI: 10.1186/s12885-017-3693-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/18/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The presence of circulating cell-free DNA from tumours in blood (ctDNA) is of major importance to those interested in early cancer detection, as well as to those wishing to monitor tumour progression or diagnose the presence of activating mutations to guide treatment. In 2014, the UK Early Cancer Detection Consortium undertook a systematic mapping review of the literature to identify blood-based biomarkers with potential for the development of a non-invasive blood test for cancer screening, and which identified this as a major area of interest. This review builds on the mapping review to expand the ctDNA dataset to examine the best options for the detection of multiple cancer types. METHODS The original mapping review was based on comprehensive searches of the electronic databases Medline, Embase, CINAHL, the Cochrane library, and Biosis to obtain relevant literature on blood-based biomarkers for cancer detection in humans (PROSPERO no. CRD42014010827). The abstracts for each paper were reviewed to determine whether validation data were reported, and then examined in full. Publications concentrating on monitoring of disease burden or mutations were excluded. RESULTS The search identified 94 ctDNA studies meeting the criteria for review. All but 5 studies examined one cancer type, with breast, colorectal and lung cancers representing 60% of studies. The size and design of the studies varied widely. Controls were included in 77% of publications. The largest study included 640 patients, but the median study size was 65 cases and 35 controls, and the bulk of studies (71%) included less than 100 patients. Studies either estimated cfDNA levels non-specifically or tested for cancer-specific mutations or methylation changes (the majority using PCR-based methods). CONCLUSION We have systematically reviewed ctDNA blood biomarkers for the early detection of cancer. Pre-analytical, analytical, and post-analytical considerations were identified which need to be addressed before such biomarkers enter clinical practice. The value of small studies with no comparison between methods, or even the inclusion of controls is highly questionable, and larger validation studies will be required before such methods can be considered for early cancer detection.
Collapse
Affiliation(s)
- Ian A. Cree
- WHO Classification of Tumours Group, International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372 Lyon, CEDEX 08 France
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
- Institute of Ophthalmology, University College London, EC1V 9EL, London, UK
| | - Lesley Uttley
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Helen Buckley Woods
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Hugh Kikuchi
- Department of Pathology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX UK
| | - Anne Reiman
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
| | - Susan Harnan
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Becky L. Whiteman
- London North West Healthcare NHS Trust, Northwick Park Hospital, Watford Road, Harrow, HA1 3UJ UK
| | | | - Michael Messenger
- Leeds Centre for Personalised Medicine and Health, University of Leeds and NIHR Diagnostic Evidence Co-Operative Leeds, Leeds Teaching Hospitals NHS Trust, Leeds, LS9 7TF UK
| | - Angela Cox
- Sheffield Institute for Nucleic Acids, Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield, S10 2RX UK
| | - Dawn Teare
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Orla Sheils
- Sir Patrick Dun Research Laboratory, Central Pathology Laboratory, St James’s Hospital & Trinity College Dublin, Dublin 8, Ireland
| | - Jacqui Shaw
- University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX UK
| | - For the UK Early Cancer Detection Consortium
- WHO Classification of Tumours Group, International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372 Lyon, CEDEX 08 France
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
- Institute of Ophthalmology, University College London, EC1V 9EL, London, UK
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
- Department of Pathology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX UK
- London North West Healthcare NHS Trust, Northwick Park Hospital, Watford Road, Harrow, HA1 3UJ UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
- Leeds Centre for Personalised Medicine and Health, University of Leeds and NIHR Diagnostic Evidence Co-Operative Leeds, Leeds Teaching Hospitals NHS Trust, Leeds, LS9 7TF UK
- Sheffield Institute for Nucleic Acids, Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield, S10 2RX UK
- Sir Patrick Dun Research Laboratory, Central Pathology Laboratory, St James’s Hospital & Trinity College Dublin, Dublin 8, Ireland
- University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX UK
| |
Collapse
|
33
|
Davalos V, Martinez-Cardus A, Esteller M. The Epigenomic Revolution in Breast Cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:2163-2174. [DOI: 10.1016/j.ajpath.2017.07.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 02/09/2023]
|
34
|
Benezeder T, Tiran V, Treitler AAN, Suppan C, Rossmann C, Stoeger H, Cote RJ, Datar RH, Balic M, Dandachi N. Multigene methylation analysis of enriched circulating tumor cells associates with poor progression-free survival in metastatic breast cancer patients. Oncotarget 2017; 8:92483-92496. [PMID: 29190932 PMCID: PMC5696198 DOI: 10.18632/oncotarget.21426] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/27/2017] [Indexed: 12/18/2022] Open
Abstract
Blood-based biomarkers such as circulating tumor cells (CTCs) provide dynamic real-time assessment of molecular tumor characteristics beyond the primary tumor. The aim of this study was to evaluate the feasibility of a size-based microfilter to assess multigene methylation analysis of enriched CTCs in a prospective proof-of principle study. We examined the quantitative methylation status of nine genes (AKR1B1, BMP6, CST6, HOXB4, HIST1H3C, ITIH5, NEUROD1, RASSF1, SOX17) in enriched CTCs from metastatic breast cancer patients. Feasibility and clinical performance testing were assessed in a test set consisting of 37 patients and 25 healthy controls. With established cut-off values from the healthy control group, methylation of enriched CTCs was detected in at least one gene in 18/37 patients (48.6%), while 97.8% of all control samples were unmethylated. Patients with CTCs unmethylated for CST6, ITIH5, or RASSF1 showed significantly longer PFS compared to patients with corresponding enriched methylated CTCs. This proof-of-principle study shows the feasibility of a size-based microfilter to enrich and analyze multigene methylation profile of CTCs from metastatic breast cancer patients. For the first time, we report that multigene methylation analysis of enriched CTCs provides prognostic information in metastatic breast cancer patients.
Collapse
Affiliation(s)
- Theresa Benezeder
- Medical University of Graz, Department of Internal Medicine, Division of Oncology, Graz, Austria
| | - Verena Tiran
- Medical University of Graz, Department of Internal Medicine, Division of Oncology, Graz, Austria
| | - Alexandra A N Treitler
- Medical University of Graz, Department of Internal Medicine, Division of Oncology, Graz, Austria
| | - Christoph Suppan
- Medical University of Graz, Department of Internal Medicine, Division of Oncology, Graz, Austria
| | - Christopher Rossmann
- Medical University of Graz, Department of Internal Medicine, Division of Oncology, Graz, Austria
| | - Herbert Stoeger
- Medical University of Graz, Department of Internal Medicine, Division of Oncology, Graz, Austria
| | - Richard J Cote
- University of Miami Miller School of Medicine, Department of Pathology, Miami, Florida, U.S.A
| | - Ram H Datar
- University of Miami Miller School of Medicine, Department of Pathology, Miami, Florida, U.S.A
| | - Marija Balic
- Medical University of Graz, Department of Internal Medicine, Division of Oncology, Graz, Austria.,Medical University of Graz, Research Unit Circulating Tumor Cells and Cancer Stem Cells, Graz, Austria
| | - Nadia Dandachi
- Medical University of Graz, Department of Internal Medicine, Division of Oncology, Graz, Austria.,Medical University of Graz, Research Unit Epigenetic and Genetic Cancer Biomarkers, Division of Oncology, Graz, Austria
| |
Collapse
|
35
|
Giannopoulou L, Chebouti I, Pavlakis K, Kasimir-Bauer S, Lianidou ES. RASSF1A promoter methylation in high-grade serous ovarian cancer: A direct comparison study in primary tumors, adjacent morphologically tumor cell-free tissues and paired circulating tumor DNA. Oncotarget 2017; 8:21429-21443. [PMID: 28206954 PMCID: PMC5400595 DOI: 10.18632/oncotarget.15249] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 11/11/2016] [Indexed: 12/12/2022] Open
Abstract
The RASSF1A promoter is frequently methylated in high-grade serous ovarian cancer (HGSC). We examined RASSF1A promoter methylation in primary tumors, adjacent morphologically tumor cell-free tissues and corresponding circulating tumor DNA (ctDNA) samples of patients with HGSC, using a real-time methylation specific PCR (real-time MSP) and a methylation-sensitive high-resolution melting analysis (MS-HRMA) assay for the detection and semi-quantitative estimation of methylation, respectively. Two groups of primary HGSC tumor FFPE samples were recruited (Group A n=67 and Group B n=61), along with matched adjacent morphologically tumor cell-free tissues (n=58) and corresponding plasma samples (n=59) for group B. Using both assays, RASSF1A promoter was found highly methylated in primary tumors of both groups, and at lower percentages in the adjacent morphologically tumor cell-free tissues. Interestingly, RASSF1A promoter methylation was also observed in ctDNA by real-time MSP. Overall survival (OS) was significantly associated with RASSF1A promoter methylation in primary tumor samples using MS-HRMA (P=0.023). Our results clearly indicate that RASSF1A promoter is methylated in adjacent tissue surrounding the tumor in HGSC patients. We report for the first time that RASSF1A promoter methylation provides significant prognostic information in HGSC patients.
Collapse
Affiliation(s)
- Lydia Giannopoulou
- Analysis of Circulating Tumor Cells Laboratory, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens, 15771, Greece
| | - Issam Chebouti
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Essen, D-45122, Germany
| | - Kitty Pavlakis
- Pathology Department, IASO Women's Hospital, 15123, Marousi, Athens, Greece
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Essen, D-45122, Germany
| | - Evi S Lianidou
- Analysis of Circulating Tumor Cells Laboratory, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens, 15771, Greece
| |
Collapse
|
36
|
Chimonidou M, Strati A, Malamos N, Kouneli S, Georgoulias V, Lianidou E. Direct comparison study of DNA methylation markers in EpCAM-positive circulating tumour cells, corresponding circulating tumour DNA, and paired primary tumours in breast cancer. Oncotarget 2017; 8:72054-72068. [PMID: 29069768 PMCID: PMC5641111 DOI: 10.18632/oncotarget.18679] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 03/29/2017] [Indexed: 01/06/2023] Open
Abstract
Circulating Tumour Cells (CTCs) and circulating tumour DNA (ctDNA) represent a non-invasive liquid biopsy approach for the follow-up and therapy management of cancer patients. We evaluated whether DNA methylation status in CTCs and ctDNA is comparable and whether it reflects the status of primary tumours. We compared the methylation status of three genes, SOX17, CST6 and BRMS1 in primary tumours, corresponding CTCs and ctDNA in 153 breast cancer patients and healthy individuals, by using real time methylation specific PCR. We report a clear association between the EpCAM-positive CTC-fraction and ctDNA for SOX17 promoter methylation both for patients with early (P = 0.001) and metastatic breast cancer (P = 0.046) but not for CST6 and BRMS1. In early breast cancer, SOX17 promoter methylation in the EpCAM-positive CTC-fraction was associated with CK-19 mRNA expression (P = 0.006) and worse overall survival (OS) (P = 0.044). In the metastatic setting SOX17 promoter methylation in ctDNA was highly correlated with CK-19 (P = 0.04) and worse OS (Ρ = 0.016). SOX17 methylation status in CTCs and ctDNA was comparable and was associated with CK-19 expression but was not reflecting the status of primary tumours in breast cancer. DNA methylation analysis of SOX17 in CTCs and matched ctDNA provides significant prognostic value.
Collapse
Affiliation(s)
- Maria Chimonidou
- Analysis of Circulating Tumour Cells Laboratory, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Areti Strati
- Analysis of Circulating Tumour Cells Laboratory, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Nikos Malamos
- Department of Pathology, Oncology Unit, Helena Venizelou Hospital, Athens, Greece
| | - Sophia Kouneli
- Department of Pathology, Oncology Unit, Helena Venizelou Hospital, Athens, Greece
| | - Vassilis Georgoulias
- Laboratory of Tumour Cell Biology, Medical School, University of Crete, Heraklion, Greece
| | - Evi Lianidou
- Analysis of Circulating Tumour Cells Laboratory, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| |
Collapse
|
37
|
Cheuk IWY, Shin VY, Kwong A. Detection of Methylated Circulating DNA as Noninvasive Biomarkers for Breast Cancer Diagnosis. J Breast Cancer 2017; 20:12-19. [PMID: 28382090 PMCID: PMC5378575 DOI: 10.4048/jbc.2017.20.1.12] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/01/2017] [Indexed: 12/31/2022] Open
Abstract
Internationally, breast cancer is the most common female cancer, and is induced by a combination of environmental, genetic, and epigenetic risk factors. Despite the advancement of imaging techniques, invasive sampling of breast epithelial cells is the only definitive diagnostic procedure for patients with breast cancer. To date, molecular biomarkers with high sensitivity and specificity for the screening and early detection of breast cancer are lacking. Recent evidence suggests that the detection of methylated circulating cell-free DNA in the peripheral blood of patients with cancer may be a promising quantitative and noninvasive method for cancer diagnosis. Methylation detection based on a multi-gene panel, rather than on the methylation status of a single gene, may be used to increase the sensitivity and specificity of breast cancer screening. In this review, the results of 14 relevant studies, investigating the efficacy of cell-free DNA methylation screening for breast cancer diagnosis, have been summarized. The genetic risk factors for breast cancer, the methods used for breast cancer detection, and the techniques and limitations related to the detection of cell-free DNA methylation status, have also been reviewed and discussed. From this review, we conclude that the analysis of peripheral blood or other samples to detect differentially methylated cell-free DNA is a promising technique for use in clinical settings, and may improve the sensitivity of screening for both, early detection and disease relapse, and thus improve the future prognosis of patients with breast cancer.
Collapse
Affiliation(s)
- Isabella Wai Yin Cheuk
- Division of Breast Surgery, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, China
| | - Vivian Yvonne Shin
- Division of Breast Surgery, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, China
| | - Ava Kwong
- Division of Breast Surgery, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, China.; Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China.; Cancer Genetics Centre, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| |
Collapse
|
38
|
DUSP1 promoter methylation in peripheral blood leukocyte is associated with triple-negative breast cancer risk. Sci Rep 2017; 7:43011. [PMID: 28220843 PMCID: PMC5318948 DOI: 10.1038/srep43011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/18/2017] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is one of the most common epigenetic alterations, providing important information regarding cancer risk and prognosis. A case-control study (423 breast cancer cases, 509 controls) and a case-only study (326 cases) were conducted to evaluate the association of DUSP1 promoter methylation with breast cancer risk and clinicopathological characteristics. No significant association between DUSP1 methylation in peripheral blood leukocyte (PBL) DNA and breast cancer risk was observed. DUSP1 methylation was significantly associated with ER/PR-negative status; in particular, triple-negative breast cancer patients showed the highest frequency of DUSP1 methylation in both tumour DNA and PBL DNA. Soybean intake was significantly correlated with methylated DUSP1 only in ER-negative (OR 2.978; 95% CI 1.245-7.124) and PR negative (OR 2.735; 95% CI 1.315-5.692) patients. Irregular menstruation was significantly associated with methylated DUSP1 only in ER-positive (OR 3.564; 95% CI 1.691-7.511) and PR-positive (OR 3.902, 95% CI 1.656-9.194) patients. Thus, DUSP1 methylation is a cancer-associated hypermethylation event that is closely linked with triple-negative status. Further investigations are warranted to confirm the association of environmental factors, including fruit and soybean intake, irregular menstruation, and ER/PR status, with DUSP1 methylation in breast tumour DNA.
Collapse
|
39
|
|
40
|
Visvanathan K, Fackler MS, Zhang Z, Lopez-Bujanda ZA, Jeter SC, Sokoll LJ, Garrett-Mayer E, Cope LM, Umbricht CB, Euhus DM, Forero A, Storniolo AM, Nanda R, Lin NU, Carey LA, Ingle JN, Sukumar S, Wolff AC. Monitoring of Serum DNA Methylation as an Early Independent Marker of Response and Survival in Metastatic Breast Cancer: TBCRC 005 Prospective Biomarker Study. J Clin Oncol 2016; 35:751-758. [PMID: 27870562 DOI: 10.1200/jco.2015.66.2080] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Purpose Epigenetic alterations measured in blood may help guide breast cancer treatment. The multisite prospective study TBCRC 005 was conducted to examine the ability of a novel panel of cell-free DNA methylation markers to predict survival outcomes in metastatic breast cancer (MBC) using a new quantitative multiplex assay (cMethDNA). Patients and Methods Ten genes were tested in duplicate serum samples from 141 women at baseline, at week 4, and at first restaging. A cumulative methylation index (CMI) was generated on the basis of six of the 10 genes tested. Methylation cut points were selected to maximize the log-rank statistic, and cross-validation was used to obtain unbiased point estimates. Logistic regression or Cox proportional hazard models were used to test associations between the CMI and progression-free survival (PFS), overall survival (OS), and disease status at first restaging. The added value of the CMI in predicting survival outcomes was evaluated and compared with circulating tumor cells (CellSearch). Results Median PFS and OS were significantly shorter in women with a high CMI (PFS, 2.1 months; OS, 12.3 months) versus a low CMI (PFS, 5.8 months; OS, 21.7 months). In multivariable models, among women with MBC, a high versus low CMI at week 4 was independently associated with worse PFS (hazard ratio, 1.79; 95% CI, 1.23 to 2.60; P = .002) and OS (hazard ratio, 1.75; 95% CI, 1.21 to 2.54; P = .003). An increase in the CMI from baseline to week 4 was associated with worse PFS ( P < .001) and progressive disease at first restaging ( P < .001). Week 4 CMI was a strong predictor of PFS, even in the presence of circulating tumor cells ( P = .004). Conclusion Methylation of this gene panel is a strong predictor of survival outcomes in MBC and may have clinical usefulness in risk stratification and disease monitoring.
Collapse
Affiliation(s)
- Kala Visvanathan
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - MaryJo S Fackler
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Zhe Zhang
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Zoila A Lopez-Bujanda
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Stacie C Jeter
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Lori J Sokoll
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Elizabeth Garrett-Mayer
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Leslie M Cope
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Christopher B Umbricht
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - David M Euhus
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Andres Forero
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Anna M Storniolo
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Rita Nanda
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Nancy U Lin
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Lisa A Carey
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - James N Ingle
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Saraswati Sukumar
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| | - Antonio C Wolff
- Kala Visvanathan, Johns Hopkins University School of Medicine and Bloomberg School of Public Health; MaryJo S. Fackler, Zhe Zhang, Zoila A. Lopez-Bujanda, Stacie C. Jeter, Lori J. Sokoll, Leslie M. Cope, Christopher B. Umbricht, David M. Euhus, Saraswati Sukumar, and Antonio C. Wolff, Johns Hopkins University School of Medicine, Baltimore, MD; Elizabeth Garrett-Mayer, Medical University of South Carolina, Charleston, SC; Andres Forero, University of Alabama at Birmingham, Birmingham, AL; Anna M. Storniolo, Indiana University, Bloomington, IN; Rita Nanda, University of Chicago, Chicago, IL; Nancy U. Lin, Dana-Farber Cancer Institute, Boston, MA; Lisa A. Carey, University of North Carolina, Chapel Hill, NC; and James N. Ingle, Mayo Clinic, Rochester, MN
| |
Collapse
|
41
|
Tang Q, Cheng J, Cao X, Surowy H, Burwinkel B. Blood-based DNA methylation as biomarker for breast cancer: a systematic review. Clin Epigenetics 2016; 8:115. [PMID: 27895805 PMCID: PMC5109688 DOI: 10.1186/s13148-016-0282-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/26/2016] [Indexed: 12/19/2022] Open
Abstract
Multiple studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop powerful screening markers for cancer. This systematic review summarizes the current evidence on methylation studies that investigated methylation level of blood-derived DNA of breast cancer (BC) patients in comparison to healthy controls by conducting a systematic literature review in PubMed and Web of Science. Essential results, such as methylation levels of BC cases and healthy controls, p values, and odds ratios, were extracted from these studies by two investigators independently. Overall, 45 publications met the inclusion criteria for this review. DNA from whole blood, as well as cell-free DNA (cfDNA) from serum or plasma, was used in these studies. The most common method used for measuring global DNA methylation was the investigation of repetitive elements as surrogates and the application of array-based genome-wide methylation analysis. For measuring gene-specific methylation level, methylation-specific PCR and pyrosequencing were the most frequently used methods. Epigenome-wide blood DNA hypomethylation in BC patients were reported in several studies; however, the evidence is still not conclusive. The most frequently investigated gene in whole blood was BRCA1, which was found more frequently methylated in patients compared to controls. RASSF1A was the most widely investigated gene in cfDNA of serum or plasma, which was also found more frequently methylated in patients compared to controls. Several of the eligible studies reported the associations of global hypomethylation and increased BC risk. Studies investigated associations between gene-specific methylation and BC risk, while got heterogeneous results. But two studies reported that hypermethylation of ATM gene was associated with increased BC risk, which suggest the potential use of this gene for BC risk stratification. Overall, our review suggests the possibility of using blood-based DNA methylation marker as promising marker for BC risk stratification, as several studies found associations between certain methylation level in blood and BC risk. However, so far, the evidence is still quite limited. Optimal markers are yet to be developed and promising results needed to be validated in prospective study cohorts and tested in large screening populations.
Collapse
Affiliation(s)
- Qiuqiong Tang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jie Cheng
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xue Cao
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Harald Surowy
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
42
|
Development and validation of a multiplex methylation specific PCR-coupled liquid bead array for liquid biopsy analysis. Clin Chim Acta 2016; 461:156-64. [DOI: 10.1016/j.cca.2016.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/06/2016] [Accepted: 08/03/2016] [Indexed: 12/21/2022]
|
43
|
Ammerpohl O, Scheufele S, Siebert R. Analysen epigenetischer Marker aus Liquid Biopsies: Informationen von jenseits des Genoms. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0093-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Zusammenfassung
Die Analyse epigenetischer Marker aus Liquid Biopsies erlaubt Einblicke in physiologische und pathologische Prozesse im Körper einer Person, die über die reine Sequenzinformation hinausgehen. Insbesondere das DNA-Methylierungsmuster sowie die Expressionsmuster von mRNA und ncRNA sind aus Liquid Biopsies erfassbar. Damit werden ganze Gruppen neuer potenzieller Biomarker einer nicht invasiven und ökonomischen Diagnostik zugänglich. Darüber hinaus und im Gegensatz zur reinen DNA-Sequenzanalyse von Liquid Biopsies erlaubt die hohe Gewebespezifität epigenetischer Marker auch die Bestimmung der Herkunft der analysierten Nukleinsäuren z. B. in Bezug auf ein betroffenes Organ. Angesichts der fallenden Kosten für Sequenzierungen und des technologischen Fortschritts, der die Nachweisgrenzen immer weiter zu immer sensitiveren Anwendungen verschiebt, könnten epigenetische Untersuchungen aus Liquid Biopsies den Trend zu einer Individualisierung in der Medizin weiter forcieren.
Collapse
Affiliation(s)
- Ole Ammerpohl
- Aff1 grid.9764.c 0000000121539986 Institut für Humangenetik Christian‑Albrechts‑Universität zu Kiel Schwanenweg 24 24105 Kiel Deutschland
- Aff2 grid.412468.d 0000000406462097 Universitätsklinikum Schleswig-Holstein Campus Kiel Kiel Deutschland
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
| | - Swetlana Scheufele
- Aff1 grid.9764.c 0000000121539986 Institut für Humangenetik Christian‑Albrechts‑Universität zu Kiel Schwanenweg 24 24105 Kiel Deutschland
- Aff2 grid.412468.d 0000000406462097 Universitätsklinikum Schleswig-Holstein Campus Kiel Kiel Deutschland
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
| | - Reiner Siebert
- Aff3 grid.452624.3 Airway Research Center North (ARCN) German Center for Lung Research (DZL) Gießen Deutschland
- Aff4 grid.6582.9 0000000419369748 Institut für Humangenetik Universität Ulm Albert-Einstein-Allee 11 89081 Ulm Deutschland
| |
Collapse
|
44
|
Canzoniero JV, Park BH. Use of cell free DNA in breast oncology. Biochim Biophys Acta Rev Cancer 2016; 1865:266-74. [PMID: 27012505 DOI: 10.1016/j.bbcan.2016.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/18/2016] [Accepted: 03/19/2016] [Indexed: 12/24/2022]
Abstract
Cell free DNA (cfDNA) are short fragments of nucleic acids present in circulation outside of cells. In patients with cancer, some portion of cfDNA is derived from tumor cells, termed circulating tumor DNA (ctDNA), and contains the same mutations and genetic changes as the cancer. The development of new, more effective methods to detect these changes has led to increased interest in developing ctDNA as a biomarker for cancer. Here we will review current literature on the use of ctDNA, with an emphasis on breast cancer, for cancer detection, prognosis, monitoring response to therapy, and tracking the rise of new mutant subclones.
Collapse
Affiliation(s)
- Jenna VanLiere Canzoniero
- Division of General Internal Medicine, Johns Hopkins, 600 N Wolfe St, Nelson 207, Baltimore, MD 21287, USA.
| | - Ben Ho Park
- The Sidney Kimmel Comprehensive Cancer Institute at Johns Hopkins, 1650 Orleans Street, CRBI, Baltimore, MD 21287, USA.
| |
Collapse
|
45
|
Lianidou ES. Gene expression profiling and DNA methylation analyses of CTCs. Mol Oncol 2016; 10:431-42. [PMID: 26880168 DOI: 10.1016/j.molonc.2016.01.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 01/26/2023] Open
Abstract
A variety of molecular assays have been developed for CTCs detection and molecular characterization. Molecular assays are based on the nucleic acid analysis in CTCs and are based on total RNA isolation and subsequent mRNA quantification of specific genes, or isolation of genomic DNA that can be for DNA methylation studies and mutation analysis. This review is mainly focused on gene expression and methylation studies in CTCs in various types of cancer.
Collapse
Affiliation(s)
- Evi S Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, 15771, Greece.
| |
Collapse
|
46
|
Terry MB, McDonald JA, Wu HC, Eng S, Santella RM. Epigenetic Biomarkers of Breast Cancer Risk: Across the Breast Cancer Prevention Continuum. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 882:33-68. [PMID: 26987530 PMCID: PMC5305320 DOI: 10.1007/978-3-319-22909-6_2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Epigenetic biomarkers, such as DNA methylation, can increase cancer risk through altering gene expression. The Cancer Genome Atlas (TCGA) Network has demonstrated breast cancer-specific DNA methylation signatures. DNA methylation signatures measured at the time of diagnosis may prove important for treatment options and in predicting disease-free and overall survival (tertiary prevention). DNA methylation measurement in cell free DNA may also be useful in improving early detection by measuring tumor DNA released into the blood (secondary prevention). Most evidence evaluating the use of DNA methylation markers in tertiary and secondary prevention efforts for breast cancer comes from studies that are cross-sectional or retrospective with limited corresponding epidemiologic data, raising concerns about temporality. Few prospective studies exist that are large enough to address whether DNA methylation markers add to the prediction of tertiary and secondary outcomes over and beyond standard clinical measures. Determining the role of epigenetic biomarkers in primary prevention can help in identifying modifiable pathways for targeting interventions and reducing disease incidence. The potential is great for DNA methylation markers to improve cancer outcomes across the prevention continuum. Large, prospective epidemiological studies will provide essential evidence of the overall utility of adding these markers to primary prevention efforts, screening, and clinical care.
Collapse
Affiliation(s)
- Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
| | - Jasmine A McDonald
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Hui Chen Wu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sybil Eng
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Regina M Santella
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| |
Collapse
|
47
|
Cava C, Bertoli G, Castiglioni I. Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential. BMC SYSTEMS BIOLOGY 2015; 9:62. [PMID: 26391647 PMCID: PMC4578257 DOI: 10.1186/s12918-015-0211-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/15/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome. Combined analyses of molecular data at multiple levels, such as DNA copy-number alteration, mRNA and miRNA expression, can clarify biological functions and pathways deregulated in cancer. The integrative methods that are used to investigate these data involve different fields, including biology, bioinformatics, and statistics. RESULTS These methodologies are presented in this review, and their implementation in breast cancer is discussed with a focus on integration strategies. We report current applications, recent studies and interesting results leading to the identification of candidate biomarkers for diagnosis, prognosis, and therapy in breast cancer by using both individual and combined analyses. CONCLUSION This review presents a state of art of the role of different technologies in breast cancer based on the integration of genetics and epigenetics, and shares some issues related to the new opportunities and challenges offered by the application of such integrative approaches.
Collapse
Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| |
Collapse
|
48
|
Warton K, Samimi G. Methylation of cell-free circulating DNA in the diagnosis of cancer. Front Mol Biosci 2015; 2:13. [PMID: 25988180 PMCID: PMC4428375 DOI: 10.3389/fmolb.2015.00013] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/07/2015] [Indexed: 01/04/2023] Open
Abstract
A range of molecular alterations found in tumor cells, such as DNA mutations and DNA methylation, is reflected in cell-free circulating DNA (circDNA) released from the tumor into the blood, thereby making circDNA an ideal candidate for the basis of a blood-based cancer diagnosis test. In many cancer types, mutations driving tumor development and progression are present in a wide range of oncogenes and tumor suppressor genes. However, even when a gene is consistently mutated in a particular cancer, the mutations can be spread over very large regions of its sequence, making evaluation difficult. This diversity of sequence changes in tumor DNA presents a challenge for the development of blood tests based on DNA mutations for cancer diagnosis. Unlike mutations, DNA methylation that can be consistently measured, as it tends to occur in specific regions of the DNA called CpG islands. Since DNA methylation is reflected within circDNA, detection of tumor-specific DNA methylation in patient plasma is a feasible approach for the development of a blood-based test. Aberrant circDNA methylation has been described in most cancer types and is actively being investigated for clinical applications. A commercial blood test for colorectal cancer based on the methylation of the SEPT9 promoter region in circDNA is under review for approval by the Federal Drug Administration (FDA) for clinical use. In this paper, we review the state of research in circDNA methylation as an application for blood-based diagnostic tests in colorectal, breast, lung, pancreatic and ovarian cancers, and we consider some of the future directions and challenges in this field. There are a number of potential circDNA biomarkers currently under investigation, and experience with SEPT9 shows that the time to clinical translation can be relatively rapid, supporting the promise of circDNA as a biomarker.
Collapse
Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Goli Samimi
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| |
Collapse
|
49
|
Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value. Nat Commun 2015; 6:5899. [PMID: 25641231 DOI: 10.1038/ncomms6899] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 11/17/2014] [Indexed: 01/09/2023] Open
Abstract
Epigenetic alterations in the cancer methylome are common in breast cancer and provide novel options for tumour stratification. Here, we perform whole-genome methylation capture sequencing on small amounts of DNA isolated from formalin-fixed, paraffin-embedded tissue from triple-negative breast cancer (TNBC) and matched normal samples. We identify differentially methylated regions (DMRs) enriched with promoters associated with transcription factor binding sites and DNA hypersensitive sites. Importantly, we stratify TNBCs into three distinct methylation clusters associated with better or worse prognosis and identify 17 DMRs that show a strong association with overall survival, including DMRs located in the Wilms tumour 1 (WT1) gene, bi-directional-promoter and antisense WT1-AS. Our data reveal that coordinated hypermethylation can occur in oestrogen receptor-negative disease, and that characterizing the epigenetic framework provides a potential signature to stratify TNBCs. Together, our findings demonstrate the feasibility of profiling the cancer methylome with limited archival tissue to identify regulatory regions associated with cancer.
Collapse
|
50
|
Fleischhacker M, Schmidt B. Extracellular Nucleic Acids and Cancer. ADVANCES IN PREDICTIVE, PREVENTIVE AND PERSONALISED MEDICINE 2015. [DOI: 10.1007/978-94-017-9168-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|