1
|
Xu YW, Peng YH, Liu CT, Chen H, Chu LY, Chen HL, Wu ZY, Wei WQ, Xu LY, Wu FC, Li EM. Machine learning technique-based four-autoantibody test for early detection of esophageal squamous cell carcinoma: a multicenter, retrospective study with a nested case-control study. BMC Med 2025; 23:235. [PMID: 40264204 PMCID: PMC12016149 DOI: 10.1186/s12916-025-04066-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 04/10/2025] [Indexed: 04/24/2025] Open
Abstract
BACKGROUND Autoantibodies represent promising diagnostic blood-based biomarkers that may be generated prior to the first clinically detectable signs of cancers. In present study, we aimed to identify a novel optimized autoantibody panel with high diagnostic accuracy for clinical and preclinical esophageal squamous cell carcinoma (ESCC) using machine learning (ML) algorithms. METHODS We identified potential autoantibodies against tumor-associated antigens with serological proteome analysis. Serum autoantibody levels were measured by ELISA. Using a training set (n = 531), 102 models based on ML algorithms were constructed, and Partial Least Squares Generalized Linear Models (plsRglm) was selected out using receiver operating characteristics (ROC), Kolmogorov-Smirnov (K-S) test, and Population Stability Index (PSI), and further validated through an internal validation set (n = 413), external validation set 1 (n = 371), and external validation set 2 (n = 202). Then, we validated the ability of plsRglm model in predicting preclinical ESCC by a nested case-control study (24 preclinical ESCCs and 112 matched controls) within a population-based prospective cohort study. RESULTS ROC analysis, K-S test, and PSI showed that plsRglm model based on four autoantibodies (ALDOA, ENO1, p53, and NY-ESO-1) exhibited the better diagnostic performance and robustness, which provided a high diagnostic accuracy in diagnosing ESCC with the respective AUCs (sensitivities and specificities) of 0.860 (68.8% and 90.4%) in the training set, 0.826 (65.3% and 89.1%) in the internal validation set, and 0.851 (69.2% and 87.3%) in the external validation set 1. For early-stage ESCC, this signature also maintained diagnostic performance [0.817 (62.3% and 90.4%) in the training set; 0.842 (62.5% and 89.1%) in the internal validation set; 0.854 (63.2% and 87.3%) in the external validation set 1; and 0.850 (67.3% and 90.1%) in the external validation set 2]. In the nested case-control study, this plsRglm model could detect the presence of preclinical ESCC with the AUC of 0.723, sensitivity of 54.2%, and specificity of 86.6%. CONCLUSIONS Our findings indicated that the plsRglm model based on four autoantibodies might help identify preclinical and early-stage ESCC.
Collapse
Affiliation(s)
- Yi-Wei Xu
- Department of Clinical Laboratory Medicine, Esophageal Cancer Prevention and Control Research Center, Chaoshan Branch of State Key Laboratory for Esophageal Cancer Prevention and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China.
- Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China.
| | - Yu-Hui Peng
- Department of Clinical Laboratory Medicine, Esophageal Cancer Prevention and Control Research Center, Chaoshan Branch of State Key Laboratory for Esophageal Cancer Prevention and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China
| | - Can-Tong Liu
- Department of Clinical Laboratory Medicine, Esophageal Cancer Prevention and Control Research Center, Chaoshan Branch of State Key Laboratory for Esophageal Cancer Prevention and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China
| | - Hao Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Ling-Yu Chu
- Department of Clinical Laboratory Medicine, Esophageal Cancer Prevention and Control Research Center, Chaoshan Branch of State Key Laboratory for Esophageal Cancer Prevention and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Hai-Lu Chen
- Department of Surgical Oncology, Shantou Central Hospital, Shantou, 515031, China
| | - Zhi-Yong Wu
- Department of Surgical Oncology, Shantou Central Hospital, Shantou, 515031, China
| | - Wen-Qiang Wei
- Department of Cancer Epidemiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Li-Yan Xu
- Institute of Oncological Pathology, Shantou University Medical College, Shantou, 515041, China.
| | - Fang-Cai Wu
- Department of Radiation Oncology, Esophageal Cancer Prevention and Control Research Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China.
| | - En-Min Li
- Esophageal Cancer Prevention and Control Research Center, Chaoshan Branch of State Key Laboratory for Esophageal Cancer Prevention and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China.
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, 515041, China.
| |
Collapse
|
2
|
Dasi S, Naab TJ, Kwabi-Addo B, Apprey V, Beyene D, Dewitty RL, Nagel S, Williams R, Bolden K, Hayes-Dixon A, Shokrani B, Stewart DA, Kassim OO, Copeland RL, Kanaan YM. Methylation of ESRα Promoters in Benign Breast Tumors Could Be a Signature for Progression to Breast Cancer in African American Women. Cancer Genomics Proteomics 2025; 22:208-230. [PMID: 39993808 PMCID: PMC11880923 DOI: 10.21873/cgp.20497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 01/20/2025] [Accepted: 01/22/2025] [Indexed: 02/26/2025] Open
Abstract
BACKGROUND/AIM Methylation in the estrogen receptor alpha (ESRα) promoter is an epigenetic abnormality associated with breast cancer (BCa), whereas hypermethylation results in the loss of ER expression. MATERIALS AND METHODS Pyrosequencing was used to investigate a potential link between aberrant methylation in the P0/P1 promoters of ESRα and the risk of progression of benign fibrocystic and fibroadenoma tumors to BCa. RESULTS Results showed a significantly elevated level of DNA methylation in ESRα P1 promoter (p=0.0001) in fibroadenoma compared to ER-negative BCa tumors and a two-fold increased ESRα expression in fibrocystic and fibroadenoma benign tissues. In addition, methylation levels of HIN-1 and RASSF1A promoters were elevated in ER-positive compared to ER-negative BCa (p-value<0.04). ANOVA Mixed Model revealed significantly higher methylation levels in the promoter of RASSF1A for fibroadenoma and ER-positive BCa (p=0.004) compared to ER-negative BCa. Tumors with unclassified molecular subtypes (ER-positive, PR-negative, HER2-negative) had elevated levels of methylation (p=0.046) in the P0 promoter compared with luminal B (ER-positive, PR-positive, HER2-positive) tumors. Grade 3 tumors showed a borderline association with ESRα P1 promoter methylation when compared with grade 2 tumors (p=0.056). CONCLUSION ESRα P0 promoter hypermethylation may occur in the early stages of breast carcinogenesis, while P1 promoter methylation appears in later stages with a poor prognosis. Therefore, methylation of the ESRα promoter and other tumor-related genes could serve as a potential biomarker for predicting fibroadenoma progression risk to BCa.
Collapse
Affiliation(s)
- Sylvia Dasi
- Howard University Cancer Center, Howard University, Washington, DC, U.S.A
| | | | - Bernard Kwabi-Addo
- Department of Biochemistry and Molecular Biology, Howard University College of Medicine, Howard University, Washington, DC, U.S.A
| | - Victor Apprey
- Howard University Cancer Center, Howard University, Washington, DC, U.S.A
| | - Desta Beyene
- Howard University Cancer Center, Howard University, Washington, DC, U.S.A
| | - Robert L Dewitty
- Department of Surgery, Howard University Hospital, Washington, DC, U.S.A
| | - Steven Nagel
- Department of Surgery, Howard University Hospital, Washington, DC, U.S.A
| | - Robin Williams
- Department of Surgery, Howard University Hospital, Washington, DC, U.S.A
| | - Kelly Bolden
- Department of Surgery, Howard University Hospital, Washington, DC, U.S.A
| | - Andrea Hayes-Dixon
- Department of Surgery, Howard University Hospital, Washington, DC, U.S.A
| | - Babak Shokrani
- Department of Pathology, Howard University Hospital, Washington, DC, U.S.A
| | - Delisha A Stewart
- Department of Microbiology, Howard University College of Medicine, Howard University, Washington, DC, U.S.A
| | - Olakunle O Kassim
- Department of Microbiology, Howard University College of Medicine, Howard University, Washington, DC, U.S.A
| | - Robert L Copeland
- Department of Pharmacology, Howard University College of Medicine, Howard University, Washington, DC, U.S.A
| | - Yasmine M Kanaan
- Howard University Cancer Center, Howard University, Washington, DC, U.S.A.;
- Department of Microbiology, Howard University College of Medicine, Howard University, Washington, DC, U.S.A
| |
Collapse
|
3
|
Li M, Xia Z, Wang R, Xi M, Hou M. Unveiling DNA methylation: early diagnosis, risk assessment, and therapy for endometrial cancer. Front Oncol 2025; 14:1455255. [PMID: 39902129 PMCID: PMC11788147 DOI: 10.3389/fonc.2024.1455255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 12/30/2024] [Indexed: 02/05/2025] Open
Abstract
Endometrial cancer (EC), one of the most common gynecologic malignancies worldwide, poses a significant burden particularly among young women, with poor treatment outcomes and prognosis for advanced and recurrent patients. Epigenetic changes, encompassing DNA methylation, are involved in the occurrence and progression of tumors and hold promise as effective tools for screening, early diagnosis, treatment strategy, efficacy evaluation, and prognosis analysis. This review provides a comprehensive summary of DNA methylation-based early diagnostic biomarkers in EC, with a focus on recent valuable research findings published in the past two years. The discussion is organized according to sample sources, including cervical scraping, vaginal fluid, urine, blood, and tissue. Additionally, we outline the role of DNA methylation in EC risk assessment, such as carcinogenesis risk, feasibility of fertility preservation approaches, and overall prognosis, aiming to provide personalized treatment decisions for patients. Finally, we review researches on DNA methylation in resistance to first-line treatment of EC and the development of new drugs, and envision the future applications of DNA methylation in EC.
Collapse
Affiliation(s)
- Minzhen Li
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Zhili Xia
- The First Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Ruiyu Wang
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Mingrong Xi
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Minmin Hou
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| |
Collapse
|
4
|
Wang X, Dong Y, Zhang H, Zhao Y, Miao T, Mohseni G, Du L, Wang C. DNA methylation drives a new path in gastric cancer early detection: Current impact and prospects. Genes Dis 2024; 11:847-860. [PMID: 37692483 PMCID: PMC10491876 DOI: 10.1016/j.gendis.2023.02.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/24/2023] [Indexed: 03/31/2023] Open
Abstract
Gastric cancer (GC) is one of the most common and deadly cancers worldwide. Early detection offers the best chance for curative treatment and reducing its mortality. However, the optimal population-based early screening for GC remains unmet. Aberrant DNA methylation occurs in the early stage of GC, exhibiting cancer-specific genetic and epigenetic changes, and can be detected in the media such as blood, gastric juice, and feces, constituting a valuable biomarker for cancer early detection. Furthermore, DNA methylation is a stable epigenetic alteration, and many innovative methods have been developed to quantify it rapidly and accurately. Nonetheless, large-scale clinical validation of DNA methylation serving as tumor biomarkers is still lacking, precluding their implementation in clinical practice. In conclusion, after a critical analysis of the recent existing literature, we summarized the evolving roles of DNA methylation during GC occurrence, expounded the newly discovered noninvasive DNA methylation biomarkers for early detection of GC, and discussed its challenges and prospects in clinical applications.
Collapse
Affiliation(s)
- Xinhui Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
| | - Yaqi Dong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
| | - Hong Zhang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
- Department of Clinical Laboratory, Fuling Hospital, Chongqing University, Chongqing 402774, China
| | - Yinghui Zhao
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
- Suzhou Research Institute of Shandong University, Suzhou, Jiangsu 215123, China
| | - Tianshu Miao
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, Shandong 250012, China
| | - Ghazal Mohseni
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong 250033, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong 250033, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong 250033, China
| |
Collapse
|
5
|
Peng S, Zhang X, Wu Y. Potential applications of DNA methylation testing technology in female tumors and screening methods. Biochim Biophys Acta Rev Cancer 2023; 1878:188941. [PMID: 37329994 DOI: 10.1016/j.bbcan.2023.188941] [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: 04/21/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/19/2023]
Abstract
DNA methylation is a common epigenetic modification, and the current commonly used methods for DNA methylation detection include methylation-specific PCR, methylation-sensitive restriction endonuclease-PCR, and methylation-specific sequencing. DNA methylation plays an important role in genomic and epigenomic studies, and combining DNA methylation with other epigenetic modifications, such as histone modifications, may lead to better DNA methylation. DNA methylation also plays an important role in the development of disease, and analyzing changes in individual DNA methylation patterns can provide individualized diagnostic and therapeutic solutions. Liquid biopsy techniques are also increasingly well established in clinical practice and may provide new methods for early cancer screening. It is important to find new screening methods that are easy to perform, minimally invasive, patient-friendly, and affordable. DNA methylation mechanisms are thought to have an important role in cancer and have potential applications in the diagnosis and treatment of female tumors. This review discussed early detection targets and screening methods for common female tumors such as breast, ovarian, and cervical cancers and discussed advances in the study of DNA methylation in these tumors. Although existing screening, diagnostic, and treatment modalities exist, the high morbidity and mortality rates of these tumors remain challenging.
Collapse
Affiliation(s)
- Shixuan Peng
- Graduate Collaborative Training Base of The First People's Hospital of Xiangtan City, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China
| | - Xinwen Zhang
- Graduate Collaborative Training Base of The First People's Hospital of Xiangtan City, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China
| | - Yongjun Wu
- Department of Pathology, The First People's Hospital of Xiangtan City, 100 Shuyuan Road, 411100 Xiangtan, Hunan Province, China.
| |
Collapse
|
6
|
Gerton TJ, Green A, Campisi M, Chen M, Gjeci I, Mahadevan N, Lee CAA, Mishra R, Vo HV, Haratani K, Li ZH, Hasselblatt KT, Testino B, Connor T, Lian CG, Elias KM, Lizotte P, Ivanova EV, Barbie DA, Dinulescu DM. Development of a Patient-Derived 3D Immuno-Oncology Platform to Potentiate Immunotherapy Responses in Ascites-Derived Circulating Tumor Cells. Cancers (Basel) 2023; 15:4128. [PMID: 37627156 PMCID: PMC10452550 DOI: 10.3390/cancers15164128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
High-grade serous ovarian cancer (HGSOC) is responsible for the majority of gynecology cancer-related deaths. Patients in remission often relapse with more aggressive forms of disease within 2 years post-treatment. Alternative immuno-oncology (IO) strategies, such as immune checkpoint blockade (ICB) targeting the PD-(L)1 signaling axis, have proven inefficient so far. Our aim is to utilize epigenetic modulators to maximize the benefit of personalized IO combinations in ex vivo 3D patient-derived platforms and in vivo syngeneic models. Using patient-derived tumor ascites, we optimized an ex vivo 3D screening platform (PDOTS), which employs autologous immune cells and circulating ascites-derived tumor cells, to rapidly test personalized IO combinations. Most importantly, patient responses to platinum chemotherapy and poly-ADP ribose polymerase inhibitors in 3D platforms recapitulate clinical responses. Furthermore, similar to clinical trial results, responses to ICB in PDOTS tend to be low and positively correlated with the frequency of CD3+ immune cells and EPCAM+/PD-L1+ tumor cells. Thus, the greatest response observed with anti-PD-1/anti-PD-L1 immunotherapy alone is seen in patient-derived HGSOC ascites, which present with high levels of systemic CD3+ and PD-L1+ expression in immune and tumor cells, respectively. In addition, priming with epigenetic adjuvants greatly potentiates ICB in ex vivo 3D testing platforms and in vivo tumor models. We further find that epigenetic priming induces increased tumor secretion of several key cytokines known to augment T and NK cell activation and cytotoxicity, including IL-6, IP-10 (CXCL10), KC (CXCL1), and RANTES (CCL5). Moreover, epigenetic priming alone and in combination with ICB immunotherapy in patient-derived PDOTS induces rapid upregulation of CD69, a reliable early activation of immune markers in both CD4+ and CD8+ T cells. Consequently, this functional precision medicine approach could rapidly identify personalized therapeutic combinations able to potentiate ICB, which is a great advantage, especially given the current clinical difficulty of testing a high number of potential combinations in patients.
Collapse
Affiliation(s)
- Thomas J. Gerton
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Allen Green
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Marco Campisi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Minyue Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Iliana Gjeci
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Navin Mahadevan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Catherine A. A. Lee
- Division of Dermatopathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ranjan Mishra
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ha V. Vo
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Koji Haratani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ze-Hua Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kathleen T. Hasselblatt
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bryanna Testino
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Trevor Connor
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Christine G. Lian
- Division of Dermatopathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin M. Elias
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Gynecologic Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Patrick Lizotte
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Elena V. Ivanova
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - David A. Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Daniela M. Dinulescu
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
7
|
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
|
8
|
Galan A, Papaluca A, Nejatie A, Matanes E, Brahimi F, Tong W, Hachim IY, Yasmeen A, Carmona E, Klein KO, Billes S, Dawod AE, Gawande P, Jeter AM, Mes-Masson AM, Greenwood CMT, Gotlieb WH, Saragovi HU. GD2 and GD3 gangliosides as diagnostic biomarkers for all stages and subtypes of epithelial ovarian cancer. Front Oncol 2023; 13:1134763. [PMID: 37124505 PMCID: PMC10145910 DOI: 10.3389/fonc.2023.1134763] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Background Ovarian cancer (OC) is the deadliest gynecological cancer, often diagnosed at advanced stages. A fast and accurate diagnostic method for early-stage OC is needed. The tumor marker gangliosides, GD2 and GD3, exhibit properties that make them ideal potential diagnostic biomarkers, but they have never before been quantified in OC. We investigated the diagnostic utility of GD2 and GD3 for diagnosis of all subtypes and stages of OC. Methods This retrospective study evaluated GD2 and GD3 expression in biobanked tissue and serum samples from patients with invasive epithelial OC, healthy donors, non-malignant gynecological conditions, and other cancers. GD2 and GD3 levels were evaluated in tissue samples by immunohistochemistry (n=299) and in two cohorts of serum samples by quantitative ELISA. A discovery cohort (n=379) showed feasibility of GD2 and GD3 quantitative ELISA for diagnosing OC, and a subsequent model cohort (n=200) was used to train and cross-validate a diagnostic model. Results GD2 and GD3 were expressed in tissues of all OC subtypes and FIGO stages but not in surrounding healthy tissue or other controls. In serum, GD2 and GD3 were elevated in patients with OC. A diagnostic model that included serum levels of GD2+GD3+age was superior to the standard of care (CA125, p<0.001) in diagnosing OC and early-stage (I/II) OC. Conclusion GD2 and GD3 expression was associated with high rates of selectivity and specificity for OC. A diagnostic model combining GD2 and GD3 quantification in serum had diagnostic power for all subtypes and all stages of OC, including early stage. Further research exploring the utility of GD2 and GD3 for diagnosis of OC is warranted.
Collapse
Affiliation(s)
- Alba Galan
- Translational Cancer Center, Lady Davis Institute-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Arturo Papaluca
- Translational Cancer Center, Lady Davis Institute-Jewish General Hospital, McGill University, Montreal, QC, Canada
- Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Ali Nejatie
- Translational Cancer Center, Lady Davis Institute-Jewish General Hospital, McGill University, Montreal, QC, Canada
- Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Emad Matanes
- Translational Cancer Center, Lady Davis Institute-Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Ob-Gyn, Jewish General Hospital, McGill University and Segal Cancer Center, Lady Davis Institute of Medical Research, Montreal, QC, Canada
| | - Fouad Brahimi
- Translational Cancer Center, Lady Davis Institute-Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Wenyong Tong
- Translational Cancer Center, Lady Davis Institute-Jewish General Hospital, McGill University, Montreal, QC, Canada
- Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Ibrahim Yaseen Hachim
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Amber Yasmeen
- Department of Ob-Gyn, Jewish General Hospital, McGill University and Segal Cancer Center, Lady Davis Institute of Medical Research, Montreal, QC, Canada
| | - Euridice Carmona
- Centre de recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM) and Institut du Cancer de Montréal, Montreal, QC, Canada
| | - Kathleen Oros Klein
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Université de Montréal, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, and Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Sonja Billes
- R&D Department, AOA Dx Inc, Cambridge, MA, United States
| | - Ahmed E. Dawod
- R&D Department, AOA Dx Inc, Cambridge, MA, United States
| | - Prasad Gawande
- R&D Department, AOA Dx Inc, Cambridge, MA, United States
| | | | - Anne-Marie Mes-Masson
- Centre de recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM) and Institut du Cancer de Montréal, Montreal, QC, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Celia M. T. Greenwood
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Université de Montréal, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, and Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Walter H. Gotlieb
- Translational Cancer Center, Lady Davis Institute-Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Ob-Gyn, Jewish General Hospital, McGill University and Segal Cancer Center, Lady Davis Institute of Medical Research, Montreal, QC, Canada
| | - H. Uri Saragovi
- Translational Cancer Center, Lady Davis Institute-Jewish General Hospital, McGill University, Montreal, QC, Canada
- Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
- Ophthalmology and Vision Science. McGill University, Montreal, QC, Canada
- *Correspondence: H. Uri Saragovi,
| |
Collapse
|
9
|
Herzog C, Marín F, Jones A, Evans I, Reisel D, Redl E, Schreiberhuber L, Paytubi S, Pelegrina B, Carmona Á, Peremiquel-Trillas P, Frias-Gomez J, Pineda M, Brunet J, Ponce J, Matias-Guiu X, de Sanjosé S, Alemany L, Olaitan A, Wong M, Jurkovic D, Crosbie EJ, Rosenthal AN, Bjørge L, Zikan M, Dostalek L, Cibula D, Sundström K, Dillner J, Costas L, Widschwendter M. A Simple Cervicovaginal Epigenetic Test for Screening and Rapid Triage of Women With Suspected Endometrial Cancer: Validation in Several Cohort and Case/Control Sets. J Clin Oncol 2022; 40:3828-3838. [PMID: 36001862 PMCID: PMC9671754 DOI: 10.1200/jco.22.00266] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Endometrial cancer (EC) incidence has been rising over the past 10 years. Delays in diagnosis reduce survival and necessitate more aggressive treatment. We aimed to develop and validate a simple, noninvasive, and reliable triage test for EC to reduce the number of invasive diagnostic procedures and improve patient survival. METHODS We developed a test to screen and triage women with suspected EC using 726 cervical smear samples from women with and without EC, and validated the test in 562 cervicovaginal samples using three different collection methods (cervical smear: n = 248; vaginal swab: n = 63; and self-collection: n = 251) and four different settings (case/control: n = 388; cohort of women presenting with postmenopausal bleeding: n = 63; a cohort of high-risk women with Lynch syndrome: n = 25; and a nested case/control setting from a screening cohort and samples taken up to 3 years before EC diagnosis: n = 86). RESULTS We describe the Women's cancer risk IDentification - quantitative polymerase chain reaction test for Endometrial Cancer (WID-qEC), a three-marker test that evaluates DNA methylation in gene regions of GYPC and ZSCAN12. In cervical, self-collected, and vaginal swab samples derived from symptomatic patients, it detected EC with sensitivities of 97.2% (95% CI, 90.2 to 99.7), 90.1% (83.6 to 94.6), and 100% (63.1 to 100), respectively, and specificities of 75.8% (63.6 to 85.5), 86.7% (79.3 to 92.2), and 89.1% (77.8 to 95.9), respectively. The WID-qEC identified 90.9% (95% CI, 70.8 to 98.9) of EC cases in samples predating diagnosis up to 1 year. Test performance was similar across menopausal status, age, stage, grade, ethnicity, and histology. CONCLUSION The WID-qEC is a noninvasive reliable test for triage of women with symptoms suggestive of ECs. Because of the potential for self-collection, it could improve early diagnosis and reduce the reliance for in-person visits.
Collapse
Affiliation(s)
- Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Innsbruck, Austria,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
| | - Fátima Marín
- Hereditary Cancer Group, Catalan Institute of Oncology, IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain,Consortium for Biomedical Research in Cancer—CIBERONC, Carlos III Institute of Health, Madrid, Spain
| | - Allison Jones
- Department of Women's Cancer, University College London, London, United Kingdom
| | - Iona Evans
- Department of Women's Cancer, University College London, London, United Kingdom
| | - Daniel Reisel
- Department of Women's Cancer, University College London, London, United Kingdom
| | - Elisa Redl
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Innsbruck, Austria,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
| | - Lena Schreiberhuber
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Innsbruck, Austria,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria
| | - Sonia Paytubi
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Beatriz Pelegrina
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Álvaro Carmona
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Paula Peremiquel-Trillas
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jon Frias-Gomez
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Group, Catalan Institute of Oncology, IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain,Consortium for Biomedical Research in Cancer—CIBERONC, Carlos III Institute of Health, Madrid, Spain
| | - Joan Brunet
- Hereditary Cancer Group, Catalan Institute of Oncology, IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain,Consortium for Biomedical Research in Cancer—CIBERONC, Carlos III Institute of Health, Madrid, Spain,Hereditary Cancer Group, Catalan Institute of Oncology, IDIBGI, Girona, Spain
| | - Jordi Ponce
- Consortium for Biomedical Research in Cancer—CIBERONC, Carlos III Institute of Health, Madrid, Spain,Department of Gynecology, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Matias-Guiu
- Consortium for Biomedical Research in Cancer—CIBERONC, Carlos III Institute of Health, Madrid, Spain,Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | - Laia Alemany
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain,Consortium for Biomedical Research in Epidemiology and Public Health—CIBERESP, Carlos III Institute of Health, Madrid, Spain
| | | | - Michael Wong
- University College Hospital, London, United Kingdom
| | | | - Emma J. Crosbie
- Department of Obstetrics and Gynaecology, Manchester Academic Health Science Center, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom,Gynaecological Oncology Research Group, Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Adam N. Rosenthal
- Department of Women's Cancer, University College London, London, United Kingdom
| | - Line Bjørge
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway,Department of Clinical Science, Center for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
| | - Michal Zikan
- Department of Gynecology and Obstetrics, Charles University in Prague, First Faculty of Medicine and Bulovka University Hospital, Czech Republic
| | - Lukas Dostalek
- Department of Obstetrics and Gynecology, First Faculty of Medicine, Gynaecologic Oncology Center, Charles University in Prague, General University Hospital in Prague, Prague, Czech Republic
| | - David Cibula
- Department of Obstetrics and Gynecology, First Faculty of Medicine, Gynaecologic Oncology Center, Charles University in Prague, General University Hospital in Prague, Prague, Czech Republic
| | - Karin Sundström
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Dillner
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Laura Costas
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain,Consortium for Biomedical Research in Epidemiology and Public Health—CIBERESP, Carlos III Institute of Health, Madrid, Spain
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Innsbruck, Austria,Institute for Biomedical Aging Research, Universität Innsbruck, Innsbruck, Austria,Department of Women's Cancer, University College London, London, United Kingdom,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden,Martin Widschwendter, MD, European Translational Oncology Prevention and Screening (EUTOPS) Institute, Milser Str 10, 6060 Hall in Tirol, Austria; e-mail:
| |
Collapse
|
10
|
Gunderson CC, Radhakrishnan R, Gomathinayagam R, Husain S, Aravindan S, Moore KM, Dhanasekaran DN, Jayaraman M. Circulating Tumor Cell-Free DNA Genes as Prognostic Gene Signature for Platinum Resistant Ovarian Cancer Diagnosis. Biomark Insights 2022; 17:11772719221088404. [PMID: 35370397 PMCID: PMC8966103 DOI: 10.1177/11772719221088404] [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: 07/08/2021] [Accepted: 02/10/2022] [Indexed: 11/17/2022] Open
Abstract
Clinical management of gynecological cancer begins by optimal debulking with first-line platinum-based chemotherapy. However, in ~80% patients, ovarian cancer will recur and is lethal. Prognostic gene signature panel identifying platinum-resistance enables better patient stratification for precision therapy. Retrospectively collected serum from 11 "poor" (<6 months progression free interval [PFI]) and 22 "favorable" (>24 months PFI) prognosis patients, were evaluated using circulating cell-free DNA (cfDNA). DNA from both groups showed 50 to 10 000 bp fragments. Pairwise analysis of sequenced cfDNA from patients showed that gene dosages were higher for 29 genes and lower for 64 genes in poor than favorable prognosis patients. Gene ontology analysis of higher dose genes predominantly grouped into cytoskeletal proteins, while lower dose genes, as hydrolases and receptors. Higher dosage genes searched for cancer-relatedness in Reactome database indicated 15 genes were referenced with cancer. Among them 3 genes, TGFBR2, ZMIZ2, and NRG2, were interacting with more than 4 cancer-associated genes. Protein expression analysis of tumor samples indicated that TGFBR2 was downregulated and ZMIZ2 was upregulated in poor prognosis patients. Our results indicate that the cfDNA gene dosage combined with protein expression in tumor samples can serve as gene signature panel for prognosis determination amongst ovarian cancer patients.
Collapse
Affiliation(s)
- Camille C Gunderson
- Section of Gynecologic Oncology, Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | | | - Rohini Gomathinayagam
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Sanam Husain
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Sheeja Aravindan
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kathleen M Moore
- Section of Gynecologic Oncology, Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Danny N Dhanasekaran
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Muralidharan Jayaraman
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA,Muralidharan Jayaraman, Department of Cell Biology, University of Oklahoma Health Sciences Center, Stephenson Cancer Center, 975 NE 10th Street, BRC416, Oklahoma City, OK 73104, USA.
| |
Collapse
|
11
|
Cao YN, Li QZ, Liu YX. Discovered Key CpG Sites by Analyzing DNA Methylation and Gene Expression in Breast Cancer Samples. Front Cell Dev Biol 2022; 10:815843. [PMID: 35178391 PMCID: PMC8844453 DOI: 10.3389/fcell.2022.815843] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/06/2022] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most common cancer in the world, and DNA methylation plays a key role in the occurrence and development of breast cancer. However, the effect of DNA methylation in different gene functional regions on gene expression and the effect of gene expression on breast cancer is not completely clear. In our study, we computed and analyzed DNA methylation, gene expression, and clinical data in the TCGA database. Firstly, we calculated the distribution of abnormal DNA methylated probes in 12 regions, found the abnormal DNA methylated probes in down-regulated genes were highly enriched, and the number of hypermethylated probes in the promoter region was 6.5 times than that of hypomethylated probes. Secondly, the correlation coefficients between abnormal DNA methylated values in each functional region of differentially expressed genes and gene expression values were calculated. Then, co-expression analysis of differentially expressed genes was performed, 34 hub genes in cancer-related pathways were obtained, of which 11 genes were regulated by abnormal DNA methylation. Finally, a multivariate Cox regression analysis was performed on 27 probes of 11 genes. Three DNA methylation probes (cg13569051 and cg14399183 of GSN, and cg25274503 of CAV2) related to survival were used to construct a prognostic model, which has a good prognostic ability. Furthermore, we found that the cg25274503 hypermethylation in the promoter region inhibited the expression of the CAV2, and the hypermethylation of cg13569051 and cg14399183 in the 5′UTR region inhibited the expression of GSN. These results may provide possible molecular targets for breast cancer.
Collapse
Affiliation(s)
- Yan-Ni Cao
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, China
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, China.,The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Yu-Xian Liu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, China
| |
Collapse
|
12
|
Yari H, Shabani S, Nafissi N, Majidzadeh T, Mahjoubi F. Investigation of promoter methylation patterns association with genes expression profile of ISL1, MGMT and DMNT3b in tissue of breast cancer patients. Mol Biol Rep 2022; 49:847-857. [PMID: 34997427 DOI: 10.1007/s11033-021-06546-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 07/02/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVES Cancer initiation and progression could influenced by both genetic and epigenetic events revealing of the overlap between epigenetic and genetic alteration can give important insights into cancer biology. METHODS AND RESULTS In this experiment ISL1, MGMT, DMNT3b genes were candidate to investigate both methylation status and expression profile by using methylation-specific PCR and real time PCR in 40 breast cancer patients, respectively, also we have assessed relation of the promoter methylation status and expression variation of the target genes. The mean level of methylation of ISL1 and MGMT in tumor tissues were significantly greater than normal tissues. In Contrast, DMNT3b gene was showed lower mean level of methylation in tumor tissue compared to normal tissues, however, this was not statistically significant. Relative expression analysis was displayed a significant reduction in expression level of ISL1 and MGMT in tumor tissues. Furthermore, there was a meaningful association between down expression of ISL1 with histological grade, Her2 and ER status. Moreover, MGMT down expression was significantly associated with tumor sizes. Any remarkable relation was not observed between DMNT3b expression level and clinic pathological features. At the end, significant relation between methylation status and expression level has been revealed. CONCLUSIONS In this study all observed results were exactly in line with the results were obtained from articles which were based on the methylation research and illustrate that the real-time PCR and methylation methods are in correlated with each other, furthermore, selected genes are capable to use as a potential biomarkers, however, more research on extended cases are needed.
Collapse
Affiliation(s)
- Hadi Yari
- Human Genetics Dept., Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology (NIGEB), Pajouhesh Blv, Tehran Karaj High Way, Tehran, Iran
| | - Samira Shabani
- Human Genetics Dept., Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology (NIGEB), Pajouhesh Blv, Tehran Karaj High Way, Tehran, Iran
| | - Nahid Nafissi
- Surgery Department of General Surgery, Iran University of Medical Science, Tehran, Iran
| | - Tayebeh Majidzadeh
- Human Genetics Dept., Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology (NIGEB), Pajouhesh Blv, Tehran Karaj High Way, Tehran, Iran
| | - Frouzandeh Mahjoubi
- Human Genetics Dept., Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology (NIGEB), Pajouhesh Blv, Tehran Karaj High Way, Tehran, Iran.
| |
Collapse
|
13
|
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: 0.3] [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
|
14
|
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: 16] [Impact Index Per Article: 4.0] [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
|
15
|
Raos D, Ulamec M, Katusic Bojanac A, Bulic-Jakus F, Jezek D, Sincic N. Epigenetically inactivated RASSF1A as a tumor biomarker. Bosn J Basic Med Sci 2021; 21:386-397. [PMID: 33175673 PMCID: PMC8292865 DOI: 10.17305/bjbms.2020.5219] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/11/2020] [Indexed: 12/18/2022] Open
Abstract
RASSF1A, one of the eight isoforms of the RASSF1 gene, is a tumor suppressor gene that influences tumor initiation and development. In cancer, RASSF1A is frequently inactivated by mutations, loss of heterozygosity, and, most commonly, by promoter hypermethylation. Epigenetic inactivation of RASSF1A was detected in various cancer types and led to significant interest; current research on RASSF1A promoter methylation focuses on its roles as an epigenetic tumor biomarker. Typically, researchers analyzed genomic DNA (gDNA) to measure the amount of RASSF1A promoter methylation. Cell-free DNA (cfDNA) from liquid biopsies is a recent development showing promise as an early cancer diagnostic tool using biomarkers, such as RASSF1A. This review discusses the evidence on aberrantly methylated RASSF1A in gDNA and cfDNA from different cancer types and its utility for early cancer diagnosis, prognosis, and surveillance. We compared methylation frequencies of RASSF1A in gDNA and cfDNA in various cancer types. The weaknesses and strengths of these analyses are discussed. In conclusion, although the importance of RASSSF1A methylation to cancer has been established and is included in several diagnostic panels, its diagnostic utility is still experimental.
Collapse
Affiliation(s)
- Dora Raos
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia; Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia; Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Monika Ulamec
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia; Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia; Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia; Department of Pathology, University of Zagreb School of Dental Medicine and School of Medicine, Zagreb, Croatia
| | - Ana Katusic Bojanac
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia; Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Floriana Bulic-Jakus
- University of Zagreb School of Medicine, Department of Medical Biology, Zagreb, Croatia
| | - Davor Jezek
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia; Department of Histology and Embryology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Nino Sincic
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia; Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia; Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| |
Collapse
|
16
|
Liu Z, Liu J, Liu R, Xue M, Zhang W, Zhao X, Zhu J, Xia P. Downregulated ZNF132 predicts unfavorable outcomes in breast Cancer via Hypermethylation modification. BMC Cancer 2021; 21:367. [PMID: 33827486 PMCID: PMC8028803 DOI: 10.1186/s12885-021-08112-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/28/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND An important mechanism that promoter methylation-mediated gene silencing for gene inactivation is identified in human tumorigenesis. Methylated genes have been found in breast cancer (BC) and beneficial biomarkers for early diagnosis. Prognostic assessment of breast cancer remain little known. Zinc finger protein 132 (ZNF132) is downregulated by promoter methylation in prostate cancer and esophageal squamous cell carcinoma. However, no study provides information on the status of ZNF132, analyzes diagnosis and prognostic significance of ZNF132 in BC. METHODS In the present study, the expression of ZNF132 mRNA and protein level was determined based on the Cancer Genome Atlas (TCGA) RNA-Seq database and clinical samples analysis and multiple cancer cell lines verification. P rognostic significance of ZNF132 in BC was assessed using the Kaplan-Meier plotter. Molecular mechanisms exploration of ZNF132 in BC was performed using the multiple bioinformatic tools. Hypermethylated status of ZNF132 in BC cell lines was confirmed via Methylation specific polymerase chain reaction (MSP) analysis. RESULTS The expression of ZNF132 both the mRNA and protein levels was downregulated in BC tissues. These results were obtained based on TCGA database and clinical sample analysis. Survival analysis from the Kaplan-Meier plotter revealed that the lower level of ZNF132 was associated with a shorter Relapse Free Survival (RFS) time. Receiver operating characteristic curve (ROC) of 0.887 confirmed ZNF132 had powerful sensitivity and specificity to distinguish between BC and adjacent normal tissues. Bioinformatic analysis showed that 6% ((58/960)) alterations of ZNF132 were identified from cBioPortal. ZNF132 participated in multiple biological pathways based on the Gene Set Enrichment Analysis (GSEA) database including the regulation of cell cycle and glycolysis. Finally, MSP analysis demonstrated that ZNF132 was hypermethylated in a panel of breast cancer cell lines and 5-aza-2'-deoxycytidine (5-Aza-dC) treatment restored ZNF132 expression in partial cell lines. CONCLUSIONS Results revealed that hypermethylation of ZNF132 contributed to its downregulated expression and could be identified as a new diagnostic and prognostic marker in BC.
Collapse
Affiliation(s)
- Zhao Liu
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xi'an, 710061, Shaanxi, China
| | - Jiaxin Liu
- Department of Gerontological Surgery, The First Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xi'an, 710061, Shaanxi, China
| | - Ruimiao Liu
- Department of Clinical Laboratory, Peoples Hospital of Xi'an (Fourth Hospital of Xi'an), Xi'an, 710004, Shaanxi, China
| | - Man Xue
- Department of General Surgery, Tongchuan Mining Bureau Central Hospital, Tongchuan, 727000, Shaanxi, China
| | - Weifan Zhang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xi'an, 710061, Shaanxi, China
| | - Xinhui Zhao
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xi'an, 710061, Shaanxi, China
| | - Jiang Zhu
- Department of Breast Disease, Shaanxi Provincial Cancer Hospital, Xi'an, 710061, Shaanxi, China
| | - Peng Xia
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xi'an, 710061, Shaanxi, China.
| |
Collapse
|
17
|
Guo Q, Wang T, Yang Y, Gao L, Zhao Q, Zhang W, Xi T, Zheng L. Transcriptional Factor Yin Yang 1 Promotes the Stemness of Breast Cancer Cells by Suppressing miR-873-5p Transcriptional Activity. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:527-541. [PMID: 32711380 PMCID: PMC7381513 DOI: 10.1016/j.omtn.2020.06.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/20/2020] [Accepted: 06/22/2020] [Indexed: 01/01/2023]
Abstract
Transcription factor Yin Yang 1 (YY1) is upregulated in multiple tumors and plays essential roles in tumor proliferation and metastasis. However, the function of YY1 in breast cancer stemness remains unclear. Herein, we found that YY1 expression was negatively correlated with the overall survival and relapse-free survival of breast cancer patients and positively correlated with the expression of stemness markers in breast cancer. Overexpression of YY1 increased the expression of stemness markers, elevated CD44+CD24- cell sub-population, and enhanced the capacity of cell spheroid formation and tumor-initiation. In contrast, YY1 knockdown exhibited the opposite effects. Mechanistically, YY1 decreased microRNA-873-5p (miR-873-5p) level by recruiting histone deacetylase 4 (HDAC4) and HDAC9 to miR-873-5p promoter and thus increasing the deacetylation level of miR-873-5p promoter. Sequentially, YY1 activated the downstream PI3K/AKT and ERK1/2 pathways, which have been confirmed to be suppressed by miR-873-5p in our recent work. Moreover, the suppressed effect of YY1/miR-873-5p axis on the stemness of breast cancer cells was partially dependent on PI3K/AKT and ERK1/2 pathways. Finally, it was found that the YY1/miR-873-5p axis is involved in the chemoresistance of breast cancer cells. Our study defines a novel YY1/miR-873-5p axis responsible for the stemness of breast cancer cells.
Collapse
Affiliation(s)
- Qianqian Guo
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, 127 Dongming Road, Zhengzhou 450003, People's Republic of China
| | - Ting Wang
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Yue Yang
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Lanlan Gao
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Qiong Zhao
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Wenzhou Zhang
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, 127 Dongming Road, Zhengzhou 450003, People's Republic of China
| | - Tao Xi
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China.
| | - Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China.
| |
Collapse
|
18
|
Abstract
Ovarian cancer has the worst survival rate because it is typically diagnosed at advanced stage. Despite treatment, the disease commonly recurs due to chemo-resistance. Liquid biopsy, based on minimally invasive blood tests, has the advantage of following tumor evolution in real time, offering novel insights on cancer prevention and treatment. Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating cell-free microRNAs (cfmiRNAs) and circulating exosomes represent the major components of liquid biopsy. In this chapter, we provide an overview of recent research on CTCs, ctDNA, cfmiRNAs and exosomes in ovarian cancer. We also focus on the clinical value of liquid biopsy in early diagnosis, prognosis, treatment response, as well as screening in the general population.
Collapse
Affiliation(s)
- Lydia Giannopoulou
- Analysis of Circulating Tumor Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens, Greece
| | - Evi S Lianidou
- Analysis of Circulating Tumor Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens, Greece.
| |
Collapse
|
19
|
Multinu F, Chen J, Madison JD, Torres M, Casarin J, Visscher D, Shridhar V, Bakkum-Gamez J, Sherman M, Wentzensen N, Mariani A, Walther-Antonio M. Analysis of DNA methylation in endometrial biopsies to predict risk of endometrial cancer. Gynecol Oncol 2020; 156:682-688. [PMID: 31902687 DOI: 10.1016/j.ygyno.2019.12.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/14/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To determine whether analysis of methylated DNA in benign endometrial biopsy (EB) specimens is associated with risk of endometrial cancer (EC). METHODS We identified 23 women with EBs performed at Mayo Clinic diagnosed as normal (n = 14) or hyperplasia (n = 9) and who later developed endometrial cancer after a median interval of 1 year. Cases were matched 1:1 with patients with benign EBs who did not develop EC (controls) by histology of benign EB (normal endometrium vs. endometrial hyperplasia without atypia), date of EB, age at EB, and length of post-biopsy follow-up. DNA extracted from formalin-fixed paraffin-embedded tissues underwent pyrosequencing to determine percent methylation of promoter region CpGs at 26 loci in 4 genes (ADCYAP1, HAND2, MME, RASSF1A) previously reported as methylated in EC. RESULTS After pathologic review, 23 matched pairs of cases and controls were identified (14 normal, 9 hyperplasia without atypia per group). Among cases, median time from benign EB to EC was 1 year (range 2 days - 9.2 years). We evaluated 26 CpG sites within 4 genes and found a consistent trend of increasing percentage of methylation from control to case to EC for all CpGs. At the gene-level, mean methylation events of ADCYAP1 and HAND2 in cases were significantly higher than control (p = 0.015 and p = 0.021, respectively). Though the other genes did not reach statistical significance, we observed an increased methylation trend among all genes. Area-under-curve (AUC) calculations (predicting future development of EC in the setting of benign EB) for ADCYAP1 and HAND2 were 0.71 (95% CI 0.55-0.88) and 0.83 (95% CI 0.64-1, respectively). CONCLUSIONS This proof-of-principle study provides evidence that specific methylation patterns in benign EB correlate with future development of EC.
Collapse
Affiliation(s)
- Francesco Multinu
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Jun Chen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States of America
| | - Joseph D Madison
- Department of Surgery, Mayo Clinic, Rochester, MN, United States of America; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Michelle Torres
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Jvan Casarin
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Daniel Visscher
- Department of Laboratory Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Viji Shridhar
- Department of Laboratory Medicine, Mayo Clinic, Rochester, MN, United States of America
| | - Jamie Bakkum-Gamez
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Mark Sherman
- Department of Health Sciences Research and Division of Epidemiology, Mayo Clinic, Jacksonville, FL, United States of America
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Andrea Mariani
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Marina Walther-Antonio
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America; Department of Surgery, Mayo Clinic, Rochester, MN, United States of America; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States of America.
| |
Collapse
|
20
|
Wu TI, Huang RL, Su PH, Mao SP, Wu CH, Lai HC. Ovarian cancer detection by DNA methylation in cervical scrapings. Clin Epigenetics 2019; 11:166. [PMID: 31775891 PMCID: PMC6881994 DOI: 10.1186/s13148-019-0773-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/24/2019] [Indexed: 02/08/2023] Open
Abstract
Background Ovarian cancer (OC) is the most lethal gynecological cancer, worldwide, largely due to its vague and nonspecific early stage symptoms, resulting in most tumors being found at advanced stages. Moreover, due to its relative rarity, there are currently no satisfactory methods for OC screening, which remains a controversial and cost-prohibitive issue. Here, we demonstrate that Papanicolaou test (Pap test) cervical scrapings, instead of blood, can reveal genetic/epigenetic information for OC detection, using specific and sensitive DNA methylation biomarkers. Results We analyzed the methylomes of tissues (50 OC tissues versus 6 normal ovarian epithelia) and cervical scrapings (5 OC patients versus 10 normal controls), and integrated public methylomic datasets, including 79 OC tissues and 6 normal tubal epithelia. Differentially methylated genes were further classified by unsupervised hierarchical clustering, and each candidate biomarker gene was verified in both OC tissues and cervical scrapings by either quantitative methylation-specific polymerase chain reaction (qMSP) or bisulfite pyrosequencing. A risk-score by logistic regression was generated for clinical application. One hundred fifty-one genes were classified into four clusters, and nine candidate hypermethylated genes from these four clusters were selected. Among these, four genes fulfilled our selection criteria and were validated in training and testing set, respectively. The OC detection accuracy was demonstrated by area under the receiver operating characteristic curves (AUCs) in 0.80–0.83 of AMPD3, 0.79–0.85 of AOX1, 0.78–0.88 of NRN1, and 0.82–0.85 of TBX15. From this, we found OC-risk score, equation generated by logistic regression in training set and validated an OC-associated panel comprising AMPD3, NRN1, and TBX15, reaching a sensitivity of 81%, specificity of 84%, and OC detection accuracy of 0.91 (95% CI, 0.82–1) in testing set. Conclusions Ovarian cancer detection from cervical scrapings is feasible, using particularly promising epigenetic biomarkers such as AMPD3/NRN1/TBX15. Further validation is warranted.
Collapse
Affiliation(s)
- Tzu-I Wu
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Obstetrics and Gynecology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Rui-Lan Huang
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Po-Hsuan Su
- Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Shih-Peng Mao
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Chen-Hsuan Wu
- Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Tao-Yuan, Taiwan.,Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan. .,Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan. .,Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan. .,Department and Graduate Institute of Biochemistry, National Defense Medical Center, No.291, Jhongjheng Rd., Jhonghe, New Taipei, 23561, Taiwan.
| |
Collapse
|
21
|
Singh A, Gupta S, Sachan M. Epigenetic Biomarkers in the Management of Ovarian Cancer: Current Prospectives. Front Cell Dev Biol 2019; 7:182. [PMID: 31608277 PMCID: PMC6761254 DOI: 10.3389/fcell.2019.00182] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer (OC) causes significant morbidity and mortality as neither detection nor screening of OC is currently feasible at an early stage. Difficulty to promptly diagnose OC in its early stage remains challenging due to non-specific symptoms in the early-stage of the disease, their presentation at an advanced stage and poor survival. Therefore, improved detection methods are urgently needed. In this article, we summarize the potential clinical utility of epigenetic signatures like DNA methylation, histone modifications, and microRNA dysregulation, which play important role in ovarian carcinogenesis and discuss its application in development of diagnostic, prognostic, and predictive biomarkers. Molecular characterization of epigenetic modification (methylation) in circulating cell free tumor DNA in body fluids offers novel, non-invasive approach for identification of potential promising cancer biomarkers, which can be performed at multiple time points and probably better reflects the prevailing molecular profile of cancer. Current status of epigenetic research in diagnosis of early OC and its management are discussed here with main focus on potential diagnostic biomarkers in tissue and body fluids. Rapid and point of care diagnostic applications of DNA methylation in liquid biopsy has been precluded as a result of cumbersome sample preparation with complicated conventional methods of isolation. New technologies which allow rapid identification of methylation signatures directly from blood will facilitate sample-to answer solutions thereby enabling next-generation point of care molecular diagnostics. To date, not a single epigenetic biomarker which could accurately detect ovarian cancer at an early stage in either tissue or body fluid has been reported. Taken together, the methodological drawbacks, heterogeneity associated with ovarian cancer and non-validation of the clinical utility of reported potential biomarkers in larger ovarian cancer populations has impeded the transition of epigenetic biomarkers from lab to clinical settings. Until addressed, clinical implementation as a diagnostic measure is a far way to go.
Collapse
Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| |
Collapse
|
22
|
Kumar R, Paul AM, Rameshwar P, Pillai MR. Epigenetic Dysregulation at the Crossroad of Women's Cancer. Cancers (Basel) 2019; 11:cancers11081193. [PMID: 31426393 PMCID: PMC6721458 DOI: 10.3390/cancers11081193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
An increasingly number of women of all age groups are affected by cancer, despite substantial progress in our understanding of cancer pathobiology, the underlying genomic alterations and signaling cascades, and cellular-environmental interactions. Though our understanding of women’s cancer is far more complete than ever before, there is no comprehensive model to explain the reasons behind the increased incidents of certain reproductive cancer among older as well as younger women. It is generally suspected that environmental and life-style factors affecting hormonal and growth control pathways might help account for the rise of women’s cancers in younger age, as well, via epigenetic mechanisms. Epigenetic regulators play an important role in orchestrating an orderly coordination of cellular signals in gene activity in response to upstream signaling and/or epigenetic modifiers present in a dynamic extracellular milieu. Here we will discuss the broad principles of epigenetic regulation of DNA methylation and demethylation, histone acetylation and deacetylation, and RNA methylation in women’s cancers in the context of gene expression, hormonal action, and the EGFR family of cell surface receptor tyrosine kinases. We anticipate that a better understanding of the epigenetics of women’s cancers may provide new regulatory leads and further fuel the development of new epigenetic biomarkers and therapeutic approaches.
Collapse
Affiliation(s)
- Rakesh Kumar
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India.
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA.
| | - Aswathy Mary Paul
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
- Graduate Degree Program, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Pranela Rameshwar
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - M Radhakrishna Pillai
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
| |
Collapse
|
23
|
Downs BM, Mercado-Rodriguez C, Cimino-Mathews A, Chen C, Yuan JP, Van Den Berg E, Cope LM, Schmitt F, Tse GM, Ali SZ, Meir-Levi D, Sood R, Li J, Richardson AL, Mosunjac MB, Rizzo M, Tulac S, Kocmond KJ, de Guzman T, Lai EW, Rhees B, Bates M, Wolff AC, Gabrielson E, Harvey SC, Umbricht CB, Visvanathan K, Fackler MJ, Sukumar S. DNA Methylation Markers for Breast Cancer Detection in the Developing World. Clin Cancer Res 2019; 25:6357-6367. [PMID: 31300453 DOI: 10.1158/1078-0432.ccr-18-3277] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/04/2019] [Accepted: 07/02/2019] [Indexed: 12/21/2022]
Abstract
PURPOSE An unmet need in low-resource countries is an automated breast cancer detection assay to prioritize women who should undergo core breast biopsy and pathologic review. Therefore, we sought to identify and validate a panel of methylated DNA markers to discriminate between cancer and benign breast lesions using cells obtained by fine-needle aspiration (FNA).Experimental Design: Two case-control studies were conducted comparing cancer and benign breast tissue identified from clinical repositories in the United States, China, and South Africa for marker selection/training (N = 226) and testing (N = 246). Twenty-five methylated markers were assayed by Quantitative Multiplex-Methylation-Specific PCR (QM-MSP) to select and test a cancer-specific panel. Next, a pilot study was conducted on archival FNAs (49 benign, 24 invasive) from women with mammographically suspicious lesions using a newly developed, 5-hour, quantitative, automated cartridge system. We calculated sensitivity, specificity, and area under the receiver-operating characteristic curve (AUC) compared with histopathology for the marker panel. RESULTS In the discovery cohort, 10 of 25 markers were selected that were highly methylated in breast cancer compared with benign tissues by QM-MSP. In the independent test cohort, this panel yielded an AUC of 0.937 (95% CI = 0.900-0.970). In the FNA pilot, we achieved an AUC of 0.960 (95% CI = 0.883-1.0) using the automated cartridge system. CONCLUSIONS We developed and piloted a fast and accurate methylation marker-based automated cartridge system to detect breast cancer in FNA samples. This quick ancillary test has the potential to prioritize cancer over benign tissues for expedited pathologic evaluation in poorly resourced countries.
Collapse
Affiliation(s)
- Bradley M Downs
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Ashley Cimino-Mathews
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chuang Chen
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Jing-Ping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Eunice Van Den Berg
- Department of Anatomical Pathology, University of Witwaterstrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Leslie M Cope
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Fernando Schmitt
- Medical Faculty of Porto University, Institute of Molecular Pathology and Immunology of Porto University, Porto, Portugal
| | - Gary M Tse
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Syed Z Ali
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Danielle Meir-Levi
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rupali Sood
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Juanjuan Li
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Andrea L Richardson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marina B Mosunjac
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Monica Rizzo
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
| | | | | | | | | | | | | | - Antonio C Wolff
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Edward Gabrielson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Susan C Harvey
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher B Umbricht
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kala Visvanathan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Bloomberg School of Public Health, Baltimore, Maryland
| | - Mary Jo Fackler
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| |
Collapse
|
24
|
Costas L, Frias-Gomez J, Guardiola M, Benavente Y, Pineda M, Pavón MÁ, Martínez JM, Climent M, Barahona M, Canet J, Paytubi S, Salinas M, Palomero L, Bianchi I, Reventós J, Capellà G, Diaz M, Vidal A, Piulats JM, Aytés Á, Ponce J, Brunet J, Bosch FX, Matias-Guiu X, Alemany L, de Sanjosé S. New perspectives on screening and early detection of endometrial cancer. Int J Cancer 2019; 145:3194-3206. [PMID: 31199503 DOI: 10.1002/ijc.32514] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/27/2019] [Accepted: 05/31/2019] [Indexed: 12/17/2022]
Abstract
Due to the anatomical continuity of the uterine cavity with the cervix, genomic exploitation of material from routine Pap smears and other noninvasive sampling methods represent a unique opportunity to detect signs of disease using biological material shed from the upper genital tract. Recent research findings offer a promising perspective in the detection of endometrial cancer, but certain questions need to be addressed in order to accelerate the implementation of novel technologies in a routine screening or clinical setting. We discuss here new perspectives on detection of endometrial cancer using genomic and other biomarkers in minimally invasive sampling methods with a special focus on public health classic screening criteria, highlighting current gaps in knowledge.
Collapse
Affiliation(s)
- Laura Costas
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Jon Frias-Gomez
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Magdalena Guardiola
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Consortium for Biomedical Research in Epidemiology and Public Health (CIBER Epidemiología y Salud Pública, CIBERESP), Madrid, Spain
| | - Marta Pineda
- Hereditary Cancer Program, IDIBELL, Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain
| | - Miquel Á Pavón
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain
| | - José M Martínez
- Department of Gynecology and Obstetrics, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Maite Climent
- Department of Gynecology and Obstetrics, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Marc Barahona
- Department of Gynecology and Obstetrics, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Júlia Canet
- Hereditary Cancer Program, IDIBELL, Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain
| | - Sonia Paytubi
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Mónica Salinas
- Hereditary Cancer Program, IDIBELL, Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain
| | - Luis Palomero
- Program Against Cancer Therapeutic Resistance (ProCURE), IDIBELL, Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain
| | - Ilaria Bianchi
- ASSIR Delta, Direcció d'Atenció Primària Costa de Ponent, SAP Delta del Llobregat, Barcelona, Spain
| | - Jaume Reventós
- Departament de Ciències Bàsiques, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Gabriel Capellà
- Hereditary Cancer Program, IDIBELL, Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain
| | - Mireia Diaz
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain
| | - August Vidal
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Josep M Piulats
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Department of Medical Oncology, IDIBELL, Catalan Institute of Cancer, Hospitalet de Llobregat, Barcelona, Spain
| | - Álvaro Aytés
- Program Against Cancer Therapeutic Resistance (ProCURE), IDIBELL, Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain
| | - Jordi Ponce
- Department of Gynecology and Obstetrics, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Joan Brunet
- Hereditary Cancer Program, IDIBELL, Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Medical Sciences Department, School of Medicine, University of Girona, Girona, Spain
| | - Francesc X Bosch
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain
| | - Xavier Matias-Guiu
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Madrid, Spain.,Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Laia Alemany
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Consortium for Biomedical Research in Epidemiology and Public Health (CIBER Epidemiología y Salud Pública, CIBERESP), Madrid, Spain
| | - Silvia de Sanjosé
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER Epidemiología y Salud Pública, CIBERESP), Madrid, Spain.,PATH, Seattle, WA
| | | |
Collapse
|
25
|
Liquid Biopsies for Ovarian Carcinoma: How Blood Tests May Improve the Clinical Management of a Deadly Disease. Cancers (Basel) 2019. [PMID: 31167492 DOI: 10.3390/cancers11060774]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Ovarian cancers (OvC) are frequent, with more than 22,000 new cases each year for 14,000 deaths in the United States. Except for patients with BRCA1 or BRCA2 mutations, diagnostic methods, prognostic tools, and therapeutic strategies have not much improved in the last two decades. High throughput tumor molecular analyses have identified important alterations involved in ovarian carcinoma growth and spreading. However, these data have not modified the clinical management of most of patients. Moreover, tumor sample collection requires invasive procedures not adapted to objectives, such as the screening, prediction, or assessment of treatment efficacy, monitoring of residual disease, and early diagnosis of relapse. In recent years, circulating tumor biomarkers (also known as "liquid biopsies") such as circulating tumor cells, circulating nucleotides (DNA or miRNA), or extracellular vesicles, have been massively explored through various indications, platforms, and goals, but their use has not yet been validated in routine practice. This review describes the methods of analysis and results related to liquid biopsies for ovarian epithelial cancer. The different settings that a patient can go through during her journey with OvC are explored: screening and early diagnosis, prognosis, prediction of response to systemic therapies for advanced stages, and monitoring of residual subclinical disease.
Collapse
|
26
|
Mari R, Mamessier E, Lambaudie E, Provansal M, Birnbaum D, Bertucci F, Sabatier R. Liquid Biopsies for Ovarian Carcinoma: How Blood Tests May Improve the Clinical Management of a Deadly Disease. Cancers (Basel) 2019; 11:E774. [PMID: 31167492 PMCID: PMC6627130 DOI: 10.3390/cancers11060774] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 02/07/2023] Open
Abstract
Ovarian cancers (OvC) are frequent, with more than 22,000 new cases each year for 14,000 deaths in the United States. Except for patients with BRCA1 or BRCA2 mutations, diagnostic methods, prognostic tools, and therapeutic strategies have not much improved in the last two decades. High throughput tumor molecular analyses have identified important alterations involved in ovarian carcinoma growth and spreading. However, these data have not modified the clinical management of most of patients. Moreover, tumor sample collection requires invasive procedures not adapted to objectives, such as the screening, prediction, or assessment of treatment efficacy, monitoring of residual disease, and early diagnosis of relapse. In recent years, circulating tumor biomarkers (also known as "liquid biopsies") such as circulating tumor cells, circulating nucleotides (DNA or miRNA), or extracellular vesicles, have been massively explored through various indications, platforms, and goals, but their use has not yet been validated in routine practice. This review describes the methods of analysis and results related to liquid biopsies for ovarian epithelial cancer. The different settings that a patient can go through during her journey with OvC are explored: screening and early diagnosis, prognosis, prediction of response to systemic therapies for advanced stages, and monitoring of residual subclinical disease.
Collapse
Affiliation(s)
- Roxane Mari
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
- CRCM-Department of Medical Oncology, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - Emilie Mamessier
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - Eric Lambaudie
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
- CRCM-Department of Medical Oncology, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - Magali Provansal
- Department of Medical Oncology, Institut Paoli-Calmettes, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - Daniel Birnbaum
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - François Bertucci
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
- CRCM-Department of Medical Oncology, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - Renaud Sabatier
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
- CRCM-Department of Medical Oncology, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| |
Collapse
|
27
|
Mari R, Mamessier E, Lambaudie E, Provansal M, Birnbaum D, Bertucci F, Sabatier R. Liquid Biopsies for Ovarian Carcinoma: How Blood Tests May Improve the Clinical Management of a Deadly Disease. Cancers (Basel) 2019. [PMID: 31167492 DOI: 10.3390/cancers11060774] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Ovarian cancers (OvC) are frequent, with more than 22,000 new cases each year for 14,000 deaths in the United States. Except for patients with BRCA1 or BRCA2 mutations, diagnostic methods, prognostic tools, and therapeutic strategies have not much improved in the last two decades. High throughput tumor molecular analyses have identified important alterations involved in ovarian carcinoma growth and spreading. However, these data have not modified the clinical management of most of patients. Moreover, tumor sample collection requires invasive procedures not adapted to objectives, such as the screening, prediction, or assessment of treatment efficacy, monitoring of residual disease, and early diagnosis of relapse. In recent years, circulating tumor biomarkers (also known as "liquid biopsies") such as circulating tumor cells, circulating nucleotides (DNA or miRNA), or extracellular vesicles, have been massively explored through various indications, platforms, and goals, but their use has not yet been validated in routine practice. This review describes the methods of analysis and results related to liquid biopsies for ovarian epithelial cancer. The different settings that a patient can go through during her journey with OvC are explored: screening and early diagnosis, prognosis, prediction of response to systemic therapies for advanced stages, and monitoring of residual subclinical disease.
Collapse
Affiliation(s)
- Roxane Mari
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
- CRCM-Department of Medical Oncology, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - Emilie Mamessier
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - Eric Lambaudie
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
- CRCM-Department of Medical Oncology, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - Magali Provansal
- Department of Medical Oncology, Institut Paoli-Calmettes, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - Daniel Birnbaum
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - François Bertucci
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
- CRCM-Department of Medical Oncology, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| | - Renaud Sabatier
- CRCM-Predictive Oncology laboratory, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
- CRCM-Department of Medical Oncology, Institut Paoli-Calmettes, Inserm, CNRS, Aix-Marseille Univ, 232 Boulevard Sainte Marguerite, 13009 Marseille, France.
| |
Collapse
|
28
|
Abstract
Over the last years, epigenetic changes, including DNA methylation and histone modifications detected in early tumorigenesis and cancer progression, have been proposed as biomarkers for cancer detection, tumor prognosis, and prediction to treatment response. Importantly for the clinical use of DNA methylation biomarkers, specific methylation signatures can be detected in many body fluids including serum/plasma samples. Several of these potential epigenetic biomarkers detected in women's cancers, colorectal cancers, prostate, pancreatic, gastric, and lung cancers are discussed. Studies conducted in breast cancer, for example, found that aberrant methylation detection of several genes in serum DNA and genome-wide epigenetic change could be used for early breast cancer diagnosis and prediction of breast cancer risk. In colorectal cancers, numerous studies have been conducted to identify specific methylation markers important for CRC detection and in fact clinical assays evaluating the methylation status of SEPT19 gene and vimentin, became commercially available. Furthermore, some epigenetic changes detected in gastric washes have been suggested as potential circulating noninvasive biomarkers for the early detection of gastric cancers. For the early detection of prostate cancer, few epigenetic markers have shown a better sensitivity and specificity than serum PSA, indicating that the inclusion of these markers together with current screening tools, could improve early diagnosis and may reduce unnecessary repeat biopsies. Similarly, in pancreatic cancers, abnormal DNA methylation of several genes including NPTX2, have been suggested as a diagnostic biomarker. Epigenetic dysregulation was also observed in several tumor suppressor genes and miRNAs in lung cancer patients, suggesting the important role of these changes in cancer initiation and progression. In conclusion, epigenetic changes detected in biological fluids could play an essential role in the early detection of several cancer types and this may have a great impact for the cancer precision medicine field.
Collapse
|
29
|
Ibrahim J, Op de Beeck K, Fransen E, Croes L, Beyens M, Suls A, Vanden Berghe W, Peeters M, Van Camp G. Methylation analysis of Gasdermin E shows great promise as a biomarker for colorectal cancer. Cancer Med 2019; 8:2133-2145. [PMID: 30993897 PMCID: PMC6536921 DOI: 10.1002/cam4.2103] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/17/2022] Open
Abstract
In addition to its implication in hereditary hearing loss, the Gasdermin E (GSDME) gene is also a tumor suppressor involved in cancer progression through programmed cell death. GSDME epigenetic silencing through methylation has been shown in some cancer types, but studies are yet to fully explore its diagnostic/prognostic potential in colorectal cancer on a large-scale. We used public data from The Cancer Genome Atlas (TCGA) to investigate differences in GSDME methylation and expression between colorectal cancer and normal colorectal tissue, and between left- and right-sided colorectal cancers in 432 samples. We also explored GSDME's diagnostic capacity as a biomarker for colorectal cancer. We observed differential methylation in all 22 GSDME CpGs between tumor and normal tissues, and in 18 CpGs between the left- and right-sided groups. In the cancer tissue, putative promoter probes were hypermethylated and gene body probes were hypomethylated, while this pattern was inversed in normal tissues. Both putative promoter and gene body CpGs correlated well together but formed distinct methylation patterns with the putative promoter exhibiting the most pronounced methylation differences between tumor and normal tissues. Clinicopathological parameters, excluding age, did not show any effect on CpG methylation. Although the methylation of 5 distinct probes was a good predictor of gene expression, we could not identify an association between GSDME methylation and expression in general. Survival analysis showed no association between GSDME methylation and expression on 5-year patient survival. Through logistic regression, we identified a combination of 2 CpGs, that can discriminate between cancer and normal tissue with high accuracy (AUC = 0.95) irrespective of age and tumor stage. We also validated our model in 3 external methylation datasets, from the Gene Expression Omnibus database, and similar results were reached. Our results suggest that GSDME is a promising biomarker for the detection of colorectal cancer.
Collapse
Affiliation(s)
- Joe Ibrahim
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Ken Op de Beeck
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Erik Fransen
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- StatUa Centre for StatisticsUniversity of AntwerpAntwerpBelgium
| | - Lieselot Croes
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Matthias Beyens
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Arvid Suls
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling, Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | - Marc Peeters
- Centre for Oncological ResearchUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
- Department of Medical OncologyAntwerp University HospitalEdegemBelgium
| | - Guy Van Camp
- Centre of Medical GeneticsUniversity of Antwerp and Antwerp University HospitalEdegemBelgium
| |
Collapse
|
30
|
Zhou C, Li J, Li Q, Liu H, Ye D, Wu Z, Shen Z, Deng H. The clinical significance of HOXA9 promoter hypermethylation in head and neck squamous cell carcinoma. J Clin Lab Anal 2019; 33:e22873. [PMID: 30843252 PMCID: PMC6595302 DOI: 10.1002/jcla.22873] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/13/2019] [Accepted: 02/10/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The purpose of the current study was to assess the association between HOXA9 (homeobox A9) promoter methylation and head and neck squamous cell carcinoma (HNSCC) and its diagnostic value. METHODS Quantitative methylation-specific PCR (qMSP) was applied to measure HOXA9 promoter methylation levels in 145 paired HNSCC and corresponding normal tissue samples. Data from the Cancer Genome Atlas (TCGA) database (n = 578; 528 HNSCC and 50 normal) were also analyzed. RESULTS Significantly higher levels of HOXA9 promoter methylation were detected in HNSCC, compared with normal, tissues (our cohort: P = 1.06E-35; TCGA cohort: P = 3.06E-39). Moreover, HOXA9 methylation was significantly increased in patients with advanced tumor (T) stage, lymph node metastasis, and advanced clinical stage. Areas under the receiver characteristic curves (AUCs) based on our cohort and TCGA data were 0.930 and 0.967, respectively. CONCLUSION In summary, our study reveals that HOXA9 promoter hypermethylation contributes to the risk of HNSCC and its progression and metastasis. Additionally, HOXA9 hypermethylation is a potential biomarker for the early diagnosis and screening of patients with HNSCC.
Collapse
Affiliation(s)
- Chongchang Zhou
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China.,Laboratory of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Jinyun Li
- Department of Oncology and Hematology, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China
| | - Qun Li
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China.,Laboratory of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Huigao Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Zhenhai Longsai Hospital, Ningbo, China
| | - Dong Ye
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China.,Laboratory of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Zhenhua Wu
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center, Lihuili Eastern Hospital, Ningbo, China
| | - Zhisen Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China.,Laboratory of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Hongxia Deng
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China.,Laboratory of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| |
Collapse
|
31
|
Samimi G, Heckman-Stoddard BM, Kay SS, Bloodgood B, Coa KI, Robinson JL, Tennant B, Ford LG, Szabo E, Minasian L. Acceptability of Localized Cancer Risk Reduction Interventions Among Individuals at Average or High Risk for Cancer. Cancer Prev Res (Phila) 2019; 12:271-282. [PMID: 30824471 DOI: 10.1158/1940-6207.capr-18-0435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/28/2019] [Accepted: 02/22/2019] [Indexed: 12/30/2022]
Abstract
Individuals at high risk for cancer, including those already diagnosed with premalignant lesions, can potentially benefit from chemopreventive interventions to reduce cancer risk. However, uptake and acceptability have been hindered due to the risk of systemic toxicity and other adverse effects. Locally delivered chemopreventive agents, where direct action on the primary organ may limit systemic toxicity, are emerging as an option for high-risk individuals. While a number of clinical trials support the development of chemopreventive agents, it is crucial to understand the factors and barriers that influence their acceptability and use. We conducted 36 focus groups with 198 individuals at average and high risk of breast/ovarian, gynecologic, and head/neck/oral and lung cancers to examine the perceptions and acceptability of chemopreventive agents. Participants' willingness to use chemopreventive agents was influenced by several factors, including perceived risk of cancer, skepticism around prevention, previous knowledge of chemopreventive agents, support from trusted sources of health information, participation in other cancer-related risk-reduction activities, previous experience with similar modalities, cost, regimen, side effects, and perceived effectiveness of the preventive intervention. Our findings indicate that individuals may be more receptive to locally delivered chemopreventive agents if they perceive themselves to be at high risk for cancer and are given the necessary information regarding regimen and side effects to make an informed decision. Clinical trials that collect additional patient-centered data including side effects and how these interventions fit into an individual's lifestyle are imperative to improve uptake of chemopreventive agents.
Collapse
Affiliation(s)
- Goli Samimi
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland.
| | | | | | | | | | | | | | - Leslie G Ford
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland
| | - Eva Szabo
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland
| | - Lori Minasian
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland
| |
Collapse
|
32
|
Giannopoulou L, Kasimir-Bauer S, Lianidou ES. Liquid biopsy in ovarian cancer: recent advances on circulating tumor cells and circulating tumor DNA. Clin Chem Lab Med 2019; 56:186-197. [PMID: 28753534 DOI: 10.1515/cclm-2017-0019] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/02/2017] [Indexed: 12/18/2022]
Abstract
Ovarian cancer remains the most lethal disease among gynecological malignancies despite the plethora of research studies during the last decades. The majority of patients are diagnosed in an advanced stage and exhibit resistance to standard chemotherapy. Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) represent the main liquid biopsy approaches that offer a minimally invasive sample collection. Both have shown a diagnostic, prognostic and predictive value in many types of solid malignancies and recent studies attempted to shed light on their role in ovarian cancer. This review is mainly focused on the clinical value of both CTCs and ctDNA in ovarian cancer and, more specifically, on their potential as diagnostic, prognostic and predictive tumor biomarkers.
Collapse
Affiliation(s)
- Lydia Giannopoulou
- Analysis of Circulating Tumor Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens, Greece
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Evi S Lianidou
- Analysis of Circulating Tumor Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, University Campus, Athens, Greece
| |
Collapse
|
33
|
Mari R, Lambaudie É, Provansal M, Sabatier R. [Circulating tumor DNA assessment for gynaecological cancers management]. Bull Cancer 2019; 106:237-252. [PMID: 30765097 DOI: 10.1016/j.bulcan.2018.11.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/19/2018] [Accepted: 11/27/2018] [Indexed: 01/05/2023]
Abstract
Gynaecological cancers are frequent, with more than 16,000 cases per year in France for 6500 deaths. Few improvements in diagnostic methods, prognostic tools, and therapeutic strategies have occurred in the last two decades. Tumour genomic analyses from, at least in part, the Cancer Genome Atlas have identified some of the molecular alterations involved in gynaecological tumours growth and spreading. However, these data remain incomplete and have not led to dramatic changes in the clinical management of our patients. Moreover, they require invasive samples that are not suitable to objectives like screening/early diagnosis, assessment of treatment efficacy, monitoring of residual disease or early diagnosis of relapse. In the last years, the analysis of circulating tumour biomarkers (also called "liquid biopsies") based on tumour cells (circulating tumour cells) or tumour nucleotides (circulating DNA or RNA) has been massively explored through various indications, platforms, objectives; data related to circulating tumour DNA being the most important in terms of number of publications and interest for clinical practice. This review aims to describe the methods of analysis as well as the observations from the analysis of circulating tumour DNA in gynaecological tumours, from screening/early diagnosis to the adaptation of treatment for advanced stages, through choice of treatments and monitoring of subclinical disease.
Collapse
Affiliation(s)
- Roxane Mari
- Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, département d'oncologie médicale, CRCM, Marseille cedex 9, France
| | - Éric Lambaudie
- Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, département de chirurgie oncologique, CRCM, Marseille cedex 9, France; Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, CRCM, laboratoire d'oncologie prédictive, Marseille cedex 9, France
| | - Magali Provansal
- Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, département d'oncologie médicale, CRCM, Marseille cedex 9, France
| | - Renaud Sabatier
- Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, département d'oncologie médicale, CRCM, Marseille cedex 9, France; Aix-Marseille university, CNRS U7258, Inserm U1068, institut Paoli-Calmettes, CRCM, laboratoire d'oncologie prédictive, Marseille cedex 9, France.
| |
Collapse
|
34
|
Loginov VI, Burdennyy AM, Filippova EA, Pronina IV, Kazubskaya TP, Kushlinsky DN, Ermilova VD, Rykov SV, Khodyrev DS, Braga EA. Hypermethylation of miR-107, miR-130b, miR-203a, miR-1258 Genes Associated with Ovarian Cancer Development and Metastasis. Mol Biol 2018. [DOI: 10.1134/s0026893318050102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
35
|
Fiano V, Trevisan M, Fasanelli F, Grasso C, Marabese F, da Graça Bicalho M, de Carvalho NS, Maestri CA, Merletti F, Sacerdote C, De Marco L, Gillio-Tos A. Methylation in host and viral genes as marker of aggressiveness in cervical lesions: Analysis in 543 unscreened women. Gynecol Oncol 2018; 151:319-326. [PMID: 30172480 DOI: 10.1016/j.ygyno.2018.08.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/02/2018] [Accepted: 08/22/2018] [Indexed: 12/13/2022]
Abstract
OBJECTIVE The present study aimed to evaluate the association between altered methylation and histologically confirmed high grade cervical intraepithelial neoplasia (hgCIN). METHODS Methylation levels in selected host (CADM1, MAL, DAPK1) and HPV (L1_I, L1_II, L2) genes were measured by pyrosequencing in DNA samples obtained from 543 women recruited in Curitiba (Brazil), 249 with hgCIN and 294 without cervical lesions. Association of methylation status with hgCIN was estimated by Odds Ratio (OR) with 95% confidence interval (CI). RESULTS The mean methylation level increased with severity of the lesion in the host and viral genes (p-trend < 0.05), with the exception of L1_II region (p-trend = 0.075). Positive association was found between methylation levels for host genes and CIN2 and CIN3 lesions respectively [CADM1: OR 4.17 (95%CI 2.03-8.56) and OR 9.54 (95%CI 4.80-18.97); MAL: OR 5.98 (95%CI 2.26-15.78) and OR 22.66 (95%CI 9.21-55.76); DAPK1: OR 3.37 (95%CI 0.93-12.13) and OR 6.74 (95%CI 1.92-23.64)]. Stronger risk estimates were found for viral genes [L1_I: OR 10.74 (95%CI 2.66-43.31) and OR 15.00 (95%CI 3.00-74.98); L1_II: OR 73.18 (95%CI 4.07-1315.94) and OR 32.50 (95%CI 3.86-273.65); L2: OR 4.73 (95%CI 1.55-14.44) and OR 10.62 (95%CI 2.60-43.39)]. The cumulative effect of the increasing number of host and viral methylated genes was associated with the risk of CIN2 and CIN3 lesions (p-trend < 0.001). CONCLUSIONS Our results, empowered by a wide cervical sample series with a large number of hgCIN, supported the role of methylation as marker of aggressiveness.
Collapse
Affiliation(s)
- Valentina Fiano
- Unit of Cancer Epidemiology-CeRMS, Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy.
| | - Morena Trevisan
- Unit of Cancer Epidemiology-CeRMS, Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy.
| | - Francesca Fasanelli
- Unit of Cancer Epidemiology-CeRMS, Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy.
| | - Chiara Grasso
- Unit of Cancer Epidemiology-CeRMS, Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy.
| | - Federica Marabese
- Unit of Cancer Epidemiology-CeRMS, Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy.
| | - Maria da Graça Bicalho
- Laboratory of Immunogenetics and Hystocompatibility (LIGH), Federal University of Paranà, Rua XV de Novembro, 1299, Curitiba, PR 80060-000, Brazil.
| | - Newton S de Carvalho
- Department of Gynecology and Obstetrics, Federal University of Paraná, Infectious Diseases in Gynecology and Obstetrics Sector, Hospital de Clínicas, Rua XV de Novembro, 1299, Curitiba, PR 80060-000, Brazil.
| | - Carlos A Maestri
- Department of Cervical Pathology, Hospital Erasto Gaertner, Curitiba, R. Dr. Ovande do Amaral, 201 - Jardim das Americas, Curitiba, PR 81520-060, Brazil.
| | - Franco Merletti
- Unit of Cancer Epidemiology-CeRMS, Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy; Unit of Cancer Epidemiology, Città della Salute e della Scienza University-Hospital and Center for Cancer Prevention (CPO), Via Santena 7, 10126 Turin, Italy.
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città della Salute e della Scienza University-Hospital and Center for Cancer Prevention (CPO), Via Santena 7, 10126 Turin, Italy.
| | - Laura De Marco
- Unit of Cancer Epidemiology-CeRMS, Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy; Unit of Cancer Epidemiology, Città della Salute e della Scienza University-Hospital and Center for Cancer Prevention (CPO), Via Santena 7, 10126 Turin, Italy.
| | - Anna Gillio-Tos
- Unit of Cancer Epidemiology-CeRMS, Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy.
| |
Collapse
|
36
|
Pisanic TR, Cope LM, Lin SF, Yen TT, Athamanolap P, Asaka R, Nakayama K, Fader AN, Wang TH, Shih IM, Wang TL. Methylomic Analysis of Ovarian Cancers Identifies Tumor-Specific Alterations Readily Detectable in Early Precursor Lesions. Clin Cancer Res 2018; 24:6536-6547. [PMID: 30108103 DOI: 10.1158/1078-0432.ccr-18-1199] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/12/2018] [Accepted: 08/09/2018] [Indexed: 12/22/2022]
Abstract
PURPOSE High-grade serous ovarian carcinoma (HGSOC) typically remains undiagnosed until advanced stages when peritoneal dissemination has already occurred. Here, we sought to identify HGSOC-specific alterations in DNA methylation and assess their potential to provide sensitive and specific detection of HGSOC at its earliest stages. EXPERIMENTAL DESIGN MethylationEPIC genome-wide methylation analysis was performed on a discovery cohort comprising 23 HGSOC, 37 non-HGSOC malignant, and 36 histologically unremarkable gynecologic tissue samples. The resulting data were processed using selective bioinformatic criteria to identify regions of high-confidence HGSOC-specific differential methylation. Quantitative methylation-specific real-time PCR (qMSP) assays were then developed for 8 of the top-performing regions and analytically validated in a cohort of 90 tissue samples. Lastly, qMSP assays were used to assess and compare methylation in 30 laser-capture microdissected (LCM) fallopian tube epithelia samples obtained from cancer-free and serous tubal intraepithelial carcinoma (STIC) positive women. RESULTS Bioinformatic selection identified 91 regions of robust, HGSOC-specific hypermethylation, 23 of which exhibited an area under the receiver-operator curve (AUC) value ≥ 0.9 in the discovery cohort. Seven of 8 top-performing regions demonstrated AUC values between 0.838 and 0.968 when analytically validated by qMSP in a 90-patient cohort. A panel of the 3 top-performing genes (c17orf64, IRX2, and TUBB6) was able to perfectly discriminate HGSOC (AUC 1.0). Hypermethylation within these loci was found exclusively in LCM fallopian tube epithelia from women with STIC lesions, but not in cancer-free fallopian tubes. CONCLUSIONS A panel of methylation biomarkers can be used to accurately identify HGSOC, even at precursor stages of the disease.
Collapse
Affiliation(s)
- Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.
| | - Leslie M Cope
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Oncology and Biostatistics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shiou-Fu Lin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ting-Tai Yen
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Pornpat Athamanolap
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ryoichi Asaka
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kentaro Nakayama
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, Japan
| | - Amanda N Fader
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Ie-Ming Shih
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tian-Li Wang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
37
|
Natanzon Y, Goode EL, Cunningham JM. Epigenetics in ovarian cancer. Semin Cancer Biol 2018; 51:160-169. [PMID: 28782606 PMCID: PMC5976557 DOI: 10.1016/j.semcancer.2017.08.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 12/24/2022]
Abstract
Ovarian cancer is a disease with a poor prognosis and little progress has been made to improve treatment. It is now recognized that there are several histotypes of ovarian cancer, each with distinct epidemiologic and genomic characteristics. Cancer therapy is moving beyond classical chemotherapy to include epigenetic approaches. Epigenetics is the dynamic regulation of gene expression by DNA methylation and histone post translational modification in response to environmental cues. Improvement in technology to study DNA methylation has enabled a more agnostic approach and, with larger samples sets, has begun to unravel how epigenetics contributes to the etiology, response to chemotherapy and prognosis in of ovarian cancer. Investigations into histone modifications in ovarian cancer are more nascent. Much more is needed to be done to fully realize the potential that epigenetics holds for ovarian cancer clinical care.
Collapse
Affiliation(s)
- Yanina Natanzon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
38
|
Croes L, Beyens M, Fransen E, Ibrahim J, Vanden Berghe W, Suls A, Peeters M, Pauwels P, Van Camp G, Op de Beeck K. Large-scale analysis of DFNA5 methylation reveals its potential as biomarker for breast cancer. Clin Epigenetics 2018; 10:51. [PMID: 29682089 PMCID: PMC5896072 DOI: 10.1186/s13148-018-0479-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background Breast cancer is the most frequent cancer among women worldwide. Biomarkers for early detection and prognosis of these patients are needed. We hypothesized that deafness, autosomal dominant 5 (DFNA5) may be a valuable biomarker, based upon strong indications for its role as tumor suppressor gene and its function in regulated cell death. In this study, we aimed to analyze DFNA5 methylation and expression in the largest breast cancer cohort to date using publicly available data from TCGA, in order to further unravel the role of DFNA5 as detection and/or prognostic marker in breast cancer. We analyzed Infinium HumanMethylation450k data, covering 22 different CpGs in the DFNA5 gene (668 breast adenocarcinomas and 85 normal breast samples) and DFNA5 expression (Agilent 244K Custom Gene Expression: 476 breast adenocarcinomas and 56 normal breast samples; RNA-sequencing: 666 breast adenocarcinomas and 71 normal breast samples). Results DFNA5 methylation and expression were significantly different between breast cancer and normal breast samples. Overall, breast cancer samples showed higher DFNA5 methylation in the putative gene promoter compared to normal breast samples, whereas in the gene body and upstream of the putative gene promoter, the opposite is true. Furthermore, DFNA5 methylation, in 10 out of 22 CpGs, and expression were significantly higher in lobular compared to ductal breast cancers. An important result of this study was the identification of a combination of one CpG in the gene promoter (CpG07504598) and one CpG in the gene body (CpG12922093) of DFNA5, which was able to discriminate between breast cancer and normal breast samples (AUC = 0.93). This model was externally validated in three independent datasets. Moreover, we showed that estrogen receptor state is associated with DFNA5 methylation and expression. Finally, we were able to find a significant effect of DFNA5 gene body methylation on a 5-year overall survival time. Conclusions We conclude that DFNA5 methylation shows strong potential as detection and prognostic biomarker for breast cancer.
Collapse
Affiliation(s)
- Lieselot Croes
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Matthias Beyens
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Erik Fransen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,3StatUa Center for Statistics, University of Antwerp, Prinsstraat 13, BE-2000 Antwerp, Belgium
| | - Joe Ibrahim
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Wim Vanden Berghe
- 4Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Arvid Suls
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium
| | - Marc Peeters
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Patrick Pauwels
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| |
Collapse
|
39
|
Croes L, de Beeck KO, Pauwels P, Vanden Berghe W, Peeters M, Fransen E, Van Camp G. DFNA5 promoter methylation a marker for breast tumorigenesis. Oncotarget 2018; 8:31948-31958. [PMID: 28404884 PMCID: PMC5458261 DOI: 10.18632/oncotarget.16654] [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: 11/15/2016] [Accepted: 03/16/2017] [Indexed: 12/28/2022] Open
Abstract
Background Identification of methylation markers that are sensitive and specific for breast cancer may improve early detection. We hypothesize that DFNA5 promoter methylation can be a valuable epigenetic biomarker, based upon strong indications for its role as tumor suppressor gene and its function in regulated cell death. Results Statistically different levels of methylation were seen, with always very low levels in healthy breast reduction samples, very high levels in part of the adenocarcinoma samples and slightly increased levels in part of the normal tissue samples adjacent the tumor. One of the CpGs (CpG4) showed the best differentiation. A ROC curve for DFNA5 CpG4 methylation showed a sensitivity of 61.8% for the detection of breast cancer with a specificity of 100%. Materials and Methods We performed methylation analysis on four CpGs in the DFNA5 promoter region by bisulfite pyrosequencing on 123 primary breast adenocarcinomas and 24 healthy breast reductions. For 16 primary tumors, corresponding histological normal tissue adjacent to the tumor was available. Conclusions We conclude that DFNA5 methylation shows strong potential as a biomarker for detection of breast cancer. Slightly increased methylation in histologically normal breast tissue surrounding the tumor suggests that it may be a good early detection marker.
Collapse
Affiliation(s)
- Lieselot Croes
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem B-2650, Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Edegem B-2650, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem B-2650, Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Edegem B-2650, Belgium
| | - Patrick Pauwels
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Edegem B-2650, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Antwerp B-2610, Belgium
| | - Marc Peeters
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Edegem B-2650, Belgium
| | - Erik Fransen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem B-2650, Belgium.,StatUa Center for Statistics, University of Antwerp, Antwerp B-2000, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem B-2650, Belgium
| |
Collapse
|
40
|
Mathieu KB, Bedi DG, Thrower SL, Qayyum A, Bast RC. Screening for ovarian cancer: imaging challenges and opportunities for improvement. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2018; 51. [PMID: 28639753 PMCID: PMC5788737 DOI: 10.1002/uog.17557] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The United Kingdom Collaborative Trial of Ovarian Cancer Screening (UKCTOCS) recently reported a reduction in the average overall mortality among ovarian cancer patients screened with an annual sequential, multimodal strategy that tracked biomarker CA125 over time, where increasing serum CA125 levels prompted ultrasound. However, multiple cases were documented wherein serum CA125 levels were rising, but ultrasound screens were normal, thus delaying surgical intervention. A significant factor which could contribute to false negatives is that many aggressive ovarian cancers are believed to arise from epithelial cells on the fimbriae of the fallopian tubes, which are not readily imaged. Moreover, because only a fraction of metastatic tumors may reach a sonographically-detectable size before they metastasize, annual screening with ultrasound may fail to detect a large fraction of early-stage ovarian cancers. The ability to detect ovarian carcinomas before they metastasize is critical and future efforts towards improving screening should focus on identifying unique features specific to aggressive, early-stage tumors, as well as improving imaging sensitivity to allow for detection of tubal lesions. Implementation of a three-stage multimodal screening strategy in which a third modality is employed in cases where the first-line blood-based assay is positive and the second-line ultrasound exam is negative may also prove fruitful in detecting early-stage cases missed by ultrasound.
Collapse
Affiliation(s)
- K B Mathieu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, 1881 East Road, Unit 1902, Houston, TX, 77054, USA
| | - D G Bedi
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - S L Thrower
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, 1881 East Road, Unit 1902, Houston, TX, 77054, USA
| | - A Qayyum
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - R C Bast
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
41
|
Yin X, Xiang T, Mu J, Mao H, Li L, Huang X, Li C, Feng Y, Luo X, Wei Y, Peng W, Ren G, Tao Q. Protocadherin 17 functions as a tumor suppressor suppressing Wnt/β-catenin signaling and cell metastasis and is frequently methylated in breast cancer. Oncotarget 2018; 7:51720-51732. [PMID: 27351130 PMCID: PMC5239510 DOI: 10.18632/oncotarget.10102] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 05/28/2016] [Indexed: 11/29/2022] Open
Abstract
Protocadherins play important roles in the regulation of cell adhesion and signaling transduction. Aberrant expression of protocadherins has been shown to be associated with multiple tumorigenesis. We previously identified PCDH17, encoding protocadherin 17, as a frequently methylated and downregulated tumor suppressor gene (TSG) in gastric and colorectal cancers. Here, we examined the abnormalities and functions of PCDH17 in breast cancer pathogenesis. We used PCR and immunohistochemistry to check its expression pattern in breast tumor cell lines and primary tumors. Methylation-specific PCR (MSP) was applied to examine its promoter methylation status in breast tumor cell lines and primary tumors. The biological functions of PCDH17 in breast tumor cells were assessed using in vitro and in vivo assays. We found that PCDH17 was frequently downregulated or silenced in 78% (7/9) of breast tumor cell lines, as well as 89% (32/36) of primary tumors. Downregulation of PCDH17 in breast cancer was mainly due to the methylation of its promoter. Ectopic expression of PCDH17 in breast tumor cells inhibited cell proliferation and mobility through arresting cell cycle and inducing apoptosis. In breast tumor cells, PCDH17 significantly suppressed the active β-catenin level and its downstream target gene expression. Thus, we found that PCDH17 functions as a tumor suppressor inhibiting Wnt/β-catenin signaling and metastasis in breast cancer but is frequently methylated in primary tumors which could be a potential biomarker.
Collapse
Affiliation(s)
- Xuedong Yin
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tingxiu Xiang
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Junhao Mu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haitao Mao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK Shenzhen Research Institute, Hong Kong
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK Shenzhen Research Institute, Hong Kong
| | - Xin Huang
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK Shenzhen Research Institute, Hong Kong
| | - Chunhong Li
- Oncology Department, Suining Sichuan Center Hospital, Sichuan, China
| | - Yixiao Feng
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xinrong Luo
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuxian Wei
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Weiyan Peng
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guosheng Ren
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qian Tao
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK Shenzhen Research Institute, Hong Kong
| |
Collapse
|
42
|
Widschwendter M, Evans I, Jones A, Ghazali S, Reisel D, Ryan A, Gentry-Maharaj A, Zikan M, Cibula D, Eichner J, Alunni-Fabbroni M, Koch J, Janni WJ, Paprotka T, Wittenberger T, Menon U, Wahl B, Rack B, Lempiäinen H. Methylation patterns in serum DNA for early identification of disseminated breast cancer. Genome Med 2017; 9:115. [PMID: 29268762 PMCID: PMC5740791 DOI: 10.1186/s13073-017-0499-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/22/2017] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Monitoring treatment and early detection of fatal breast cancer (BC) remains a major unmet need. Aberrant circulating DNA methylation (DNAme) patterns are likely to provide a highly specific cancer signal. We hypothesized that cell-free DNAme markers could indicate disseminated breast cancer, even in the presence of substantial quantities of background DNA. METHODS We used reduced representation bisulfite sequencing (RRBS) of 31 tissues and established serum assays based on ultra-high coverage bisulfite sequencing in two independent prospective serum sets (n = 110). The clinical use of one specific region, EFC#93, was validated in 419 patients (in both pre- and post-adjuvant chemotherapy samples) from SUCCESS (Simultaneous Study of Gemcitabine-Docetaxel Combination adjuvant treatment, as well as Extended Bisphosphonate and Surveillance-Trial) and 925 women (pre-diagnosis) from the UKCTOCS (UK Collaborative Trial of Ovarian Cancer Screening) population cohort, with overall survival and occurrence of incident breast cancer (which will or will not lead to death), respectively, as primary endpoints. RESULTS A total of 18 BC specific DNAme patterns were discovered in tissue, of which the top six were further tested in serum. The best candidate, EFC#93, was validated for clinical use. EFC#93 was an independent poor prognostic marker in pre-chemotherapy samples (hazard ratio [HR] for death = 7.689) and superior to circulating tumor cells (CTCs) (HR for death = 5.681). More than 70% of patients with both CTCs and EFC#93 serum DNAme positivity in their pre-chemotherapy samples relapsed within five years. EFC#93-positive disseminated disease in post-chemotherapy samples seems to respond to anti-hormonal treatment. The presence of EFC#93 serum DNAme identified 42.9% and 25% of women who were diagnosed with a fatal BC within 3-6 and 6-12 months of sample donation, respectively, with a specificity of 88%. The sensitivity with respect to detecting fatal BC was ~ 4-fold higher compared to non-fatal BC. CONCLUSIONS Detection of EFC#93 serum DNAme patterns offers a new tool for early diagnosis and management of disseminated breast cancers. Clinical trials are required to assess whether EFC#93-positive women in the absence of radiological detectable breast cancers will benefit from anti-hormonal treatment before the breast lesions become clinically apparent.
Collapse
Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK.
| | - Iona Evans
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Shohreh Ghazali
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Andy Ryan
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Aleksandra Gentry-Maharaj
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Michal Zikan
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University Prague, Prague, Czech Republic
| | - David Cibula
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University Prague, Prague, Czech Republic
| | | | - Marianna Alunni-Fabbroni
- Department of Gynaecology and Obstetrics, Klinikum Innenstadt, Ludwig-Maximilians Universitaet Muenchen, Maistrasse 11, 80337, Munich, Germany
| | - Julian Koch
- Department of Gynaecology and Obstetrics, Klinikum Innenstadt, Ludwig-Maximilians Universitaet Muenchen, Maistrasse 11, 80337, Munich, Germany
| | - Wolfgang J Janni
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Prittwitzstrasse 43, 89075, Ulm, Germany
| | - Tobias Paprotka
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | | | - Usha Menon
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, 74 Huntley Street, London, WC1E 6AU, UK
| | - Benjamin Wahl
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
- Boehringer Ingelheim Pharma, GmbH & Co. KG, Target Discovery Research, Biberach, Germany
| | - Brigitte Rack
- Department of Gynaecology and Obstetrics, Klinikum Innenstadt, Ludwig-Maximilians Universitaet Muenchen, Maistrasse 11, 80337, Munich, Germany
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Prittwitzstrasse 43, 89075, Ulm, Germany
| | | |
Collapse
|
43
|
Widschwendter M, Zikan M, Wahl B, Lempiäinen H, Paprotka T, Evans I, Jones A, Ghazali S, Reisel D, Eichner J, Rujan T, Yang Z, Teschendorff AE, Ryan A, Cibula D, Menon U, Wittenberger T. The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer. Genome Med 2017; 9:116. [PMID: 29268796 PMCID: PMC5740748 DOI: 10.1186/s13073-017-0500-7] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/24/2017] [Indexed: 02/07/2023] Open
Abstract
Background Despite a myriad of attempts in the last three decades to diagnose ovarian cancer (OC) earlier, this clinical aim still remains a significant challenge. Aberrant methylation patterns of linked CpGs analyzed in DNA fragments shed by cancers into the bloodstream (i.e. cell-free DNA) can provide highly specific signals indicating cancer presence. Methods We analyzed 699 cancerous and non-cancerous tissues using a methylation array or reduced representation bisulfite sequencing to discover the most specific OC methylation patterns. A three-DNA-methylation-serum-marker panel was developed using targeted ultra-high coverage bisulfite sequencing in 151 women and validated in 250 women with various conditions, particularly in those associated with high CA125 levels (endometriosis and other benign pelvic masses), serial samples from 25 patients undergoing neoadjuvant chemotherapy, and a nested case control study of 172 UKCTOCS control arm participants which included serum samples up to two years before OC diagnosis. Results The cell-free DNA amount and average fragment size in the serum samples was up to ten times higher than average published values (based on samples that were immediately processed) due to leakage of DNA from white blood cells owing to delayed time to serum separation. Despite this, the marker panel discriminated high grade serous OC patients from healthy women or patients with a benign pelvic mass with specificity/sensitivity of 90.7% (95% confidence interval [CI] = 84.3–94.8%) and 41.4% (95% CI = 24.1–60.9%), respectively. Levels of all three markers plummeted after exposure to chemotherapy and correctly identified 78% and 86% responders and non-responders (Fisher’s exact test, p = 0.04), respectively, which was superior to a CA125 cut-off of 35 IU/mL (20% and 75%). 57.9% (95% CI 34.0–78.9%) of women who developed OC within two years of sample collection were identified with a specificity of 88.1% (95% CI = 77.3–94.3%). Sensitivity and specificity improved further when specifically analyzing CA125 negative samples only (63.6% and 87.5%, respectively). Conclusions Our data suggest that DNA methylation patterns in cell-free DNA have the potential to detect a proportion of OCs up to two years in advance of diagnosis and may potentially guide personalized treatment. The prospective use of novel collection vials, which stabilize blood cells and reduce background DNA contamination in serum/plasma samples, will facilitate clinical implementation of liquid biopsy analyses. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0500-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK.
| | - Michal Zikan
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University, Prague, Czech Republic
| | - Benjamin Wahl
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | | | - Tobias Paprotka
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | - Iona Evans
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Shohreh Ghazali
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | | | - Tamas Rujan
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - Zhen Yang
- CAS Max-Planck Partner Institute for Computational Biology, Shanghai Institute of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrew E Teschendorff
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK.,CAS Max-Planck Partner Institute for Computational Biology, Shanghai Institute of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andy Ryan
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - David Cibula
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University, Prague, Czech Republic
| | - Usha Menon
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | | |
Collapse
|
44
|
Wang H, Liu Z, Xie J, Wang Z, Zhou X, Fang Y, Pan H, Han W. Quantitation of cell-free DNA in blood is a potential screening and diagnostic maker of breast cancer: a meta-analysis. Oncotarget 2017; 8:102336-102345. [PMID: 29254249 PMCID: PMC5731959 DOI: 10.18632/oncotarget.21827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 09/22/2017] [Indexed: 12/25/2022] Open
Abstract
INTRODUCTION Increased cell-free DNA (cfDNA) levels in circulating blood have been associated with higher possibility of breast cancer, however, researchers have not reached an agreement on its analysis. MATERIALS AND METHODS We conducted a meta-analysis of 12 retrospective studies to clarify the value of cfDNA quantification in screening and diagnosis of breast cancer. PubMed, EMBASE, Web of Science and Cochrane library were searched from January, 2000 to October, 2016. Pooled analyses were estimated using a random effects model. RESULTS In total, 1003 primary breast cancer patients, 283 cases with benign breast disease and 575 healthy individuals were included. Pooled diagnostic odds ratio (DOR) was 27.63 (95% confidence interval [CI]: 10.96~69.61, I2 = 86.2%, P < 0.001) in discriminating between breast cancer and healthy controls; the area under the summary receiver operating characteristic (SROC) curve measured 0.91 (95% CI: 0.17~1.00). Analysis of available data in distinguishing breast cancer and benign breast disease showed a pooled DOR of 35.30 (95% CI: 7.58~164.39, I2 = 79.9%, P = 0.002) with an area under SROC of 0.91 (95% CI: 0.89~0.93). Ethnic group distribution based geographical factors suggested by meta-regression and subgroup analyses explained most of the heterogeneity. CONCLUSIONS Quantification of cfDNA is a promising test in screening and diagnostic of breast cancer, but population-based standardization of test methods require completion prior to clinical use.
Collapse
Affiliation(s)
- Huadi Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Liu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiansheng Xie
- Laboratory of Cancer Biology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhanggui Wang
- Department of Radiotherapy, The Second People's Hospital of Anhui Province, Hefei, Anhui, China
| | - Xiaoyun Zhou
- Department of Medical Oncology, Xiasha Campus, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yong Fang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
45
|
Gong M, Shi W, Qi J, Shao G, Shi Z, Wang J, Chen J, Chu R. Alu hypomethylation and MGMT hypermethylation in serum as biomarkers of glioma. Oncotarget 2017; 8:76797-76806. [PMID: 29100349 PMCID: PMC5652743 DOI: 10.18632/oncotarget.20012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/12/2017] [Indexed: 02/05/2023] Open
Abstract
In order to improve prognosis of glioma patients, better tools are required for early diagnosis and treatment. Serum cell-free DNA methylation levels of Alu, MGMT, P16, RASSF1A from 124 glioma patients and 58 healthy controls were detected by the bisulfite sequencing. The median methylation level of Alu was 46.15% (IQR, 36.57%-54.00%) and 60.85% (IQR, 57.23%-65.68%) in glioma patients and healthy controls respectively. The median methylation level of MGMT in glioma samples was 64.65% (IQR, 54.87%-74.37%) compared to 38.30% (IQR, 34.13%-45.45%) in healthy controls, and all revealed significant differences including P16. However, the median methylation level of RASSF1A was not significantly altered in glioma patients. Furthermore, the methylation levels of Alu and MGMT in serum had a good diagnostic value, and was higher than P16. Interestingly, combination of Alu and MGMT identified additional patients, which were missed by either diagnosis alone. In the Alu group, the patients with high levels were associated with an increased survival rate compared to those who with low levels, with similar results observed in the MGMT group. In the present study, we demonstrated that the methylation level of Alu and MGMT in serum had a better diagnostic value than P16. Moreover, combined analysis of Alu and MGMT showed higher sensitivity for glioma diagnosis. Therefore, both serum Alu and MGMT methylation levels may represent a novel prognostic factor for glioma patients.
Collapse
Affiliation(s)
- Mingjie Gong
- Department of Neurosurgery, Changshu No. 2 People's Hospital (The 5th Clinical Medical College of Yangzhou University), Changshu, Jiangsu Province, China
| | - Wei Shi
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Jing Qi
- Comprehensive Surgical Laboratory, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Guoping Shao
- Department of Neurosurgery, Changshu No. 2 People's Hospital (The 5th Clinical Medical College of Yangzhou University), Changshu, Jiangsu Province, China
| | - Zhenghua Shi
- Department of Neurosurgery, Changshu No. 2 People's Hospital (The 5th Clinical Medical College of Yangzhou University), Changshu, Jiangsu Province, China
| | - Junxiang Wang
- Department of Neurosurgery, Changshu No. 2 People's Hospital (The 5th Clinical Medical College of Yangzhou University), Changshu, Jiangsu Province, China
| | - Jian Chen
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Rongtao Chu
- Department of Neurosurgery, Changshu No. 2 People's Hospital (The 5th Clinical Medical College of Yangzhou University), Changshu, Jiangsu Province, China
| |
Collapse
|
46
|
Tumor and serum DNA methylation in women receiving preoperative chemotherapy with or without vorinostat in TBCRC008. Breast Cancer Res Treat 2017; 167:107-116. [PMID: 28918548 DOI: 10.1007/s10549-017-4503-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND Methylated gene markers have shown promise in predicting breast cancer outcomes and treatment response. We evaluated whether baseline and changes in tissue and serum methylation levels would predict pathological complete response (pCR) in patients with HER2-negative early breast cancer undergoing preoperative chemotherapy. METHODS The TBCRC008 trial investigated pCR following 12 weeks of preoperative carboplatin and albumin-bound paclitaxel + vorinostat/placebo (n = 62). We measured methylation of a 10-gene panel by quantitative multiplex methylation-specific polymerase chain reaction and expressed results as cumulative methylation index (CMI). We evaluated association between CMI level [baseline, day 15 (D15), and change] and pCR using univariate and multivariable logistic regression models controlling for treatment and hormone receptor (HR) status, and performed exploratory subgroup analyses. RESULTS In univariate analysis, one log unit increase in tissue CMI levels at D15 was associated with 40% lower chance of obtaining pCR (odds ratio, OR 0.60, 95% CI 0.37-0.97; p = 0.037). Subgroup analyses suggested a significant association between tissue D15 CMI levels and pCR in vorinostat-treated [OR 0.44 (0.20, 0.93), p = 0.03], but not placebo-treated patients. CONCLUSION In this study investigating the predictive roles of tissue and serum CMI levels in patients with early breast cancer for the first time, we demonstrate that high D15 tissue CMI levels may predict poor response. Larger studies and improved analytical procedures to detect methylated gene markers in early stage breast cancer are needed. TBCRC008 is registered on ClinicalTrials.gov (NCT00616967).
Collapse
|
47
|
Thivyah Prabha A, Sekar D. Deciphering the molecular signaling pathways in breast cancer pathogenesis and their role in diagnostic and treatment modalities. GENE REPORTS 2017; 7:1-17. [DOI: 10.1016/j.genrep.2017.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
48
|
Han X, Wang J, Sun Y. Circulating Tumor DNA as Biomarkers for Cancer Detection. GENOMICS, PROTEOMICS & BIOINFORMATICS 2017; 15:59-72. [PMID: 28392479 PMCID: PMC5414889 DOI: 10.1016/j.gpb.2016.12.004] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 12/13/2016] [Accepted: 12/20/2016] [Indexed: 12/23/2022]
Abstract
Detection of circulating tumor DNAs (ctDNAs) in cancer patients is an important component of cancer precision medicine ctDNAs. Compared to the traditional physical and biochemical methods, blood-based ctDNA detection offers a non-invasive and easily accessible way for cancer diagnosis, prognostic determination, and guidance for treatment. While studies on this topic are currently underway, clinical translation of ctDNA detection in various types of cancers has been attracting much attention, due to the great potential of ctDNA as blood-based biomarkers for early diagnosis and treatment of cancers. ctDNAs are detected and tracked primarily based on tumor-related genetic and epigenetic alterations. In this article, we reviewed the available studies on ctDNA detection and described the representative methods. We also discussed the current understanding of ctDNAs in cancer patients and their availability as potential biomarkers for clinical purposes. Considering the progress made and challenges involved in accurate detection of specific cell-free nucleic acids, ctDNAs hold promise to serve as biomarkers for cancer patients, and further validation is needed prior to their broad clinical use.
Collapse
Affiliation(s)
- Xiao Han
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junyun Wang
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingli Sun
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
49
|
Next-Generation Sequencing Approach in Methylation Analysis of HNF1B and GATA4 Genes: Searching for Biomarkers in Ovarian Cancer. Int J Mol Sci 2017; 18:ijms18020474. [PMID: 28241454 PMCID: PMC5344006 DOI: 10.3390/ijms18020474] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 02/14/2017] [Accepted: 02/16/2017] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is well-known to be associated with ovarian cancer (OC) and has great potential to serve as a biomarker in monitoring response to therapy and for disease screening. The purpose of this study was to investigate methylation of HNF1B and GATA4 and correlate detected methylation with clinicopathological characteristic of OC patients. The study group consisted of 64 patients with OC and 35 control patients. To determine the most important sites of HNF1B and GATA4, we used next-generation sequencing. For further confirmation of detected methylation of selected regions, we used high-resolution melting analysis and methylation-specific real-time polymerase chain reaction (PCR). Selected regions of HNF1B and GATA4 were completely methylation free in all control samples, whereas methylation-positive pattern was observed in 32.8% (HNF1B) and 45.3% (GATA4) of OC samples. Evaluating both genes together, we were able to detect methylation in 65.6% of OC patients. We observed a statistically significant difference in HNF1B methylation between samples with different stages of OC. We also detected subtype specific methylation in GATA4 and a decrease of methylation in late stages of OC. The combination of unmethylated HNF1B and methylated GATA4 was associated with longer overall survival. In our study, we employed innovative approach of methylation analysis of HNF1B and GATA4 to search for possible epigenetic biomarkers. We confirmed the significance of the HNF1B and GATA4 hypermethylation with emphasis on the need of selecting the most relevant sites for analysis. We suggest selected CpGs to be further examined as a potential positive prognostic factor.
Collapse
|
50
|
Shan M, Yin H, Li J, Li X, Wang D, Su Y, Niu M, Zhong Z, Wang J, Zhang X, Kang W, Pang D. Detection of aberrant methylation of a six-gene panel in serum DNA for diagnosis of breast cancer. Oncotarget 2017; 7:18485-94. [PMID: 26918343 PMCID: PMC4951303 DOI: 10.18632/oncotarget.7608] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/11/2016] [Indexed: 01/05/2023] Open
Abstract
Detection of breast cancer at an early stage is the key for successful treatment and improvement of outcome. However the limitations of mammography are well recognized, especially for those women with premenopausal breast cancer. Novel approaches to breast cancer screening are necessary, especially in the developing world where mammography is not feasible. In this study, we examined the promoter methylation of six genes (SFN, P16, hMLH1, HOXD13, PCDHGB7 and RASSF1a) in circulating free DNA (cfDNA) extracted from serum. We used a high-throughput DNA methylation assay (MethyLight) to examine serum from 749 cases including breast cancer patients, patients with benign breast diseases and healthy women. The six-gene methylation panel test achieved 79.6% and 82.4% sensitivity with a specificity of 72.4% and 78.1% in diagnosis of breast cancer when compared with healthy and benign disease controls, respectively. Moreover, the methylation panel positive group showed significant differences in the following independent variables: (a) involvement of family history of tumors; (b) a low proliferative index, ki-67; (c) high ratios in luminal subtypes. Additionally the panel also complemented some breast cancer cases which were neglected by mammography or ultrasound. These data suggest that epigenetic markers in serum have potential for diagnosis of breast cancer.
Collapse
Affiliation(s)
- Ming Shan
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, P.R. China
| | - Huizi Yin
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Junnan Li
- Department of Epidemiology and Biostatistics, Harbin Medical University, Harbin, P.R. China
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, P.R. China
| | - Dong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P.R. China
| | - Yonghui Su
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Ming Niu
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Zhenbin Zhong
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Ji Wang
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Xianyu Zhang
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China
| | - Wenli Kang
- Department of Oncology, General Hospital of Heilongjiang Province Land Reclamation Headquarters, Harbin, P.R. China
| | - Da Pang
- Department of Breast Cancer Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, P.R. China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, P.R. China
| |
Collapse
|