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Bagheri-Hosseinabadi Z, Eshkevari SMS, Khalighfard S, Alizadeh AM, Khori V, Amiriani T, Poorkhani A, Sadani S, Esmati E, Lashgari M, Mahmoodi M, Hajizadeh MR. A systematic approach introduced some immune system targets in rectal cancer by considering cell-free DNA methylation in response to radiochemotherapy. Cytokine 2024; 181:156666. [PMID: 38906038 DOI: 10.1016/j.cyto.2024.156666] [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: 03/03/2024] [Revised: 05/12/2024] [Accepted: 05/26/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND This study aims to investigate cell-free DNA (cfDNA) methylation of genes involved in some immune system targets as biomarkers of radioresistance in patients with non-metastatic rectal cancer. METHODS Gene expression (GSE68204, GPL6480, and GSE15781) and DNA methylation profiles (GSE75548 and GSE139404) of rectal cancer patients were obtained from the Gene Expression Omnibus (GEO) database. GEO2R and FunRich software were first used to identify genes with significant expression differences. Enricher softwer was then used to analyze Gene Ontology and detect pathway enrichment of hub genes. Blood samples were then taken from 43 rectal cancer patients. After cfDNA extraction from samples, it was treated with bisulfite and analyzed by methylation-specific PCR. RESULTS 1088 genes with high and 629 with low expression were identified by GEO2R and FunRich software. A total of five high-expression hub genes, including CDH24, FGF18, CCND1, IFITM1, UBE2V1, and three low-expression hub genes, including CBLN2, VIPR2, and IRF4, were identified from UALCAN and DNMIVD databases. Methylation-specific PCR indicated a significant difference in hub gene methylation between cancerous and non-cancerous individuals. Radiochemotherapy significantly affected hub gene methylation. There was a considerable difference in the methylation rate of hub genes between patients who responded to radiochemotherapy and those who did not. CONCLUSIONS Evaluating gene methylation patterns might be an appropriate diagnostic tool to predict radiochemotherapy response and develop targeted therapeutic agents.
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Affiliation(s)
- Zahra Bagheri-Hosseinabadi
- Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Department of Clinical Biochemistry, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | | | | | - Ali Mohammad Alizadeh
- Radiation Oncology Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran; Cancer Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Vahid Khori
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Taghi Amiriani
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Amirhoushang Poorkhani
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Somayeh Sadani
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ebrahim Esmati
- Radiation Oncology Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzih Lashgari
- Radiation Oncology Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Mahmoodi
- Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Reza Hajizadeh
- Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Department of Clinical Biochemistry, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
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Bai Y, Wang Y, Qin J, Wang T, Zhou X, Ma Z, Wang A, Yang W, Wang J, Li J, Hu Y. Systematic pan-cancer analysis identified RASSF1 as an immunological and prognostic biomarker and validated in lung cancer. Heliyon 2024; 10:e33304. [PMID: 39022053 PMCID: PMC11253667 DOI: 10.1016/j.heliyon.2024.e33304] [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: 12/26/2023] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
Background Ras association domain family member 1 (RASSF1) encodes the RASSF1A protein, serving as a scaffold protein situated at the intersection of a complex signalling network. Aims To evaluate the immunological and prognostic significance of RASSF1 expression in various types of human cancers, with a specific focus on lung cancer. Methods Differential expression analysis of RASSF1 was conducted based on data from The Cancer Genome Atlas, Genotype-Tissue Expression, and Cancer Cell Line Encyclopaedia databases. Prognostic analysis was performed using the Cox regression test and Kaplan-Meier test. Spearman's test was utilized for correlation analysis. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) gene sets were employed to enrich the associated signaling pathways. Immunohistochemical staining and quantitative real-time PCR were employed to detect protein and mRNA expression levels, respectively. Results RASSF1 expression was significantly lower in tumour tissues than in normal tissues in most cancers, and Cox regression analysis demonstrated a significant correlation between RASSF1 expression and the prognosis of over 12 types of cancer. Specifically, high RASSF1 expression was associated with poor OS in nine cancer types, including GBMLGG (HR = 4.98, P = 1.2e-31), LGG (HR = 3.72, P = 2.5e-10), and LAML (HR = 1.48, P = 2.4e-3). Further analysis showed that RASSF1 expression was significantly correlated with immune checkpoint- and immune-related genes. Moreover, RASSF1 expression is involved in tumour microenvironment (TME), RNA modification, genomic heterogeneity, and tumour stemness. GO and KEGG analyses showed that RASSF1 was closely related to tumour immune-related pathways. Finally, RASSF1A was moderately correlated with PD-L1 (R = 0.556), and RASSF1A overexpression significantly affected the expression of several genes involved in the Th17 cell differentiation signalling pathway in lung cancer. Conclusions RASSF1 was differentially expressed in 29 human cancers and played a critical role in tumour immunity. Thus, RASSF1 has the potential to be used as a prognostic marker and reference for achieving more precise immunotherapy, particularly in lung cancer.
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Affiliation(s)
- Yibing Bai
- Medical School of Chinese PLA, Beijing, China
- Department of Oncology, The First Medical Center of PLA General Hospital, Beijing, China
| | - Yuanyong Wang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Jiapei Qin
- Medical School of Chinese PLA, Beijing, China
- Department of Oncology, The First Medical Center of PLA General Hospital, Beijing, China
| | - Ting Wang
- Department of Oncology, The First Medical Center of PLA General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Xin Zhou
- Medical School of Chinese PLA, Beijing, China
- Department of Oncology, The First Medical Center of PLA General Hospital, Beijing, China
| | - Zhiqiang Ma
- Department of Oncology, The First Medical Center of PLA General Hospital, Beijing, China
| | - An Wang
- Medical School of Chinese PLA, Beijing, China
- Department of Oncology, The First Medical Center of PLA General Hospital, Beijing, China
| | - Wenyu Yang
- Department of Oncology, The First Medical Center of PLA General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Jinliang Wang
- Medical School of Chinese PLA, Beijing, China
- Department of Oncology, The First Medical Center of PLA General Hospital, Beijing, China
| | - Jinfeng Li
- Institute of Oncology, Senior Department of Oncology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yi Hu
- Medical School of Chinese PLA, Beijing, China
- Department of Oncology, The First Medical Center of PLA General Hospital, Beijing, China
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Rendek T, Pos O, Duranova T, Saade R, Budis J, Repiska V, Szemes T. Current Challenges of Methylation-Based Liquid Biopsies in Cancer Diagnostics. Cancers (Basel) 2024; 16:2001. [PMID: 38893121 PMCID: PMC11171112 DOI: 10.3390/cancers16112001] [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: 04/23/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
In current clinical practice, effective cancer testing and screening paradigms are limited to specific types of cancer, exhibiting varying efficiency, acceptance, and adherence. Cell-free DNA (cfDNA) methylation profiling holds promise in providing information about the presence of malignity regardless of its type and location while leveraging blood-based liquid biopsies as a method to obtain analytical samples. However, technical difficulties, costs and challenges resulting from biological variations, tumor heterogeneity, and exogenous factors persist. This method exploits the mechanisms behind cfDNA release but faces issues like fragmentation, low concentrations, and high background noise. This review explores cfDNA methylation's origins, means of detection, and profiling for cancer diagnostics. The critical evaluation of currently available multi-cancer early detection methods (MCEDs) as well as tests targeting single genes, emphasizing their potential and limits to refine strategies for early cancer detection, are explained. The current methodology limitations, workflows, comparisons of clinically approved liquid biopsy-based methylation tests for cancer, their utilization in companion diagnostics as well as the biological limitations of the epigenetics approach are discussed, aiming to help healthcare providers as well as researchers to orient themselves in this increasingly complex and evolving field of diagnostics.
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Affiliation(s)
- Tomas Rendek
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Ondrej Pos
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | | | - Rami Saade
- 2nd Department of Gynaecology and Obstetrics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Tomas Szemes
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
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Gonzalez T, Nie Q, Chaudhary LN, Basel D, Reddi HV. Methylation signatures as biomarkers for non-invasive early detection of breast cancer: A systematic review of the literature. Cancer Genet 2024; 282-283:1-8. [PMID: 38134587 DOI: 10.1016/j.cancergen.2023.12.003] [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: 10/04/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
BACKGROUND Early detection of breast cancer would help alleviate the burden of treatment for early-stage breast cancer and help patient prognosis. There is currently no established gene panel that utilizes the potential of DNA methylation as a molecular signature for the early detection of breast cancer. This systematic review aims to identify the optimal methylation biomarkers for a non-invasive liquid biopsy assay and the gaps in knowledge regarding biomarkers for early detection of breast cancer. METHODS Following the PRISMA-ScR method, Pubmed and Google Scholar was searched for publications related to methylation biomarkers in breast cancer over a five-year period. Eligible publications were mined for key data fields such as study aims, cohort demographics, types of breast cancer studied, technologies used, and outcomes. Data was analyzed to address the objectives of the review. RESULTS Literature search identified 112 studies of which based on eligibility criteria, 13 studies were included. 28 potential methylation gene targets were identified, of which 23 were methylated at the promoter region, 1 was methylated in the body of the gene and 4 were methylated at yet to be identified locations. CONCLUSIONS Our evaluation shows that at minimum APC, RASSFI, and FOXA1 genes would be a promising set of genes to start with for the early detection of breast cancer, based on the sensitivity and specificity outlined in the studies. Prospective studies are needed to optimize biomarkers for broader impact in early detection of breast cancer.
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Affiliation(s)
- Tessa Gonzalez
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA
| | - Qian Nie
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA
| | - Lubna N Chaudhary
- Division of Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, CT, USA
| | - Donald Basel
- Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, CT, USA
| | - Honey V Reddi
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA.
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Morshed AKMH, Al Azad S, Mia MAR, Uddin MF, Ema TI, Yeasin RB, Srishti SA, Sarker P, Aurthi RY, Jamil F, Samia NSN, Biswas P, Sharmeen IA, Ahmed R, Siddiquy M, Nurunnahar. Oncoinformatic screening of the gene clusters involved in the HER2-positive breast cancer formation along with the in silico pharmacodynamic profiling of selective long-chain omega-3 fatty acids as the metastatic antagonists. Mol Divers 2023; 27:2651-2672. [PMID: 36445532 DOI: 10.1007/s11030-022-10573-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022]
Abstract
The HER2-positive patients occupy ~ 30% of the total breast cancer patients globally where no prevalent drugs are available to mitigate the frequent metastasis clinically except lapatinib and neratinib. This scarcity reinforced researchers' quest for new medications where natural substances are significantly considered. Valuing the aforementioned issues, this research aimed to study the ERBB2-mediated string networks that work behind the HER2-positive breast cancer formation regarding co-expression, gene regulation, GAMA-receptor-signaling pathway, cellular polarization, and signal inhibition. Following the overexpression, promotor methylation, and survivability profiles of ERBB2, the super docking position of HER2 was identified using the quantum tunneling algorithm. Supramolecular docking was conducted to study the target specificity of EPA and DHA fatty acids followed by a comprehensive molecular dynamic simulation (100 ns) to reveal the RMSD, RMSF, Rg, SASA, H-bonds, and MM/GBSA values. Finally, potential drug targets for EPA and DHA in breast cancer were constructed to determine the drug-protein interactions (DPI) at metabolic stages. Considering the values resulting from the combinational models of the oncoinformatic, pharmacodynamic, and metabolic parameters, long-chain omega-3 fatty acids like EPA and DHA can be considered as potential-targeted therapeutics for HER2-positive breast cancer treatment.
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Affiliation(s)
- A K M Helal Morshed
- Pathology and Pathophysiology Major, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001, Henan Province, People's Republic of China
| | - Salauddin Al Azad
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu Province, People's Republic of China.
| | - Md Abdur Rashid Mia
- Department of Pharmaceutical Technology, Faculty of Pharmacy, International Islamic University Malaysia, 25200, Pahang, Kuantan, Malaysia
| | - Mohammad Fahim Uddin
- College of Material Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, People's Republic of China
| | - Tanzila Ismail Ema
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | - Rukaiya Binte Yeasin
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | | | - Pallab Sarker
- Department of Medicine, Sher-E-Bangla Medical College Hospital, South Alekanda, Barisal, 8200, Bangladesh
| | - Rubaita Younus Aurthi
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Palashi, Dhaka, 1205, Bangladesh
| | - Farhan Jamil
- Department of Pharmacy, University of Asia Pacific, Farmgate, Dhaka, 1205, Bangladesh
| | | | - Partha Biswas
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Iffat Ara Sharmeen
- School of Data Sciences, Department of Mathematics & Natural Sciences, BRAC University, 66 Mohakhali, Dhaka, 1212, Bangladesh
| | - Rasel Ahmed
- School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough, TS1 3BX, Tees Valley, UK
| | - Mahbuba Siddiquy
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, People's Republic of China
| | - Nurunnahar
- Department of Mathematics, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
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Zhang Y, Wang JW, Su X, Li JE, Wei XF, Yang JR, Gao S, Fan YC, Wang K. F-box protein 43 promoter methylation as a novel biomarker for hepatitis B virus-associated hepatocellular carcinoma. Front Microbiol 2023; 14:1267844. [PMID: 38029156 PMCID: PMC10652413 DOI: 10.3389/fmicb.2023.1267844] [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: 07/27/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) has a high prevalence and poor prognosis worldwide. Therefore, it is urgent to find effective and timely diagnostic markers. The objective of this study was to evaluate the diagnostic value of F-box protein 43 promoter methylation in peripheral blood mononuclear cells (PBMCs) for HCC. Method A total of 247 participants were included in this study, comprising individuals with 123 hepatitis B virus-associated HCC, 79 chronic hepatitis B, and 45 healthy controls. F-box protein 43 methylation and mRNA levels in PBMCs were detected by MethyLight and quantitative real-time PCR. Result F-box protein 43 promoter methylation levels were significantly lower in HCC PBMCs than the chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Relative mRNA expression levels of F-box protein 43 in HCC PBMCs were significantly higher than those in chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Receiver operating characteristic analysis of F-box protein 43 promoter methylation levels yielded an area under curve (AUC) of 0.793 with 76.42% sensitivity and 68.35% specificity when differentiating HCC from chronic hepatitis. These values for the F-box protein 43 promoter methylation level were superior to those of the alpha-fetoprotein serum (AFP) level (AUC: 0.780, sensitivity: 47.97%, and specificity: 96.20%), with increments in values for the combination of F-box protein 43 promoter methylation AFP levels (AUC: 0.888, sensitivity: 76.42%, and specificity: 86.08%). Conclusion Hypomethylation of the F-box protein 43 promoter in PBMCs is a promising biochemical marker for HBV-associated HCC.
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Affiliation(s)
- Ying Zhang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jing-Wei Wang
- Department of Hepatology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xing Su
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jin-E Li
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Xue-Fei Wei
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jie-Ru Yang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Shuai Gao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Department of Hepatology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
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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.
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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.
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An Optimized CoBRA Method for the Microfluidic Electrophoresis Detection of Breast Cancer Associated RASSF1 Methylation. BIOTECH (BASEL (SWITZERLAND)) 2023; 12:biotech12010007. [PMID: 36648833 PMCID: PMC9844460 DOI: 10.3390/biotech12010007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023]
Abstract
Although breast cancer screening assays exist, many are inaccessible and have high turnaround times, leaving a significant need for better alternatives. Hypermethylation of tumor suppressor genes is a common epigenetic marker of breast cancer. Methylation tends to occur most frequently in the promoter and first exon regions of genes. Preliminary screening tests are crucial for informing patients whether they should pursue more involved testing. We selected RASSF1, previously demonstrated to be aberrantly methylated in liquid biopsies from breast cancer patients, as our gene of interest. Using CoBRA as our method for methylation quantification, we designed unique primer sets that amplify a portion of the CpG island spanning the 5' end of the RASSF1 first exon. We integrated the CoBRA approach with a microfluidics-based electrophoresis quantification system (LabChip) and optimized the assay such that insightful results could be obtained without post-PCR purification or concentration, two steps traditionally included in CoBRA assays. Circumventing these steps resulted in a decreased turnaround time and mitigated the laboratory machinery and reagent requirements. Our streamlined technique has an estimated limit of detection of 9.1 ng/μL of input DNA and was able to quantify methylation with an average error of 4.3%.
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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.
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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
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10
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Khan NG, Eswaran S, Adiga D, Sriharikrishnaa S, Chakrabarty S, Rai PS, Kabekkodu SP. Integrated bioinformatic analysis to understand the association between phthalate exposure and breast cancer progression. Toxicol Appl Pharmacol 2022; 457:116296. [PMID: 36328110 DOI: 10.1016/j.taap.2022.116296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
Phthalates have been extensively used as plasticizers while manufacturing plastic-based consumer products. Estradiol mimicking properties and association studies suggest phthalates may contribute to breast cancer (BC). We performed an in-silico analysis and functional studies to understand the association between phthalate exposure and BC progression. Search for phthalate-responsive genes using the comparative toxicogenomics database identified 20 genes as commonly altered in response to multiple phthalates exposure. Of the 20 genes, 12 were significantly differentially expressed between normal and BC samples. In BC samples, 9 out of 20 genes showed a negative correlation between promoter methylation and its expression. AHR, BAX, BCL2, CAT, ESR2, IL6, and PTGS2 expression differed significantly between metastatic and non-metastatic BC samples. Gene set enrichment analysis identified metabolism, ATP-binding cassette transporters, insulin signaling, and type II diabetes as highly enriched pathways. The diagnostic assessment based on 20 genes expression suggested a sensitivity and a specificity >0.91. The aberrantly expressed phthalate interactive gene influenced the overall survival of BC patients. Drug-gene interaction analysis identified 14 genes and 523 candidate drugs, including 19 BC treatment-approved drugs. Di(2-ethylhexyl) phthlate (DEHP) exposure increased the growth, proliferation, and migration of MCF-7 and MDA-MB-231 cells in-vitro. DEHP exposure induced morphological changes, actin cytoskeletal remodeling, increased ROS content, reduced basal level lipid peroxidation, and induced epithelial to mesenchymal transition (EMT). The present approach can help to explore the potentially damaging effects of environmental agents on cancer risk and understand the underlined pathways and molecular mechanisms.
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Affiliation(s)
- Nadeem G Khan
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sangavi Eswaran
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - S Sriharikrishnaa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Centre for DNA repair and Genome Stability (CDRGS), Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Padmalatha S Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Centre for DNA repair and Genome Stability (CDRGS), Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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11
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Duque G, Manterola C, Otzen T, Arias C, Palacios D, Mora M, Galindo B, Holguín JP, Albarracín L. Cancer Biomarkers in Liquid Biopsy for Early Detection of Breast
Cancer: A Systematic Review. Clin Med Insights Oncol 2022; 16:11795549221134831. [PMCID: PMC9634213 DOI: 10.1177/11795549221134831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022] Open
Abstract
Background: Breast cancer (BC) is the most common neoplasm in women worldwide. Liquid
biopsy (LB) is a non-invasive diagnostic technique that allows the analysis
of biomarkers in different body fluids, particularly in peripheral blood and
also in urine, saliva, nipple discharge, volatile respiratory fluids, nasal
secretions, breast milk, and tears. The objective was to analyze the
available evidence related to the use of biomarkers obtained by LB for the
early diagnosis of BC. Methods: Articles related to the use of biomarkers for the early diagnosis of BC due
to LB, published between 2010 and 2022, from the databases (WoS, EMBASE,
PubMed, and SCOPUS) were included. The MInCir diagnostic scale was applied
in the articles to determine their methodological quality (MQ). Descriptive
statistics were used, as well as determination of weighted averages of each
variable, to analyze the extracted data. Sensitivity, specificity, and area
under the curve values for specific biomarkers (individual or in panels) are
described. Results: In this systematic review (SR), 136 articles met the selection criteria,
representing 17 709 patients with BC. However, 95.6% were case-control
studies. In 96.3% of cases, LB was performed in peripheral blood samples.
Most of the articles were based on microRNA (miRNA) analysis. The mean MQ
score was 25/45 points. Sensitivity, specificity, and area under the curve
values for specific biomarkers (individual or in panels) have been
found. Conclusions: The determination of biomarkers through LB is a useful mechanism for the
diagnosis of BC. The analysis of miRNA in peripheral blood is the most
studied methodology. Our results indicate that LB has a high sensitivity and
specificity for the diagnosis of BC, especially in early stages.
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Affiliation(s)
- Galo Duque
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile,Faculty of Medicine, Universidad del
Azuay, Cuenca, Ecuador,Galo Duque, Faculty of Medicine,
Universidad del Azuay. Postal address: Av. 24 de Mayo y Hernán Malo, Cuenca,
Ecuador 010107.
| | - Carlos Manterola
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile,Center of Excellence in Morphological
and Surgical Studies (CEMyQ), Universidad de La Frontera, Temuco, Chile
| | - Tamara Otzen
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile,Center of Excellence in Morphological
and Surgical Studies (CEMyQ), Universidad de La Frontera, Temuco, Chile
| | - Cristina Arias
- Faculty of Medicine, Universidad del
Azuay, Cuenca, Ecuador
| | | | - Miriann Mora
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile,Faculty of Medicine, Universidad del
Azuay, Cuenca, Ecuador
| | - Bryan Galindo
- Faculty of Medicine, Universidad del
Azuay, Cuenca, Ecuador
| | - Juan Pablo Holguín
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile,Faculty of Medicine, Universidad del
Azuay, Cuenca, Ecuador
| | - Lorena Albarracín
- Medical Sciences PhD Program,
Universidad de La Frontera, Temuco, Chile
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12
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Baldi S, He Y, Ivanov I, Khamgan H, Safi M, Alradhi M, Shopit A, Al-Danakh A, Al-Nusaif M, Gao Y, Tian H. Aberrantly hypermethylated ARID1B is a novel biomarker and potential therapeutic target of colon adenocarcinoma. Front Genet 2022; 13:914354. [PMID: 36313455 PMCID: PMC9614077 DOI: 10.3389/fgene.2022.914354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/21/2022] [Indexed: 11/18/2022] Open
Abstract
Background and Objective: Understanding the tumor microenvironment (TME) and immune cell infiltration (ICI) may help guide immunotherapy efforts for colon cancer (COAD). However, whether ARID1B is truly regulated by hypermethylation or linked to immune infiltration remains unknown. The current work focused on the ARID1B gene expression and methylation in COAD, as well as its relation with ICI. Methods and Results: Multiple tools based on TCGA were used to analyze the differences in the expression of the ARID1B gene, DNA methylation, and its association with various clinicopathological features, somatic mutations, copy number variation, and the prognosis of patients with COAD. According to the analysis results, patients with high mRNA, low methylation levels showed better overall survival than patients with low mRNA, high methylation levels. The correlation analysis of immune cell infiltration and immune checkpoint gene expression showed that the infiltration rates of the main ICI subtypes, cancer-associated fibroblast, and myeloid cells were significantly enriched and correlated with ARID1B in COAD. An association between ARID1B expression and immune infiltration in COAD was found by correlating ICI indicators with ARID1B expression in the immune cell composition of the COAD microenvironment. Notably, M2 chemokines were related to ARID1B expression, while M1 chemokines were not. Conclusion: This study provided evidence that ARID1B may have a role in the pathogenesis of COAD. The specific underlying mechanisms that could be responsible for ARID1B’s downregulation in COAD will need to be investigated in the future.
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Affiliation(s)
- Salem Baldi
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co.,Ltd, Shenzhen, Guangdong, China
- *Correspondence: Salem Baldi, ; Yaping Gao, ; Hui Tian,
| | - Yun He
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co.,Ltd, Shenzhen, Guangdong, China
| | - Igor Ivanov
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co.,Ltd, Shenzhen, Guangdong, China
| | - Hassan Khamgan
- Department of Molecular Diagnostics and Therapeutics, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat, Egypt
| | - Mohammed Safi
- Department of respiratory, Shandong Second Provincial General Hospital, Shandong University, Jinan, China
| | - Mohammed Alradhi
- Department of Urology, The Affiliated Hospital of Qingdao Binhai University, Qingdao, China
| | - Abdullah Shopit
- Academic Integrated Medicine and Collage of Pharmacy, School of Pharmacy, Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Abdullah Al-Danakh
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Murad Al-Nusaif
- Center for Clinical Research on Neurological Diseases, First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Yaping Gao
- Research Center of Molecular Diagnostics and Sequencing, Research Institute of Tsinghua University in Shenzhen, Shenzhen, Guangdong, China
- *Correspondence: Salem Baldi, ; Yaping Gao, ; Hui Tian,
| | - Hui Tian
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co.,Ltd, Shenzhen, Guangdong, China
- *Correspondence: Salem Baldi, ; Yaping Gao, ; Hui Tian,
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13
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Sarvari P, Sarvari P, Ramírez-Díaz I, Mahjoubi F, Rubio K. Advances of Epigenetic Biomarkers and Epigenome Editing for Early Diagnosis in Breast Cancer. Int J Mol Sci 2022; 23:ijms23179521. [PMID: 36076918 PMCID: PMC9455804 DOI: 10.3390/ijms23179521] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022] Open
Abstract
Epigenetic modifications are known to regulate cell phenotype during cancer progression, including breast cancer. Unlike genetic alterations, changes in the epigenome are reversible, thus potentially reversed by epi-drugs. Breast cancer, the most common cause of cancer death worldwide in women, encompasses multiple histopathological and molecular subtypes. Several lines of evidence demonstrated distortion of the epigenetic landscape in breast cancer. Interestingly, mammary cells isolated from breast cancer patients and cultured ex vivo maintained the tumorigenic phenotype and exhibited aberrant epigenetic modifications. Recent studies indicated that the therapeutic efficiency for breast cancer regimens has increased over time, resulting in reduced mortality. Future medical treatment for breast cancer patients, however, will likely depend upon a better understanding of epigenetic modifications. The present review aims to outline different epigenetic mechanisms including DNA methylation, histone modifications, and ncRNAs with their impact on breast cancer, as well as to discuss studies highlighting the central role of epigenetic mechanisms in breast cancer pathogenesis. We propose new research areas that may facilitate locus-specific epigenome editing as breast cancer therapeutics.
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Affiliation(s)
- Pourya Sarvari
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Frouzandeh Mahjoubi
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Correspondence:
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14
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Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies. NPJ Precis Oncol 2022; 6:28. [PMID: 35468987 PMCID: PMC9038724 DOI: 10.1038/s41698-022-00270-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/16/2022] [Indexed: 01/23/2023] Open
Abstract
Cell-free RNA (cfRNA) in plasma reflects phenotypic alterations of both localized sites of cancer and the systemic host response. Here we report that cfRNA sequencing enables the discovery of messenger RNA (mRNA) biomarkers in plasma with the tissue of origin-specific to cancer types and precancerous conditions in both solid and hematologic malignancies. To explore the diagnostic potential of total cfRNA from blood, we sequenced plasma samples of eight hepatocellular carcinoma (HCC) and ten multiple myeloma (MM) patients, 12 patients of their respective precancerous conditions, and 20 non-cancer (NC) donors. We identified distinct gene sets and built classification models using Random Forest and linear discriminant analysis algorithms that could distinguish cancer patients from premalignant conditions and NC individuals with high accuracy. Plasma cfRNA biomarkers of HCC are liver-specific genes and biomarkers of MM are highly expressed in the bone marrow compared to other tissues and are related to cell cycle processes. The cfRNA level of these biomarkers displayed a gradual transition from noncancerous states through precancerous conditions and cancer. Sequencing data were cross-validated by quantitative reverse transcription PCR and cfRNA biomarkers were validated in an independent sample set (20 HCC, 9 MM, and 10 NC) with AUC greater than 0.86. cfRNA results observed in precancerous conditions require further validation. This work demonstrates a proof of principle for using mRNA transcripts in plasma with a small panel of genes to distinguish between cancers, noncancerous states, and precancerous conditions.
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15
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Wu HJ, Chu PY. Current and Developing Liquid Biopsy Techniques for Breast Cancer. Cancers (Basel) 2022; 14:2052. [PMID: 35565189 PMCID: PMC9105073 DOI: 10.3390/cancers14092052] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer and leading cause of cancer mortality among woman worldwide. The techniques of diagnosis, prognosis, and therapy monitoring of breast cancer are critical. Current diagnostic techniques are mammography and tissue biopsy; however, they have limitations. With the development of novel techniques, such as personalized medicine and genetic profiling, liquid biopsy is emerging as the less invasive tool for diagnosing and monitoring breast cancer. Liquid biopsy is performed by sampling biofluids and extracting tumor components, such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), cell-free mRNA (cfRNA) and microRNA (miRNA), proteins, and extracellular vehicles (EVs). In this review, we summarize and focus on the recent discoveries of tumor components and biomarkers applied in liquid biopsy and novel development of detection techniques, such as surface-enhanced Raman spectroscopy (SERS) and microfluidic devices.
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Affiliation(s)
- Hsing-Ju Wu
- Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan;
- Department of Medical Research, Chang Bing Show Chwan Memorial Hospital, Lukang Town, Changhua 505, Taiwan
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan
| | - Pei-Yi Chu
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Pathology, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
- Department of Health Food, Chung Chou University of Science and Technology, Changhua 510, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
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16
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Challenges in promoter methylation analysis in the new era of translational oncology: a focus on liquid biopsy. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166390. [PMID: 35296416 DOI: 10.1016/j.bbadis.2022.166390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/01/2022] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Toward the discovery of novel reliable biomarkers, epigenetic alterations have been repeatedly proposed for the diagnosis and the development of therapeutic strategies against cancer. Indeed, for promoter methylation to actively become a tumor marker for clinical use, it must be combined with a highly informative technology evaluated in an appropriate biospecimen. Methodological standardization related to epigenetic research is, in fact, one of the most challenging tasks. Moreover, tissue-based biopsy is being complemented and, in some cases, replaced by liquid biopsy. This review will highlight the advancements made for both pre-analytical and analytical implementation for the prospective use of methylation biomarkers in clinical settings, with particular emphasis on liquid biopsy.
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17
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Karaglani M, Panagopoulou M, Baltsavia I, Apalaki P, Theodosiou T, Iliopoulos I, Tsamardinos I, Chatzaki E. Tissue-Specific Methylation Biosignatures for Monitoring Diseases: An In Silico Approach. Int J Mol Sci 2022; 23:2959. [PMID: 35328380 PMCID: PMC8952417 DOI: 10.3390/ijms23062959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 02/06/2023] Open
Abstract
Tissue-specific gene methylation events are key to the pathogenesis of several diseases and can be utilized for diagnosis and monitoring. Here, we established an in silico pipeline to analyze high-throughput methylome datasets to identify specific methylation fingerprints in three pathological entities of major burden, i.e., breast cancer (BrCa), osteoarthritis (OA) and diabetes mellitus (DM). Differential methylation analysis was conducted to compare tissues/cells related to the pathology and different types of healthy tissues, revealing Differentially Methylated Genes (DMGs). Highly performing and low feature number biosignatures were built with automated machine learning, including: (1) a five-gene biosignature discriminating BrCa tissue from healthy tissues (AUC 0.987 and precision 0.987), (2) three equivalent OA cartilage-specific biosignatures containing four genes each (AUC 0.978 and precision 0.986) and (3) a four-gene pancreatic β-cell-specific biosignature (AUC 0.984 and precision 0.995). Next, the BrCa biosignature was validated using an independent ccfDNA dataset showing an AUC and precision of 1.000, verifying the biosignature's applicability in liquid biopsy. Functional and protein interaction prediction analysis revealed that most DMGs identified are involved in pathways known to be related to the studied diseases or pointed to new ones. Overall, our data-driven approach contributes to the maximum exploitation of high-throughput methylome readings, helping to establish specific disease profiles to be applied in clinical practice and to understand human pathology.
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Affiliation(s)
- Makrina Karaglani
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.K.); (M.P.); (P.A.); (T.T.)
| | - Maria Panagopoulou
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.K.); (M.P.); (P.A.); (T.T.)
| | - Ismini Baltsavia
- Department of Basic Sciences, School of Medicine, University of Crete, GR-71003 Heraklion, Greece; (I.B.); (I.I.)
| | - Paraskevi Apalaki
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.K.); (M.P.); (P.A.); (T.T.)
| | - Theodosis Theodosiou
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.K.); (M.P.); (P.A.); (T.T.)
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, GR-71003 Heraklion, Greece; (I.B.); (I.I.)
| | - Ioannis Tsamardinos
- JADBio Gnosis DA S.A., Science and Technology Park of Crete, GR-70013 Heraklion, Greece;
- Department of Computer Science, University of Crete, GR-70013 Heraklion, Greece
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology—Hellas, GR-70013 Heraklion, Greece
| | - Ekaterini Chatzaki
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.K.); (M.P.); (P.A.); (T.T.)
- Institute of Agri-Food and Life Sciences, Hellenic Mediterranean University Research Centre, GR-71410 Heraklion, Greece
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18
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Rajkumar T, Amritha S, Sridevi V, Gopal G, Sabitha K, Shirley S, Swaminathan R. Identification and validation of plasma biomarkers for diagnosis of breast cancer in South Asian women. Sci Rep 2022; 12:100. [PMID: 34997107 PMCID: PMC8742108 DOI: 10.1038/s41598-021-04176-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 12/16/2021] [Indexed: 01/26/2023] Open
Abstract
Breast cancer is the most common malignancy among women globally. Development of a reliable plasma biomarker panel might serve as a non-invasive and cost-effective means for population-based screening of the disease. Transcriptomic profiling of breast tumour, paired normal and apparently normal tissues, followed by validation of the shortlisted genes using TaqMan® Low density arrays and Quantitative real-time PCR was performed in South Asian women. Fifteen candidate protein markers and 3 candidate epigenetic markers were validated first in primary breast tumours and then in plasma samples of cases [N = 202 invasive, 16 DCIS] and controls [N = 203 healthy, 37 benign] using antibody array and methylation specific PCR. Diagnostic efficiency of single and combined markers was assessed. Combination of 6 protein markers (Adipsin, Leptin, Syndecan-1, Basic fibroblast growth factor, Interleukin 17B and Dickopff-3) resulted in 65% sensitivity and 80% specificity in detecting breast cancer. Multivariate diagnostic analysis of methylation status of SOSTDC1, DACT2, WIF1 showed 100% sensitivity and up to 91% specificity in discriminating BC from benign and controls. Hence, combination of SOSTDC1, DACT2 and WIF1 was effective in differentiating breast cancer [non-invasive and invasive] from benign diseases of the breast and healthy individuals and could help as a complementary diagnostic tool for breast cancer.
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Affiliation(s)
- Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India.
| | - Sathyanarayanan Amritha
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
| | - Veluswami Sridevi
- Department of Surgical Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
| | - Gopisetty Gopal
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
| | - Kesavan Sabitha
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
| | - Sundersingh Shirley
- Department of Pathology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
| | - Rajaraman Swaminathan
- Department of Epidemiology and Biostatistics, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai, 600036, India
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19
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Ray SK, Mukherjee S. Epigenetic Reprogramming and Landscape of Transcriptomic Interactions: Impending Therapeutic Interference of Triple-Negative Breast Cancer in Molecular Medicine. Curr Mol Med 2021; 22:835-850. [PMID: 34872474 DOI: 10.2174/1566524021666211206092437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022]
Abstract
The mechanisms governing the development and progression of cancers are believed to be the consequence of hereditary deformities and epigenetic modifications. Accordingly, epigenetics has become an incredible and progressively explored field of research to discover better prevention and therapy for neoplasia, especially triple-negative breast cancer (TNBC). It represents 15-20% of all invasive breast cancers and will, in general, have bellicose histological highlights and poor clinical outcomes. In the early phases of triple-negative breast carcinogenesis, epigenetic deregulation modifies chromatin structure and influences the plasticity of cells. It up-keeps the oncogenic reprogramming of malignant progenitor cells with the acquisition of unrestrained selfrenewal capacities. Genomic impulsiveness in TNBC prompts mutations, copy number variations, as well as genetic rearrangements, while epigenetic remodeling includes an amendment by DNA methylation, histone modification, and noncoding RNAs of gene expression profiles. It is currently evident that epigenetic mechanisms assume a significant part in the pathogenesis, maintenance, and therapeutic resistance of TNBC. Although TNBC is a heterogeneous malaise that is perplexing to describe and treat, the ongoing explosion of genetic and epigenetic research will help to expand these endeavors. Latest developments in transcriptome analysis have reformed our understanding of human diseases, including TNBC at the molecular medicine level. It is appealing to envision transcriptomic biomarkers to comprehend tumor behavior more readily regarding its cellular microenvironment. Understanding these essential biomarkers and molecular changes will propel our capability to treat TNBC adequately. This review will depict the different aspects of epigenetics and the landscape of transcriptomics in triple-negative breast carcinogenesis and their impending application for diagnosis, prognosis, and treatment decision with the view of molecular medicine.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry All India Institute of Medical Sciences. Bhopal, Madhya pradesh-462020. India
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20
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Vietri MT, D'Elia G, Benincasa G, Ferraro G, Caliendo G, Nicoletti GF, Napoli C. DNA methylation and breast cancer: A way forward (Review). Int J Oncol 2021; 59:98. [PMID: 34726251 DOI: 10.3892/ijo.2021.5278] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/01/2021] [Indexed: 11/05/2022] Open
Abstract
The current management of breast cancer (BC) lacks specific non‑invasive biomarkers able to provide an early diagnosis of the disease. Epigenetic‑sensitive signatures are influenced by environmental exposures and are mediated by direct molecular mechanisms, mainly guided by DNA methylation, which regulate the interplay between genetic and non‑genetic risk factors during cancerogenesis. The inactivation of tumor suppressor genes due to promoter hypermethylation is an early event in carcinogenesis. Of note, targeted tumor suppressor genes are frequently hypermethylated in patient‑derived BC tissues and peripheral blood biospecimens. In addition, epigenetic alterations in triple‑negative BC, as the most aggressive subtype, have been identified. Thus, detecting both targeted and genome‑wide DNA methylation changes through liquid‑based assays appears to be a useful clinical strategy for early detection, more accurate risk stratification and a personalized prediction of therapeutic response in patients with BC. Of note, the DNA methylation profile may be mapped by isolating the circulating tumor DNA from the plasma as a more accessible biospecimen. Furthermore, the sensitivity to treatment with chemotherapy, hormones and immunotherapy may be altered by gene‑specific DNA methylation, suggesting novel potential drug targets. Recently, the use of epigenetic drugs administered alone and/or with anticancer therapies has led to remarkable results, particularly in patients with BC resistant to anticancer treatment. The aim of the present review was to provide an update on DNA methylation changes that are potentially involved in BC development and their putative clinical utility in the fields of diagnosis, prognosis and therapy.
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Affiliation(s)
- Maria Teresa Vietri
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanna D'Elia
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giuseppe Ferraro
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Gemma Caliendo
- Unit of Clinical and Molecular Pathology, AOU, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Giovanni Francesco Nicoletti
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Plastic Surgery Unit, University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania 'Luigi Vanvitelli', I-80138 Naples, Italy
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21
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Seale KN, Tkaczuk KHR. Circulating Biomarkers in Breast Cancer. Clin Breast Cancer 2021; 22:e319-e331. [PMID: 34756687 DOI: 10.1016/j.clbc.2021.09.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/22/2021] [Accepted: 09/19/2021] [Indexed: 12/11/2022]
Abstract
Breast cancer management has progressed immensely over the decades, but the disease is still a major source of morbidity and mortality worldwide. Even with enhanced imaging detection and tissue biopsy capabilities, disease can progress on an ineffective treatment before additional information is obtained through standard methods of response evaluation, including the RECIST 1.1 criteria, widely used for assessment of treatment response and benefit from therapy.6 Circulating biomarkers have the potential to provide valuable insight into disease progression and response to therapy, and they can serve to identify actionable mutations and tumor characteristics that can direct therapy. These biomarkers can be collected at higher frequencies than imaging or tissue sampling, potentially allowing for more informed management. This review will evaluate the roles of circulating biomarkers in breast cancer, including the serum markers Carcinoembryonic antigen CA15-3, CA27-29, HER2 ECD, and investigatory markers such as GP88; and the components of the liquid biopsy, including circulating tumor cells, cell free DNA/DNA methylation, circulating tumor DNA, and circulating microRNA.
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Affiliation(s)
- Katelyn N Seale
- University of Maryland, School of Medicine, Marlene and Stewart Greenebaum Comprehensive Cancer Center, 22 South Greene Street, S9D12, Baltimore, MD 21201
| | - Katherine H R Tkaczuk
- University of Maryland, School of Medicine, Marlene and Stewart Greenebaum Comprehensive Cancer Center, 22 South Greene Street, S9D12, Baltimore, MD 21201.
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22
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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: 6] [Impact Index Per Article: 2.0] [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.
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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
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23
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Lianidou E. Detection and relevance of epigenetic markers on ctDNA: recent advances and future outlook. Mol Oncol 2021; 15:1683-1700. [PMID: 33942482 PMCID: PMC8169441 DOI: 10.1002/1878-0261.12978] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsy, a minimally invasive approach, is a highly powerful clinical tool for the real-time follow-up of cancer and overcomes many limitations of tissue biopsies. Epigenetic alterations have a high potential to provide a valuable source of innovative biomarkers for cancer, owing to their stability, frequency, and noninvasive accessibility in bodily fluids. Numerous DNA methylation markers are now tested in circulating tumor DNA (ctDNA) as potential biomarkers, in various types of cancer. DNA methylation in combination with liquid biopsy is very powerful in identifying circulating epigenetic biomarkers of clinical importance. Blood-based epigenetic biomarkers have a high potential for early detection of cancer since DNA methylation in plasma can be detected early during cancer pathogenesis. In this review, we summarize the latest findings on DNA methylation markers in ctDNA for early detection, prognosis, minimal residual disease, risk of relapse, treatment selection, and resistance, for breast, prostate, lung, and colorectal cancer.
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Affiliation(s)
- Evi Lianidou
- Analysis of Circulating Tumor CellsLaboratory of Analytical ChemistryDepartment of ChemistryUniversity of AthensGreece
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24
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Swellam M, Saad EA, Sabry S, Denewer A, Abdel Malak C, Abouzid A. Alterations of PTEN and SMAD4 methylation in diagnosis of breast cancer: implications of methyl II PCR assay. J Genet Eng Biotechnol 2021; 19:54. [PMID: 33825073 PMCID: PMC8024427 DOI: 10.1186/s43141-021-00154-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/26/2021] [Indexed: 12/22/2022]
Abstract
Background Diagnosis of breast cancer is more complicated due to lack of minimal invasive biomarker with sufficient precision. DNA methylation is a promising marker for cancer diagnosis. In this study, authors evaluated methylation patterns for PTEN and SMAD4 in blood samples using EpiTect Methyl II QPCR assay quantitative PCR technology. Results Methylation status for PTEN and SMAD4 were statistically significant as breast cancer patients reported hypermethylation compared to benign and control groups (77.1 ± 17.9 vs. 24.9 ± 4.5 and 15.1 ± 1.4 and 70.1 ± 14.4 vs. 28.2 ± 0.61 and 29.5 ± 3.6, respectively). ROC curve analysis revealed that both PTEN (AUC = 0.992) and SMAD4 (AUC = 0.853) had good discriminative power for differentiating BC from all non-cancer individuals (benign and healthy combined) compared to routine tumor markers CEA (AUC = 0.538) and CA15.3 (AUC = 0.686). High PTEN methylation degree was associated with late stages (84.2 ± 17.4), positive lymph node (84.2 ± 18.5), positive ER (81.3 ± 19.7), positive PgR (79.5 ± 19.1), and positive HER2 (80.7 ± 19.0) vs. 67.4 ± 13.8, 70.6 ± 14.8, 72.8 ± 14.9, 72.5 ± 14.7, and 70.2 ± 13.5 in early stages, negative lymph node, negative ER, negative PgR, and negative HER2, respectively. Similar results were obtained regarding SMAD4 methylation. Sensitivity, specificity, positive and negative predictive values, and accuracy for methylated PTEN were 100%, 95%, 99.1%, 100%, and 95%, respectively when differentiated BC from all-non cancer controls. Interestingly, PTEN could distinguish early BC stages with good sensitivity 84.4%, 51.4%, 69.1%, 72%, and 70%, respectively. Conclusion Methylation status of PTEN and SMAD4 is a promising blood marker for early detection of breast cancer. Future studies are needed for their role as prognostic markers.
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Affiliation(s)
- Menha Swellam
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, High Throughput Molecular and Genetic Laboratory, Center for Excellences for Advanced Sciences, National Research Centre, Dokki, Giza, Egypt
| | - Entsar A Saad
- Chemistry Department, Faculty of Science, Damietta University, Damietta, 34517, Egypt
| | - Shimaa Sabry
- Chemistry Department, Faculty of Science, Damietta University, Damietta, 34517, Egypt.
| | - Adel Denewer
- Surgical Oncology Department, Mansoura Oncology Centre, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Camelia Abdel Malak
- Chemistry Department, Faculty of Science, Damietta University, Damietta, 34517, Egypt
| | - Amr Abouzid
- Surgical Oncology Department, Mansoura Oncology Centre, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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25
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Panagopoulou M, Karaglani M, Manolopoulos VG, Iliopoulos I, Tsamardinos I, Chatzaki E. Deciphering the Methylation Landscape in Breast Cancer: Diagnostic and Prognostic Biosignatures through Automated Machine Learning. Cancers (Basel) 2021; 13:1677. [PMID: 33918195 PMCID: PMC8037759 DOI: 10.3390/cancers13071677] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 12/24/2022] Open
Abstract
DNA methylation plays an important role in breast cancer (BrCa) pathogenesis and could contribute to driving its personalized management. We performed a complete bioinformatic analysis in BrCa whole methylome datasets, analyzed using the Illumina methylation 450 bead-chip array. Differential methylation analysis vs. clinical end-points resulted in 11,176 to 27,786 differentially methylated genes (DMGs). Innovative automated machine learning (AutoML) was employed to construct signatures with translational value. Three highly performing and low-feature-number signatures were built: (1) A 5-gene signature discriminating BrCa patients from healthy individuals (area under the curve (AUC): 0.994 (0.982-1.000)). (2) A 3-gene signature identifying BrCa metastatic disease (AUC: 0.986 (0.921-1.000)). (3) Six equivalent 5-gene signatures diagnosing early disease (AUC: 0.973 (0.920-1.000)). Validation in independent patient groups verified performance. Bioinformatic tools for functional analysis and protein interaction prediction were also employed. All protein encoding features included in the signatures were associated with BrCa-related pathways. Functional analysis of DMGs highlighted the regulation of transcription as the main biological process, the nucleus as the main cellular component and transcription factor activity and sequence-specific DNA binding as the main molecular functions. Overall, three high-performance diagnostic/prognostic signatures were built and are readily available for improving BrCa precision management upon prospective clinical validation. Revisiting archived methylomes through novel bioinformatic approaches revealed significant clarifying knowledge for the contribution of gene methylation events in breast carcinogenesis.
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Affiliation(s)
- Maria Panagopoulou
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.P.); (M.K.); (V.G.M.)
| | - Makrina Karaglani
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.P.); (M.K.); (V.G.M.)
| | - Vangelis G. Manolopoulos
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.P.); (M.K.); (V.G.M.)
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, GR-71003 Heraklion, Greece;
| | - Ioannis Tsamardinos
- JADBio, Gnosis Data Analysis PC, Science and Technology Park of Crete, GR-70013 Heraklion, Greece;
- Department of Computer Science, University of Crete, GR-70013 Heraklion, Greece
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology–Hellas, GR-70013 Heraklion, Greece
| | - Ekaterini Chatzaki
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece; (M.P.); (M.K.); (V.G.M.)
- Institute of Agri-Food and Life Sciences, Hellenic Mediterranean University Research Centre, GR-71410 Heraklion, Greece
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Ruscito I, Gasparri ML, De Marco MP, Costanzi F, Besharat AR, Papadia A, Kuehn T, Gentilini OD, Bellati F, Caserta D. The Clinical and Pathological Profile of BRCA1 Gene Methylated Breast Cancer Women: A Meta-Analysis. Cancers (Basel) 2021; 13:cancers13061391. [PMID: 33808555 PMCID: PMC8003261 DOI: 10.3390/cancers13061391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/09/2021] [Accepted: 03/16/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND DNA aberrant hypermethylation is the major cause of transcriptional silencing of the breast cancer gene 1 (BRCA1) gene in sporadic breast cancer patients. The aim of the present meta-analysis was to analyze all available studies reporting clinical characteristics of BRCA1 gene hypermethylated breast cancer in women, and to pool the results to provide a unique clinical profile of this cancer population. METHODS On September 2020, a systematic literature search was performed. Data were retrieved from PubMed, MEDLINE, and Scopus by searching the terms: "BRCA*" AND "methyl*" AND "breast". All studies evaluating the association between BRCA1 methylation status and breast cancer patients' clinicopathological features were considered for inclusion. RESULTS 465 studies were retrieved. Thirty (6.4%) studies including 3985 patients met all selection criteria. The pooled analysis data revealed a significant correlation between BRCA1 gene hypermethylation and advanced breast cancer disease stage (OR = 0.75: 95% CI: 0.58-0.97; p = 0.03, fixed effects model), lymph nodes involvement (OR = 1.22: 95% CI: 1.01-1.48; p = 0.04, fixed effects model), and pre-menopausal status (OR = 1.34: 95% CI: 1.08-1.66; p = 0.008, fixed effects model). No association could be found between BRCA1 hypermethylation and tumor histology (OR = 0.78: 95% CI: 0.59-1.03; p = 0.08, fixed effects model), tumor grading (OR = 0.78: 95% CI :0.46-1.32; p = 0.36, fixed effects model), and breast cancer molecular classification (OR = 1.59: 95% CI: 0.68-3.72; p = 0.29, random effects model). CONCLUSIONS hypermethylation of the BRCA1 gene significantly correlates with advanced breast cancer disease, lymph nodes involvement, and pre-menopausal cancer onset.
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Affiliation(s)
- Ilary Ruscito
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
- Correspondence: ; Tel.: +39-06-3377-5696
| | - Maria Luisa Gasparri
- Department of Gynecology and Obstetrics, Ente Ospedaliere Cantonale (EOC), Via Tesserete 46, 6900 Lugano, Switzerland; (M.L.G.); (A.P.)
- University of the Italian Switzerland (USI), Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
| | - Maria Paola De Marco
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Flavia Costanzi
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Aris Raad Besharat
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Andrea Papadia
- Department of Gynecology and Obstetrics, Ente Ospedaliere Cantonale (EOC), Via Tesserete 46, 6900 Lugano, Switzerland; (M.L.G.); (A.P.)
- University of the Italian Switzerland (USI), Via Giuseppe Buffi 13, 6900 Lugano, Switzerland
| | - Thorsten Kuehn
- Interdisciplinary Breast Center, Department of Gynecology and Obstetrics, Klinikum Esslingen, 73730 Neckar, Germany;
| | - Oreste Davide Gentilini
- Breast Surgery Unit, San Raffaele University Hospital, via Olgettina 60, 20132 Milan, Italy;
| | - Filippo Bellati
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
| | - Donatella Caserta
- Gynecology Division, Department of Medical and Surgical Sciences and Translational Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy; (M.P.D.M.); (F.C.); (A.R.B.); (F.B.); (D.C.)
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Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13040728. [PMID: 33578793 PMCID: PMC7916622 DOI: 10.3390/cancers13040728] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed. Abstract Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.
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Ray SK, Mukherjee S. Cell free DNA as an evolving liquid biopsy biomarker for initial diagnosis and therapeutic nursing in Cancer- An evolving aspect in Medical Biotechnology. Curr Pharm Biotechnol 2020; 23:112-122. [PMID: 33308128 DOI: 10.2174/1389201021666201211102710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/26/2020] [Accepted: 10/20/2020] [Indexed: 11/22/2022]
Abstract
Cell-free DNA (cfDNA) is present in numerous body fluids in addition to initiates generally from blood cells. It is undoubtedly the utmost promising tool among all components of liquid biopsy. Liquid biopsy is a specialized method investigating the nonsolid biological tissue by revealing of circulating cells, cell free DNA etc. that enter body fluids. Since, cancer cells disengage from compact tumors circulate in peripheral blood, evaluating blood of cancer patients holds the opportunities for capture and molecular level analysis of various tumor-derived constituents. Cell free DNA samples can deliver a significant perceptions into oncology, for instance tumor heterogeneity, instantaneous tumor development, response to therapy and treatment, comprising immunotherapy and mechanisms of cancer metastasis. Malignant growth at any phase can outhouse tumor cells in addition to fragments of neoplasticity causing DNA into circulatory system giving noble sign of mutation in the tumor at sampling time. Liquid biopsy distinguishes diverse blood based evolving biomarkers comprising circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) or cfDNA, circulating RNA (cfRNA) and exosomes. Cell free DNA are little DNA fragments found circulating in plasma or serum, just as other fluids present in our body. Cell free DNA involves primarily double stranded nuclear DNA and mitochondrial DNA, present both on a surface level and in the lumen of vesicles. The probable origins of the tumor-inferred portion of cfDNA are apoptosis or tumor necrosis, lysis of CTCs or release of DNA from the tumor cells into circulation. The evolution of innovations, refinement and improvement in therapeutics for determination of cfDNA fragment size and its distribution provide significant information related with pathological conditions of the cell, thus emerging as promising indicator for clinical output in medical biotechnology.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry. All India Institute of Medical Sciences. Bhopal, Madhya pradesh-462020. India
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Crimi S, Falzone L, Gattuso G, Grillo CM, Candido S, Bianchi A, Libra M. Droplet Digital PCR Analysis of Liquid Biopsy Samples Unveils the Diagnostic Role of hsa-miR-133a-3p and hsa-miR-375-3p in Oral Cancer. BIOLOGY 2020; 9:biology9110379. [PMID: 33172167 PMCID: PMC7694750 DOI: 10.3390/biology9110379] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022]
Abstract
Simple Summary Despite the availability of screening programs, oral cancer is often diagnosed due to the lack of effective biomarkers. Therefore, the identification of new effective diagnostic and late prognostic biomarkers is of fundamental importance for the management of this tumor type. In our previous computational study, we have identified a set of microRNAs (miRNAs) significantly dysregulated in oral cancer and with a potential diagnostic and prognostic significance for oral cancer patients. Starting from our preliminary bioinformatics results, the aim of the present study was to validate the diagnostic potential of four selected miRNAs, hsa-miR-133a-3p, hsa-miR-375-3p, hsa-miR-503-5p and hsa-miR-196a-5p, in liquid biopsy samples obtained from oral cancer patients and healthy donors. For this purpose, the expression levels of the selected miRNAs were determined in plasma samples by using specific miRNA probes and droplet digital PCR (ddPCR). The ddPCR results showed that the hsa-miR-133a-3p and hsa-miR-375-3p were significantly down-regulated in oral cancer and their evaluation in liquid biopsy samples can predict the risk of oral cancer development with high sensitivity and specificity. Finally, the computational analysis of miRNA expression and clinical-pathological features of patients allowed us to establish the functional role and prognostic significance of the two validated miRNAs. Abstract Despite the availability of screening programs, oral cancer deaths are increasing due to the lack of diagnostic biomarkers leading to late diagnosis and a poor prognosis. Therefore, there is an urgent need to discover novel effective biomarkers for this tumor. On these bases, the aim of this study was to validate the diagnostic potential of microRNAs (miRNAs) through the analysis of liquid biopsy samples obtained from ten oral cancer patients and ten healthy controls. The expression of four selected miRNAs was evaluated by using droplet digital PCR (ddPCR) in a pilot cohort of ten oral cancer patients and ten healthy donors. Bioinformatics analyses were performed to assess the functional role of these miRNAs. The expression levels of the predicted down-regulated hsa-miR-133a-3p and hsa-miR-375-3p were significantly reduced in oral cancer patients compared to normal individuals while no significant results were obtained for the up-regulated hsa-miR-503-5p and hsa-miR-196a-5p. ROC analysis confirmed the high sensitivity and specificity of hsa-miR-375-3p and hsa-miR-133a-3p. Therefore, both miRNAs are significantly down-regulated in cancer patients and can be used as biomarkers for the early diagnosis of oral cancer. The analysis of circulating miRNAs in a larger series of patients is mandatory to confirm the results obtained in this pilot study.
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Affiliation(s)
- Salvatore Crimi
- Department of General Surgery, Section of Maxillo Facial Surgery, Policlinico San Marco, University of Catania, 95123 Catania, Italy; (S.C.); (A.B.)
| | - Luca Falzone
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori “Fondazione G. Pascale”, 80131 Naples, Italy
- Correspondence: ; Tel.: +39-095-478-1271
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (G.G.); (S.C.); (M.L.)
| | - Caterina Maria Grillo
- Otolaryngology Unit, Department of Medical Sciences, Surgical and Advanced Technologies, University of Catania, 95123 Catania, Italy;
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (G.G.); (S.C.); (M.L.)
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy
| | - Alberto Bianchi
- Department of General Surgery, Section of Maxillo Facial Surgery, Policlinico San Marco, University of Catania, 95123 Catania, Italy; (S.C.); (A.B.)
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (G.G.); (S.C.); (M.L.)
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy
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Sher G, Salman NA, Khan AQ, Prabhu KS, Raza A, Kulinski M, Dermime S, Haris M, Junejo K, Uddin S. Epigenetic and breast cancer therapy: Promising diagnostic and therapeutic applications. Semin Cancer Biol 2020; 83:152-165. [PMID: 32858230 DOI: 10.1016/j.semcancer.2020.08.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
The global burden of breast cancer (BC) is increasing significantly. This trend is caused by several factors such as late diagnosis, limited treatment options for certain BC subtypes, drug resistance which all lead to poor clinical outcomes. Recent research has reported the role of epigenetic alterations in the mechanism of BC pathogenesis and its hallmarks include drug resistance and stemness features. The understanding of these modifications and their significance in the management of BC carcinogenesis is challenging and requires further attention. Nevertheless, it promises to provide novel insight needed for utilizing these alterations as potential diagnostic, prognostic markers, predict treatment efficacy, as well as therapeutic agents. This highlights the importance of continuing research development to further advance the existing knowledge on epigenetics and BC carcinogenesis to overcome the current challenges. Hence, this review aims to shed light and discuss the current state of epigenetics research in the diagnosis and management of BC.
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Affiliation(s)
- Gulab Sher
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Nadia Aziz Salman
- Kingston University London, School of Life Science, Pharmacy and Chemistry, SEC Faculty, Kingston, upon Thames, London, KT1 2EE, UK
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Afsheen Raza
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Michal Kulinski
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Said Dermime
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Mohammad Haris
- Functional and Molecular Imaging Laboratory, Sidra Medicine, P.O. Box 26999, Qatar; Laboratory Animal Research Center, Qatar University, Doha, P.O. Box 2713, Qatar
| | - Kulsoom Junejo
- General Surgery Department, Hamad General Hospital, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar.
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31
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Zhang C, Zhao N, Zhang X, Xiao J, Li J, Lv D, Zhou W, Li Y, Xu J, Li X. SurvivalMeth: a web server to investigate the effect of DNA methylation-related functional elements on prognosis. Brief Bioinform 2020; 22:5890509. [PMID: 32778890 DOI: 10.1093/bib/bbaa162] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/04/2020] [Accepted: 06/27/2020] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a fundamental characterization of epigenetics for carcinogenesis. Abnormality of DNA methylation-related functional elements (DMFEs) may lead to dysfunction of regulatory genes in the progression of cancers, contributing to prognosis of many cancers. There is an urgent need to construct a tool to comprehensively assess the impact of DMFEs on prognosis. Therefore, we developed SurvivalMeth (http://bio-bigdata.hrbmu.edu.cn/survivalmeth) to explore the prognosis-related DMFEs, which documented many kinds of DMFEs, including 309,465 CpG island-related elements, 104,748 transcript-related elements, 77,634 repeat elements, as well as cell-type specific 1,689,653 super enhancers (SE) and 1,304,902 CTCF binding regions for analysis. SurvivalMeth is a convenient tool which collected DNA methylation profiles of 36 cancers and allowed users to query their genes of interest in different datasets for prognosis. Furthermore, SurvivalMeth not only integrated different combinations, including single DMFE, multiple DMFEs, SEs and clinical data, to perform survival analysis on preupload data but also allowed for uploading customized DNA methylation profile of DMFEs from various diseases to analyze. SurvivalMeth provided a comprehensive resource and automated analysis for prognostic DMFEs, including DMFE methylation level, correlation analysis, clinical analysis, differential analysis, DMFE annotation, survival-related detailed result and visualization of survival analysis. In summary, we believe that SurvivalMeth will facilitate prognostic research of DMFEs in diverse cancers.
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Affiliation(s)
- Chunlong Zhang
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Ning Zhao
- School of Life Sciences and Technology at Harbin Institute of Technology
| | - Xue Zhang
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Jun Xiao
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Junyi Li
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Dezhong Lv
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Weiwei Zhou
- College of Bioinformatics Science and Technology at Harbin Medical University
| | - Yongsheng Li
- College of Bioinformatics Science and Technology at Harbin Medical University
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Juan Xu
- College of Bioinformatics Science and Technology at Harbin Medical University
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Xia Li
- College of Bioinformatics Science and Technology at Harbin Medical University
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
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32
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Demircan B, Yucel B, Radosevich JA. DNA Methylation in Human Breast Cancer Cell Lines Adapted to High Nitric Oxide. In Vivo 2020; 34:169-176. [PMID: 31882476 DOI: 10.21873/invivo.11758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 09/13/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Nitric oxide (NO) exposure has been suggested to cause alterations in DNA methylation in breast cancer. We investigated the effect of NO on DNA methylation of promoters in cell lines of breast cancer. MATERIAL AND METHODS The methylation status of the promoters of breast cancer 1 (BRCA1), deleted in colon cancer (DCC), Ras-association domain family 1A (RASSF1A), O6-methylguanine-DNA methyltransferase (MGMT), and secreted frizzled related protein 1 (SFRP1) were analyzed in the parental and high nitric oxide-adapted cell lines of breast cancer using Illumina MiSequencing. RESULTS Methylation of RASSF1A promoter in BT-20-HNO (74.7%) was significantly higher than that in BT-20 cells (72%) (p<0.05), whereas in MCF-7-HNO cells, methylation of MGMT promoter was found to have significantly decreased as compared to its parental cell line (45.1% versus 50.1%; p<0.0001). Promoter methylation of SFRP and DCC was elevated in T-47D-HNO relative to its parent cell line (p<0.05). CONCLUSION Similarly to the double-edged effects of NO on tumorigenesis, its epigenetic effects through DNA methylation are diverse and contradictory in breast cancer.
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Affiliation(s)
- Berna Demircan
- Department of Medical Biology, Medical School, Istanbul Medeniyet University, Istanbul, Turkey
| | - Burcu Yucel
- Department of Medical Biology, Medical School, Istanbul Medeniyet University, Istanbul, Turkey
| | - James A Radosevich
- Oral Medicine and Diagnostic Sciences, College of Dentistry, University of Illinois, Chicago, IL, U.S.A
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33
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Matsutani A, Udagawa C, Matsunaga Y, Nakamura S, Zembutsu H. Liquid biopsy for the detection of clinical biomarkers in early breast cancer: new insights and challenges. Pharmacogenomics 2020; 21:359-367. [PMID: 32284011 DOI: 10.2217/pgs-2019-0130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The widespread use of breast screening programs has contributed to the detection of early stage breast cancer, which is often asymptomatic. Early diagnosis is essential to avoid overtreatment and improve clinical outcomes, as early stage breast cancer is rarely life-threatening if detected quickly. Despite this, tissue biopsy remains the principle method for detecting these cancers. Liquid biopsy has been recently proposed as a promising detection method in oncology that is not only less invasive but also contributes to the early diagnosis of breast cancer. Here, we describe the clinical utility of liquid biopsy as a tool for the early detection of breast cancer.
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Affiliation(s)
- Akiko Matsutani
- Division of Breast Surgical Oncology, Department of Surgery, School of Medicine, Showa University, Tokyo, Japan.,Project for Development of Liquid Biopsy, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Chihiro Udagawa
- Project for Development of Liquid Biopsy, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuki Matsunaga
- Division of Breast Surgical Oncology, Department of Surgery, School of Medicine, Showa University, Tokyo, Japan
| | - Seigo Nakamura
- Division of Breast Surgical Oncology, Department of Surgery, School of Medicine, Showa University, Tokyo, Japan
| | - Hitoshi Zembutsu
- Project for Development of Liquid Biopsy, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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34
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Constâncio V, Nunes SP, Henrique R, Jerónimo C. DNA Methylation-Based Testing in Liquid Biopsies as Detection and Prognostic Biomarkers for the Four Major Cancer Types. Cells 2020; 9:E624. [PMID: 32150897 PMCID: PMC7140532 DOI: 10.3390/cells9030624] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022] Open
Abstract
Lung, breast, colorectal, and prostate cancers are the most incident worldwide. Optimal population-based cancer screening methods remain an unmet need, since cancer detection at early stages increases the prospects of successful and curative treatment, leading to a lower incidence of recurrences. Moreover, the current parameters for cancer patients' stratification have been associated with divergent outcomes. Therefore, new biomarkers that could aid in cancer detection and prognosis, preferably detected by minimally invasive methods are of major importance. Aberrant DNA methylation is an early event in cancer development and may be detected in circulating cell-free DNA (ccfDNA), constituting a valuable cancer biomarker. Furthermore, DNA methylation is a stable alteration that can be easily and rapidly quantified by methylation-specific PCR methods. Thus, the main goal of this review is to provide an overview of the most important studies that report methylation biomarkers for the detection and prognosis of the four major cancers after a critical analysis of the available literature. DNA methylation-based biomarkers show promise for cancer detection and management, with some studies describing a "PanCancer" detection approach for the simultaneous detection of several cancer types. Nonetheless, DNA methylation biomarkers still lack large-scale validation, precluding implementation in clinical practice.
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Affiliation(s)
- Vera Constâncio
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Sandra P. Nunes
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
| | - Rui Henrique
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
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35
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Bin Y, Ding Y, Xiao W, Liao A. RASSF1A: A promising target for the diagnosis and treatment of cancer. Clin Chim Acta 2020; 504:98-108. [PMID: 31981586 DOI: 10.1016/j.cca.2020.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
Abstract
The Ras association domain family 1 isoform A (RASSF1A), a tumor suppressor, regulates several tumor-related signaling pathways and interferes with diverse cellular processes. RASSF1A is frequently demonstrated to be inactivated by hypermethylation in numerous types of solid cancers. It is also associated with lymph node metastasis, vascular invasion, and chemo-resistance. Therefore, reactivation of RASSF1A may be a viable strategy to block tumor progress and reverse drug resistance. In this review, we have summarized the clinical value of RASSF1A for screening, staging, and therapeutic management of human malignancies. We also highlighted the potential mechanism of RASSF1A in chemo-resistance, which may help identify novel drugs in the future.
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Affiliation(s)
- Yuling Bin
- Digestive System Department, the First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, China
| | - Yong Ding
- Department of Vascular Surgery, Zhongshan Hospital, Institue of Vascular Surgery, Fudan University, Shanghai 200032, China
| | - Weisheng Xiao
- Digestive System Department, the First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, China
| | - Aijun Liao
- Digestive System Department, the First Affiliated Hospital of University of South China, Hengyang, Hunan 421001, China.
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36
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Novel Epigenetic Biomarkers in Pregnancy-Related Disorders and Cancers. Cells 2019; 8:cells8111459. [PMID: 31752198 PMCID: PMC6912400 DOI: 10.3390/cells8111459] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/08/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
As the majority of cancers and gestational diseases are prognostically stage- and grade-dependent, the ultimate goal of ongoing studies in precision medicine is to provide early and timely diagnosis of such disorders. These studies have enabled the development of various new diagnostic biomarkers, such as free circulating nucleic acids, and detection of their epigenetic changes. Recently, extracellular vesicles including exosomes, microvesicles, oncosomes, and apoptotic bodies have been recognized as powerful diagnostic tools. Extracellular vesicles carry specific proteins, lipids, DNAs, mRNAs, and miRNAs of the cells that produced them, thus reflecting the function of these cells. It is believed that exosomes, in particular, may be the optimal biomarkers of pathological pregnancies and cancers, especially those that are frequently diagnosed at an advanced stage, such as ovarian cancer. In the present review, we survey and critically appraise novel epigenetic biomarkers related to free circulating nucleic acids and extracellular vesicles, focusing especially on their status in trophoblasts (pregnancy) and neoplastic cells (cancers).
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37
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Mijnes J, Tiedemann J, Eschenbruch J, Gasthaus J, Bringezu S, Bauerschlag D, Maass N, Arnold N, Weimer J, Anzeneder T, Fasching PA, Rübner M, Bruno B, Heindrichs U, Freres J, Schulz H, Hilgers RD, Ortiz-Brüchle N, von Serenyi S, Knüchel R, Kloten V, Dahl E. SNiPER: a novel hypermethylation biomarker panel for liquid biopsy based early breast cancer detection. Oncotarget 2019; 10:6494-6508. [PMID: 31741713 PMCID: PMC6849652 DOI: 10.18632/oncotarget.27303] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/19/2019] [Indexed: 01/02/2023] Open
Abstract
Introduction Mammography is the gold standard for early breast cancer detection, but shows important limitations. Blood-based approaches on basis of cell-free DNA (cfDNA) provide minimally invasive screening tools to characterize epigenetic alterations of tumor suppressor genes and could serve as a liquid biopsy, complementing mammography. Methods Potential biomarkers were identified from The Cancer Genome Atlas (TCGA), using HumanMethylation450-BeadChip data. Promoter methylation status was evaluated quantitatively by pyrosequencing in a serum test cohort (n = 103), a serum validation cohort (n = 368) and a plasma cohort (n = 125). Results SPAG6, NKX2-6 and PER1 were identified as novel biomarker candidates. ITIH5 was included on basis of our previous work. In the serum test cohort, a panel of SPAG6 and ITIH5 showed 63% sensitivity for DCIS and 51% sensitivity for early invasive tumor (pT1, pN0) detection at 80% specificity. The serum validation cohort revealed 50% sensitivity for DCIS detection on basis of NKX2-6 and ITIH5. Furthermore, an inverse correlation between methylation frequency and cfDNA concentration was uncovered. Therefore, markers were tested in a plasma cohort, achieving a 64% sensitivity for breast cancer detection using SPAG6, PER1 and ITIH5. Conclusions Although liquid biopsy remains challenging, a combination of SPAG6, NKX2-6, ITIH5 and PER1 (SNiPER) provides a promising tool for blood-based breast cancer detection.
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Affiliation(s)
- Jolein Mijnes
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Janina Tiedemann
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Julian Eschenbruch
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Janina Gasthaus
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Sarah Bringezu
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Dirk Bauerschlag
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Nicolai Maass
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Norbert Arnold
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Clinical Molecular Biology, University Medical Centre Schleswig-Holstein, Campus Kiel, Christian-Albrechts-University, Kiel, Germany
| | - Jörg Weimer
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Tobias Anzeneder
- Patients' Tumor Bank of Hope (PATH-Biobank) Foundation, München, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Matthias Rübner
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Benjamin Bruno
- Department of Gynecology and Obstetrics Luisenhospital, Aachen, Germany
| | - Uwe Heindrichs
- Department of Gynecology and Obstetrics Luisenhospital, Aachen, Germany
| | - Jennifer Freres
- Department of Gynecology and Obstetrics Luisenhospital, Aachen, Germany
| | - Hanna Schulz
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ralf-Dieter Hilgers
- Institute of Medical Statistics, University Hospital RWTH Aachen, Aachen, Germany
| | - Nadina Ortiz-Brüchle
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Sonja von Serenyi
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ruth Knüchel
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Vera Kloten
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany.,Current address: Bayer AG, Pharmaceuticals Division, Biomarker Research, Wuppertal, Germany.,Share equal senior authorship
| | - Edgar Dahl
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany.,RWTH centralized Biomaterial Bank (RWTH cBMB) at the Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany.,Share equal senior authorship
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Zhang Y, Chen C, Duan M, Liu S, Huang L, Zhou F. BioDog, biomarker detection for improving identification power of breast cancer histologic grade in methylomics. Epigenomics 2019; 11:1717-1732. [PMID: 31625763 DOI: 10.2217/epi-2019-0230] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: Breast cancer histologic grade (HG) is a well-established prognostic factor. This study aimed to select methylomic biomarkers to predict breast cancer HGs. Materials & methods: The proposed algorithm BioDog firstly used correlation bias reduction strategy to eliminate redundant features. Then incremental feature selection was applied to find the features with a high HG prediction accuracy. The sequential backward feature elimination strategy was employed to further refine the biomarkers. A comparison with existing algorithms were conducted. The HG-specific somatic mutations were investigated. Results & conclusions: BioDog achieved accuracy 0.9973 using 92 methylomic biomarkers for predicting breast cancer HGs. Many of these biomarkers were within the genes and lncRNAs associated with the HG development in breast cancer or other cancer types.
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Affiliation(s)
- Yexian Zhang
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Chaorong Chen
- College of Software, Jilin University, Changchun, Jilin 130012, PR China
| | - Meiyu Duan
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Shuai Liu
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Lan Huang
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
| | - Fengfeng Zhou
- College of Computer Science & Technology, & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, PR China
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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: 9.6] [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.
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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
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40
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Diagnostic value of RASSF1A methylation for breast cancer: a meta-analysis. Biosci Rep 2019; 39:BSR20190923. [PMID: 31196964 PMCID: PMC6597854 DOI: 10.1042/bsr20190923] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 01/26/2023] Open
Abstract
Background: Numerous studies reported that RAS-association domain family 1 isoform A (RASSF1A) methylation might act as diagnostic biomarker for breast cancer (BC), this meta-analysis aimed to evaluate the value of RASSF1A methylation for diagnosing BC. Methods: Such databases as PubMed, Cochrane Library and Web of Science databases were searched for literatures until May 2019. A meta-analysis was performed utilizing STATA and Revman softwares. Furthermore, subgroup analysis was adopted to determine likely sources of heterogeneity. Results: Totally 19 literatures with 1849 patients and 1542 controls were included in the present study. Sensitivity, specificity, diagnostic odds ratio (DOR) and the area under the summary receiver operating characteristic curve (AUC) of RASSF1A methylation for diagnosing BC were 0.49, 0.95, 19.0 and 0.83, respectively. The sensitivity (0.54 vs 0.43), DOR (30.0 vs 10.0) and AUC (0.84 vs 0.81) of RASSF1A methylation in Caucasian were higher than other ethnicities. The sensitivity (0.64 vs 0.57), DOR (21.0 vs 14.0) and AUC (0.89 vs 0.86) of methylation-specific PCR (MSP) were superior to other methods (q-MSP, OS-MSP and MethyLight). The sensitivity, DOR and AUC of serum RASSF1A methylation vs RASSF1A methylation in other samples (tissue or plasma) were 0.55 vs 0.40, 22.0 vs 14.0 and 0.86 vs 0.74, respectively. Conclusions: RASSF1A methylation might be a potential diagnostic biomarker for BC. Considering its low sensitivity and high specificity, it should combine with others to upgrade the sensitivity. Besides, under such conditions, MSP detection, serum RASSF1A methylation and Caucasian are shown to be more effective and suitable for diagnosing BC.
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